Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 71 of 97
Found at i:28457397 original size:3 final size:3
Alignment explanation
Indices: 28457389--28457413 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28457379 ACCAAATTTA
28457389 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
28457414 CTGCAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28460954 original size:284 final size:281
Alignment explanation
Indices: 28460455--28460990 Score: 772
Period size: 284 Copynumber: 1.9 Consensus size: 281
28460445 AAATCAAATC
* *
28460455 TGGTTGGTTAGTAGACAAGTTATGATGGATTGCTTCTCCTTTGTATGGGATCAAATTTTTTGATG
1 TGGTTGGTTAGGAGACAAGTTATGATGGATTGCTTCTCCTTTCTATGGGATCAAATTTTTTGATG
* * *
28460520 CCATACATATTTTTAATTCCTCCAACCTAGATTAATATAAATTGATTTATATTTTTATTTGGTTA
66 CCATACATATTTTTAATTCCTCCAACCTAGATTAATATAAATTAATTTATATTTTCATTTGATTA
* * * * *
28460585 TTAGAATTTTGAGATATTAACAAAACACAAATTTTTCTCTATTTAAATATTAACAAAACATATAT
131 TCAGAATTCTGAGATATTAACAAAACACAAACTTTTCTCTATTTAAATATTAACAAAACAAAGAT
* *
28460650 TTTTGTTTCATTTTAAAATTTGGGTACTTCATATATCAAGATAATAGAATTTTGCTTATATCTTT
196 TTTTGTTTCATTTCAAAATTTGGGTACTTCACATATCAAGATAATAGAATTTTGCTTATATCTTT
28460715 GTATGATGGCAAAATGCAGTG
261 GTATGATGGCAAAATGCAGTG
*
28460736 TGGTTGGTTAGGAGACAAGTTATGGTGGATTG-TTACTCCTTTACT-TGGGATCAAACAATTTTT
1 TGGTTGGTTAGGAGACAAGTTATGATGGATTGCTT-CTCCTTT-CTATGGGATC--A-AATTTTT
* * * * **
28460799 TTATGCCATAC-TGATTTTTTATTCCTCCAACCTATATTAATGTGTATTAATTTATATTTTCATT
61 TGATGCCATACAT-ATTTTTAATTCCTCCAACCTAGATTAATATAAATTAATTTATATTTTCATT
* * * *
28460863 TGATTGTCAGAATTCTGAGATATTAACAAAACACATACTTTTCTTTATTTAAATATTAATAAAAC
125 TGATTATCAGAATTCTGAGATATTAACAAAACACAAACTTTTCTCTATTTAAATATTAACAAAAC
* *
28460928 AAAGATTTTTGTTTCATTTCAAAATTTGGGTAGTTCACATATCAAGATACTAGAATTTTGCTT
190 AAAGATTTTTGTTTCATTTCAAAATTTGGGTACTTCACATATCAAGATAATAGAATTTTGCTT
28460991 CTATTTCTAT
Statistics
Matches: 224, Mismatches: 25, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
280 2 0.01
281 44 0.20
282 1 0.00
283 2 0.01
284 175 0.78
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (281 bp):
TGGTTGGTTAGGAGACAAGTTATGATGGATTGCTTCTCCTTTCTATGGGATCAAATTTTTTGATG
CCATACATATTTTTAATTCCTCCAACCTAGATTAATATAAATTAATTTATATTTTCATTTGATTA
TCAGAATTCTGAGATATTAACAAAACACAAACTTTTCTCTATTTAAATATTAACAAAACAAAGAT
TTTTGTTTCATTTCAAAATTTGGGTACTTCACATATCAAGATAATAGAATTTTGCTTATATCTTT
GTATGATGGCAAAATGCAGTG
Found at i:28461377 original size:20 final size:20
Alignment explanation
Indices: 28461352--28461399 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
28461342 ACAAGGATCT
*
28461352 GATATGATGCTATCTTGACA
1 GATATGACGCTATCTTGACA
28461372 GATATGACGCTATCTTGACA
1 GATATGACGCTATCTTGACA
*
28461392 AATATGAC
1 GATATGAC
28461400 TAACTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
GATATGACGCTATCTTGACA
Found at i:28466179 original size:27 final size:27
Alignment explanation
Indices: 28466144--28466197 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
28466134 AAAATTGAAT
*
28466144 AAAATAAAATAAAATAATTATTTTATA
1 AAAATAAAATAAAATAATTATTATATA
*
28466171 AAAATAAAATAAAATTATTATTATATA
1 AAAATAAAATAAAATAATTATTATATA
28466198 TTTTAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATAAAATAAAATAATTATTATATA
Found at i:28466191 original size:22 final size:22
Alignment explanation
Indices: 28466149--28466191 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28466139 TGAATAAAAT
*
28466149 AAAATAAAATAATTATTTTATA
1 AAAATAAAATAATAATTTTATA
28466171 AAAATAAAATAA-AATTATTAT
1 AAAATAAAATAATAATT-TTAT
28466192 TATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAAATAATAATTTTATA
Found at i:28466435 original size:23 final size:24
Alignment explanation
Indices: 28466409--28466463 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
28466399 TAATATTTTT
28466409 TAATTTTTTATTAAATTA-TTAAA
1 TAATTTTTTATTAAATTAGTTAAA
* * *
28466432 TAATTTATTATTAACTTAGTTATA
1 TAATTTTTTATTAAATTAGTTAAA
*
28466456 TGATTTTT
1 TAATTTTT
28466464 AATTTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TAATTTTTTATTAAATTAGTTAAA
Found at i:28475551 original size:24 final size:23
Alignment explanation
Indices: 28475494--28475539 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28475484 ATACAATAAC
**
28475494 CTTATCCTAATTTAATTAGAAAT
1 CTTATCCTAATAGAATTAGAAAT
28475517 CTTATCCTAATAGAATTAGAAAT
1 CTTATCCTAATAGAATTAGAAAT
28475540 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGAAAT
Found at i:28479126 original size:14 final size:15
Alignment explanation
Indices: 28479107--28479140 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28479097 TAGTTTGTAG
28479107 ACCTTA-CCTTCATA
1 ACCTTATCCTTCATA
*
28479121 ACCTTATTCTTCATA
1 ACCTTATCCTTCATA
28479136 ACCTT
1 ACCTT
28479141 CAAGTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.41
Consensus pattern (15 bp):
ACCTTATCCTTCATA
Found at i:28482544 original size:21 final size:21
Alignment explanation
Indices: 28482518--28482561 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28482508 TAATGAGTTC
28482518 AACCAGAAATCCATGTTTTTT
1 AACCAGAAATCCATGTTTTTT
28482539 AACCAGAAATCCATGTTTTTT
1 AACCAGAAATCCATGTTTTTT
28482560 AA
1 AA
28482562 TGGGATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (21 bp):
AACCAGAAATCCATGTTTTTT
Found at i:28487094 original size:21 final size:21
Alignment explanation
Indices: 28487069--28487128 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
28487059 CTGAAAAAAT
28487069 TGTATCGATACATTATGAACA
1 TGTATCGATACATTATGAACA
* * *
28487090 TGTATCAATACATCATAAACA
1 TGTATCGATACATTATGAACA
*
28487111 TGTATGGATACATT-TGAA
1 TGTATCGATACATTATGAA
28487129 ACATAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTATGAACA
Found at i:28487284 original size:16 final size:16
Alignment explanation
Indices: 28487255--28487296 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28487245 TTTAGATTCG
*
28487255 ATAAAAATATCAAAAAA
1 ATAAAAAT-CCAAAAAA
*
28487272 ATAAAAATCCAAAAGA
1 ATAAAAATCCAAAAAA
28487288 ATAAAAATC
1 ATAAAAATC
28487297 TAAAGTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.17
Consensus pattern (16 bp):
ATAAAAATCCAAAAAA
Found at i:28502021 original size:18 final size:19
Alignment explanation
Indices: 28501987--28502045 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
28501977 ATCTATTTCG
*
28501987 TAAAC-AATTAATTAAAAC
1 TAAACTAATTAATGAAAAC
*
28502005 TAAATTTAATT-A-GAAAAC
1 TAAA-CTAATTAATGAAAAC
28502023 TAAACTAATTAATGAAAAC
1 TAAACTAATTAATGAAAAC
28502042 TAAA
1 TAAA
28502046 AATTCACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 5 0.15
18 14 0.41
19 11 0.32
20 4 0.12
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAACTAATTAATGAAAAC
Found at i:28502107 original size:12 final size:12
Alignment explanation
Indices: 28502090--28502114 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28502080 GGATTATGGG
28502090 TTCATTCAACAC
1 TTCATTCAACAC
28502102 TTCATTCAACAC
1 TTCATTCAACAC
28502114 T
1 T
28502115 AGTTTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (12 bp):
TTCATTCAACAC
Found at i:28503710 original size:80 final size:79
Alignment explanation
Indices: 28503611--28503772 Score: 236
Period size: 80 Copynumber: 2.0 Consensus size: 79
28503601 TTAATGTTAA
* *
28503611 TGGCACCTCAAAATGATTTTTTAATTTTTTGTTC-ATAGATAACTGTAACGAATGAAAATAGATA
1 TGGCACCTAAAAATAATTTTTTAATTTTTTG-TCAATAGATAACTGTAACGAATGAAAATAGATA
28503675 GAACAATTATATTTTG
65 GAACAATTATA-TTTG
* ** *
28503691 TGGCACTTAAAAATAATTTTTTAATTTTTTGTCAATAGATAACTGTAACGGTTGGAAATAGATAG
1 TGGCACCTAAAAATAATTTTTTAATTTTTTGTCAATAGATAACTGTAACGAATGAAAATAGATAG
*
28503756 AATAATTATATTTG
66 AACAATTATATTTG
28503770 TGG
1 TGG
28503773 TTTGAAAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 9 0.12
80 65 0.88
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (79 bp):
TGGCACCTAAAAATAATTTTTTAATTTTTTGTCAATAGATAACTGTAACGAATGAAAATAGATAG
AACAATTATATTTG
Found at i:28503890 original size:26 final size:26
Alignment explanation
Indices: 28503847--28503897 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
28503837 ATTCTGTTTG
* * *
28503847 AAATAGATATAAATAGATTTTGTCTA
1 AAATAGATAGAAACAGATTGTGTCTA
28503873 AAATAGATAGAAACAGATTGTGTCT
1 AAATAGATAGAAACAGATTGTGTCT
28503898 GAAACGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (26 bp):
AAATAGATAGAAACAGATTGTGTCTA
Found at i:28504070 original size:105 final size:105
Alignment explanation
Indices: 28503883--28504077 Score: 264
Period size: 105 Copynumber: 1.9 Consensus size: 105
28503873 AAATAGATAG
* * * * * * * *
28503883 AAACAGATTGTGTCTGAAACGGATATAATTGTGTTTATTGGAAAATTATCTCGATTGCCTATAAA
1 AAACAAATTCTGTCTGAAACAGATATAATTATGTCTATTGGAAAACTATCTCGAATACCTATAAA
*
28503948 TAAAACCCTTCTCTGAAACAAAAAAGACATAGAAAAATAA
66 TAAAACCCTCCTCTGAAACAAAAAAGACATAGAAAAATAA
* * * *
28503988 AAACAAATTCTGTCTGAAACAGATGTAATTATGTCTGTTGGAAAACTGTCTCGAATACTTATAAA
1 AAACAAATTCTGTCTGAAACAGATATAATTATGTCTATTGGAAAACTATCTCGAATACCTATAAA
*
28504053 TAAAACCCTCCTTTGAAACAAAAAA
66 TAAAACCCTCCTCTGAAACAAAAAA
28504078 TAACATTCCT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 76 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (105 bp):
AAACAAATTCTGTCTGAAACAGATATAATTATGTCTATTGGAAAACTATCTCGAATACCTATAAA
TAAAACCCTCCTCTGAAACAAAAAAGACATAGAAAAATAA
Found at i:28506077 original size:20 final size:21
Alignment explanation
Indices: 28506041--28506079 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28506031 TTTTTTTAAA
*
28506041 TATTTAATGTCTTTTAAATTT
1 TATTTAATCTCTTTTAAATTT
28506062 TATTTAATCT-TTTTAAAT
1 TATTTAATCTCTTTTAAAT
28506080 GATTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTAATCTCTTTTAAATTT
Found at i:28506116 original size:19 final size:19
Alignment explanation
Indices: 28506092--28506129 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28506082 TTGAAAATTA
28506092 AATTATATA-TAATTTTTTT
1 AATTATATAGT-ATTTTTTT
*
28506111 AATTATTTAGTATTTTTTT
1 AATTATATAGTATTTTTTT
28506130 TGTTTGACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
AATTATATAGTATTTTTTT
Found at i:28506582 original size:18 final size:18
Alignment explanation
Indices: 28506559--28506597 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28506549 GTTACCAATT
28506559 TAGGAAGAGCTTG-ATGAG
1 TAGGAAGA-CTTGCATGAG
*
28506577 TAGGAATACTTGCATGAG
1 TAGGAAGACTTGCATGAG
28506595 TAG
1 TAG
28506598 AAAAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.26
Consensus pattern (18 bp):
TAGGAAGACTTGCATGAG
Found at i:28510307 original size:74 final size:75
Alignment explanation
Indices: 28510178--28510400 Score: 246
Period size: 75 Copynumber: 3.0 Consensus size: 75
28510168 GTTTTAGGGA
*
28510178 AACTTGGTTGCTCGAATATTGTA-CT-TAAAGTTTC-AACAATTTGTATTAATCAAGGGATGGAG
1 AACTTGGTTGCTCGAATATT-TATATATAAAGTTTCGAA-AATTTGTATTAATCAAGGGATGGAG
28510240 ATCTAAAAATAC-
64 ATCTAAAAAT-CT
* * * * *
28510252 AACTTGGTTGCTTGAATATTTCTATATAAAGTTTCGATAATTTTTATT-ATGAAGGGATTGGAGA
1 AACTTGGTTGCTCGAATATTTATATATAAAGTTTCGAAAATTTGTATTAATCAAGGGA-TGGAGA
*
28510316 TCTAAAACTCT
65 TCTAAAAATCT
* * * * *
28510327 AACTTGATTGCTCAAATATTAATATATAAAGTTTTGAAAATTTGTATTAATCAAGGGAT--AAAT
1 AACTTGGTTGCTCGAATATTTATATATAAAGTTTCGAAAATTTGTATTAATCAAGGGATGGAGAT
28510390 CT-AAAATCT
66 CTAAAAATCT
28510399 AA
1 AA
28510401 GCTCTTGTTG
Statistics
Matches: 125, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
72 8 0.06
73 6 0.05
74 29 0.23
75 73 0.58
76 9 0.07
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (75 bp):
AACTTGGTTGCTCGAATATTTATATATAAAGTTTCGAAAATTTGTATTAATCAAGGGATGGAGAT
CTAAAAATCT
Found at i:28522904 original size:58 final size:58
Alignment explanation
Indices: 28522835--28522954 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
28522825 ATTTCGTATA
28522835 TATAGTACATCAAATTAATCATTATTATTTTTTTTTGTAAAAGTTTCAAATTTATCAT
1 TATAGTACATCAAATTAATCATTATTATTTTTTTTTGTAAAAGTTTCAAATTTATCAT
*
28522893 TATANTACATCAAATTAATCATTATTATTTTTTTTTGTAAAAGTTTCAAATTTATCAT
1 TATAGTACATCAAATTAATCATTATTATTTTTTTTTGTAAAAGTTTCAAATTTATCAT
28522951 TATA
1 TATA
28522955 TAAGTTATAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.50
Consensus pattern (58 bp):
TATAGTACATCAAATTAATCATTATTATTTTTTTTTGTAAAAGTTTCAAATTTATCAT
Found at i:28528975 original size:2 final size:2
Alignment explanation
Indices: 28528968--28528992 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28528958 ATTATGTTGG
28528968 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28528993 GTTGTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28529137 original size:40 final size:38
Alignment explanation
Indices: 28529092--28529213 Score: 129
Period size: 40 Copynumber: 3.1 Consensus size: 38
28529082 AGGGAGATGG
* *
28529092 ATGATGATAGTGCTCGTGTGCACAATGTGGGGGGATGTAC
1 ATGATGATAGTGCT--TGTGCACGATGTGGGGGGATGCAC
** * *
28529132 ATGATGGCACTGATTGTGCACGATGTGGGGGGATGCAC
1 ATGATGATAGTGCTTGTGCACGATGTGGGGGGATGCAC
*
28529170 ATGATGACTCCG-GCTATGTGCACGATGTGGGGGGATGCAC
1 ATGATGA-T-AGTGCT-TGTGCACGATGTGGGGGGATGCAC
28529210 ATGA
1 ATGA
28529214 GCTGGATGTG
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
38 28 0.41
39 2 0.03
40 38 0.56
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.25
Consensus pattern (38 bp):
ATGATGATAGTGCTTGTGCACGATGTGGGGGGATGCAC
Found at i:28529151 original size:38 final size:40
Alignment explanation
Indices: 28529108--28529213 Score: 144
Period size: 38 Copynumber: 2.7 Consensus size: 40
28529098 ATAGTGCTCG
* * * *
28529108 TGTGCACAATGTGGGGGGATGTACATGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGCACATGATGACTACGGATA
* *
28529146 TGTGCACGATGTGGGGGGATGCACATGATGACTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACATGATGACTACGGATA
28529186 TGTGCACGATGTGGGGGGATGCACATGA
1 TGTGCACGATGTGGGGGGATGCACATGA
28529214 GCTGGATGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 29 0.48
39 3 0.05
40 28 0.47
ACGTcount: A:0.22, C:0.16, G:0.39, T:0.24
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACATGATGACTACGGATA
Found at i:28532518 original size:203 final size:203
Alignment explanation
Indices: 28532168--28532571 Score: 758
Period size: 203 Copynumber: 2.0 Consensus size: 203
28532158 ACATTTGTTG
28532168 TTAGTTAATATTGAGGGTAAAATACCATGATCCTCTTACGTTTTGATCGAAATTACATGGAAGTC
1 TTAGTTAATATTGAGGGTAAAATACCATGATCCTCTTACGTTTTGATCGAAATTACATGGAAGTC
28532233 CATTAGTTTTCGAAATGGAAACTCCGCCCCAAGACTACAAACACCGTTAATAGAAATAATAAAAA
66 CATTAGTTTTCGAAATGGAAACTCCGCCCCAAGACTACAAACACCGTTAATAGAAATAATAAAAA
28532298 GATAAAATACTTTTTTTTAATTAATTTTAAAAATTATTATT-TATATTTAAAAAAAT-AAAAAAA
131 GATAAAATACTTTTTTTTAATTAATTTTAAAAATTATTATTATAT-TTTAAAAAAATAAAAAAAA
28532361 TAAAAACCA
195 TAAAAACCA
28532370 NTTAGTTAATATTGAGGGTAAAATACCATGATCCTCTTACGTTTTGATCGAAATTACATGGAAGT
1 -TTAGTTAATATTGAGGGTAAAATACCATGATCCTCTTACGTTTTGATCGAAATTACATGGAAGT
28532435 CCATTAGTTTTCGAAATGGAAACTCCGCCCCAAGACTACAAACACCGTTAATAGAAATAATAAAA
65 CCATTAGTTTTCGAAATGGAAACTCCGCCCCAAGACTACAAACACCGTTAATAGAAATAATAAAA
*
28532500 AGACTAAAATACTTTTTTTTAATTAATTTTAAAAATTATTATTATATTTTTAAAAAATAAAAAAA
130 AGA-TAAAATACTTTTTTTTAATTAATTTTAAAAATTATTATTATATTTTAAAAAAATAAAAAAA
28532565 ATAAAAA
194 ATAAAAA
28532572 ACACTGATCG
Statistics
Matches: 197, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
203 132 0.67
204 49 0.25
205 16 0.08
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (203 bp):
TTAGTTAATATTGAGGGTAAAATACCATGATCCTCTTACGTTTTGATCGAAATTACATGGAAGTC
CATTAGTTTTCGAAATGGAAACTCCGCCCCAAGACTACAAACACCGTTAATAGAAATAATAAAAA
GATAAAATACTTTTTTTTAATTAATTTTAAAAATTATTATTATATTTTAAAAAAATAAAAAAAAT
AAAAACCA
Found at i:28534886 original size:29 final size:28
Alignment explanation
Indices: 28534836--28534897 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
28534826 ATAACACTTC
* *
28534836 TTTTTTCAATTTTTATAAATTTTGTATT
1 TTTTTTCAATTTTTATAAATTTTGGATG
*
28534864 TTTTTTC-ATTTTATAATACATTTTGGATG
1 TTTTTTCAATTTT-T-ATAAATTTTGGATG
28534893 TTTTT
1 TTTTT
28534898 AATACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 8 0.28
29 16 0.55
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.66
Consensus pattern (28 bp):
TTTTTTCAATTTTTATAAATTTTGGATG
Found at i:28536143 original size:20 final size:20
Alignment explanation
Indices: 28536120--28536158 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28536110 TATGGGTAAT
28536120 AAAAGAAAAATATAAAAATA
1 AAAAGAAAAATATAAAAATA
* *
28536140 AAAATAAAAATATGAAAAT
1 AAAAGAAAAATATAAAAAT
28536159 TGTTATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAGAAAAATATAAAAATA
Found at i:28541784 original size:26 final size:26
Alignment explanation
Indices: 28541732--28541786 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
28541722 GGAGGCCCTA
*
28541732 TAATTATATAATAATTATAATATAAT
1 TAATTATATAAAAATTATAATATAAT
28541758 TAATTATATTAAAAATATATAA-A-AAT
1 TAATTATA-TAAAAAT-TATAATATAAT
28541784 TAA
1 TAA
28541787 GATAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 14 0.54
27 7 0.27
28 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAATTATATAAAAATTATAATATAAT
Found at i:28542476 original size:247 final size:247
Alignment explanation
Indices: 28542024--28542526 Score: 965
Period size: 247 Copynumber: 2.0 Consensus size: 247
28542014 CTTTTTCTCC
28542024 TATTTCAA-ATCAATAGGGATTTGCATCTGTTATGATTTCTTCTACAGAAATTGCATCTAAAATG
1 TATTT-AACATCAATAGGGATTTGCATCTGTTATGATTTCTTCTACAGAAATTGCATCTAAAATG
28542088 AACATATATAGAACCTAATTTCCATGATACACATATCATCATAGAAAAAAACAATTTGACGAGAA
65 AACATATATAGAACCTAATTTCCATGATACACATATCATCATAGAAAAAAACAATTTGACGAGAA
28542153 TGTTGATAATGAAATAACAAGATCTCTTGAAGAATAATTTAGAATTAATATATTAGATCAAAAAA
130 TGTTGATAATGAAATAACAAGATCTCTTGAAGAATAATTTAGAATTAATATATTAGATCAAAAAA
28542218 AATTTTCACTCCAAAGTAGATTGAAACAATTTAAGATATATTAAAGTA-TTTT
195 AATTTTCACTCCAAAGTAGATTGAAACAATTTAAGATATATTAAAGTATTTTT
*
28542270 TATTTAACANTCAATATGGATTTGCATCTGTTATGATTTCTTCTACAGAAATTGCATCTAAAATG
1 TATTTAACA-TCAATAGGGATTTGCATCTGTTATGATTTCTTCTACAGAAATTGCATCTAAAATG
28542335 AACATATATAGAACCTAATTTCCATGATACACATATCATCATAGAAAAAAACAATTTGACGAGAA
65 AACATATATAGAACCTAATTTCCATGATACACATATCATCATAGAAAAAAACAATTTGACGAGAA
28542400 TGTTGATAATGAAATAACAAGATCTCTTGAAGAATAATTTAGAATTAATATATTAGATCAAAAAA
130 TGTTGATAATGAAATAACAAGATCTCTTGAAGAATAATTTAGAATTAATATATTAGATCAAAAAA
28542465 AATTTTCACTCCAAAGTAGATTGAAACAATTTAAGATATATTAAAGTATTTTT
195 AATTTTCACTCCAAAGTAGATTGAAACAATTTAAGATATATTAAAGTATTTTT
28542518 TATTTAACA
1 TATTTAACA
28542527 GTAAAATGTT
Statistics
Matches: 253, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
245 2 0.01
246 6 0.02
247 232 0.92
248 13 0.05
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (247 bp):
TATTTAACATCAATAGGGATTTGCATCTGTTATGATTTCTTCTACAGAAATTGCATCTAAAATGA
ACATATATAGAACCTAATTTCCATGATACACATATCATCATAGAAAAAAACAATTTGACGAGAAT
GTTGATAATGAAATAACAAGATCTCTTGAAGAATAATTTAGAATTAATATATTAGATCAAAAAAA
ATTTTCACTCCAAAGTAGATTGAAACAATTTAAGATATATTAAAGTATTTTT
Found at i:28543858 original size:25 final size:25
Alignment explanation
Indices: 28543824--28543871 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
28543814 TGTCAGGGTA
28543824 CGTAGTGAGTG-TTTAGTTTGAAATG
1 CGTAGTGAGTGCTTT-GTTTGAAATG
28543849 CGTAGTGAGTGCTTTGTTTGAAA
1 CGTAGTGAGTGCTTTGTTTGAAA
28543872 AGTTTCGACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.23, C:0.06, G:0.31, T:0.40
Consensus pattern (25 bp):
CGTAGTGAGTGCTTTGTTTGAAATG
Found at i:28552396 original size:14 final size:14
Alignment explanation
Indices: 28552377--28552408 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28552367 AATCAAAATT
*
28552377 AATTAATTAACTAA
1 AATTAATTAACCAA
28552391 AATTAATTAACCAA
1 AATTAATTAACCAA
28552405 AATT
1 AATT
28552409 TAAACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAATTAACCAA
Found at i:28554903 original size:16 final size:15
Alignment explanation
Indices: 28554864--28554903 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
28554854 AACATAACTT
28554864 AAAATAAAAGCAAAA
1 AAAATAAAAGCAAAA
*
28554879 ACAATTAAAAGCAAATA
1 A-AAATAAAAGCAAA-A
28554896 AAAATAAA
1 AAAATAAA
28554904 TAAACCTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGCAAAA
Found at i:28554948 original size:24 final size:25
Alignment explanation
Indices: 28554891--28554948 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
28554881 AATTAAAAGC
*
28554891 AAATAAAAATAAATAAACCTAACAT
1 AAATAAAAAAAAATAAACCTAACAT
*
28554916 -AACAAAAAAAAATAAA-CTAA-AT
1 AAATAAAAAAAAATAAACCTAACAT
*
28554938 AAATAATAAAA
1 AAATAAAAAAA
28554949 GTCTCCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 12 0.43
24 14 0.50
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (25 bp):
AAATAAAAAAAAATAAACCTAACAT
Found at i:28564978 original size:2 final size:2
Alignment explanation
Indices: 28564971--28565015 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
28564961 TTATCCCATT
28564971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28565013 TA T
1 TA T
28565016 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28572344 original size:2 final size:2
Alignment explanation
Indices: 28572331--28572364 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28572321 TACATATAAC
*
28572331 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28572365 TCAAAACGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28572659 original size:2 final size:2
Alignment explanation
Indices: 28572654--28572685 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28572644 AAACCCACTA
28572654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28572686 TATTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28573537 original size:16 final size:16
Alignment explanation
Indices: 28573516--28573554 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
28573506 CTTCCAATTC
*
28573516 TTTTATTTTCTTA-TTA
1 TTTTATTAT-TTATTTA
28573532 TTTTATTATTTATTTA
1 TTTTATTATTTATTTA
28573548 TTTTATT
1 TTTTATT
28573555 CTCTCCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTATTTATTTA
Found at i:28573952 original size:18 final size:19
Alignment explanation
Indices: 28573915--28573955 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28573905 TTAATATTTT
* *
28573915 AATATTATTTTTTTCATAA
1 AATAATATTTTATTCATAA
28573934 AATAATATTTTATTC-TAA
1 AATAATATTTTATTCATAA
28573952 AATA
1 AATA
28573956 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATATTTTATTCATAA
Found at i:28578074 original size:20 final size:22
Alignment explanation
Indices: 28578041--28578084 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
28578031 TATTAAATTA
28578041 TTAATATATATTTTTATTTATT
1 TTAATATATATTTTTATTTATT
*
28578063 TTAAT-TAT-TTTTTTTTTATT
1 TTAATATATATTTTTATTTATT
28578083 TT
1 TT
28578085 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 3 0.14
22 5 0.24
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTAATATATATTTTTATTTATT
Found at i:28578122 original size:22 final size:21
Alignment explanation
Indices: 28578097--28578155 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
28578087 TAAAAAAATA
*
28578097 AAAATATATTAATATTTTA-AT
1 AAAATATATTAAT-TTATACAT
28578118 CAAAATAATATTAATTTATACAT
1 -AAAAT-ATATTAATTTATACAT
28578141 AAAATATTATTAATT
1 AAAATA-TATTAATT
28578156 AAAATATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.03
22 22 0.67
23 10 0.30
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATATATTAATTTATACAT
Found at i:28578160 original size:15 final size:15
Alignment explanation
Indices: 28578140--28578178 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28578130 AATTTATACA
* *
28578140 TAAAATATTATTAAT
1 TAAAATATAAGTAAT
28578155 TAAAATATAAGTAAT
1 TAAAATATAAGTAAT
*
28578170 TAAATTATA
1 TAAAATATA
28578179 TAAAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAATATAAGTAAT
Found at i:28578164 original size:22 final size:22
Alignment explanation
Indices: 28578119--28578164 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
28578109 TATTTTAATC
* *
28578119 AAAATAATATTAATTTATACAT
1 AAAATAATATTAATTAAAACAT
* *
28578141 AAAATATTATTAATTAAAATAT
1 AAAATAATATTAATTAAAACAT
28578163 AA
1 AA
28578165 GTAATTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAATATTAATTAAAACAT
Found at i:28578198 original size:23 final size:24
Alignment explanation
Indices: 28578155--28578217 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
28578145 TATTATTAAT
28578155 TAAAATATAAGTAATTAAATTATA
1 TAAAATATAAGTAATTAAATTATA
28578179 TAAAATATTAA-T-ATTAAATTAT-
1 TAAAATA-TAAGTAATTAAATTATA
* * *
28578201 TAATATTTAATTAATTA
1 TAAAATATAAGTAATTA
28578218 TAAATATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 3 0.09
22 6 0.18
23 14 0.41
24 8 0.24
25 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAAATATAAGTAATTAAATTATA
Found at i:28578201 original size:14 final size:14
Alignment explanation
Indices: 28578179--28578213 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28578169 TTAAATTATA
*
28578179 TAAAATATTAATAT
1 TAAATTATTAATAT
28578193 TAAATTATTAATAT
1 TAAATTATTAATAT
*
28578207 TTAATTA
1 TAAATTA
28578214 ATTATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATTATTAATAT
Found at i:28578230 original size:24 final size:25
Alignment explanation
Indices: 28578185--28578234 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
28578175 TATATAAAAT
28578185 ATTAATATTAAATTATTAATATTTA
1 ATTAATATTAAATTATTAATATTTA
28578210 ATTAAT-TATAAA-TATTAATATTTA
1 ATTAATAT-TAAATTATTAATATTTA
28578234 A
1 A
28578235 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTAATATTAAATTATTAATATTTA
Found at i:28580576 original size:22 final size:22
Alignment explanation
Indices: 28580551--28580605 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
28580541 GCTTGAATGA
*
28580551 TTTTTTAACTTATTTAAATAAG
1 TTTTTGAACTTATTTAAATAAG
* *
28580573 TTTTTGAACTTATTTGAATGAG
1 TTTTTGAACTTATTTAAATAAG
28580595 -TTTTGAACTTA
1 TTTTTGAACTTA
28580606 AGTTATTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (22 bp):
TTTTTGAACTTATTTAAATAAG
Found at i:28587625 original size:18 final size:18
Alignment explanation
Indices: 28587602--28587724 Score: 65
Period size: 18 Copynumber: 6.7 Consensus size: 18
28587592 TATAAGTTAT
28587602 AACATATATAATAATATA
1 AACATATATAATAATATA
*
28587620 AACATAT-TAA-AACATA
1 AACATATATAATAATATA
* ** *
28587636 TATGTTTAT-ATAAATATA
1 AACATATATAAT-AATATA
* *
28587654 AATATATATAATAGTA-A
1 AACATATATAATAATATA
* *
28587671 ACATATATATAAACAAATTATA
1 A-ACATATAT-AA-TAA-TATA
*
28587693 TGACATATATAATAATATA
1 -AACATATATAATAATATA
28587712 AACATATTATAAT
1 AACATA-TATAAT
28587725 TTGTTGGAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
16 9 0.12
17 6 0.08
18 34 0.44
19 14 0.18
20 3 0.04
21 4 0.05
22 8 0.10
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (18 bp):
AACATATATAATAATATA
Found at i:28590680 original size:21 final size:21
Alignment explanation
Indices: 28590656--28590699 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28590646 ATCAAATATT
28590656 GAAAACAAATCACATAACTGA
1 GAAAACAAATCACATAACTGA
28590677 GAAAACAAATCACATAACTGA
1 GAAAACAAATCACATAACTGA
28590698 GA
1 GA
28590700 CGTAAACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.18, G:0.11, T:0.14
Consensus pattern (21 bp):
GAAAACAAATCACATAACTGA
Found at i:28605308 original size:27 final size:29
Alignment explanation
Indices: 28605258--28605314 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
28605248 TGGAGCATAA
**
28605258 GGGCAAAATGGTAATTTTACCACC-CTAG
1 GGGCAAAACAGTAATTTTACCACCACTAG
*
28605286 GGGCAAAACAGTAATTTT-TCACCACTAG
1 GGGCAAAACAGTAATTTTACCACCACTAG
28605314 G
1 G
28605315 ATACTTGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (29 bp):
GGGCAAAACAGTAATTTTACCACCACTAG
Found at i:28615885 original size:19 final size:20
Alignment explanation
Indices: 28615858--28615903 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
28615848 AAGAGACAAG
*
28615858 ATAAAATTTTTA-TAATAAA
1 ATAATATTTTTATTAATAAA
*
28615877 ATAATA-TTTTATTAATGAA
1 ATAATATTTTTATTAATAAA
28615896 ATAATATT
1 ATAATATT
28615904 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATATTTTTATTAATAAA
Found at i:28620336 original size:35 final size:35
Alignment explanation
Indices: 28620245--28620343 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
28620235 AAGGGAAATG
*
28620245 AGCTTTTTTACGGGATCAAGCGAAACCCTCATAAT
1 AGCTTTTTTACGGGATCAAGTGAAACCCTCATAAT
* * ** * * *
28620280 ATCTTTTTCACAAGATAAAGTGAAACCTTTATAAT
1 AGCTTTTTTACGGGATCAAGTGAAACCCTCATAAT
*
28620315 AGCTTTTTTATGGGATCAAGTGAAACCCT
1 AGCTTTTTTACGGGATCAAGTGAAACCCT
28620344 TCAACAATGG
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (35 bp):
AGCTTTTTTACGGGATCAAGTGAAACCCTCATAAT
Found at i:28622239 original size:19 final size:21
Alignment explanation
Indices: 28622199--28622241 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28622189 TAATAAAAGC
28622199 AAGAAAAATATATACATAATA
1 AAGAAAAATATATACATAATA
*
28622220 AAGAACAATATATA-AT-ATA
1 AAGAAAAATATATACATAATA
28622239 AAG
1 AAG
28622242 GTTTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (21 bp):
AAGAAAAATATATACATAATA
Found at i:28623859 original size:19 final size:19
Alignment explanation
Indices: 28623835--28623879 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28623825 CTAAGGAGAC
28623835 AAAATAAAATTTT-TAAAAT
1 AAAATAAAATTTTAT-AAAT
*
28623854 AAAATAAAATTTTATTAAT
1 AAAATAAAATTTTATAAAT
28623873 AAAATAA
1 AAAATAA
28623880 TATTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATAAAATTTTATAAAT
Found at i:28628036 original size:64 final size:65
Alignment explanation
Indices: 28627942--28628073 Score: 194
Period size: 64 Copynumber: 2.0 Consensus size: 65
28627932 TTGATGTACA
*
28627942 TAGATCAACAATGTACATAAACTGTTAGTTGAGTTGCCTATGGTTGGTGAG-AATTTACATGGTG
1 TAGATCAACAATGTACATAAACTATTAGTTGAGTTGCCTATGGTTGGTGAGAAATTTACATGGTG
* * * * * *
28628006 TAGATCGATAATGTACATATACTATTAGTTGATTTGCTTATGGTTGGTGGGAAATTTACATGGTG
1 TAGATCAACAATGTACATAAACTATTAGTTGAGTTGCCTATGGTTGGTGAGAAATTTACATGGTG
28628071 TAG
1 TAG
28628074 TAGAAGAGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
64 44 0.73
65 16 0.27
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.37
Consensus pattern (65 bp):
TAGATCAACAATGTACATAAACTATTAGTTGAGTTGCCTATGGTTGGTGAGAAATTTACATGGTG
Found at i:28637483 original size:27 final size:27
Alignment explanation
Indices: 28637452--28637527 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
28637442 CTTATTTCTA
*
28637452 TTGGGCCATGCCCATTTTTCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTCTTG
28637479 TTGGGCCATGCCCATTTTCCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTCTTG
*
28637506 TTGGGTCATGCCCATTTTCCTT
1 TTGGGCCATGCCCATTTTCCTT
28637528 CCTTATTACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.08, C:0.28, G:0.18, T:0.46
Consensus pattern (27 bp):
TTGGGCCATGCCCATTTTCCTTTCTTG
Found at i:28637547 original size:5 final size:5
Alignment explanation
Indices: 28637537--28637571 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
28637527 TCCTTATTAC
28637537 TTTCT TTTCT TTTCT TTTCT TTT-T TTTC- TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
28637572 CTTCCACTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:28638087 original size:36 final size:39
Alignment explanation
Indices: 28638025--28638112 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 39
28638015 CTCAACTCAG
28638025 CTCTCTTT-TTCTTTTGTTTTTCTTTCT-T-TCTCGGCT
1 CTCTCTTTGTTCTTTTGTTTTTCTTTCTGTCTCTCGGCT
* *
28638061 TTCTCTTTGTT-TTTT-TTTTGTTTTTCTGTCTCTCGGCT
1 CTCTCTTTGTTCTTTTGTTTT-TCTTTCTGTCTCTCGGCT
*
28638099 CTATCTTTGTTCTT
1 CTCTCTTTGTTCTT
28638113 CTTCATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
35 4 0.09
36 17 0.40
37 3 0.07
38 17 0.40
39 2 0.05
ACGTcount: A:0.01, C:0.22, G:0.10, T:0.67
Consensus pattern (39 bp):
CTCTCTTTGTTCTTTTGTTTTTCTTTCTGTCTCTCGGCT
Found at i:28638106 original size:38 final size:39
Alignment explanation
Indices: 28638030--28638115 Score: 111
Period size: 38 Copynumber: 2.2 Consensus size: 39
28638020 CTCAGCTCTC
* * *
28638030 TTTTTCTTTTGTTTTTCTTTCTTTCTCGGCTTTCTCTTTG
1 TTTTTCTTTTGTTTTTCTGTC-TTCTCGGCTCTATCTTTG
*
28638070 TTTTTTTTTTGTTTTTCTGTC-TCTCGGCTCTATCTTTG
1 TTTTTCTTTTGTTTTTCTGTCTTCTCGGCTCTATCTTTG
*
28638108 TTCTTCTT
1 TTTTTCTT
28638116 CATTTAACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
38 21 0.52
40 19 0.47
ACGTcount: A:0.01, C:0.20, G:0.10, T:0.69
Consensus pattern (39 bp):
TTTTTCTTTTGTTTTTCTGTCTTCTCGGCTCTATCTTTG
Found at i:28638140 original size:2 final size:2
Alignment explanation
Indices: 28638133--28638187 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
28638123 CTCATTCAAT
28638133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28638175 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
28638188 TTTATGCCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28638372 original size:2 final size:2
Alignment explanation
Indices: 28638367--28638399 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28638357 TGGTTTTTTA
*
28638367 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28638400 CTATTATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:28642218 original size:35 final size:35
Alignment explanation
Indices: 28642173--28642252 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
28642163 TTAGTTTTTG
* * *
28642173 GGTTTTGGTTGATCCCATGAAAAACCATTGTTG-TA
1 GGTTGTGGTTGAGCCCATGAAAAACCATTG-TGAAA
* *
28642208 GGTTGTGGTTGAGCCCGTGGAAAACCATTGTGAAA
1 GGTTGTGGTTGAGCCCATGAAAAACCATTGTGAAA
28642243 GGTTGTGGTT
1 GGTTGTGGTT
28642253 AAGCTTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 2 0.05
35 37 0.95
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34
Consensus pattern (35 bp):
GGTTGTGGTTGAGCCCATGAAAAACCATTGTGAAA
Found at i:28644188 original size:15 final size:15
Alignment explanation
Indices: 28644168--28644205 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28644158 TATATATATA
28644168 TTATAATTAATAA-TT
1 TTATAATT-ATAATTT
28644183 TTATAAGTTATAATTT
1 TTATAA-TTATAATTT
28644199 TTATAAT
1 TTATAAT
28644206 GTTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTATAATTT
Found at i:28644254 original size:23 final size:23
Alignment explanation
Indices: 28644228--28644271 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28644218 TAAAAGGCAA
* *
28644228 ATATATTTATATTTAAAGTATAT
1 ATATATATATATTAAAAGTATAT
28644251 ATATATATATATTAAAAGTAT
1 ATATATATATATTAAAAGTAT
28644272 TTTAGTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATATATATATTAAAAGTATAT
Found at i:28644778 original size:348 final size:339
Alignment explanation
Indices: 28644160--28645124 Score: 1139
Period size: 348 Copynumber: 2.8 Consensus size: 339
28644150 AAAGTGTGTA
*
28644160 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAAAAGG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAAAA-G
*
28644225 CAAATATATTTATATTTAAAGTATATATATATATATATTAAAAGTATTTTAGTGTATATATATAA
65 CAAATATATTTATATTTAAAGTATATATATA-A-A-ACTAAAAGTATTTTA--GTATATATATAA
* * * *
28644290 TAGTAATTATATTCCTTATAAAAGAACCCAATACATATAAAG-AATAGATATTAAAAAGCATTAC
125 TAGTAATTATATTCTTTATAAATGAACCCAATATATATAAAGTAA-ATATATTAAAAA-CATTAC
* * *
28644354 AAGTTAATTAATAAGCATAGTTTCATTAATTAATTTAATTAATTATATGGATTTGTCCTTAATTA
188 AAGTTAATTAATAATCATAGTTTAATGAATTAATTTAATTAATTATATGG-TTTGTCCTTAATTA
* * * * *
28644419 CATGAAATTAAAAAAATAGCTAATTTTCAAAACTATTCTAATATCTCAACTTCTTTTTA-G-A-T
252 CATGAAATTAAAAAAATAACTAAGTCTCAAAACTATTCTAATATCACAACTTCTTTTAAGGTATT
*
28644481 AAT-TAAGTTTATATAAACAAAAG
317 AATATAAGTTTATAGAAA-AAAAG
*
28644504 TATTTATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATA-AAAG
* * *
28644569 CAAATATGTTTATATTTAAAGTGTATTTATATATACACACACACGAAAAGTATTTTACTATATAT
65 CAAATATATTTATATTTAAA--GTA--TATATAT--A-A-A-ACTAAAAGTATTTTAGTATATAT
*
28644634 ATAATAGTAATTATATTCTTTATAAATGAACACAATATATATAAAGTAAATATATTAAAAGACAT
121 ATAATAGTAATTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAA-ACAT
* * *
28644699 TACAAGGTAATTAATAATCATAATTTTATGAATTAATTTAATTAATTATATGAGTTTGTCCTTAA
185 TACAAGTTAATTAATAATCATAGTTTAATGAATTAATTTAATTAATTATATG-GTTTGTCCTTAA
* * *
28644764 TTACATGAAATTAAAAAAAAATAACTAGGTCTGAAAACTATTCTAATCTCACAACTTCTTTTAAG
249 TTACATGAAATT--AAAAAAATAACTAAGTCTCAAAACTATTCTAATATCACAACTTCTTTTAAG
* *
28644829 GTTTATTTATTATAAGTTTTTAGAAAAAAAG
312 G--TA-TTAATATAAGTTTATAGAAAAAAAG
* * * * *
28644860 TGTATATATTATAATTAATAATTTTACAAGTTATAGTTTTTGTAATGTTAATATAAAATAAAAAG
1 TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAAT-AAAAG
* *
28644925 TAAATATATTTATATTTAAAGTATATATAT---GCTAAAAGTA--TTAGTATATATATAATATAG
65 CAAATATATTTATATTTAAAGTATATATATAAAACTAAAAGTATTTTAGTATATATAT-A-ATAG
* ** *
28644985 TAATTATATT-TCTTATAAATGAACCCAATTTATAT-AA-TGCATATATTAAAAAACATTCCAAG
128 TAATTATATTCT-TTATAAATGAACCCAATATATATAAAGTAAATATATT-AAAAACATTACAAG
* * *
28645047 TTAATTAATAATCATAGTTTAATGAA-TAAGTTTAATTAACTATATGGGTTTGTCTTTCATTACA
191 TTAATTAATAATCATAGTTTAATGAATTAA-TTTAATTAATTATAT-GGTTTGTCCTTAATTACA
*
28645111 TAAAATTAAAAAAA
254 TGAAATTAAAAAAA
28645125 ATAGTTAGTT
Statistics
Matches: 542, Mismatches: 53, Indels: 56
0.83 0.08 0.09
Matches are distributed among these distances:
340 7 0.01
341 3 0.01
342 87 0.16
343 9 0.02
344 121 0.22
345 3 0.01
346 3 0.01
348 139 0.26
349 4 0.01
350 58 0.11
351 1 0.00
352 7 0.01
354 4 0.01
356 83 0.15
357 13 0.02
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (339 bp):
TATATATATTATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAAAAGC
AAATATATTTATATTTAAAGTATATATATAAAACTAAAAGTATTTTAGTATATATATAATAGTAA
TTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAACATTACAAGTTAAT
TAATAATCATAGTTTAATGAATTAATTTAATTAATTATATGGTTTGTCCTTAATTACATGAAATT
AAAAAAATAACTAAGTCTCAAAACTATTCTAATATCACAACTTCTTTTAAGGTATTAATATAAGT
TTATAGAAAAAAAG
Found at i:28667084 original size:27 final size:27
Alignment explanation
Indices: 28667054--28667133 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
28667044 GTGTGCAATG
*
28667054 CATAAGGACGATCTCAAGTGCGTAACA
1 CATAAGGACGTTCTCAAGTGCGTAACA
* ** **
28667081 CATAAGTAATTTCTCAAGTTTGTAACA
1 CATAAGGACGTTCTCAAGTGCGTAACA
*
28667108 CACTAGGGACGTTC-CAAGTGCGTAAC
1 CA-TAAGGACGTTCTCAAGTGCGTAAC
28667134 GCATTAGTGG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
27 33 0.82
28 7 0.17
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (27 bp):
CATAAGGACGTTCTCAAGTGCGTAACA
Found at i:28669179 original size:30 final size:30
Alignment explanation
Indices: 28669104--28669206 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
28669094 TTAGAAAAAT
* * * * *
28669104 TCAAATGAGCCCTTATATTTTTATTGTG-T
1 TCAAATAAGCCCTTGTACTTTTATTTTGAG
*
28669133 TC-AATCAAGCCGTTGTACTTTTATTTTGAG
1 TCAAAT-AAGCCCTTGTACTTTTATTTTGAG
28669163 -CTAAATAAGCCCTTGTACTTTTATTTTGAG
1 TC-AAATAAGCCCTTGTACTTTTATTTTGAG
*
28669193 TCCAATAAGCCCTT
1 TCAAATAAGCCCTT
28669207 ATGATTTATG
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.05
29 20 0.33
30 34 0.56
31 4 0.07
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (30 bp):
TCAAATAAGCCCTTGTACTTTTATTTTGAG
Found at i:28673264 original size:29 final size:29
Alignment explanation
Indices: 28673232--28673294 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
28673222 GACTGTTAAT
*
28673232 TATAATGA-TTTATTTAATTAAAATAAAAA
1 TATAA-GAGTTTAATTAATTAAAATAAAAA
* *
28673261 TATAAGAGTTTAATTGATTATAATAAAAA
1 TATAAGAGTTTAATTAATTAAAATAAAAA
*
28673290 AATAA
1 TATAA
28673295 ATACTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (29 bp):
TATAAGAGTTTAATTAATTAAAATAAAAA
Found at i:28682711 original size:3 final size:3
Alignment explanation
Indices: 28682696--28682725 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28682686 TTGAACTATA
*
28682696 ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28682726 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:28683229 original size:514 final size:503
Alignment explanation
Indices: 28682320--28684428 Score: 2416
Period size: 514 Copynumber: 4.2 Consensus size: 503
28682310 TATTATTATC
* * * *
28682320 ACTTGTTACGTTAACTATCACACATTTACCTTAAGATTTTAAATTT-GCTTATTCCACTTTTATA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCCACCTTTATA
* * * * ** ** **
28682384 AGATTTTACATTAGTTCTTACAACTTTACACCAAACCTTTTCAATAACAACTTTT-AACTATAAT
65 AGATTTTACGTCAATTCTTACAATTTTACGTCAAAATTTTTCAATAGTAACTTTTGAACTATAAT
* *
28682448 TATCTTTATCTTTATTATTCTTTATTTAAAATAAAAATTTAAATATCGTTACATACTTTTAGCCC
130 TATCTTTATCTTTATTATTCTTTATTTAAAATAAAAATTTGAATATCGTTACATACTTTTAGCTC
*
28682513 GATAATATAAATATAAATGCTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTAACTTATTA
195 GATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTAACTTATTA
* * *
28682578 TGTTAACTCTCACATATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTA-
260 CGTTAACTCTCACAAATTTATGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTAC
* * * * * **
28682642 TGTTAATTGTTACAGTTTTACGTTAAAATTTATCTATACCAATTTTGAACTATAATTATTTTTAT
325 T-TCAATTCTTACAGTTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTA----T-T
**
28682707 TATTATTATTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAA-CCAG
384 T-TTATCCTTATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAACCCAG
** * *
28682771 AGAATATATTTTTGAATATTTATTTTTCACTAAAATTAGATTTATTTTTTTTTTACTTAATTG
447 AGAATATAAATTTAAATATTTA-TTTTCACTAAAATT--ATTTA---TTTTTTTACTTAATTA
* * * *
28682834 ACTTGTTACGTTAACTCTCACACATTTACGTTAAAATTTTAAATTT-GCTTATTCCACTTTTAAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCCACCTTTATA
* * ** *
28682898 AGATTTTACGTTAATTCTTACAATTTTATGTCAAGCTTTTTCAATAGTAACTTTT-AATTATAAT
65 AGATTTTACGTCAATTCTTACAATTTTACGTCAAAATTTTTCAATAGTAACTTTTGAACTATAAT
28682962 TATCTTTATCTTTATTATTCTTTATTTAAAATAAAAATTTGAATATCGTTACATACTTTTAGCTC
130 TATCTTTATCTTTATTATTCTTTATTTAAAATAAAAATTTGAATATCGTTACATACTTTTAGCTC
* *
28683027 GATAATATAAATATAAATGCTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTAACTTATTA
195 GATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTAACTTATTA
*
28683092 CGTTAACTCTCACAAATTTATGTTAAGATTTAAAATTTAGTTATTCCACTTTTATAAGTTTTTAC
260 CGTTAACTCTCACAAATTTATGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTAC
* * * * * *
28683157 TTCAGTTCTTACAGTTTTACATTAGGGCTTATCTATGTCAATTTTAAACTATAATTATTTTTATC
325 TTCAATTCTTACAGTTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTATTTTTATC
* * * ** *
28683222 CTTATTATTTTTATTTAAAAATTATAATTTGTATATCGTTAAATACTTTT-ATTCTGAGAATATA
390 CTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAACCCAGAGAATATA
* * * * *
28683286 AATTTAAATATTTGTTTTTTAATTAAATTA--AATTTTTTTACTTAATTA
455 AATTTAAATATTT-ATTTTCACTAAAATTATTTATTTTTTTACTTAATTA
* * * * **
28683334 ACTTATTATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGATATTTTACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * *
28683399 -ATCTTTACGTCAATTCTTATAGTTTTACTTCAAGATTTTTC--TACGT-CCATTTTGAACTATA
66 GAT-TTTACGTCAATTCTTACAATTTTACGTCAAAATTTTTCAATA-GTAAC-TTTTGAACTATA
* * * * *
28683460 ATTATTTTTATCTTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTGA-ACACTTTTA
128 ATTATCTTTATCTTTATTATTCTTTATTT-AAAATAAAAATTTGAATATCGTT-ACATACTTTTA
* * * * * * * *
28683524 G-TCTAAAAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTGA-
191 GCTC-GATAATATAAATATAAATACTTATTTTTCATTAAAATTAGA-CTTTTTTACTTAATTAAC
* * * *
28683587 TATGTTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTTCACATTTATAAG
254 T-TATTACGTTAACTCTCACAAATTTATGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAG
* * * * *
28683652 TTTTTACATCAATTCTTACAATTTTACGTCAAGACATATCTATGTTAATTTTCAACTATAATTAT
318 TTTTTACTTCAATTCTTACAGTTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTAT
* * * * *
28683717 TTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTAATCC-GA
383 TTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAACCCAGA
* * * ** * *
28683781 TAATACAAATATAAATGCTTATTTTCATTAAAA-T-TTGATTTTTTTACTTAATTA
448 GAATATAAATTTAAATATTTATTTTCACTAAAATTATTTATTTTTTTACTTAATTA
* *
28683835 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * *
28683900 GTTTTTAAGTCAATTGTTACAGA-TTTACGTCAAAATTTTT-TAT-GTTAA-TTTTGAACTATAA
66 GATTTTACGTCAATTCTTACA-ATTTTACGTCAAAATTTTTCAATAG-TAACTTTTGAACTATAA
* * * *
28683961 TTATTTTTATCCTTATTATTTTTTATTTAAAAGTAAAAATTTGAATATCATTACATACTTTTAGC
129 TTATCTTTATCTTTATTATTCTTTATTTAAAA-TAAAAATTTGAATATCGTTACATACTTTTAGC
* *
28684026 TCGATAATATAAATATAAATATTTATTTTTCATTAAAATTA-ATTTTTTTACTTAATTAACTTAT
193 TCGATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTAACTTAT
* * *
28684090 TACGTTAACTTTCA-AATATTTATATTAAGATTTAAAATTTATTTATTCCACCTTTATAAGTTTT
258 TACGTTAACTCTCACAA-ATTTATGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTT
** * * * *
28684154 TACGTT-AATTCTTGTAGTTTTACGTCAAGATTTATTTATGTTAATTTTGAATTATAA-T-TTTT
322 TAC-TTCAATTCTTACAGTTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTATTTT
* * *
28684216 T-TCATTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTTAATCACTTTTAACCCA-AAA
386 TATCCTTATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAACCCAGAGA
* * * *
28684279 ATATAAATTTAAAT-GTTATTTTCACTAGAATTA--GA-TTTTTTATTTAATTA
450 ATATAAATTTAAATATTTATTTTCACTAAAATTATTTATTTTTTTACTTAATTA
* * *
28684329 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCATCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * *
28684394 GTTTTTACATCAATTGTTACAGA-TTTACGTCAAAA
66 GATTTTACGTCAATTCTTACA-ATTTTACGTCAAAA
28684429 CTTAAAAATT
Statistics
Matches: 1397, Mismatches: 166, Indels: 84
0.85 0.10 0.05
Matches are distributed among these distances:
494 109 0.08
495 25 0.02
496 60 0.04
497 2 0.00
498 123 0.09
499 16 0.01
500 236 0.17
501 187 0.13
502 203 0.15
503 4 0.00
505 1 0.00
506 1 0.00
507 69 0.05
508 12 0.01
509 2 0.00
510 1 0.00
514 345 0.25
515 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (503 bp):
ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
GATTTTACGTCAATTCTTACAATTTTACGTCAAAATTTTTCAATAGTAACTTTTGAACTATAATT
ATCTTTATCTTTATTATTCTTTATTTAAAATAAAAATTTGAATATCGTTACATACTTTTAGCTCG
ATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTAACTTATTAC
GTTAACTCTCACAAATTTATGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACT
TCAATTCTTACAGTTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTATTTTTATCC
TTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAACCCAGAGAATATAA
ATTTAAATATTTATTTTCACTAAAATTATTTATTTTTTTACTTAATTA
Found at i:28683885 original size:249 final size:251
Alignment explanation
Indices: 28682320--28684432 Score: 2189
Period size: 250 Copynumber: 8.4 Consensus size: 251
28682310 TATTATTATC
* * * * *
28682320 ACTTGTTACGTTAACTATCACACATTTACCTTAAGATTTTAAATTT-GCTTATTCCACTTTTATA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCCACCTTTATA
* * * * ** * * **
28682384 AGATTTTACATTAGTTCTTACAACTTTACACCAA-ACCTTTTCAATAACAACTTTT-AACTATAA
65 AGTTTTTACATCAATTCTTACAATTTTACGTCAAGA-CTTATCTATGTCAA-TTTTGAACTATAA
* * * ** **
28682447 TTATCTTTATCTTTATTATTCTTTATTT-AAAATAAAAATTTAAATATCGTTACATACTTTTAGC
128 TTATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTTAAT
* *
28682511 CCGATAATATAAATATAAATGCTTATTTTTCATTAAAATTAGACTTTTTTACTTAATTA
193 CCGATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* *
28682570 ACTTATTATGTTAACTCTCACATATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
** * * * * * * **
28682635 GTTTTTATGTTAATTGTTACAGTTTTACGTTAAAATTTATCTATACCAATTTTGAACTATAATTA
66 GTTTTTACATCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTA
** * * * *
28682700 TTTTTATTATTATTATTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTT
131 ----T-TT-TTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTT
* ** * * * *
28682765 AA-CCAGAGAATATATTTTTGAATATTTATTTTTCACTAAAATTAGATTTATTTTTTTTTTACTT
190 AATCC-GATAATATAAATATAAATGTTTATTTTTCATTAAAATTAG----A---TTTTTTTACTT
*
28682829 AATTG
247 AATTA
* * * * *
28682834 ACTTGTTACGTTAACTCTCACACATTTACGTTAAAATTTTAAATTT-GCTTATTCCACTTTTAAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCCACCTTTATA
* * * * * * *
28682898 AGATTTTACGTTAATTCTTACAATTTTATGTCAAG-CTTTTTCAATAGT-AACTTTT-AATTATA
65 AGTTTTTACATCAATTCTTACAATTTTACGTCAAGAC-TTATCTAT-GTCAA-TTTTGAACTATA
* * * *
28682960 ATTATCTTTATCTTTATTATTCTTTATTT-AAAATAAAAATTTGAATATCGTTACATACTTTT-A
127 ATTATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTTAA
* * * *
28683023 GCTCGATAATATAAATATAAATGCTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTA
192 TC-CGATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * *
28683084 ACTTATTACGTTAACTCTCACAAATTTATGTTAAGATTTAAAATTTAGTTATTCCACTTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * * * * *
28683149 GTTTTTACTTCAGTTCTTACAGTTTTACATTAGGGCTTATCTATGTCAATTTTAAACTATAATTA
66 GTTTTTACATCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTA
* * * *
28683214 TTTTTATCCTTATTATT-TTTATTTAAAAATTATAATTTGTATATCGTTAAATACTTTTATTCTG
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTTAATCCG
* * * * * *
28683278 AGAATATAAATTTAAATATTTGTTTTTTAATT-AAATTAAATTTTTTTACTTAATTA
196 ATAATATAAATATAAATGTTT-ATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * **
28683334 ACTTATTATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGATATTTTACCTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * * * * * * *
28683399 ATCTTTACGTCAATTCTTATAGTTTTACTTCAAGATTTTTCTACGTCCATTTTGAACTATAATTA
66 GTTTTTACATCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTA
* * * * *
28683464 TTTTTATCTTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTGA-ACACTTTTAGTCT
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTT-ACATACTTTTAATCC
* * * * * * *
28683528 AAAAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTG
195 GATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGA-TTTTTTTACTTAATTA
* * * *
28683586 A-TATGTTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTTCACATTTATA
1 ACT-TATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATA
* * *
28683650 AGTTTTTACATCAATTCTTACAATTTTACGTCAAGACATATCTATGTTAATTTTCAACTATAATT
65 AGTTTTTACATCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATT
*
28683715 ATTTTTATCCTTATTATT-TTTATTTAAAAATTAAAATTTGTATATTGTTACATACTTTTAATCC
130 ATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTTAATCC
* * *
28683779 GATAATACAAATATAAATGCTTA-TTTTCATTAAAATTTGATTTTTTTACTTAATTA
195 GATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
*
28683835 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTTCACCTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * *
28683900 GTTTTTA-AGTCAATTGTTACAGA-TTTACGTCAA-AATTTTTTATGTTAATTTTGAACTATAAT
66 GTTTTTACA-TCAATTCTTACA-ATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAAT
* * * * * *
28683962 TATTTTTATCCTTATTATTTTTTATTTAAAAGTAAAAATTTGAATATCATTACATACTTTT-AGC
129 TATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTTAATC
*
28684026 TCGATAATATAAATATAAATATTTATTTTTCATTAAAATTA-ATTTTTTTACTTAATTA
194 -CGATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * ** *
28684084 ACTTATTACGTTAACTTTCAAATATTTATATTAAGATTTAAAATTTATTTATTCCACCTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * ** * * * * *
28684149 GTTTTTACGTTAATTCTTGTAGTTTTACGTCAAGATTTATTTATGTTAATTTTGAATTATAA-T-
66 GTTTTTACATCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTA
* * *
28684212 TTTTT-TCATTATTATTCTTTATTTAAAAATTAAAATTTATATATCGTTA-ATCACTTTTAACCC
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACAT-ACTTTTAATCC
* * * * * *
28684275 AAAAATATAAATTTAAATG-TTA-TTTTCACTAGAATTAGA-TTTTTTATTTAATTA
195 GATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
* * * *
28684329 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTTCATCTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* *
28684394 GTTTTTACATCAATTGTTACAGA-TTTACGTCAAAACTTA
66 GTTTTTACATCAATTCTTACA-ATTTTACGTCAAGACTTA
28684433 AAAATTAAAT
Statistics
Matches: 1567, Mismatches: 246, Indels: 105
0.82 0.13 0.05
Matches are distributed among these distances:
245 113 0.07
246 6 0.00
247 59 0.04
248 53 0.03
249 278 0.18
250 487 0.31
251 139 0.09
252 142 0.09
253 1 0.00
254 1 0.00
255 1 0.00
256 22 0.01
257 122 0.08
258 20 0.01
259 1 0.00
260 1 0.00
261 1 0.00
263 1 0.00
264 115 0.07
265 4 0.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (251 bp):
ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
GTTTTTACATCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTGAACTATAATTA
TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTACATACTTTTAATCCG
ATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
Found at i:28684589 original size:200 final size:196
Alignment explanation
Indices: 28684234--28684608 Score: 536
Period size: 200 Copynumber: 1.9 Consensus size: 196
28684224 TATTCTTTAT
** *
28684234 TTAAAAATTAAAATTTATATATCGTTAATCACTTTTAACCCAAAAATATAAATTTAAATGTTATT
1 TTAAAAATTAAAATTTATATATCGTTAAAAACTTTTAACACAAAAATATAAATTTAAATGTTATT
* * *
28684299 TTCACTAGAATTAGATTTTTTATTTAATTAACTTGTTACGTTAACTCTCACACATTTACGTTAAG
66 TTAACTAAAATTAGATTTTTTATTTAATTAACTTATTACGTTAACTCTCACACATTTACGTTAAG
* *
28684364 ATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTACATCAATTGTTACAGATTTACGTCAAAA
131 ATTAAAAATTTAATTATTCCATCTTTATAAGTTTTTACATCAATTGTTACAGATTTACGTCAAAA
28684429 C
196 C
* ** * * *
28684430 TTAAAAATT-AAATTTGTATATCGTTAAAAACTTTTAGTACAAGAATATAAATTTAAATATTTGT
1 TTAAAAATTAAAATTTATATATCGTTAAAAACTTTTAACACAAAAATATAAATTTAAAT-GTT-A
* *
28684494 TTTTAACTAAAATTAGATTTTTTTTTATTTAATTAACTTATTACGTTAACTTTCACACGTTTACG
64 TTTTAACTAAAATTAGA---TTTTTTATTTAATTAACTTATTACGTTAACTCTCACACATTTACG
* *
28684559 TTAAGATTAAAAATTTAGTTATTCCATCTTTATAAGTTTTTACGTCAATT
126 TTAAGATTAAAAATTTAATTATTCCATCTTTATAAGTTTTTACATCAATT
28684609 CTCACAGTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
195 42 0.27
196 11 0.07
197 15 0.10
200 88 0.56
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (196 bp):
TTAAAAATTAAAATTTATATATCGTTAAAAACTTTTAACACAAAAATATAAATTTAAATGTTATT
TTAACTAAAATTAGATTTTTTATTTAATTAACTTATTACGTTAACTCTCACACATTTACGTTAAG
ATTAAAAATTTAATTATTCCATCTTTATAAGTTTTTACATCAATTGTTACAGATTTACGTCAAAA
C
Found at i:28687856 original size:503 final size:501
Alignment explanation
Indices: 28686669--28688440 Score: 2529
Period size: 503 Copynumber: 3.5 Consensus size: 501
28686659 TTAGAACCTT
* * *
28686669 ATAATTATACTTCAAAGTTGAAACGGAAAAACCTTGACGTAAAACTGGAAGAATTGAAGTAAAAA
1 ATAATTATAATTCAAAGTTGAAACGGAAAAACCTTGACGTAAAACTAGAAGAATTGATGTAAAAA
* * *
28686734 TTTGTAAAGGTAGAATAACTAAATTTTAAAT-TTGAACGTAAGTGTGTAAGAGTTAACATAACAA
66 CTTGTAAAGGTGGAATAACTAAATTTTAAATCTT-AACGTAAGTGTATAAGAGTTAACATAACAA
* * *
28686798 ATCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTCTCGGGTT
130 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
* *
28686863 AAAAATGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATAATTA
195 AAAAGTGTTTAACGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATAATTA
* * *
28686928 TAGTTCAAAGTTGACATGGAAAAGTCTTGACATAAAACTAT--GATTGACGTAAAATTTTGTAAA
260 TAATTCAAAGTTGACATGGAAAAGTCTTGACATAAAACTATAAAATTGACGTAAAAATTTGTAAA
* * * * *
28686991 GATGGAATAATTAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAATGTAACAAGTCAATTAA
325 GGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTGAAAGTTAACGTAACAAGTCAATTAA
* * * * *
28687056 GTAAAAATAATTTAAATTTAATAAAAAATAAATATTTAAATTTATATTATCGAATTAAAAGTGTT
390 GTAAAAACAA-TTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTTGAGTTAAAAGTGTT
*
28687121 TAACGATATACAAATTTTAATTTTTAAATAAAAAATAATAAGCATAAAA
454 TAACGATATACAAATTTTAATTTTTAAAT-AAAAATAATAAGGATAAAA
* * * * * *
28687170 ATAATTATAAATCAAAGTTGACATGG-AAAACTTTAGACGTAAAACTATAAGAATTGATATAAAA
1 ATAATTATAATTCAAAGTTGAAACGGAAAAACCTT-GACGTAAAACTAGAAGAATTGATGTAAAA
* * * * * *
28687234 ACTTGTAAAGGTGAAATAACTAAATTTAAAATCTTAACGTAAATGTGTGAA-AGTTAACGTAATA
65 ACTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTAT-AAGAGTTAACATAACA
* *
28687298 AGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTATCGGGT
129 AGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGAT
*
28687363 TAAAAGTGTTTAACGATATACAGATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATT
194 TAAAAGTGTTTAACGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATAATT
* * * *
28687428 ATAATTCAAAGTTAACATGGAAAAGTCTTGCCATAAAACTATAAAAATTAACCTAAAAATTTGTA
259 ATAATTCAAAGTTGACATGGAAAAGTCTTGACATAAAACTAT-AAAATTGACGTAAAAATTTGTA
* * * *
28687493 AAGGTGGAATAACTAAATTTTAAATCTTAACATAAGTGTGTGATAGTTAACGTAACAAGTTAATT
323 AAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTGAAAGTTAACGTAACAAGTCAATT
28687558 AAGTAAAAACAAGTTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTTGAGTTAAAAGTG
388 AAGTAAAAACAA-TTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTTGAGTTAAAAGTG
28687623 TTTAACGATATACAAATTTTAATTTTTAAATAAAAATAATAAGGATAAAA
452 TTTAACGATATACAAATTTTAATTTTTAAATAAAAATAATAAGGATAAAA
* *
28687673 ATAATTATAATTTAAAGTTGAAACGGAAAAGCCTTGACGTAAAACTAGAAGAATT-AGTGTAAAA
1 ATAATTATAATTCAAAGTTGAAACGGAAAAACCTTGACGTAAAACTAGAAGAATTGA-TGTAAAA
* * * * *
28687737 ACTTGTGAAGGTGGTATAACTAAATTTTAAATCTTAACGTAAGTGTATAAGTGCTAACATAATAA
65 ACTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTATAAGAGTTAACATAACAA
* * **
28687802 GTCAATTAAGTAAAAACAATATAAATTTCATGAAAAATAAATATTTAAATTTATATTTTTAGATT
130 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
* * *
28687867 AAAAGTTTTTAACAATATACA-AGTTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATT
195 AAAAGTGTTTAACGATATACAGA-TTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATAATT
* * * * *
28687931 ATAATTCAAAATTGACATGGAAAAATCTT-ATCGTAAAACTATAAGAATTGACGTAAAAACTTAT
259 ATAATTCAAAGTTGACATGGAAAAGTCTTGA-CATAAAACTATAA-AATTGACGTAAAAATTTGT
* *
28687995 AAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTTACAAGTCAAT
322 AAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTGAAAGTTAACGTAACAAGTCAAT
* *
28688060 TAAGTAAAAACAATCTCAATTTAATGAAAAATAAATATTTAAATTTATA-TTTTCAGATTAAAAG
387 TAAGTAAAAACAAT-TAAATTTAATGAAAAATAAATATTTAAATTTATATTTTTGAG-TTAAAAG
* *
28688124 TGTTTAACGATGTGCAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
450 TGTTTAACGATATACAAATTTTAATTTTTAAATAAA-AATAATAAGGATAAAA
* * * * * *
28688177 ATAATTATAATTCAAAATTGACATGGAAAAATCTT-ATCGTAAAACTATAAGAATTGACGTAAAA
1 ATAATTATAATTCAAAGTTGAAACGGAAAAACCTTGA-CGTAAAACTAGAAGAATTGATGTAAAA
* * * * * *
28688241 ACTTATAAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTTACAA
65 ACTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTATAAGAGTTAACATAACAA
28688306 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
130 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
* ** * *
28688371 AAAAGTGTTTAATGATATGTAGATTTTAATTTTTATATAAAGAATAATAAAGATGAAAATAATTA
195 AAAAGTGTTTAACGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATAATTA
28688436 TAATT
260 TAATT
28688441 TACAGTTACT
Statistics
Matches: 1135, Mismatches: 118, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
500 7 0.01
501 262 0.23
502 17 0.01
503 435 0.38
504 412 0.36
505 2 0.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (501 bp):
ATAATTATAATTCAAAGTTGAAACGGAAAAACCTTGACGTAAAACTAGAAGAATTGATGTAAAAA
CTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTATAAGAGTTAACATAACAAG
TCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATTA
AAAGTGTTTAACGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATAATTAT
AATTCAAAGTTGACATGGAAAAGTCTTGACATAAAACTATAAAATTGACGTAAAAATTTGTAAAG
GTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTGAAAGTTAACGTAACAAGTCAATTAAG
TAAAAACAATTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTTGAGTTAAAAGTGTTTA
ACGATATACAAATTTTAATTTTTAAATAAAAATAATAAGGATAAAA
Found at i:28688123 original size:755 final size:752
Alignment explanation
Indices: 28686728--28688447 Score: 2516
Period size: 755 Copynumber: 2.3 Consensus size: 752
28686718 AGAATTGAAG
* * *
28686728 TAAAAATTTGTAAAGGTAGAATAACTAAATTTTAAAT-TTGAACGTAAGTGTGTAAGAGTTAACA
1 TAAAAATTTGTAAAGGTGGAATAACTAAATTTTAAATCTT-AACGTAAGTGTGTAAAAGTTAACG
* *
28686792 TAACAAATCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTCT
65 TAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTT
*
28686857 CGGGTTAAAAATGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAA
130 C-GGTTAAAAGTGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAA
* * * * * * **
28686922 TAATTATAGTTCAAAGTTGACATGGAAAAGTCTTGACATAAAACTATGATTGACGTAAAATTTTG
194 TAATTATAATTTAAAGTTGAAACGGAAAAGCCTTGACATAAAACTAAGATTGACGTAAAAACTTG
* * * * **
28686987 TAAAGATGGAATAATTAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAATGTAACAAGTCAA
259 TAAAGATGGAATAACTAAATTTTAAATCTTAACGTAAATATATAAGAGCTAACATAACAAGTCAA
* * *
28687052 TTAAGTAAAAATAATTTAAATTTAATAAAAAATAAATATTTAAATTTATATTATCGAATTAAAAG
324 TTAAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTTATATTATAGAATTAAAAG
*
28687117 TGTTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAATAAGCATAAAAATAATTATAAAT
389 TGTTTAACAATATACAAATTTTAATTTTTAAATAAAAAATAATAAGCATAAAAATAATTATAAAT
* * * *
28687182 CAAAGTTGACATGGAAAACTTTAGACGTAAAACTATAAGAATTGATATAAAAACTTGTAAAGGTG
454 CAAAATTGACATGGAAAAATTTAGACGTAAAACTATAAGAATTGACATAAAAACTTATAAAGGTG
* *
28687247 AAATAACTAAATTTAAAATCTTAACGTAAATGTGTGAAAGTTAACGTAATAAGTCAATTAAGTAA
519 AAATAACTAAATTTAAAATCTTAACGTAAATGTGTAAAAGTTAACGTAACAAGTCAATTAAGTAA
* *
28687312 AAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTATCGGGTTAAAAGTGTTTAAC
584 AAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTATCAGATTAAAAGTGTTTAAC
* *
28687377 GATATACAGATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTA
649 GATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAATTCAAAATTA
* *
28687442 ACATGGAAAAGTCTTGCCATAAAACTATAAAAATTAACC
714 ACATGGAAAAATCTTACCATAAAACTATAAAAATTAACC
* * *
28687481 TAAAAATTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACATAAGTGTGTGATAGTTAACGT
1 TAAAAATTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGT
*
28687546 AACAAGTTAATTAAGTAAAAACAAGT-TAAATTTAATGAAAAATAAATATTTAAATTTATATTTT
66 AACAAGTCAATTAAGTAAAAACAA-TCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTT
* * * *
28687610 TGAGTTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAA-AATAATAAGGATAAAAA
130 CG-GTTAAAAGTGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAA
* *
28687674 TAATTATAATTTAAAGTTGAAACGGAAAAGCCTTGACGTAAAACTAGAAGAATT-AGTGTAAAAA
194 TAATTATAATTTAAAGTTGAAACGGAAAAGCCTTGACATAAAACT--AAG-ATTGA-CGTAAAAA
* * * * * * *
28687738 CTTGTGAAGGTGGTATAACTAAATTTTAAATCTTAACGTAAGTGTATAAGTGCTAACATAATAAG
255 CTTGTAAAGATGGAATAACTAAATTTTAAATCTTAACGTAAATATATAAGAGCTAACATAACAAG
* * *
28687803 TCAATTAAGTAAAAACAATATAAATTTCATGAAAAATAAATATTTAAATTTATATTTTTAG-ATT
320 TCAATTAAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTTATA-TTATAGAATT
* * * *
28687867 AAAAGTTTTTAACAATATACAAGTTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTA
384 AAAAGTGTTTAACAATATACAAATTTTAATTTTTAAATAAAAAATAATAAGCATAAAAATAATTA
* * *
28687932 TAATTCAAAATTGACATGGAAAAATCTTA-TCGTAAAACTATAAGAATTGACGTAAAAACTTATA
449 TAAATCAAAATTGACATGGAAAAAT-TTAGACGTAAAACTATAAGAATTGACATAAAAACTTATA
* * * * *
28687996 AAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTTACAAGTCAATT
513 AAGGTGAAATAACTAAATTTAAAATCTTAACGTAAATGTGTAAAAGTTAACGTAACAAGTCAATT
* *
28688061 AAGTAAAAACAATCTCAATTTAATGAAAAATAAATATTTAAATTTATATTTTCAGATTAAAAGTG
578 AAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTATCAGATTAAAAGTG
* *
28688126 TTTAACGATGTGCAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAATTCA
643 TTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAATTCA
* * * * * *
28688191 AAATTGACATGGAAAAATCTTATCGTAAAACTATAAGAATTGACG
708 AAATTAACATGGAAAAATCTTACCATAAAACTATAAAAATTAACC
* * *
28688236 TAAAAACTTATAAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGT
1 TAAAAATTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGT
*
28688301 TACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTC
66 AACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTC
** * *
28688366 GGATTAAAAGTGTTTAATGATATGTAGATTTTAATTTTTATATAAAGAATAATAAAGATGAAAAT
131 GG-TTAAAAGTGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAAT
*
28688431 AATTATAATTTACAGTT
195 AATTATAATTTAAAGTT
28688448 ACTATCAGAA
Statistics
Matches: 861, Mismatches: 94, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
752 56 0.07
753 157 0.18
754 8 0.01
755 601 0.70
756 39 0.05
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34
Consensus pattern (752 bp):
TAAAAATTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGT
AACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTC
GGTTAAAAGTGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAAATA
ATTATAATTTAAAGTTGAAACGGAAAAGCCTTGACATAAAACTAAGATTGACGTAAAAACTTGTA
AAGATGGAATAACTAAATTTTAAATCTTAACGTAAATATATAAGAGCTAACATAACAAGTCAATT
AAGTAAAAACAATATAAATTTAATAAAAAATAAATATTTAAATTTATATTATAGAATTAAAAGTG
TTTAACAATATACAAATTTTAATTTTTAAATAAAAAATAATAAGCATAAAAATAATTATAAATCA
AAATTGACATGGAAAAATTTAGACGTAAAACTATAAGAATTGACATAAAAACTTATAAAGGTGAA
ATAACTAAATTTAAAATCTTAACGTAAATGTGTAAAAGTTAACGTAACAAGTCAATTAAGTAAAA
ACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTATCAGATTAAAAGTGTTTAACGA
TATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAATTCAAAATTAAC
ATGGAAAAATCTTACCATAAAACTATAAAAATTAACC
Found at i:28688534 original size:252 final size:252
Alignment explanation
Indices: 28686669--28688440 Score: 2455
Period size: 252 Copynumber: 7.0 Consensus size: 252
28686659 TTAGAACCTT
* * * * * ** *
28686669 ATAATTATACTTCAAAGTTGAAACGGAAAAACCTTGACGTAAAACTGGAAGAATTGAAGTAAAAA
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGACGTAAAAA
* * * *
28686734 TTTGTAAAGGTAGAATAACTAAATTTTAAAT-TTGAACGTAAGTGTGTAAGAGTTAACATAACAA
66 CTTGTAAAGGTGGAATAACTAAATTTTAAATCTT-AACGTAAGTGTGTAAAAGTTAACGTAACAA
* * *
28686798 ATCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTCTCGGGTT
130 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
* * * *
28686863 AAAAATGTTTAATGATATACAGATTTTAATTTTTAAATAAAGAATAATAAAGATAAAA
195 AAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
* * * * *
28686921 ATAATTATAGTTCAAAGTTGACATGGAAAAGTCTTGACATAAAACTAT--G-ATTGACGTAAAAT
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGACGTAAAAA
* * * * * * * *
28686983 TTTGTAAAGATGGAATAATTAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAATGTAACAAG
66 CTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAAG
* * * * *
28687048 TCAATTAAGTAAAAATAATTTAAATTTAATAAAAAATAAATATTTAAATTTATATTATCGAATTA
131 TCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATTA
* *
28687113 AAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAATAAGCATAAAA
196 AAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
* * * **
28687170 ATAATTATAAATCAAAGTTGACATGGAAAACT-TTAGACGTAAAACTATAAGAATTGATATAAAA
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTT-GTCGTAAAACTATAAGAATTGACGTAAAA
* * * * *
28687234 ACTTGTAAAGGTGAAATAACTAAATTTAAAATCTTAACGTAAATGTGTGAAAGTTAACGTAATAA
65 ACTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAA
* *
28687299 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTATCGGGTT
130 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
*
28687364 AAAAGTGTTTAACGATATACAGATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
195 AAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
* * * * * * *
28687422 ATAATTATAATTCAAAGTTAACATGGAAAAGTCTTGCCATAAAACTATAAAAATTAACCTAAAAA
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGACGTAAAAA
* * * *
28687487 TTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACATAAGTGTGTGATAGTTAACGTAACAAG
66 CTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAAG
* *
28687552 TTAATTAAGTAAAAACAAGT-TAAATTTAATGAAAAATAAATATTTAAATTTATATTTT-TGAGT
131 TCAATTAAGTAAAAACAA-TCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGA-T
28687615 TAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAA-AATAATAAGGATAAAA
194 TAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
* * * ** * * *
28687673 ATAATTATAATTTAAAGTTGAAACGGAAAAGCCTTGACGTAAAACTAGAAGAATT-AGTGTAAAA
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGA-CGTAAAA
* * * ** * * *
28687737 ACTTGTGAAGGTGGTATAACTAAATTTTAAATCTTAACGTAAGTGTATAAGTGCTAACATAATAA
65 ACTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAA
* * **
28687802 GTCAATTAAGTAAAAACAATATAAATTTCATGAAAAATAAATATTTAAATTTATATTTTTAGATT
130 GTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATT
* * *
28687867 AAAAGTTTTTAACAATATACAAGTTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
195 AAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
* *
28687925 ATAATTATAATTCAAAATTGACATGGAAAAATCTTATCGTAAAACTATAAGAATTGACGTAAAAA
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGACGTAAAAA
* * *
28687990 CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTTACAAG
66 CTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAAG
* *
28688055 TCAATTAAGTAAAAACAATCTCAATTTAATGAAAAATAAATATTTAAATTTATATTTTCAGATTA
131 TCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATTA
* *
28688120 AAAGTGTTTAACGATGTGCAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
196 AAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
* *
28688177 ATAATTATAATTCAAAATTGACATGGAAAAATCTTATCGTAAAACTATAAGAATTGACGTAAAAA
1 ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGACGTAAAAA
* * *
28688242 CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTTACAAG
66 CTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAAG
28688307 TCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATTA
131 TCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATTA
* ** * * * *
28688372 AAAGTGTTTAATGATATGTAGATTTTAATTTTTATATAAAGAATAATAAAGATGAAA
196 AAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
28688429 ATAATTATAATT
1 ATAATTATAATT
28688441 TACAGTTACT
Statistics
Matches: 1364, Mismatches: 143, Indels: 26
0.89 0.09 0.02
Matches are distributed among these distances:
248 2 0.00
249 215 0.16
250 5 0.00
251 218 0.16
252 920 0.67
253 4 0.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (252 bp):
ATAATTATAATTCAAAGTTGACATGGAAAAATCTTGTCGTAAAACTATAAGAATTGACGTAAAAA
CTTGTAAAGGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGTAAAAGTTAACGTAACAAG
TCAATTAAGTAAAAACAATCTAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCGGATTA
AAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAA
Found at i:28716717 original size:48 final size:48
Alignment explanation
Indices: 28716668--28717867 Score: 1222
Period size: 48 Copynumber: 24.8 Consensus size: 48
28716658 ATCTGCTCCT
* * *
28716668 CCTCCATATGTTTACAAGTCTCCACCACCTCCATCTCCATCACCCCCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* *
28716716 CCACCTTATGTTTACAAATCTCCACCTCCTCCATCTCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* * * * * * *
28716764 CCTCCTTATGTTTATAAATCTCCGCCACCACCATCACCTTCACCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* *
28716812 CCTCCGTATGTTTACAAGTCTCCACCACCTCCATCTCCATCACCCCCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
*
28716860 CCACCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* * *
28716908 CCACCTTATGTTTACAAATCTCCACCACCTCCATCCCCATC-CCCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* ** * * * * *
28716956 CCTCCATACT-ACTACAAGTCTCCACCACCACCA-ATACATTCA-CCACA
1 CCTCCTTA-TGTTTACAAATCTCCACCACCTCCATCTCCA-TCACCCCCA
* * *
28717003 TCCACCTTATGTTTACAAATCTCCACCTCCTCCATCTCCATCACCACCA
1 -CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
*
28717052 CCTCCTTATGTTTACAAATCTCCACCTCCTCCATCTCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* * * * * * *
28717100 CCTCTTTATGTTTATAAATCTCCACCACCACCATCACCTTCACCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* * * * ** *
28717148 CCTCCATATGTTTACAAGTCACCTCCACCTCCTCCATATAAGTATAAGTCACCACCTCCT
1 CCTCCTTATGTTTACAA---ATCTCCACCACCTCC--AT--CT-CCA-TCA-C-CC-CCA
* * * *
28717208 CCTCCATATGTTTACAAGTCTCCACCTCCTCCATCTCCATCACCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
*
28717256 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCGCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* * * * * *
28717304 CCTCCTTATGTTTATAAATCTCCACCACCACCATCACCTTCACCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* * *
28717352 CCTCCATATGTTTACAAGTCTCCACCTCCTCCATCTCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* * * * * * *
28717400 CCTCTTTATGTTTATAAATCTCCACCACCACCATCGCCTTCACCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* * *
28717448 CCTCCATATGTTTACAAGTCTCCACCTCCTCCATCTCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
*
28717496 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCGCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* * * * * * * *
28717544 CCTCCTTATGTTTATAAATATCCACCACCACCATCACCTTCGCCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* * * *
28717592 CCTCCATATGTTTACAAGTCTCCACCTCCTCCATCTCCATC-CCCACTA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
* * * * * * *
28717640 CCTTCTTATGTTTATAAATCTCCACCACCACCATCACCTTCACCACCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* * *
28717688 TCTCCATATGTTTACAAGTCTCCACCACCTCCATCTCCATCACCCCCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
* *
28717736 CCACCTTATGTTTACAAATCTCCACCTCCTCCATCTCCATC-CCCACCA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
28717784 CCT-CTATATGTTTACAAATCTCCACCACCTCCATCTCCATC-CCCACCA
1 CCTCCT-TATGTTTACAAATCTCCACCACCTCCATCTCCATCACCC-CCA
*
28717832 CCTCCTTATGTTTATAAATCTCCACCACCTCCATCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCT
28717868 TCATACATGT
Statistics
Matches: 947, Mismatches: 170, Indels: 70
0.80 0.14 0.06
Matches are distributed among these distances:
47 25 0.03
48 840 0.89
49 22 0.02
50 1 0.00
51 15 0.02
52 1 0.00
53 3 0.00
55 2 0.00
57 16 0.02
58 1 0.00
59 1 0.00
60 20 0.02
ACGTcount: A:0.24, C:0.45, G:0.03, T:0.28
Consensus pattern (48 bp):
CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCCCCA
Found at i:28716830 original size:144 final size:144
Alignment explanation
Indices: 28716668--28717867 Score: 1418
Period size: 144 Copynumber: 8.2 Consensus size: 144
28716658 ATCTGCTCCT
* * *
28716668 CCTCCATATGTTTACAAGTCTCCACCACCTCCATCTCCATCACCCCCTCCACCTTATGTTTACAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
* * *
28716733 ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTATAAATCTCCGCCACCACCAT
66 ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCAT
* * * *
28716798 CACCTTCACCACCT
131 CTCCATCCCCACCA
* * * *
28716812 CCTCCGTATGTTTACAAGTCTCCACCACCTCCATCTCCATCACCCCCACCACCTTATGTTTACAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
* *
28716877 ATCTCCACCACCTCCATCTCCATCACCC-CCACCACCTTATGTTTACAAATCTCCACCACCTCCA
66 ATCTCCACCTCCTCCATCTCCATC-CCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCA
* *
28716941 TCCCCATCCCCACCT
130 TCTCCATCCCCACCA
* ** * * * * *
28716956 CCTCCATACT-ACTACAAGTCTCCACCACCACCA-ATACATTCACCACATCCACCTTATGTTTAC
1 CCTCCTTA-TGTTTACAAATCTCCACCACCTCCATCTCCA-TCACCACCTCCACCTTATGTTTAC
* *
28717019 AAATCTCCACCTCCTCCATCTCCATCACCACCACCTCCTTATGTTTACAAATCTCCACCTCCTCC
64 AAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCC
28717084 ATCTCCATCCCCACCA
129 ATCTCCATCCCCACCA
* * * * * * *
28717100 CCTCTTTATGTTTATAAATCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
* * ** * * *
28717165 GTCACCTCCACCTCCTCCATATAAGTATAAGTCACCACCTCCTCCTCCATATGTTTACAAGTCTC
66 ---ATCTCCACCTCCTCC--AT--CT-CCA-TCCCCACCACCTCCT---TATGTTTACAAATCTC
* *
28717230 CACCTCCTCCATCTCCATCACCACCA
119 CACCACCTCCATCTCCATCCCCACCA
* * * * *
28717256 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCGCCATCCCCACCACCTCCTTATGTTTATAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
* * * * * * * * *
28717321 ATCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCTCCTCCAT
66 ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCAT
28717386 CTCCATCCCCACCA
131 CTCCATCCCCACCA
* * * * * * *
28717400 CCTCTTTATGTTTATAAATCTCCACCACCACCATCGCCTTCACCACCTCCTCCATATGTTTACAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
*
28717465 GTCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCAT
66 ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCAT
*
28717530 CGCCATCCCCACCA
131 CTCCATCCCCACCA
* * * * * * * *
28717544 CCTCCTTATGTTTATAAATATCCACCACCACCATCACCTTCGCCACCTCCTCCATATGTTTACAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
* * * * *
28717609 GTCTCCACCTCCTCCATCTCCATCCCCACTACCTTCTTATGTTTATAAATCTCCACCACCACCAT
66 ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCAT
* * * *
28717674 CACCTTCACCACCT
131 CTCCATCCCCACCA
* * * * *
28717688 TCTCCATATGTTTACAAGTCTCCACCACCTCCATCTCCATCACCCCCACCACCTTATGTTTACAA
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
28717753 ATCTCCACCTCCTCCATCTCCATCCCCACCACCT-CTATATGTTTACAAATCTCCACCACCTCCA
66 ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCT-TATGTTTACAAATCTCCACCACCTCCA
28717817 TCTCCATCCCCACCA
130 TCTCCATCCCCACCA
*
28717832 CCTCCTTATGTTTATAAATCTCCACCACCTCCATCT
1 CCTCCTTATGTTTACAAATCTCCACCACCTCCATCT
28717868 TCATACATGT
Statistics
Matches: 917, Mismatches: 120, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
143 8 0.01
144 748 0.82
145 5 0.01
147 28 0.03
149 2 0.00
151 3 0.00
152 1 0.00
153 26 0.03
156 96 0.10
ACGTcount: A:0.24, C:0.45, G:0.03, T:0.28
Consensus pattern (144 bp):
CCTCCTTATGTTTACAAATCTCCACCACCTCCATCTCCATCACCACCTCCACCTTATGTTTACAA
ATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTACAAATCTCCACCACCTCCAT
CTCCATCCCCACCA
Found at i:28716865 original size:24 final size:24
Alignment explanation
Indices: 28716833--28716913 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
28716823 TTACAAGTCT
28716833 CCACCACCTCCATCTCCATCACCC
1 CCACCACCTCCATCTCCATCACCC
* * * * * *
28716857 CCACCACCT-TATGTTTACA-AATCT
1 CCACCACCTCCA--TCTCCATCACCC
28716881 CCACCACCTCCATCTCCATCACCC
1 CCACCACCTCCATCTCCATCACCC
28716905 CCACCACCT
1 CCACCACCT
28716914 TATGTTTACA
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
23 5 0.12
24 31 0.76
25 5 0.12
ACGTcount: A:0.23, C:0.54, G:0.01, T:0.21
Consensus pattern (24 bp):
CCACCACCTCCATCTCCATCACCC
Found at i:28717176 original size:30 final size:30
Alignment explanation
Indices: 28717142--28717241 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
28717132 ATCACCTTCA
28717142 CCACCTCCTCCATATGTTTACAAGTCACCT
1 CCACCTCCTCCATATGTTTACAAGTCACCT
*** * *
28717172 CCACCTCCTCCATATAAGTATAAGTCACCA
1 CCACCTCCTCCATATGTTTACAAGTCACCT
*
28717202 CCTCCTCCTCCATATGTTTACAAGT---CT
1 CCACCTCCTCCATATGTTTACAAGTCACCT
28717229 CCACCTCCTCCAT
1 CCACCTCCTCCAT
28717242 CTCCATCACC
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
27 13 0.22
30 45 0.78
ACGTcount: A:0.24, C:0.41, G:0.06, T:0.29
Consensus pattern (30 bp):
CCACCTCCTCCATATGTTTACAAGTCACCT
Found at i:28720749 original size:26 final size:26
Alignment explanation
Indices: 28720705--28720774 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
28720695 GCTGCATGAG
* **
28720705 AAACCAACCTTGATGTATACTGATTT
1 AAACCAACCTTAACATATACTGATTT
* *
28720731 AGACCAACCTTAACATATATTGATTT
1 AAACCAACCTTAACATATACTGATTT
* *
28720757 AAACTAACCTTGACATAT
1 AAACCAACCTTAACATAT
28720775 GAATAAAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (26 bp):
AAACCAACCTTAACATATACTGATTT
Found at i:28726912 original size:41 final size:41
Alignment explanation
Indices: 28726867--28726976 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
28726857 GATTTGCAGG
28726867 CATGATTGTATTCATATCTTCCAAGAATCAGCTACACTTTT
1 CATGATTGTATTCATATCTTCCAAGAATCAGCTACACTTTT
* * * *
28726908 CATGATTGCATTCATATTTTTCAAGAATCAGCTACATTTTT
1 CATGATTGTATTCATATCTTCCAAGAATCAGCTACACTTTT
28726949 CATGATTGTATTCATATCTTCCAAGAAT
1 CATGATTGTATTCATATCTTCCAAGAAT
28726977 TTATTAAGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (41 bp):
CATGATTGTATTCATATCTTCCAAGAATCAGCTACACTTTT
Found at i:28726929 original size:21 final size:21
Alignment explanation
Indices: 28726904--28726965 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
28726894 TCAGCTACAC
28726904 TTTTCATGATTGCATTCATAT
1 TTTTCATGATTGCATTCATAT
* * * *
28726925 TTTTCAAGAAT-CA-GCTACAT
1 TTTTCATGATTGCATTC-ATAT
*
28726945 TTTTCATGATTGTATTCATAT
1 TTTTCATGATTGCATTCATAT
28726966 CTTCCAAGAA
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 13 0.45
22 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTTCATGATTGCATTCATAT
Found at i:28748121 original size:3 final size:3
Alignment explanation
Indices: 28748113--28748141 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28748103 AAGTTAAAGC
28748113 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28748142 CTATATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28754821 original size:21 final size:20
Alignment explanation
Indices: 28754797--28754844 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
28754787 TCTTACCTTT
*
28754797 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
28754818 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
28754839 TTTTTC
1 TTTTTC
28754845 CACATAGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:28754844 original size:22 final size:22
Alignment explanation
Indices: 28754802--28754842 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28754792 CCTTTTTTTT
*
28754802 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
28754824 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
28754843 TCCACATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:28756714 original size:24 final size:23
Alignment explanation
Indices: 28756687--28756741 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
28756677 CATTATTAAC
*
28756687 TTAAAATAAA-TATTTAAACATAAA
1 TTAAAATAAACTA-ATAAA-ATAAA
*
28756711 TTAAATTAAACTAATAAAATAAA
1 TTAAAATAAACTAATAAAATAAA
*
28756734 TAAAAATA
1 TTAAAATA
28756742 CTTAAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.42
24 13 0.50
25 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
TTAAAATAAACTAATAAAATAAA
Found at i:28756965 original size:51 final size:51
Alignment explanation
Indices: 28756917--28757013 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
28756907 TCCCCACCTT
* * *
28756917 CTCCATTTGTATATAAGTCTCCTCCACCACCAGTTCATTCACCACCACCAC
1 CTCCATATGTATATAAGTCTCCACCACCACCAGTTCACTCACCACCACCAC
* * * *
28756968 CTCTATATGTATATAAGTTTCCACCACCACCTGTTTACTCACCACC
1 CTCCATATGTATATAAGTCTCCACCACCACCAGTTCACTCACCACC
28757014 TCATTTTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.26, C:0.38, G:0.06, T:0.30
Consensus pattern (51 bp):
CTCCATATGTATATAAGTCTCCACCACCACCAGTTCACTCACCACCACCAC
Found at i:28757769 original size:48 final size:48
Alignment explanation
Indices: 28757659--28757751 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
28757649 CACCACTTGC
* * *
28757659 AAAACACTTACCATCACCTCCTTATGTATACAAATCCCCACCACCCCT
1 AAAACAGTTACCACCACCTCCTTATATATACAAATCCCCACCACCCCT
* * * *
28757707 AAAATAGTCACCACCACCTCTTTATATATACAAGTCCCCACCACC
1 AAAACAGTTACCACCACCTCCTTATATATACAAATCCCCACCACC
28757752 ACCAGTACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.34, C:0.40, G:0.03, T:0.23
Consensus pattern (48 bp):
AAAACAGTTACCACCACCTCCTTATATATACAAATCCCCACCACCCCT
Found at i:28757770 original size:45 final size:45
Alignment explanation
Indices: 28757719--28757838 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 45
28757709 AATAGTCACC
*
28757719 ACCACCTCTTTATATATACAAGTCCCCACCACCACCAGTACATTT
1 ACCACCTCTTTATATATACAAGTCCCCACCACCACCAGTACATTA
* ** * *
28757764 ACCACCTCCTTACT-TATACAAGTCCCTTCCACCATCAGTCCATTA
1 ACCACCTCTTTA-TATATACAAGTCCCCACCACCACCAGTACATTA
* *
28757809 ACCACCTTCTTCCTACATCTACAAGTCCCC
1 ACCACC-TCTT--TATATATACAAGTCCCC
28757839 TGCACCACTA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
45 43 0.72
46 4 0.07
48 13 0.22
ACGTcount: A:0.28, C:0.41, G:0.04, T:0.28
Consensus pattern (45 bp):
ACCACCTCTTTATATATACAAGTCCCCACCACCACCAGTACATTA
Found at i:28760461 original size:22 final size:23
Alignment explanation
Indices: 28760431--28760477 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
28760421 AAATAGAGTT
28760431 ATTTGAGCTTAATT-TTGATAGTA
1 ATTTGAGCTTAATTCTT-ATAGTA
*
28760454 ATTT-AGCTTAGTTCTTATAGTA
1 ATTTGAGCTTAATTCTTATAGTA
28760476 AT
1 AT
28760478 GCATAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (23 bp):
ATTTGAGCTTAATTCTTATAGTA
Found at i:28771158 original size:30 final size:30
Alignment explanation
Indices: 28771124--28771186 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
28771114 CACATCTCCT
* * *
28771124 CCTCCATATGTAGATAAGTCTCCTCCACCA
1 CCTCCATATGTAGACAAATCTCCACCACCA
*
28771154 CCTCCATATGTATACAAATCTCCACCACCA
1 CCTCCATATGTAGACAAATCTCCACCACCA
28771184 CCT
1 CCT
28771187 GTTCACTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.40, G:0.06, T:0.25
Consensus pattern (30 bp):
CCTCCATATGTAGACAAATCTCCACCACCA
Found at i:28771229 original size:30 final size:30
Alignment explanation
Indices: 28771202--28771293 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 30
28771192 CTCACCACTT
* *
28771202 CCTCCTTACGTATACAAATCCCCACCACCA
1 CCTCCTTACATATACAAGTCCCCACCACCA
* *
28771232 CCTCCTTATATATACAAGTCCCCATCACCA
1 CCTCCTTACATATACAAGTCCCCACCACCA
* * *
28771262 CCTACTTACCTATACAAGTCCCCTCCACCA
1 CCTCCTTACATATACAAGTCCCCACCACCA
28771292 CC
1 CC
28771294 AGTCCACTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.28, C:0.46, G:0.03, T:0.23
Consensus pattern (30 bp):
CCTCCTTACATATACAAGTCCCCACCACCA
Found at i:28771264 original size:108 final size:105
Alignment explanation
Indices: 28771139--28771368 Score: 235
Period size: 108 Copynumber: 2.2 Consensus size: 105
28771129 ATATGTAGAT
* * * ** * * * *
28771139 AAGTCTCCTCCACCACCTCCATATGTATACAAATCTCCACCACCACCTGTTCACTCACCACTTCC
1 AAGTCCCCACCACCACCTACATACCTATACAAATCCCCACCACCACCAGTCCACTCACCACCTCC
28771204 TCCTTACGTATACAAATCCCCACCACCACCTCCTTATATATAC
66 TCCTTACGTATACAAAT--CC-CCACCACCTCCTTATATATAC
* * * * * *
28771247 AAGTCCCCATCACCACCTACTTACCTATACAAGTCCCCTCCACCACCAGTCCACTCTCCTCCTCC
1 AAGTCCCCACCACCACCTACATACCTATACAAATCCCCACCACCACCAGTCCACTCACCACCTCC
* * * * * * *
28771312 TCCTTATGTGTACAAGTCCCCACTACCTCCTTATCTCTAT
66 TCCTTACGTATACAAATCCCCACCACCTCCTTATATATAC
28771352 AAGTCCCCACCACCACC
1 AAGTCCCCACCACCACC
28771369 AATACATTCA
Statistics
Matches: 99, Mismatches: 23, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
105 33 0.33
106 2 0.02
108 64 0.65
ACGTcount: A:0.25, C:0.45, G:0.05, T:0.25
Consensus pattern (105 bp):
AAGTCCCCACCACCACCTACATACCTATACAAATCCCCACCACCACCAGTCCACTCACCACCTCC
TCCTTACGTATACAAATCCCCACCACCTCCTTATATATAC
Found at i:28771340 original size:27 final size:27
Alignment explanation
Indices: 28771310--28771361 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28771300 CTCTCCTCCT
* *
28771310 CCTCCTTATGTGTACAAGTCCCCACTA
1 CCTCCTTATCTCTACAAGTCCCCACTA
*
28771337 CCTCCTTATCTCTATAAGTCCCCAC
1 CCTCCTTATCTCTACAAGTCCCCAC
28771362 CACCACCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.31
Consensus pattern (27 bp):
CCTCCTTATCTCTACAAGTCCCCACTA
Found at i:28771367 original size:75 final size:74
Alignment explanation
Indices: 28771227--28771488 Score: 238
Period size: 75 Copynumber: 3.4 Consensus size: 74
28771217 AAATCCCCAC
* * * *
28771227 CACCACCTCCTTATATATACAAGTCCCCATCACCACCTACTTACCTATACAAGTCCCCTCCACCA
1 CACCTCCTCCTTATAT-TACAAGT-CCC--CACCACCTCCTTATCTATACAAGTCCCCACCACCA
* *
28771292 CCAGTCCACTC-T
62 CCAATACACTCAT
* * * * *
28771304 CCTCCTCCTCCTTATGTGTACAAGTCCCCACTACCTCCTTATCTCTATAAGTCCCCACCACCACC
1 -CACCTCCTCCTTATAT-TACAAGTCCCCACCACCTCCTTATCTATACAAGTCCCCACCACCACC
*
28771369 AATACATTCAT
64 AATACACTCAT
* * * * *
28771380 CACCTCTTCCTTACCATTACAAGTCCCCACCACTTCCTTATGTATACAAGTCTCCACCACCACCA
1 CACCTCCTCCTTA-TATTACAAGTCCCCACCACCTCCTTATCTATACAAGTCCCCACCACCACCA
* * *
28771445 ACACATTCAC
65 ATACACTCAT
* * *
28771455 CACCTCATCCTTATCTATACAAGTCCCCTCCACC
1 CACCTCCTCCTTATAT-TACAAGTCCCCACCACC
28771489 ACCAGTCCAC
Statistics
Matches: 151, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
74 1 0.01
75 125 0.83
76 2 0.01
77 3 0.02
78 20 0.13
ACGTcount: A:0.26, C:0.44, G:0.04, T:0.26
Consensus pattern (74 bp):
CACCTCCTCCTTATATTACAAGTCCCCACCACCTCCTTATCTATACAAGTCCCCACCACCACCAA
TACACTCAT
Found at i:28771458 original size:48 final size:48
Alignment explanation
Indices: 28771414--28772179 Score: 572
Period size: 48 Copynumber: 15.8 Consensus size: 48
28771404 CCCCACCACT
* *
28771414 TCCTTATGTATACAAGTCTCCACCACCACCAACACATTCACCACCTCA
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * * * * *
28771462 TCCTTATCTATACAAGTCCCCTCCACCACCAGTC-CACTT-TCCTCCTCT
1 TCCTTATGTATACAAGTCCCCACCACCACCA-ACACA-TTCACCACCTCC
* * * * * *
28771510 TCCTTATGTCTATAAGTCCCCACCACCTCCAAAACACTCACCACCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * *
28771558 TACTTATGTGTACAAGTCTCCACCACCACCAACACATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* ** * * * * *
28771606 TACTTACCTATACAAGTCCCCTCCACCACCAATC-CACTCTCCTCTTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAA-CACATTCACCACCTCC
* * * * * * * * *
28771654 TCTTTATGTGTACAAGTTCCCACCACCTCCAAAATACTCACCGCCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
**
28771702 TCCTTATGTATACAAGTCCCCACCACCACCAATGCATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
** * * * ** *
28771750 TCCTTACATATACAAGTCACCTCCACCACCTATTCATTCACCGCCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * ** ** * *
28771798 TCCTTACT-TATATAAGTCCCCTCCTTCACCGGTC-CACTCTCCTCCTCCTCCTTC
1 TCCTTA-TGTATACAAGTCCCCACCACCACC-AACACA-T-T-CACCACCT-C--C
* * * *
28771852 TCCTTATGTTTACAAGTCCCCACCACCTCCAAAACATTCACCACCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * **
28771900 TCTTTATGTATACAAGTCTCCACCACCACCAGTACATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * * * * *
28771948 TCCTTATCTATACAAGTCCCCTCCACCACCAGTC-CATTCTCCTCCTTC
1 TCCTTATGTATACAAGTCCCCACCACCACCA-ACACATTCACCACCTCC
* * * * * * *
28771996 TCCTTATGTCTATAAGTCCCCACCGCCTCCAAAACACTCACCACCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * *
28772044 TCCTTATGTATACAAGTCTCCACCACCACCACCTATTTATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAAC-A--CATTCACCACCTCC
** * * *
28772095 TCCTTACCTATACAAGTCTCCACCACCACCAATACATTCACCACATCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * * * * *
28772143 ACCTTATGTTTACAAATCTCCACCTCCACCATCACAT
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACAT
28772180 CCTAAGCCTC
Statistics
Matches: 555, Mismatches: 142, Indels: 42
0.75 0.19 0.06
Matches are distributed among these distances:
47 1 0.00
48 465 0.84
49 6 0.01
50 3 0.01
51 51 0.09
52 2 0.00
53 2 0.00
54 25 0.05
ACGTcount: A:0.26, C:0.43, G:0.05, T:0.26
Consensus pattern (48 bp):
TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
Found at i:28772048 original size:198 final size:193
Alignment explanation
Indices: 28771510--28772149 Score: 572
Period size: 198 Copynumber: 3.3 Consensus size: 193
28771500 TTCCTCCTCT
* * * * * * * * * *
28771510 TCCTTATGTCTATAAGTCCCCACCACCTCCAAAACACTCACCACCACCTACTTAT-GTGTACAAG
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
* * * * * * * * *
28771574 TCTCCACCACCACC-AACACATTCACCACCTCCTACTTACCTATACAAGTCCCCTCCACCACCAA
66 TCACCTCCACCACCTATC-CATTCACCGCCTCCTCCTTACTTATATAAGTCCCCACCGCCACCAA
** * * ** * * * * *
28771638 TCCACTCTCCTCTTCCTCTTTATGTGTACAAGTTCCCACCACCTCCAAAATACTCACCGCCACC
130 AACACTCACCACCACCTCCTTATGTATACAAGTCCCCACCACCTCCAAAATATTCACCACCACC
* *
28771702 TCCTTATGTATACAAGTCCCCACCACCACCAATGCATTCACCACCTCCTCCTTA-CATATACAAG
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
* * ** *
28771766 TCACCTCCACCACCTATTCATTCACCGCCTCCTCCTTACTTATATAAGTCCCCTCCTTCACCGGT
66 TCACCTCCACCACCTATCCATTCACCGCCTCCTCCTTACTTATATAAGTCCCCACCGCCACC--A
** * * * * * *
28771831 CCACTCTCCTCCTCCTCCTTCTCCTTATGTTTACAAGTCCCCACCACCTCCAAAACATTCACCAC
129 AAACACT-CACCACC-AC--CTCCTTATGTATACAAGTCCCCACCACCTCCAAAATATTCACCAC
28771896 CACC
190 CACC
* *
28771900 TCTTTATGTATACAAGTCTCCACCACCACCAGTACATTCACCACCTCCTCCTTATC-TATACAAG
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
* * * * * *
28771964 TCCCCTCCACCACC-AGTCCATTCTCCTCCTTCTCCTTA-TGTCTATAAGTCCCCACCGCCTCCA
66 TCACCTCCACCACCTA-TCCATTCACCGCCTCCTCCTTACT-TATATAAGTCCCCACCGCCACCA
* * **
28772027 AAACACTCACCACCACCTCCTTATGTATACAAGTCTCCACCACCACCACCTATTTATTCACCACC
129 AAACACTCACCACCACCTCCTTATGTATACAAG--TCC-CCACCACCTCCAAAATATTCACCACC
*
28772092 TCC
191 ACC
** * *
28772095 TCCTTACCTATACAAGTCTCCACCACCACCAATACATTCACCACATCCACCTTAT
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTAT
28772150 GTTTACAAAT
Statistics
Matches: 367, Mismatches: 67, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
192 119 0.32
193 1 0.00
194 7 0.02
195 83 0.23
196 5 0.01
197 2 0.01
198 149 0.41
199 1 0.00
ACGTcount: A:0.25, C:0.44, G:0.05, T:0.26
Consensus pattern (193 bp):
TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
TCACCTCCACCACCTATCCATTCACCGCCTCCTCCTTACTTATATAAGTCCCCACCGCCACCAAA
ACACTCACCACCACCTCCTTATGTATACAAGTCCCCACCACCTCCAAAATATTCACCACCACC
Found at i:28772222 original size:21 final size:22
Alignment explanation
Indices: 28772198--28772241 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
28772188 TCATCCCTCT
*
28772198 CATCCCCCTCATCCTAA-ACCC
1 CATCCCCCGCATCCTAAGACCC
28772219 CATCCCCCGCATCCTAAGACCC
1 CATCCCCCGCATCCTAAGACCC
28772241 C
1 C
28772242 TTCAACGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.23, C:0.57, G:0.05, T:0.16
Consensus pattern (22 bp):
CATCCCCCGCATCCTAAGACCC
Found at i:28772787 original size:10 final size:9
Alignment explanation
Indices: 28772769--28772793 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28772759 TATTATATGA
28772769 TTTTATTTT
1 TTTTATTTT
28772778 TTTTATTTT
1 TTTTATTTT
28772787 TTTTATT
1 TTTTATT
28772794 AATTCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTATTTT
Found at i:28776776 original size:78 final size:78
Alignment explanation
Indices: 28776646--28776857 Score: 264
Period size: 78 Copynumber: 2.7 Consensus size: 78
28776636 AAAATGTTAA
* * * * * *
28776646 ATTTATATATTGGCACCATTTTATCTTCATGTATAATAGGAATGCCAAATGCCCACCTATCGCAT
1 ATTTACATATTGGCATCATTTTACCTTAATGTATAATAGGAATGCCACATGCCCACCTATCACAT
* *
28776711 AGACCTTGATGGT
66 AGACCATGATGAT
** *
28776724 ATTTACATATTGGCATCATTACACCTTAATGTATAATAGGAATGCCACATGCCTACCTATCACAT
1 ATTTACATATTGGCATCATTTTACCTTAATGTATAATAGGAATGCCACATGCCCACCTATCACAT
* *
28776789 GGATCATGATGAT
66 AGACCATGATGAT
* * *
28776802 ATTTATC-TATTGACATCATTTTACCTTAATATATAATAAGAATGCCACATGCCCAC
1 ATTTA-CATATTGGCATCATTTTACCTTAATGTATAATAGGAATGCCACATGCCCAC
28776858 ACCTTATGTC
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
78 113 0.99
79 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (78 bp):
ATTTACATATTGGCATCATTTTACCTTAATGTATAATAGGAATGCCACATGCCCACCTATCACAT
AGACCATGATGAT
Found at i:28778798 original size:3 final size:3
Alignment explanation
Indices: 28778790--28778848 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
28778780 ATAAATTTCC
*
28778790 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28778838 TAT TAT TAT TA
1 TAT TAT TAT TA
28778849 CAAAAACTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28782088 original size:19 final size:19
Alignment explanation
Indices: 28782058--28782126 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
28782048 ATTTTTTCTT
* *
28782058 TTTTCATTTTTTT-GTTTC
1 TTTTCTTTTTTTTCTTTTC
28782076 TTCTT-TTTTTTTTCTTTTC
1 TT-TTCTTTTTTTTCTTTTC
*
28782095 TTTTCTTTTTTCTCTTTT-
1 TTTTCTTTTTTTTCTTTTC
28782113 TTTTCATTTTTTTT
1 TTTTC-TTTTTTTT
28782127 GTTATTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 16 0.37
19 27 0.63
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (19 bp):
TTTTCTTTTTTTTCTTTTC
Found at i:28782093 original size:23 final size:21
Alignment explanation
Indices: 28782051--28782115 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
28782041 GTCGTACATT
*
28782051 TTTTCTTTTTTCATTTTTTTGT
1 TTTTCTTTTTTCATTTTTTT-C
*
28782073 TTCTTCTTTTTT-TTTTCTTTTC
1 TT-TTCTTTTTTCATTT-TTTTC
*
28782095 TTTTCTTTTTTCTCTTTTTTT
1 TTTTCTTTTTTC-ATTTTTTT
28782116 TCATTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 9 0.25
22 11 0.31
23 16 0.44
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTCTTTTTTCATTTTTTTC
Found at i:28782098 original size:28 final size:27
Alignment explanation
Indices: 28782051--28782129 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 27
28782041 GTCGTACATT
*
28782051 TTTTCTTTTTTCATTTTTTTGTTTCTTC
1 TTTT-TTTTTTCTTTTTTTTGTTTCTTC
* *
28782079 TTTTTTTTTTCTTTTCTTTTCTTTTTTC
1 TTTTTTTTTTCTTTT-TTTTGTTTCTTC
*
28782107 TCTTTTTTTTCATTTTTTTTGTT
1 TTTTTTTTTTC-TTTTTTTTGTT
28782130 ATTATTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
27 10 0.23
28 30 0.68
29 4 0.09
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (27 bp):
TTTTTTTTTTCTTTTTTTTGTTTCTTC
Found at i:28782107 original size:31 final size:30
Alignment explanation
Indices: 28782049--28782116 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
28782039 CAGTCGTACA
*
28782049 TTTTTTCTTTTTTCATTTTTTTGTTTCTTCT
1 TTTTTTTTTTTTTCATTTTTTTGTTTC-TCT
28782080 TTTTTTTTTCTTTTC-TTTTCTTT-TTTCTCT
1 TTTTTTTTT-TTTTCATTTT-TTTGTTTCTCT
28782110 TTTTTTT
1 TTTTTTT
28782117 CATTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 10 0.29
31 16 0.47
32 8 0.24
ACGTcount: A:0.01, C:0.13, G:0.01, T:0.84
Consensus pattern (30 bp):
TTTTTTTTTTTTTCATTTTTTTGTTTCTCT
Found at i:28782122 original size:17 final size:19
Alignment explanation
Indices: 28782076--28782122 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
28782066 TTTTTGTTTC
28782076 TTCTTTT-T-TTTT-TCTT
1 TTCTTTTCTATTTTCTCTT
*
28782092 TTCTTTTCTTTTTTCTCTT
1 TTCTTTTCTATTTTCTCTT
28782111 TT-TTTTC-ATTTT
1 TTCTTTTCTATTTT
28782123 TTTTGTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 5 0.19
18 9 0.33
19 6 0.22
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTCTTTTCTATTTTCTCTT
Found at i:28782140 original size:28 final size:26
Alignment explanation
Indices: 28782051--28782140 Score: 67
Period size: 28 Copynumber: 3.3 Consensus size: 26
28782041 GTCGTACATT
*
28782051 TTTTCTTTTTTCA-TTTTTTTGTTTCTTC
1 TTTT-TTTTTTCATTTTTTTTG-TT-TTA
* *
28782079 TTTTTTTTTTC-TTTTCTTTTCTTTTT
1 TTTTTTTTTTCATTTT-TTTTGTTTTA
28782105 TCTCTTTTTTTTCATTTTTTTTGTTATTA
1 T-T-TTTTTTTTCATTTTTTTTGTT-TTA
*
28782134 TTATTTT
1 TTTTTTT
28782141 GTCTTTTGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
26 3 0.06
27 17 0.33
28 24 0.47
29 7 0.14
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (26 bp):
TTTTTTTTTTCATTTTTTTTGTTTTA
Found at i:28783249 original size:48 final size:48
Alignment explanation
Indices: 28783183--28783296 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
28783173 TGCATCTCCT
* *
28783183 CCACCACCAGAGCACCCATATCATCCACCAGGCCACTACGAA-TCACCA
1 CCACCTCCAGAGCACCCATATCAGCCACCAGGCCACTAC-AAGTCACCA
* * *
28783231 TCACCTCCCA-AGCACCCATATCAGCCACCCGGCCATTACAAGTCACCA
1 CCACCT-CCAGAGCACCCATATCAGCCACCAGGCCACTACAAGTCACCA
28783279 CCACCTCCAGAGCACCCA
1 CCACCTCCAGAGCACCCA
28783297 CTACACCCAC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
47 5 0.09
48 49 0.86
49 3 0.05
ACGTcount: A:0.31, C:0.47, G:0.11, T:0.11
Consensus pattern (48 bp):
CCACCTCCAGAGCACCCATATCAGCCACCAGGCCACTACAAGTCACCA
Found at i:28783307 original size:48 final size:48
Alignment explanation
Indices: 28783183--28783334 Score: 148
Period size: 48 Copynumber: 3.1 Consensus size: 48
28783173 TGCATCTCCT
* * * *
28783183 CCACCACCAGAGCACCCATATCATCCACCAGGCCACTACGAA-TCACCA
1 CCACCTCCAGAGCACCCATATCACCCACCCGGCCATTAC-AAGTCACCA
* *
28783231 TCACCTCCCA-AGCACCCATATCAGCCACCCGGCCATTACAAGTCACCA
1 CCACCT-CCAGAGCACCCATATCACCCACCCGGCCATTACAAGTCACCA
** *
28783279 CCACCTCCAGAGCACCCACTA-CACCCACCATCGTATCATTACAAGTCTCCA
1 CCACCTCCAGAGCACCCA-TATCACCCACC--CG-GCCATTACAAGTCACCA
28783330 CCACC
1 CCACC
28783335 CTCGGAACAT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
47 5 0.06
48 56 0.64
49 5 0.06
50 2 0.02
51 19 0.22
ACGTcount: A:0.30, C:0.47, G:0.09, T:0.14
Consensus pattern (48 bp):
CCACCTCCAGAGCACCCATATCACCCACCCGGCCATTACAAGTCACCA
Found at i:28783512 original size:66 final size:66
Alignment explanation
Indices: 28783423--28783558 Score: 218
Period size: 66 Copynumber: 2.1 Consensus size: 66
28783413 CTATAAATCT
* * *
28783423 CCACCTCCTCATCCCAAGTCACCACCACCTCATTACGTCTATAAGTCTCCACCACCTCCATCACA
1 CCACCTCCTCATCCAAAGTCACCACCACCTCATTACGTCTATAAATCTCCACCACCCCCATCACA
28783488 C
66 C
* * *
28783489 CCACCTCCTCATTCAAAGTCACCACCACCTCATTATGTTTATAAATCTCCACCACCCCCATCACA
1 CCACCTCCTCATCCAAAGTCACCACCACCTCATTACGTCTATAAATCTCCACCACCCCCATCACA
28783554 C
66 C
28783555 CCAC
1 CCAC
28783559 TGCCGGTCCA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.22
Consensus pattern (66 bp):
CCACCTCCTCATCCAAAGTCACCACCACCTCATTACGTCTATAAATCTCCACCACCCCCATCACA
C
Found at i:28783586 original size:63 final size:66
Alignment explanation
Indices: 28783423--28783607 Score: 216
Period size: 66 Copynumber: 2.8 Consensus size: 66
28783413 CTATAAATCT
* * *
28783423 CCACCTCCTCA-TCCCAAGTCACCACCACCTCATTACGTCTATAAGTCTCCACCACCTCCATCAC
1 CCACCTCCTCAGT-CAAAGTCACCACCACCTCATTATGTCTATAAGTCTCCACCACCCCCATCAC
28783487 AC
65 AC
* * *
28783489 CCACCTCCTCATTCAAAGTCACCACCACCTCATTATGTTTATAAATCTCCACCACCCCCATCACA
1 CCACCTCCTCAGTCAAAGTCACCACCACCTCATTATGTCTATAAGTCTCCACCACCCCCATCACA
28783554 C
66 C
* * * * * * *
28783555 CCA-CTGC-CGGTC-CATTCACCACCTCCTCATTATGTCTACAAGTCCCCACCACC
1 CCACCTCCTCAGTCAAAGTCACCACCACCTCATTATGTCTATAAGTCTCCACCACC
28783608 AGCACATCCC
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
63 34 0.33
64 3 0.03
65 3 0.03
66 62 0.60
67 1 0.01
ACGTcount: A:0.25, C:0.46, G:0.05, T:0.23
Consensus pattern (66 bp):
CCACCTCCTCAGTCAAAGTCACCACCACCTCATTATGTCTATAAGTCTCCACCACCCCCATCACA
C
Found at i:28783658 original size:60 final size:59
Alignment explanation
Indices: 28783571--28783757 Score: 270
Period size: 60 Copynumber: 3.2 Consensus size: 59
28783561 CCGGTCCATT
*
28783571 CACCACCTCCTCATTATGTCTACAAGTCCCCACCACCAGCACATCCCAAACCCTACAAAG
1 CACCACCTCCTCATTATGTCTACAAGTCCCCTCCACCA-CACATCCCAAACCCTACAAAG
* ** *
28783631 CACCTCCTCCTCATTACATCTATAAGTCCCCTCCA-C-CACATCCCAAACCCTACAAAG
1 CACCACCTCCTCATTATGTCTACAAGTCCCCTCCACCACACATCCCAAACCCTACAAAG
* * *
28783688 CACCTCCTCCTCATTATGTCTACAAGTCCCCTCCCCCACCACATCCCAAACACTACAAAG
1 CACCACCTCCTCATTATGTCTACAAGTCCCCTCCACCA-CACATCCCAAACCCTACAAAG
28783748 CACCACCTCC
1 CACCACCTCC
28783758 ACATCCCAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
57 52 0.46
58 1 0.01
59 1 0.01
60 59 0.52
ACGTcount: A:0.29, C:0.47, G:0.05, T:0.19
Consensus pattern (59 bp):
CACCACCTCCTCATTATGTCTACAAGTCCCCTCCACCACACATCCCAAACCCTACAAAG
Found at i:28783815 original size:63 final size:63
Alignment explanation
Indices: 28783748--28783907 Score: 159
Period size: 63 Copynumber: 2.6 Consensus size: 63
28783738 CACTACAAAG
* * *
28783748 CACCACC-TCCACATCCCAAACCTTACAAAGCAT-CTCCTCCTCATTACGTTTACAAGTCCCCAC
1 CACCACCAT-CACATCCCAAACCCTACAAAGC-TCCACCTCCTCATTACATTTACAAGTCCCCAC
* * * * *
28783811 CACCACCATCACATCCCGAGCCCTACAAATCTCCACCTCCTCATTACATTTATAAGT--TC-C
1 CACCACCATCACATCCCAAACCCTACAAAGCTCCACCTCCTCATTACATTTACAAGTCCCCAC
* * * *
28783871 CACCACCATCTCATCCCGAGCCCTACAAATCTCCACC
1 CACCACCATCACATCCCAAACCCTACAAAGCTCCACC
28783908 ACCATCACAT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
60 37 0.43
61 1 0.01
62 1 0.01
63 46 0.53
64 1 0.01
ACGTcount: A:0.28, C:0.45, G:0.05, T:0.22
Consensus pattern (63 bp):
CACCACCATCACATCCCAAACCCTACAAAGCTCCACCTCCTCATTACATTTACAAGTCCCCAC
Found at i:28783847 original size:33 final size:33
Alignment explanation
Indices: 28783810--28783923 Score: 89
Period size: 33 Copynumber: 3.6 Consensus size: 33
28783800 CAAGTCCCCA
28783810 CCACCACCATCACATCCCGAGCCCTACAAATCT
1 CCACCACCATCACATCCCGAGCCCTACAAATCT
* ** ** * *
28783843 CCACCTCC-T--CATTAC-A--TTTATAAGT-T
1 CCACCACCATCACATCCCGAGCCCTACAAATCT
*
28783869 CCCACCACCATCTCATCCCGAGCCCTACAAATCT
1 C-CACCACCATCACATCCCGAGCCCTACAAATCT
*
28783903 CCACCACCATCACATCTCGAG
1 CCACCACCATCACATCCCGAG
28783924 ACTCCTGCCC
Statistics
Matches: 57, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
26 2 0.04
27 11 0.19
28 1 0.02
29 1 0.02
30 8 0.14
31 1 0.02
32 1 0.02
33 30 0.53
34 2 0.04
ACGTcount: A:0.28, C:0.45, G:0.06, T:0.21
Consensus pattern (33 bp):
CCACCACCATCACATCCCGAGCCCTACAAATCT
Found at i:28783910 original size:63 final size:62
Alignment explanation
Indices: 28783783--28783907 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 62
28783773 CAAAGCATCT
*
28783783 CCTCCTCATTACGTTTACAAGTCCCCACCACCACCATCACATCCCGAGCCCTACAAATCTCCA
1 CCTCCTCATTACATTTACAAGT-CCCACCACCACCATCACATCCCGAGCCCTACAAATCTCCA
* * *
28783846 CCTCCTCATTACATTTATAAGT-TC-CCACCACCATCTCATCCCGAGCCCTACAAATCTCCA
1 CCTCCTCATTACATTTACAAGTCCCACCACCACCATCACATCCCGAGCCCTACAAATCTCCA
28783906 CC
1 CC
28783908 ACCATCACAT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
60 37 0.64
61 1 0.02
63 20 0.34
ACGTcount: A:0.26, C:0.45, G:0.06, T:0.23
Consensus pattern (62 bp):
CCTCCTCATTACATTTACAAGTCCCACCACCACCATCACATCCCGAGCCCTACAAATCTCCA
Found at i:28793323 original size:27 final size:29
Alignment explanation
Indices: 28793267--28793324 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
28793257 CCACATCCTC
* *
28793267 ATAAGTCTCCACCACCTCCGACCTACTATT
1 ATAAATCTCCACCACCACCGACCTA-TATT
28793297 ATAAATCTCCACCACCACC-ACCT-TATT
1 ATAAATCTCCACCACCACCGACCTATATT
28793324 A
1 A
28793325 CTACAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
29 4 0.15
30 17 0.65
ACGTcount: A:0.31, C:0.40, G:0.03, T:0.26
Consensus pattern (29 bp):
ATAAATCTCCACCACCACCGACCTATATT
Found at i:28793333 original size:30 final size:30
Alignment explanation
Indices: 28793272--28793342 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
28793262 TCCTCATAAG
* * *
28793272 TCTCCACCACCTCCGACCTACTATTATAAA
1 TCTCCACCACCACCGACCTACTACTACAAA
*
28793302 TCTCCACCACCACC-ACCTTATTACTACAAA
1 TCTCCACCACCACCGACC-TACTACTACAAA
* *
28793332 TCCCCTCCACC
1 TCTCCACCACC
28793343 CCCATCACCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.28, C:0.46, G:0.01, T:0.24
Consensus pattern (30 bp):
TCTCCACCACCACCGACCTACTACTACAAA
Found at i:28793408 original size:48 final size:48
Alignment explanation
Indices: 28793335--28793597 Score: 168
Period size: 48 Copynumber: 5.5 Consensus size: 48
28793325 CTACAAATCC
* * *
28793335 CCTCCACCCCCATCACCATCTCCTCCTCCGCCATACTATTATAAGTCT
1 CCTCCACCACCTTCACCATCACCTCCTCCGCCATACTATTATAAGTCT
* * ** * * *
28793383 CCTCCACCACCTTCTCCTTCACCTCCTCTTCCATA-TGTGTACAAATCT
1 CCTCCACCACCTTCACCATCACCTCCTCCGCCATACTAT-TATAAGTCT
* * * * * * * * * *
28793431 CCTCCACCTCCATCGCCATCTCCCCCTTCGCCCTATTATTACAAGTCC
1 CCTCCACCACCTTCACCATCACCTCCTCCGCCATACTATTATAAGTCT
* * * * * * * * * *
28793479 CCACCACCACCTTCACCATCCCCACCACCACCTTATTACTATAAATCC
1 CCTCCACCACCTTCACCATCACCTCCTCCGCCATACTATTATAAGTCT
** * * *
28793527 CCTCCACCACCTTCACCATTGCCTCCACCTCCCTACTATTATAAGTCT
1 CCTCCACCACCTTCACCATCACCTCCTCCGCCATACTATTATAAGTCT
* * *
28793575 CCACCTCCACCATCACCATCACC
1 CCTCCACCACCTTCACCATCACC
28793598 ACCACCACCA
Statistics
Matches: 162, Mismatches: 51, Indels: 4
0.75 0.24 0.02
Matches are distributed among these distances:
47 2 0.01
48 158 0.98
49 2 0.01
ACGTcount: A:0.22, C:0.49, G:0.03, T:0.26
Consensus pattern (48 bp):
CCTCCACCACCTTCACCATCACCTCCTCCGCCATACTATTATAAGTCT
Found at i:28793525 original size:96 final size:96
Alignment explanation
Indices: 28793308--28793636 Score: 338
Period size: 96 Copynumber: 3.4 Consensus size: 96
28793298 TAAATCTCCA
* *
28793308 CCACCACCACCTTATTACTACAAATCCCCTCCACCCCCATCACCATCTCCTCCTCCGCCATACTA
1 CCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCTCCTCCTCCGCCCTACTA
* * * *
28793373 TTATAAGTCTCCTCCACCACCTTCTCCTTCA
66 TTATAAGTCTCCACCACCACCTTCACCATCC
* * ** * * * * * * *
28793404 CCTCCTCTTCCATATGT-GTACAAATCTCCTCCACCTCCATCGCCATCTCCCCCTTCGCCCTATT
1 CCACCACCACCTTAT-TACTACAAATCCCCTCCACCTCCATCACCATCTCCTCCTCCGCCCTACT
* *
28793468 ATTACAAGTCCCCACCACCACCTTCACCATCC
65 ATTATAAGTCTCCACCACCACCTTCACCATCC
* * * * *
28793500 CCACCACCACCTTATTACTATAAATCCCCTCCACCACCTTCACCAT-TGCCTCCACCTCCCTACT
1 CCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCT-CCTCCTCCGCCCTACT
* *
28793564 ATTATAAGTCTCCACCTCCACCATCACCATCACC
65 ATTATAAGTCTCCACCACCACCTTCACCAT--CC
* * *
28793598 ACCACCACCACCTTATTATTACAAGTCACCTCCACCTCC
1 -CCACCACCACCTTATTACTACAAATCCCCTCCACCTCC
28793637 TTCTCGATCT
Statistics
Matches: 183, Mismatches: 44, Indels: 9
0.78 0.19 0.04
Matches are distributed among these distances:
95 2 0.01
96 145 0.79
97 1 0.01
98 2 0.01
99 33 0.18
ACGTcount: A:0.23, C:0.48, G:0.03, T:0.26
Consensus pattern (96 bp):
CCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCTCCTCCTCCGCCCTACTA
TTATAAGTCTCCACCACCACCTTCACCATCC
Found at i:28793603 original size:48 final size:48
Alignment explanation
Indices: 28793551--28794665 Score: 826
Period size: 48 Copynumber: 23.2 Consensus size: 48
28793541 ACCATTGCCT
* * * *
28793551 CCACCTCCCTACTATTATAAGTCTCCACCTCCACCATCACCATCACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * * * * * * *
28793599 CCACCACCACCTTATTATTACAAGTCACCTCCACCTCCTTCTCGATCTCTC-
1 CCACCTCCA---TACTATTACAAGTCACCACCTCCACCATCTCCATCAC-CA
* * *
28793650 CCACCTCCGTACTATTACAAGTCACCACCTCCGCCATCTCCTAGTTCTCCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-A--TCACCA
* * * *
28793701 CCA---ACATACTATTACAAGACTCCACCCCCACCATCTCCATCACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * * * *
28793746 CCACCTCCTTACTATTACAAGTCACCACCACCTCCTTCACC-T-AGTCCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCA--CCA
* * *
28793794 CCACCTCCATACTACTACAAGTCACCACCTCCACCATCCCCTAGC-CCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-ATCACCA
* * * ** * *
28793842 CCACCACCATACTACTACAAAT--CC-CCTCCACC-TC-CTTTGAAGTCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCAT-CA-CCA
*
28793887 CCACCTCCATATTATTACAAGTCACCACCTCCACCATCTCCTAGTC-CC-
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-A-TCACCA
* * *
28793935 CCACCACCATATTATTACAAGTCACCACCCCCACCATCTCCATCACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
** * *
28793983 CCACCTCTTTACTACTACAAGTCACCACCTCCTCCATCTCCTAGTC-CC-
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-A-TCACCA
* * * *
28794031 CCACCACCATACAACTACAAGTCACCACCCCCACCATCTCCATCACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * *
28794079 CCACCTCCTTACTACTACAAGTCACCACCTCCGCCATCTCCTAGTC-CC-
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-A-TCACCA
* * *
28794127 CCACCACCATACTACTACAAGTCACCACCTCCGCCATCTCCTAGTC-CC-
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-A-TCACCA
* * *
28794175 CCACCACCATACTACTACAAGTCACCACCCCCACCATCTCCATCACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * * * *
28794223 CCACCTCCTTATTATTACAAGTCACCACCACCACCTTCACC--CAGTCCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCA--CCA
* * * *
28794271 CCACCACCATACTATTACAAGTCACCACCTCCACCATCCCCTAGC-CCG
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-ATCACCA
* * * * *
28794319 CCACCACCATACTATTATAAGTCACCACCTCCGCCATCCCCTAGC-CCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-ATCACCA
* * * * * * * * ** *
28794367 CCACCACCATACTACTACAAATCCCCTCCACCTCC-TTTGAAGTCACCG
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCA-TCACCA
* *
28794415 CCTCCTCCATACTATTACAAGTCACCACCTCCGCCATCTCCTAGTC-CC-
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCC-A-TCACCA
* * *
28794463 CCACCACCATACTATTACAAGTCACCACCCCCACCATCTCCATTACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * * * * * * *
28794511 TCACCTCCTTATTACTACAGGTCGCCACCTCCACCATCTCCTTCACCC
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * * * * * *
28794559 CCACCTCCTTACTACTACAAATCACCACCACCTCCTTCCCCATCACCA
1 CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
* * * * *
28794607 CCACCACCACGTTACTATTATAAGTCACCCCCTCCACCATCTCCTTCCCCA
1 CCACCTCCA---TACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
28794658 CCACCTCC
1 CCACCTCC
28794666 TCACTACTAG
Statistics
Matches: 855, Mismatches: 162, Indels: 97
0.77 0.15 0.09
Matches are distributed among these distances:
43 1 0.00
44 2 0.00
45 36 0.04
46 13 0.02
47 18 0.02
48 681 0.80
49 14 0.02
50 10 0.01
51 78 0.09
52 2 0.00
ACGTcount: A:0.26, C:0.48, G:0.04, T:0.21
Consensus pattern (48 bp):
CCACCTCCATACTATTACAAGTCACCACCTCCACCATCTCCATCACCA
Found at i:28793630 original size:99 final size:99
Alignment explanation
Indices: 28793305--28793687 Score: 334
Period size: 96 Copynumber: 3.9 Consensus size: 99
28793295 TTATAAATCT
* * *
28793305 CCACCACCACCACCTTATTACTACAAATCCCCTCCACCCCCATCACCATCTCCTCCTCCGCCATA
1 CCACCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCTCCTCCACCGCCCTA
* * * * *
28793370 CTATTATAAGTCTCCTCCACCACCTTCTCCTTCA
66 CTATTACAAGTCTCCACCACCACCATCACCATCA
* * ** * * * * **
28793404 CCTCCTCTTCCA---TATGT-GTACAAATCTCCTCCACCTCCATCGCCATCTCCCCCTTCGCCCT
1 CCACCACCACCACCTTAT-TACTACAAATCCCCTCCACCTCCATCACCATCTCCTCCACCGCCCT
* * *
28793465 ATTATTACAAGTCCCCACCACCACCTTCACCAT--
65 ACTATTACAAGTCTCCACCACCACCATCACCATCA
* * * *
28793498 CC-CCACCACCACCTTATTACTATAAATCCCCTCCACCACCTTCACCAT-TGCCTCCACCTCCCT
1 CCACCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCT-CCTCCACCGCCCT
* *
28793561 ACTATTATAAGTCTCCACCTCCACCATCACCATCA
65 ACTATTACAAGTCTCCACCACCACCATCACCATCA
* * * * * * * *
28793596 CCACCACCACCACCTTATTATTACAAGTCACCTCCACCTCCTTCTCGATCT-CTCCCACCTCCGT
1 CCACCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCTCCT-CCACCGCCCT
* * *
28793660 ACTATTACAAGTCACCACCTCCGCCATC
65 ACTATTACAAGTCTCCACCACCACCATC
28793688 TCCTAGTTCT
Statistics
Matches: 227, Mismatches: 46, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
93 6 0.03
94 2 0.01
95 2 0.01
96 130 0.57
97 1 0.00
98 4 0.02
99 81 0.36
100 1 0.00
ACGTcount: A:0.23, C:0.48, G:0.04, T:0.26
Consensus pattern (99 bp):
CCACCACCACCACCTTATTACTACAAATCCCCTCCACCTCCATCACCATCTCCTCCACCGCCCTA
CTATTACAAGTCTCCACCACCACCATCACCATCA
Done.