Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 176 of 208
Found at i:55865640 original size:128 final size:128
Alignment explanation
Indices: 55865412--55865713 Score: 604
Period size: 128 Copynumber: 2.4 Consensus size: 128
55865402 GCACACGCCC
55865412 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTTG
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTTG
55865477 TGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
66 TGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
55865540 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTTG
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTTG
55865605 TGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
66 TGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
55865668 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACA
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACA
55865714 CACCCGTGTG
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 174 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.29
Consensus pattern (128 bp):
GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTTG
TGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
Found at i:55865714 original size:64 final size:64
Alignment explanation
Indices: 55865412--55865714 Score: 534
Period size: 64 Copynumber: 4.7 Consensus size: 64
55865402 GCACACGCCC
* *
55865412 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACACGCCTGTGTCCCCTACCT
* *
55865476 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACACGCCTGTGTCCCCTACCT
* *
55865540 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACACGCCTGTGTCCCCTACCT
* *
55865604 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACACGCCTGTGTCCCCTACCT
55865668 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAC
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAC
55865715 ACCCGTGTGC
Statistics
Matches: 226, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 226 1.00
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACACGCCTGTGTCCCCTACCT
Found at i:55866451 original size:10 final size:10
Alignment explanation
Indices: 55866436--55866460 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55866426 ACAATTACCA
55866436 AAAAAAAAAG
1 AAAAAAAAAG
55866446 AAAAAAAAAG
1 AAAAAAAAAG
55866456 AAAAA
1 AAAAA
55866461 GGAGAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:55870208 original size:49 final size:49
Alignment explanation
Indices: 55870151--55870250 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
55870141 ATTTGAGAAT
55870151 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
1 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
55870200 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
1 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
55870249 GA
1 GA
55870251 ACGTAGTCAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (49 bp):
GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
Found at i:55874272 original size:21 final size:21
Alignment explanation
Indices: 55874215--55874265 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
55874205 GCAAATTGTT
*
55874215 GATTTTCAAAAGAAAATAGAG
1 GATTTTCAAAAGAAAACAGAG
*
55874236 GATTTTCAAAAGAAAACAGTG
1 GATTTTCAAAAGAAAACAGAG
55874257 GATTTTCAA
1 GATTTTCAA
55874266 CATAAAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACAGAG
Found at i:55875685 original size:14 final size:14
Alignment explanation
Indices: 55875643--55875693 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
55875633 AGGCAACCCA
55875643 ATTTTA-TTTT-TT
1 ATTTTATTTTTATT
* *
55875655 ATTTT-GTTGTATAT
1 ATTTTATTTTTAT-T
55875669 ATTTTATTTTTATT
1 ATTTTATTTTTATT
55875683 ATTTTATTTTT
1 ATTTTATTTTT
55875694 TTGCATGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 8 0.25
13 1 0.03
14 18 0.56
15 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (14 bp):
ATTTTATTTTTATT
Found at i:55876674 original size:109 final size:110
Alignment explanation
Indices: 55876476--55876674 Score: 312
Period size: 109 Copynumber: 1.8 Consensus size: 110
55876466 TTAAACAAAA
*
55876476 AATAAATTAAGAGCTTGTTGGCCTGAGTAACTGGGGAGGGATGCTTGGGTTGTCATTCCACTTCG
1 AATAAATTAAGAGCTTGTTGGCCTAAGTAACTGGGGAGGGATGCTTGGGTTGTCATTCCACTTCG
*
55876541 CGTCACAAGGGCCAAAACATTCTTAAACTAATATATATATAATAT
66 CGTCAAAAGGGCCAAAACATTCTTAAACTAATATATATATAATAT
* * *
55876586 AATAAATTAAGAG-TATGTTGGGCTAAGTAACTGGGGTGGGGTGCTT-GGTTGTCATTCCACTTC
1 AATAAATTAAGAGCT-TGTTGGCCTAAGTAACTGGGGAGGGATGCTTGGGTTGTCATTCCACTTC
* *
55876649 GCGTCAAAAGTGCCAATACATTCTTA
65 GCGTCAAAAGGGCCAAAACATTCTTA
55876675 TGCATTAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
109 41 0.51
110 40 0.49
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (110 bp):
AATAAATTAAGAGCTTGTTGGCCTAAGTAACTGGGGAGGGATGCTTGGGTTGTCATTCCACTTCG
CGTCAAAAGGGCCAAAACATTCTTAAACTAATATATATATAATAT
Found at i:55877735 original size:6 final size:6
Alignment explanation
Indices: 55877714--55877752 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
55877704 GACAATTACC
55877714 AAAAA- AAAAGAG AAAAAG AAAAAG AAAAAGG AAAAAG AA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAA-G AAAAAG AA
55877753 TGAGATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.13
6 17 0.55
7 10 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:55877735 original size:13 final size:12
Alignment explanation
Indices: 55877714--55877752 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
55877704 GACAATTACC
55877714 AAAAA-AAAAGAG
1 AAAAAGAAAA-AG
55877726 AAAAAGAAAAAG
1 AAAAAGAAAAAG
55877738 AAAAAGGAAAAAG
1 AAAAA-GAAAAAG
55877751 AA
1 AA
55877753 TGAGATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:55878339 original size:64 final size:63
Alignment explanation
Indices: 55878128--55878339 Score: 280
Period size: 64 Copynumber: 3.3 Consensus size: 63
55878118 TGGGGTGTTA
* * * *
55878128 CACAAACAGCGAGTCACATGACCTGGACACACACCCGTGTCTTTGGCCCTTGTAGTTTCTAAAT
1 CACAAATAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGT-GTTTCTAAAT
* * * * * * *
55878192 CACAAATAGTGAGTCAGACAAGCTGGACACACACCCATATGTCTGGCCCGTGTGGTTTCTAAAT
1 CACAAATAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGT-GTTTCTAAAT
* *
55878256 CACAAATAGTGAGTCACACGACCTGGACACACAACCGTGTCTCTAGCCCTTGTGTTTTCTAAAT
1 CACAAATAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGTG-TTTCTAAAT
55878320 CACAAATAGTGAGTCACACG
1 CACAAATAGTGAGTCACACG
55878340 GCCTACCACA
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
63 1 0.01
64 125 0.99
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (63 bp):
CACAAATAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGTGTTTCTAAAT
Found at i:55880548 original size:14 final size:14
Alignment explanation
Indices: 55880531--55880562 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55880521 TAAAATATAT
55880531 TTATATTAGTATTA
1 TTATATTAGTATTA
*
55880545 TTATATTATTATTA
1 TTATATTAGTATTA
55880559 TTAT
1 TTAT
55880563 TATAATAAAG
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:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTATATTAGTATTA
Found at i:55880560 original size:17 final size:17
Alignment explanation
Indices: 55880534--55880566 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55880524 AATATATTTA
55880534 TATTAGTATTATTATAT
1 TATTAGTATTATTATAT
*
55880551 TATTATTATTATTATA
1 TATTAGTATTATTATA
55880567 ATAAAGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTAGTATTATTATAT
Found at i:55881059 original size:21 final size:21
Alignment explanation
Indices: 55881033--55881074 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55881023 ATAGAGTGTG
55881033 AATTGAATTAAGAAAATAAGT
1 AATTGAATTAAGAAAATAAGT
* *
55881054 AATTGAATTAGGAAAGTAAGT
1 AATTGAATTAAGAAAATAAGT
55881075 GAACTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (21 bp):
AATTGAATTAAGAAAATAAGT
Found at i:55881352 original size:3 final size:3
Alignment explanation
Indices: 55881344--55881380 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
55881334 TGAGGTAAGC
55881344 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55881381 AGATGAGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55890032 original size:23 final size:22
Alignment explanation
Indices: 55889980--55890032 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55889970 TCCACGTCTT
*
55889980 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55890002 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55890025 TTTCTTTT
1 TTTCTTTT
55890033 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55890056 original size:26 final size:26
Alignment explanation
Indices: 55890027--55890076 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
55890017 TTCTTCAATT
55890027 TCTTTTTCACTCTCAATCTCTTTTGC
1 TCTTTTTCACTCTCAATCTCTTTTGC
* **
55890053 TCTTTTTCATTCTCTTTCTCTTTT
1 TCTTTTTCACTCTCAATCTCTTTT
55890077 TCCTCACTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.08, C:0.28, G:0.02, T:0.62
Consensus pattern (26 bp):
TCTTTTTCACTCTCAATCTCTTTTGC
Found at i:55891224 original size:55 final size:55
Alignment explanation
Indices: 55891161--55891270 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
55891151 AACAGAAAAC
55891161 CCGAAAAACTGCGGAGTAACTTGACAACTTCGTTCGAGGTGTTCCCGATCTCAAA
1 CCGAAAAACTGCGGAGTAACTTGACAACTTCGTTCGAGGTGTTCCCGATCTCAAA
55891216 CCGAAAAACTGCGGAGTAACTTGACAACTTCGTTCGAGGTGTTCCCGATCTCAAA
1 CCGAAAAACTGCGGAGTAACTTGACAACTTCGTTCGAGGTGTTCCCGATCTCAAA
55891271 AATCACAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (55 bp):
CCGAAAAACTGCGGAGTAACTTGACAACTTCGTTCGAGGTGTTCCCGATCTCAAA
Found at i:55893944 original size:162 final size:162
Alignment explanation
Indices: 55893699--55894050 Score: 605
Period size: 162 Copynumber: 2.2 Consensus size: 162
55893689 TGCAATTGGG
55893699 AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
1 AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
* * *
55893764 AATTTCAATTTGTTGCATTCTCTGACTTGTAATTTCCTTAGGCATTGGAAGCTTATGGTTGATAC
66 AATTTCAACTTATTGCATTCTCTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
* *
55893829 TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
131 TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
* * * *
55893861 AGCACCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGTGAAGAGA
1 AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
* *
55893926 AATTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
66 AATTTCAACTTATTGCATTCTCTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
55893991 TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
131 TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
55894023 AACAACTCTCTATCTTCAGAGTTTGCAA
1 AACAACTCTCTATCTTCAGAGTTTGCAA
55894051 ATTGGGCGCA
Statistics
Matches: 177, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 177 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (162 bp):
AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
AATTTCAACTTATTGCATTCTCTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
Found at i:55898829 original size:19 final size:19
Alignment explanation
Indices: 55898805--55898849 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
55898795 AAAATTACAA
*
55898805 AAAAATT-AAAATAATTTTT
1 AAAAATTGAAAAT-ATTTAT
55898824 AAAAATTGAAAATATTTAT
1 AAAAATTGAAAATATTTAT
55898843 AAAAATT
1 AAAAATT
55898850 CTAACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATTGAAAATATTTAT
Found at i:55900260 original size:16 final size:16
Alignment explanation
Indices: 55900226--55900275 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
55900216 AAAACTAAAG
* *
55900226 TTTTTAAAACATTTA-
1 TTTTTAAAATATTCAT
*
55900241 TTTTTATAATATTCAT
1 TTTTTAAAATATTCAT
*
55900257 TTTTTAAAATTTTCAT
1 TTTTTAAAATATTCAT
55900273 TTT
1 TTT
55900276 AAATTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAATATTCAT
Found at i:55902367 original size:42 final size:42
Alignment explanation
Indices: 55902262--55902416 Score: 150
Period size: 43 Copynumber: 3.6 Consensus size: 42
55902252 ATGTGATTTT
* * *
55902262 GTGTAAGACCACGTCTGGGACGTTGGCTTCG-ATTTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGTATTT--GA-TTAC
* *
55902306 GTGTAAGACCATGTTTGGGACATTGACATCGTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTAC
* * * *
55902348 GTGTAAGACCTTGTCTGGGATAGTGGCATTGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATTAC
* ** *
55902391 ATGTAAGACCACATCTGGGACGTTGG
1 GTGTAAGACCATGTCTGGGACATTGG
55902417 TATTGTACGA
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 29 0.32
43 32 0.35
44 26 0.29
45 4 0.04
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTAC
Found at i:55902398 original size:43 final size:42
Alignment explanation
Indices: 55902262--55902411 Score: 133
Period size: 42 Copynumber: 3.5 Consensus size: 42
55902252 ATGTGATTTT
* * *
55902262 GTGTAAGACCACGTCTGGGAC-GTTGGCTTCG-ATTTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACAG-TGACATCGTATTT--GA-TTAC
* *
55902306 GTGTAAGACCATGTTTGGGACATTGACATCGTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGTGACATCGTATTTGATTAC
* * * *
55902348 GTGTAAGACCTTGTCTGGGATAGTGGCATTGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGTGACATCG-TATTTGATTAC
* **
55902391 ATGTAAGACCACATCTGGGAC
1 GTGTAAGACCATGTCTGGGAC
55902412 GTTGGTATTG
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 29 0.33
43 29 0.33
44 25 0.29
45 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACAGTGACATCGTATTTGATTAC
Found at i:55905317 original size:15 final size:13
Alignment explanation
Indices: 55905297--55905349 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 13
55905287 AATAAAAAGG
55905297 AAATAATAAGTAAAT
1 AAATAA-AA-TAAAT
55905312 AAATAAAATAAAAT
1 AAATAAAAT-AAAT
55905326 AAAATAAAATAAA-
1 -AAATAAAATAAAT
55905339 AAAT-AAATAAA
1 AAATAAAATAAA
55905350 AATAATAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.19
12 4 0.11
13 1 0.03
14 9 0.25
15 15 0.42
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:55905322 original size:5 final size:5
Alignment explanation
Indices: 55905308--55905350 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
55905298 AATAATAAGT
*
55905308 AAAT- AAATA AAATA AAATA AAATA AAATA AAAAA TAAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAA
55905351 ATAATAACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
4 4 0.11
5 27 0.77
6 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:55905342 original size:27 final size:26
Alignment explanation
Indices: 55905285--55905367 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 26
55905275 AAATCAATTT
*
55905285 TAAATAAAAAGGAAATAATAAGTAAATAAA
1 TAAATAAAAA--AAATAACAA-TAAA-AAA
55905315 TAAAATAAAATAAAATAA-AATAAAAAA
1 TAAA-TAAAA-AAAATAACAATAAAAAA
*
55905342 TAAATAAAAATAATAACACATAAAAA
1 TAAATAAAAAAAATAACA-ATAAAAA
55905368 TGAATAATCT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
25 6 0.12
26 6 0.12
27 14 0.29
28 4 0.08
29 2 0.04
30 10 0.21
31 5 0.10
32 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (26 bp):
TAAATAAAAAAAATAACAATAAAAAA
Found at i:55905346 original size:11 final size:11
Alignment explanation
Indices: 55905261--55905351 Score: 58
Period size: 11 Copynumber: 8.1 Consensus size: 11
55905251 AAAAATGCAC
55905261 AATAAATAAAA
1 AATAAATAAAA
* * *
55905272 AACAAATCAAT
1 AATAAATAAAA
**
55905283 TTTAAATAAAA
1 AATAAATAAAA
** *
55905294 AGGAAATAATA
1 AATAAATAAAA
*
55905305 AGTAAATAAATAA
1 AATAAAT-AA-AA
*
55905318 AATAAA-ATAA
1 AATAAATAAAA
55905328 AATAAAATAAAA
1 AAT-AAATAAAA
55905340 AATAAATAAAA
1 AATAAATAAAA
55905351 A
1 A
55905352 TAATAACACA
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
10 5 0.08
11 40 0.68
12 8 0.14
13 6 0.10
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:55906040 original size:3 final size:3
Alignment explanation
Indices: 55906032--55906063 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
55906022 AAAAAGGTAA
55906032 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
55906064 AGTTTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55906445 original size:89 final size:89
Alignment explanation
Indices: 55906267--55906749 Score: 416
Period size: 89 Copynumber: 5.4 Consensus size: 89
55906257 TTTGTAGTTC
* ** * * * *
55906267 TAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTT-ATAGCTTTAATCTGCTCCACCG-AACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* * *
55906330 TCAGAGAGATAAGATTTATGTTTT
66 TCAGGGAGATAAGATTTGTGTCTT
* * * *
55906354 TAATCTGCTCTACTACAACTTCAGAAAGATAAGATTTGCTATCTTCAAACTGCTCTACTGCAACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
*
55906419 TCAGGGAGATAAGATTTGTGGCTT
66 TCAGGGAGATAAGATTTGTGTCTT
* * * *
55906443 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTTAATCTACTCCACTGCAACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* * *
55906508 TCAAGGAAATAAGATTTGCTATCTT
66 TCAGGGAGATAAGATTTG-TGTCTT
* ** * * * * * *
55906533 CAATCTGCTCCACTGTGACTTTAGGAAGATAAGATTTTCTATCTTCAATCTTCTCTACTGCGACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* * * *
55906598 TCGGGGAGATAAGGTTTGCTATCAT
66 TCAGGGAGATAAGATTTG-TGTCTT
* ** * ** * * * **
55906623 CAATCTGCTCCACTGTGACTTTAGGGAGATAAGATTTG-TGGT-TTTAATCTGCTCAACTATAAC
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCT-ATCTTCAATCTGCTCCACTGCAAC
* * *
55906686 TTCAGAGAGATAGGATTTGTGGCTT
65 TTCAGGGAGATAAGATTTGTGTCTT
* * * ** *
55906711 TAATCTACTCCACCGCAACTTTAGGGAGATAATATTTGC
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGC
55906750 CATAATAACT
Statistics
Matches: 327, Mismatches: 64, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
87 32 0.10
88 51 0.16
89 130 0.40
90 114 0.35
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (89 bp):
TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
TCAGGGAGATAAGATTTGTGTCTT
Found at i:55906748 original size:44 final size:44
Alignment explanation
Indices: 55906267--55906748 Score: 437
Period size: 45 Copynumber: 10.9 Consensus size: 44
55906257 TTTGTAGTTC
* * *
55906267 TAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* * * * *
55906311 TAATCTGCTCCACCG-AACTTCAGAGAGATAAGATTTATGTTTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* * **
55906354 TAATCTGCTCTACTACAACTTCAGAAAGATAAGATTTGCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* * * **
55906399 CAAACTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTGGCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* *
55906443 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* * *
55906488 TAATCTACTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* ** * * *
55906533 CAATCTGCTCCACTGTGACTTTAGGAAGATAAGATTTTCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTATCTT
* * * * * * *
55906578 CAATCTTCTCTACTGCGACTTCGGGGAGATAAGGTTTGCTATCAT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* ** * *
55906623 CAATCTGCTCCACTGTGACTTTAGGGAGATAAGATTTGTGGT-TT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ATCTT
* ** * * **
55906667 TAATCTGCTCAACTATAACTTCAGAGAGATAGGATTTGTGGCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* * * *
55906711 TAATCTACTCCACCGCAACTTTAGGGAGATAATATTTG
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
55906749 CCATAATAAC
Statistics
Matches: 358, Mismatches: 73, Indels: 14
0.80 0.16 0.03
Matches are distributed among these distances:
43 37 0.10
44 140 0.39
45 178 0.50
46 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (44 bp):
TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
Found at i:55908332 original size:13 final size:13
Alignment explanation
Indices: 55908314--55908338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55908304 TAATTTATAT
55908314 GTGTGAAAATTTC
1 GTGTGAAAATTTC
55908327 GTGTGAAAATTT
1 GTGTGAAAATTT
55908339 TACCATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:55912382 original size:16 final size:15
Alignment explanation
Indices: 55912357--55912386 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
55912347 TTAATTTCAT
55912357 TCATTTCACAATTTC
1 TCATTTCACAATTTC
55912372 TCATATTCACAATTT
1 TCAT-TTCACAATTT
55912387 AAAATCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATTTCACAATTTC
Found at i:55915278 original size:38 final size:37
Alignment explanation
Indices: 55915206--55915278 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 37
55915196 CTTTCATAAT
*
55915206 TTCACTTTTTCACTTTCTATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCTATCACAATTCAATTCAAAA
55915243 TTCACTTTTCCA-TTTCTAAGTCA-ATATTCAATTCAA
1 TTCACTTTTCCACTTTCT-A-TCACA-ATTCAATTCAA
55915279 TTCCACACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 5 0.16
37 13 0.41
38 14 0.44
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.44
Consensus pattern (37 bp):
TTCACTTTTCCACTTTCTATCACAATTCAATTCAAAA
Found at i:55915281 original size:36 final size:36
Alignment explanation
Indices: 55915206--55915278 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
55915196 CTTTCATAAT
*
55915206 TTCACTTTTTCACTTTCTATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCTATCACAATTCAATTC-AAA
55915243 TTCACTTTTCCA-TTTCTAAGTCA-ATATTCAATTCAA
1 TTCACTTTTCCACTTTCT-A-TCACA-ATTCAATTCAA
55915279 TTCCACACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 5 0.16
37 15 0.47
38 12 0.38
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.44
Consensus pattern (36 bp):
TTCACTTTTCCACTTTCTATCACAATTCAATTCAAA
Found at i:55915484 original size:51 final size:50
Alignment explanation
Indices: 55915408--55915843 Score: 342
Period size: 51 Copynumber: 8.6 Consensus size: 50
55915398 CCGGCTCACA
* * *
55915408 TAGTAGCATGCACATAGTACTACACAGGTGACCATCA-CTATCCGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGCTATCCGATACACG
* * * * *
55915459 TAGTAGCCTTCACATAGTACCACACACGTGATCGAAGCTATCCAATACGCA
1 TAGTAGCCTTCACATAGTACTACACACGTGA-CCAAGCTATCCGATACACG
* * * * * *
55915510 TAGTAGCCTGCACATAGTACTACACATGCGACCTATC-ATTCTGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTA-TCCGATACACG
** * * * * * *
55915560 TAGTAGCCCACACATAGTACTACACACGTGATCAAGTTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTATCCGATACACG
* * * * * *
55915610 AAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGA-CCAAGCTATCCGATACACG
* * **
55915661 TAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGCTATCCGATACACG
* * * *
55915712 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCT-TCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTATC-CGATACACG
** * * ** *
55915763 TTTTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACATG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGCTATCCGATACACG
*
55915814 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
55915844 TTCATCGATA
Statistics
Matches: 300, Mismatches: 72, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
49 2 0.01
50 80 0.27
51 209 0.70
52 8 0.03
53 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTATCCGATACACG
Found at i:55915585 original size:101 final size:102
Alignment explanation
Indices: 55915406--55915592 Score: 288
Period size: 101 Copynumber: 1.8 Consensus size: 102
55915396 TACCGGCTCA
* **
55915406 CATAGTAGCATGCACATAGTACTACACAGGTGACCATCACTATCCGATACACGTAGTAGCCTTCA
1 CATAGTAGCATGCACATAGTACTACACAGGCGACCATCACTATCCGATACACGTAGTAGCCCACA
55915471 CATAGTACCACACACGTGATCGAAGCTATCCAATACG
66 CATAGTACCACACACGTGATCGAAGCTATCCAATACG
* * *
55915508 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGATACACGTAGTAGCCCAC
1 CATAGTAGCATGCACATAGTACTACACAGGCGACC-ATCACTATCCGATACACGTAGTAGCCCAC
*
55915571 ACATAGTACTACACACGTGATC
65 ACATAGTACCACACACGTGATC
55915593 AAGTTTTACG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 40 0.52
102 33 0.43
103 4 0.05
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACAGGCGACCATCACTATCCGATACACGTAGTAGCCCACA
CATAGTACCACACACGTGATCGAAGCTATCCAATACG
Found at i:55915683 original size:151 final size:152
Alignment explanation
Indices: 55915455--55915742 Score: 400
Period size: 151 Copynumber: 1.9 Consensus size: 152
55915445 CTATCCGATA
* * *
55915455 CACGTAGTAGCCTTCACATAGTACCACACACGTGATCGAAGCTATCCAATACGCATAGTAGCCTG
1 CACGAAGTAGCCTTCACATAGTACCACACACGTGATCAAAGCTATCCAATACACATAGTAGCCTG
* *
55915520 CACATAGTACTACACATGCGACCTATCA-TTCT-GATACACGTAGTAGCCCACACATAGTACTAC
66 CACATAGTACTACACATGCGACC-ATCATTTATCGATACACGTAGTAGCCCACACACAGTACTAC
*
55915583 ACACGTGATCAAGTTTTACGGTT
130 ACAAGTGATCAAGTTTTACGGTT
* * * ** *
55915606 CACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTT
1 CACGAAGTAGCCTTCACATAGTACCACACACGTGATCAAAGCTATCCAATACACATAGTAGCCTG
* * * **
55915671 CACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAGTAGCCTTCACACAGTACTACA
66 CACATAGTACTACACATGCGACCATCATTTATCGATACACGTAGTAGCCCACACACAGTACTACA
55915736 CAAGTGA
131 CAAGTGA
55915743 CCAAAGCTTC
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
150 3 0.03
151 80 0.68
152 35 0.30
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (152 bp):
CACGAAGTAGCCTTCACATAGTACCACACACGTGATCAAAGCTATCCAATACACATAGTAGCCTG
CACATAGTACTACACATGCGACCATCATTTATCGATACACGTAGTAGCCCACACACAGTACTACA
CAAGTGATCAAGTTTTACGGTT
Found at i:55915748 original size:102 final size:102
Alignment explanation
Indices: 55915510--55915839 Score: 398
Period size: 102 Copynumber: 3.3 Consensus size: 102
55915500 CCAATACGCA
* * * * * * * * **
55915510 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCT-GATACACGTAGTAGCCCACAC
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGC-TTCTCGGTACACATAGTAGCCTTCAC
* * * * * *
55915573 ATAGTACTACACACGTGATCAAGT-TTTA-CGGTTCACG
65 TTAGTACTACACATGTGA-CCATTATTTATCGATACACG
* * * * *
55915610 AAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTTCACT
55915675 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
**
55915712 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTTTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTTCACT
*
55915777 TAGTACTACACATGTGACCATTATTTATCGATACATG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
55915814 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTTCACACAGTACTACACA
55915840 CGTGTTCATC
Statistics
Matches: 200, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 34 0.17
101 39 0.19
102 127 0.63
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTTCACT
TAGTACTACACATGTGACCATTATTTATCGATACACG
Found at i:55915818 original size:153 final size:150
Alignment explanation
Indices: 55915453--55915839 Score: 395
Period size: 151 Copynumber: 2.5 Consensus size: 150
55915443 CACTATCCGA
* * * * * * * *
55915453 TACACGTAGTAGCCTTCACATAGTACCACACACGTGATCGAAGCTATCCAATACGCATAGTAGCC
1 TACACGAAGTAGCCTTCACATAGTACTACACACGTGA-CCAAACTTTTCGATACACATAGTAGCC
* * *
55915518 TGCACATAGTACTACACATGCGACCTATCATTCTGATACACGTAGTAGCCCACACATAGTACTAC
65 TTCACATAGTACTACACATGCGACCTATCATTATGATACACGTAGTAGCCCACACACAGTACTAC
* * *
55915583 ACACGTGATCAAGTTTTACGG
130 ACAAGTGACCAAGTTCTACGG
* * *
55915604 TTCACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCC
1 TACACGAAGTAGCCTTCACATAGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCC
* * * **
55915669 TTCACTTAGTACTACACATGTGACC-ATTATTTATCGATACACGTAGTAGCCTTCACACAGTACT
65 TTCACATAGTACTACACATGCGACCTATCA-TTAT-GATACACGTAGTAGCCCACACACAGTACT
55915733 ACACAAGTGACCAAAGCTTCT-CGG
128 ACACAAGTGACC-AAG-TTCTACGG
** * * * **
55915757 TACAC-ATTTTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACATGTAGTAG
1 TACACGA-AGTAGCCTTCACATAGTACTACACACGTGACCA-AACTTT-TCGATACACATAGTAG
*
55915820 CCTTCACACAGTACTACACA
63 CCTTCACATAGTACTACACA
55915840 CGTGTTCATC
Statistics
Matches: 194, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
150 5 0.03
151 76 0.39
152 40 0.21
153 69 0.36
154 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (150 bp):
TACACGAAGTAGCCTTCACATAGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCT
TCACATAGTACTACACATGCGACCTATCATTATGATACACGTAGTAGCCCACACACAGTACTACA
CAAGTGACCAAGTTCTACGG
Found at i:55920306 original size:43 final size:42
Alignment explanation
Indices: 55920241--55920368 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 42
55920231 TACTTCACAT
*
55920241 TGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGA
1 TGCCAACGTCCCAGACGTGGTCTTACACGTAA-CACATATCGA
*
55920284 TGCC-ACTGTCCCAGACAG-GGTCTTACACGTAACA-AAAGTCGA
1 TGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAACACATA-TCGA
* *
55920326 TGCCAACATCCCAGACGTGGTCTTACACGAAAACACATATCGA
1 TGCCAACGTCCCAGACGTGGTCTTACACG-TAACACATATCGA
55920369 AAATCCTATG
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
41 3 0.04
42 31 0.42
43 36 0.49
44 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (42 bp):
TGCCAACGTCCCAGACGTGGTCTTACACGTAACACATATCGA
Found at i:55923790 original size:46 final size:42
Alignment explanation
Indices: 55923736--55923855 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 42
55923726 AAATTATACA
55923736 TTTTAATATTTTCATTAATATATTAATATTAATATAAAAACATAT
1 TTTTAATATTTT-ATTAATATA-TAATATTAATATAAAAA-ATAT
*
55923781 TTTTAAATATTTTTATT--TATATAA-ATTTATAT-AAAAATAT
1 TTTT-AATA-TTTTATTAATATATAATATTAATATAAAAAATAT
* *
55923821 TTTTATTATTTT-TTAAAAGTAATAATATTAATATA
1 TTTTAATATTTTATTAATA-T-ATAATATTAATATA
55923856 TTATTTTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
37 2 0.03
38 4 0.06
39 4 0.06
40 9 0.14
41 8 0.13
42 14 0.22
43 3 0.05
44 4 0.06
45 4 0.06
46 7 0.11
47 4 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (42 bp):
TTTTAATATTTTATTAATATATAATATTAATATAAAAAATAT
Found at i:55923873 original size:29 final size:27
Alignment explanation
Indices: 55923827--55923893 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
55923817 ATATTTTTAT
*
55923827 TATTTTTTAAAAGTAATAATATTAATA
1 TATTTTTTAAAAATAATAATATTAATA
* * *
55923854 TATTATTTTAAACAATAATAATTTTATTT
1 TATT-TTTTAAA-AATAATAATATTAATA
55923883 TATTGTTTTAA
1 TATT-TTTTAA
55923894 TATTTTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 4 0.12
28 7 0.21
29 22 0.67
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (27 bp):
TATTTTTTAAAAATAATAATATTAATA
Found at i:55923885 original size:26 final size:25
Alignment explanation
Indices: 55923816--55923886 Score: 63
Period size: 28 Copynumber: 2.7 Consensus size: 25
55923806 TTTATATAAA
* *
55923816 AATATTTTTATTATT-TTTTAAAAGT
1 AATAATTTTATT-TTATTTTAAAAAT
*
55923841 AATAATATTAATATATTATTTTAAACAAT
1 AATAAT-TT--TATTTTATTTTAAA-AAT
55923870 AATAATTTTATTTTATT
1 AATAATTTTATTTTATT
55923887 GTTTTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
25 5 0.14
26 10 0.27
27 2 0.05
28 12 0.32
29 8 0.22
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
AATAATTTTATTTTATTTTAAAAAT
Found at i:55925116 original size:29 final size:29
Alignment explanation
Indices: 55925082--55925138 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
55925072 CTAGTCTTCG
55925082 AAGGTACAAGAGTGAGGAATCATCATTCA
1 AAGGTACAAGAGTGAGGAATCATCATTCA
*
55925111 AAGGTACAAGAGTGAGGAATCTTCATTC
1 AAGGTACAAGAGTGAGGAATCATCATTC
55925139 TGTATAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
AAGGTACAAGAGTGAGGAATCATCATTCA
Found at i:55928782 original size:162 final size:162
Alignment explanation
Indices: 55928544--55929052 Score: 883
Period size: 162 Copynumber: 3.1 Consensus size: 162
55928534 TTGGGAACAG
* *
55928544 CTCTCTATCCTTAGAGTTTGCAATTGCCCGAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
* *
55928609 CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTAGATACTTGTA
66 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTA
55928674 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
* * *
55928706 CTCTCTATCTTTAGAGTTTGTAATTTCCCAAGACTATTAGCAACACACATTGAGAAGAGAAATTT
1 CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
* * *
55928771 CAATTTATTGCATTTTGTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTA
* *
55928836 ACTCTTGGATTATTTCTTCCATTCCAAAGCAG
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
*
55928868 CTCTCTATCTTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
55928933 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTA
66 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTA
*
55928998 AGTATTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
*
55929030 CTCTCTATCCTCAGAGTTTGCAA
1 CTCTCTATCCTTAGAGTTTGCAA
55929053 ATTGGGCGCA
Statistics
Matches: 325, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 325 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (162 bp):
CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTA
AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
Found at i:55931531 original size:24 final size:24
Alignment explanation
Indices: 55931499--55931548 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
55931489 AAATGAGCTG
55931499 AGCTAGATAGCTGCTGGTCTCGAT
1 AGCTAGATAGCTGCTGGTCTCGAT
*
55931523 AGCTCGATAGCTGCTGGTCTCGAT
1 AGCTAGATAGCTGCTGGTCTCGAT
55931547 AG
1 AG
55931549 TAGCATGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (24 bp):
AGCTAGATAGCTGCTGGTCTCGAT
Found at i:55936118 original size:24 final size:24
Alignment explanation
Indices: 55936086--55936135 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
55936076 AAATGAGCTG
55936086 AGCTAGATAGCTGCTGGTCTCGAT
1 AGCTAGATAGCTGCTGGTCTCGAT
*
55936110 AGCTCGATAGCTGCTGGTCTCGAT
1 AGCTAGATAGCTGCTGGTCTCGAT
55936134 AG
1 AG
55936136 TAGCATGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (24 bp):
AGCTAGATAGCTGCTGGTCTCGAT
Found at i:55938658 original size:28 final size:28
Alignment explanation
Indices: 55938624--55938680 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
55938614 GAGCAAAAGT
55938624 ATGTAAAACTTAATACAAAAAGAAAGGA
1 ATGTAAAACTTAATACAAAAAGAAAGGA
*
55938652 ATGTAAAACTTAATACAAAAGGAAAGGA
1 ATGTAAAACTTAATACAAAAAGAAAGGA
55938680 A
1 A
55938681 CTTGAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.60, C:0.07, G:0.16, T:0.18
Consensus pattern (28 bp):
ATGTAAAACTTAATACAAAAAGAAAGGA
Found at i:55939051 original size:15 final size:14
Alignment explanation
Indices: 55939022--55939065 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
55939012 AAAATATCTA
* *
55939022 CTTTTCTTCAGTTT
1 CTTTTCTTAATTTT
55939036 CTTTTTCTTAATTTT
1 C-TTTTCTTAATTTT
*
55939051 CATTTCTTAATTTT
1 CTTTTCTTAATTTT
55939065 C
1 C
55939066 AGTTGATCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.14, C:0.18, G:0.02, T:0.66
Consensus pattern (14 bp):
CTTTTCTTAATTTT
Found at i:55939056 original size:14 final size:14
Alignment explanation
Indices: 55939039--55939066 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55939029 TCAGTTTCTT
55939039 TTTCTTAATTTTCA
1 TTTCTTAATTTTCA
55939053 TTTCTTAATTTTCA
1 TTTCTTAATTTTCA
55939067 GTTGATCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTCTTAATTTTCA
Found at i:55939567 original size:56 final size:56
Alignment explanation
Indices: 55939506--55939618 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
55939496 ATACGAGAGA
55939506 CTTTCAAAAATTCCAATGTTAAAATTATGGATTTGGATTAAATTATCTAAAAATAT
1 CTTTCAAAAATTCCAATGTTAAAATTATGGATTTGGATTAAATTATCTAAAAATAT
55939562 CTTTCAAAAATTCCAATGTTAAAATTATGGATTTGGATTAAATTATCTAAAAATAT
1 CTTTCAAAAATTCCAATGTTAAAATTATGGATTTGGATTAAATTATCTAAAAATAT
55939618 C
1 C
55939619 GAAAAACAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (56 bp):
CTTTCAAAAATTCCAATGTTAAAATTATGGATTTGGATTAAATTATCTAAAAATAT
Found at i:55939612 original size:28 final size:28
Alignment explanation
Indices: 55939525--55939613 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
55939515 ATTCCAATGT
55939525 TAAAATTATGGATTTGGATTAAATTATC
1 TAAAATTATGGATTTGGATTAAATTATC
* * * * *
55939553 TAAAAATAT--CTTT-CA-AAAATTCCAATGT
1 TAAAATTATGGATTTGGATTAAATT---AT-C
55939581 TAAAATTATGGATTTGGATTAAATTATC
1 TAAAATTATGGATTTGGATTAAATTATC
55939609 TAAAA
1 TAAAA
55939614 ATATCGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 16
0.62 0.14 0.23
Matches are distributed among these distances:
24 5 0.12
25 1 0.02
26 3 0.07
27 2 0.05
28 21 0.49
29 2 0.05
30 3 0.07
31 1 0.02
32 5 0.12
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (28 bp):
TAAAATTATGGATTTGGATTAAATTATC
Found at i:55943100 original size:30 final size:30
Alignment explanation
Indices: 55943028--55943140 Score: 140
Period size: 30 Copynumber: 3.8 Consensus size: 30
55943018 TTTGGCCTGT
* * *
55943028 GCCCTATACAGTAGCA-A-TGTGTGGCCATA
1 GCCCAATACAGTAACAGAGTGTG-GGCCTTA
*
55943057 GCCCAATATAGTAACAGAGTGTGGGCCTTA
1 GCCCAATACAGTAACAGAGTGTGGGCCTTA
*
55943087 GCCTAATACAGTAACAGAGTGTGGGCCTTA
1 GCCCAATACAGTAACAGAGTGTGGGCCTTA
* *
55943117 TCCCAATACAGTAATAGAGTGTGG
1 GCCCAATACAGTAACAGAGTGTGG
55943141 TGCAAGTATA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.18
30 56 0.77
31 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (30 bp):
GCCCAATACAGTAACAGAGTGTGGGCCTTA
Found at i:55943375 original size:32 final size:32
Alignment explanation
Indices: 55943320--55943522 Score: 291
Period size: 32 Copynumber: 6.4 Consensus size: 32
55943310 GAATGACTAC
* * *
55943320 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
55943351 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
55943383 CAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
55943415 CAGCCATTAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
55943447 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
55943479 AAGCCATCAATAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
55943511 AAGCCATCAGTA
1 AAGCCATCAGTA
55943523 GCATCGCAGC
Statistics
Matches: 155, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 10 0.06
32 145 0.94
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:55943581 original size:27 final size:26
Alignment explanation
Indices: 55943550--55943610 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
55943540 CCAACAATAG
55943550 TAACAGTATATGTGGCCA-AGCCACCAA
1 TAACAGTAT-TGTGG-CAGAGCCACCAA
*
55943577 TAACAGTGATTGTGGCAGAGCCACCAG
1 TAACAGT-ATTGTGGCAGAGCCACCAA
55943604 T-ACAGTA
1 TAACAGTA
55943611 CTTCCTCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 21 0.68
28 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (26 bp):
TAACAGTATTGTGGCAGAGCCACCAA
Found at i:55943709 original size:24 final size:24
Alignment explanation
Indices: 55943673--55943750 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
55943663 TACATGCTCA
* *
55943673 AAATCAGTCATACAAATCACAGAC
1 AAATCAATTATACAAATCACAGAC
*
55943697 AAATCAATTATACTAATCACAGAC
1 AAATCAATTATACAAATCACAGAC
*
55943721 AAATCAACTATTA-AAATCACAGAC
1 AAATCAATTA-TACAAATCACAGAC
55943745 AAATCA
1 AAATCA
55943751 GTCATTTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.53, C:0.22, G:0.05, T:0.21
Consensus pattern (24 bp):
AAATCAATTATACAAATCACAGAC
Found at i:55943763 original size:24 final size:24
Alignment explanation
Indices: 55943686--55943783 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
55943676 TCAGTCATAC
* *
55943686 AAATCACAGACAAATCAATTATACT
1 AAATCACAGACAAATCAATCAT-TT
*
55943711 -AATCACAGACAAATCAA-CTATTA
1 AAATCACAGACAAATCAATC-ATTT
*
55943734 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAATCATTT
* *
55943758 ACATCAC-GAAAAAATCAATCATTT
1 AAATCACAG-ACAAATCAATCATTT
55943782 AA
1 AA
55943784 CCTCGAGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 58 0.97
25 1 0.02
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.23
Consensus pattern (24 bp):
AAATCACAGACAAATCAATCATTT
Found at i:55943923 original size:27 final size:27
Alignment explanation
Indices: 55943855--55943998 Score: 157
Period size: 27 Copynumber: 5.4 Consensus size: 27
55943845 AGGTACTATA
* *
55943855 GTCATTTTA-CCTATAGGGGCATCACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * **
55943881 GTCATTTTACTTTACAGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
*
55943908 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
55943935 GTCATTATACCCTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* *
55943962 ATCATTTTACCCTACA-GGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
55943988 ATCATTTTACC
1 GTCATTTTACC
55943999 AATATTGGGG
Statistics
Matches: 97, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
26 28 0.29
27 69 0.71
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:55950299 original size:18 final size:17
Alignment explanation
Indices: 55950273--55950320 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
55950263 AAATAAAAAA
55950273 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAA-TGAAT
*
55950291 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
*
55950309 AATGTTTTGAAA
1 AACGTTTTGAAA
55950321 ACGAACGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:55952530 original size:38 final size:38
Alignment explanation
Indices: 55952452--55952530 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
55952442 AGTCCCTTTA
**
55952452 TATTTTTTATATATTAATTAATTTTCATTTTTATTTTG
1 TATTTTTTATATATTAATTAATTTTCATTTAAATTTTG
55952490 TATTTTTCTCATAT-TTAATT-ATTTT-ATTTAAATTTATG
1 TATTTTT-T-ATATATTAATTAATTTTCATTTAAATTT-TG
55952528 TAT
1 TAT
55952531 GTATGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
37 8 0.22
38 17 0.47
39 7 0.19
40 4 0.11
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (38 bp):
TATTTTTTATATATTAATTAATTTTCATTTAAATTTTG
Found at i:55952625 original size:22 final size:22
Alignment explanation
Indices: 55952568--55952629 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
55952558 TGCATACGCA
*
55952568 TATTTTTT-TAATGTAATGTAAT
1 TATTTTTTATAAT-TTATGTAAT
*
55952590 TATTTTTTAT--TTTATGTGAT
1 TATTTTTTATAATTTATGTAAT
55952610 TATTTTTTATAATTTATGTA
1 TATTTTTTATAATTTATGTA
55952630 TGTATACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 15 0.44
23 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (22 bp):
TATTTTTTATAATTTATGTAAT
Found at i:55952700 original size:6 final size:6
Alignment explanation
Indices: 55952689--55952713 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55952679 TTAATTATTT
55952689 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
55952714 ATATGGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:55975095 original size:20 final size:20
Alignment explanation
Indices: 55975070--55975135 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
55975060 TTAAGATATA
55975070 AATAAACAAACATAAATAAT
1 AATAAACAAACATAAATAAT
*
55975090 AATAAACAAATTATAAATAAAT
1 AATAAACAAA-CATAAAT-AAT
*
55975112 AA-AAGA-AACACATAAACAAT
1 AATAA-ACAA-ACATAAATAAT
55975132 AATA
1 AATA
55975136 GTATTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 15 0.39
21 16 0.42
22 7 0.18
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (20 bp):
AATAAACAAACATAAATAAT
Found at i:55975708 original size:22 final size:23
Alignment explanation
Indices: 55975665--55975713 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 23
55975655 CCTATCGGAT
55975665 AAAACTAGTTATTTTTCCTTTTAA
1 AAAACTAGTTATTTTT-CTTTTAA
55975689 AAAATCTAGTTA-TTTT-TTTTAA
1 AAAA-CTAGTTATTTTTCTTTTAA
55975711 AAA
1 AAA
55975714 GTAATGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
24 8 0.33
25 7 0.29
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (23 bp):
AAAACTAGTTATTTTTCTTTTAA
Found at i:55975867 original size:20 final size:20
Alignment explanation
Indices: 55975842--55975901 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
55975832 ATTATGCATT
55975842 TTAATATTTATATTTATATA
1 TTAATATTTATATTTATATA
** * ** *
55975862 TTAATATAAAAACATATATT
1 TTAATATTTATATTTATATA
*
55975882 TTAATATTTTTATTTATATA
1 TTAATATTTATATTTATATA
55975902 CATTAATATA
Statistics
Matches: 27, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATATTTATATTTATATA
Found at i:55975995 original size:31 final size:30
Alignment explanation
Indices: 55975922--55976001 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
55975912 TAAATATTTT
*
55975922 TATTATTTTATTATTTTAAAAAAGTAATAA
1 TATTATTTTATTATTTTAAAAAAATAATAA
* * *
55975952 TATTAATATATTATTTGTAAAAAAATAATTA
1 TATTATTTTATTATTT-TAAAAAAATAATAA
*
55975983 TTTTATTTTATTATTTTAA
1 TATTATTTTATTATTTTAA
55976002 TATTTCATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TATTATTTTATTATTTTAAAAAAATAATAA
Found at i:55979862 original size:16 final size:16
Alignment explanation
Indices: 55979841--55979909 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
55979831 TTTGGTTCGC
55979841 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55979857 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55979873 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
55979890 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55979906 TGTA
1 TGTA
55979910 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55979887 original size:33 final size:32
Alignment explanation
Indices: 55979841--55979909 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
55979831 TTTGGTTCGC
55979841 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
55979873 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
55979906 TGTA
1 TGTA
55979910 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:55979974 original size:44 final size:45
Alignment explanation
Indices: 55979890--55979980 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
55979880 GGATTAGAGG
* * *
55979890 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
55979935 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
55979979 TG
1 TG
55979981 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:55980166 original size:18 final size:19
Alignment explanation
Indices: 55980145--55980181 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55980135 TTATTATTAA
55980145 ATAT-ATTT-TAATTAAAAT
1 ATATAATTTATAA-TAAAAT
55980163 ATATAATTTATAATAAAAT
1 ATATAATTTATAATAAAAT
55980182 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 10 0.59
20 3 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATTTATAATAAAAT
Found at i:55980346 original size:120 final size:120
Alignment explanation
Indices: 55980125--55980414 Score: 447
Period size: 120 Copynumber: 2.4 Consensus size: 120
55980115 TTAATCATAT
55980125 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTATAATAAAATTCTTAATA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAA-TT-TAATAAAATTCTTAATA
* * *
55980190 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
64 ATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * *
55980247 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAACTATATGATTTAATAAAATTCTTAATAT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
55980311 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
** *
55980367 TTTAACATAATTATTATTAAATATAAGTTAATAAAAATATATAATTTA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTA
55980415 TCATCATACT
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
119 2 0.01
120 108 0.71
121 2 0.01
122 38 0.25
123 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:55982440 original size:18 final size:17
Alignment explanation
Indices: 55982417--55982484 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
55982407 AATTATTATT
55982417 AAATATAT-A-TTAATTA
1 AAATATATAATTTAA-TA
55982433 AAATATATAATTTAATA
1 AAATATATAATTTAATA
*
55982450 AAAT-TCTTAA--TAAT-
1 AAATAT-ATAATTTAATA
55982464 AAATATATAATTTAATA
1 AAATATATAATTTAATA
55982481 AAAT
1 AAAT
55982485 TCTCAATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
14 7 0.16
15 5 0.12
16 13 0.30
17 14 0.33
18 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAATTTAATA
Found at i:55982447 original size:14 final size:15
Alignment explanation
Indices: 55982410--55982449 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
55982400 TTAACATAAT
55982410 TATT-ATTAAATATA
1 TATTAATTAAATATA
55982424 TATTAATTAAA-ATA
1 TATTAATTAAATATA
*
55982438 TA-TAATTTAATA
1 TATTAATTAAATA
55982450 AAATTCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 10 0.43
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATTAAATATA
Found at i:55982481 original size:16 final size:15
Alignment explanation
Indices: 55982416--55982482 Score: 50
Period size: 16 Copynumber: 4.3 Consensus size: 15
55982406 TAATTATTAT
55982416 TAAATATATA-TTAA
1 TAAATATATATTTAA
55982430 TTAAAATATATAATTTAA
1 -T-AAATATAT-ATTTAA
*
55982448 TAAA-AT-TCTTAATAA
1 TAAATATATATT--TAA
55982463 TAAATATATAATTTAA
1 TAAATATAT-ATTTAA
55982479 TAAA
1 TAAA
55982483 ATTCTCAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
13 2 0.05
14 1 0.02
15 10 0.24
16 20 0.48
17 3 0.07
18 6 0.14
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATATATATTTAA
Found at i:55985317 original size:52 final size:50
Alignment explanation
Indices: 55985240--55985375 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 50
55985230 TTGCATGTTC
55985240 GATTGAAAAATTTGTTCAATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
1 GATTGAAAAA-TTGTT--ATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
*
55985293 GATTGAAGAATATTTGTT-TCCTTAAGCGAAATAGTTTTATGGGTTGCGTTGT
1 GATTGAA-AA-A-TTGTTATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
55985345 GATTGAAAAATTGTTCAATCCTTAAGCTAAA
1 GATTGAAAAATTGTT--ATCCTTAAGCTAAA
55985376 ACTCTTTGTA
Statistics
Matches: 76, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
49 5 0.07
50 1 0.01
51 2 0.03
52 52 0.68
53 7 0.09
54 2 0.03
55 7 0.09
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (50 bp):
GATTGAAAAATTGTTATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
Found at i:55987073 original size:18 final size:18
Alignment explanation
Indices: 55987050--55987084 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55987040 ATTGGTTAAA
*
55987050 ATAAAAATACTTAAATTC
1 ATAAAAATAATTAAATTC
*
55987068 ATAAAACTAATTAAATT
1 ATAAAAATAATTAAATT
55987085 ATATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAATAATTAAATTC
Found at i:55987448 original size:33 final size:33
Alignment explanation
Indices: 55987411--55987476 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
55987401 AAATAGAATT
55987411 TTAATTTTAGCTCAATTATACATATACCAACAA
1 TTAATTTTAGCTCAATTATACATATACCAACAA
*
55987444 TTAATTTTAGCTCAATTATACATATACCTACAA
1 TTAATTTTAGCTCAATTATACATATACCAACAA
55987477 ATTTTAATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAATTTTAGCTCAATTATACATATACCAACAA
Found at i:55989351 original size:49 final size:49
Alignment explanation
Indices: 55989294--55989397 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
55989284 TCATGTGTTA
* * *
55989294 TAATTTTATACA-GTGTTGAGCTTTTGATTCATGATATTTAACTTAATTT
1 TAATTTTATA-AGGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
55989343 TAATTTTATAAGGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAGGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
55989392 TAATTT
1 TAATTT
55989398 GTTTTTTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.98
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAGGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:55990729 original size:15 final size:16
Alignment explanation
Indices: 55990701--55990730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55990691 TAAATTCATA
55990701 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
55990717 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
55990731 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:55990808 original size:120 final size:120
Alignment explanation
Indices: 55990675--55991261 Score: 1093
Period size: 120 Copynumber: 4.9 Consensus size: 120
55990665 ATTCTCAAGT
*
55990675 TATATTATCATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
55990740 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
55990795 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
55990860 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
* *
55990915 TTTATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATCATATA
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
*
55990980 TTTTTATTAAATTATATTTAATAATAATCATTTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
*
55991035 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATCATATA
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
* *
55991100 TTTTTATTAAATTATATTTAATTATTATTATTTTAAATTATATTTTATAGTATTA
66 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
55991155 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
* *
55991220 TTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATA
66 TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATA
55991262 ATTAAATTAT
Statistics
Matches: 454, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 454 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (120 bp):
TATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATA
TTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTA
Found at i:55990849 original size:15 final size:16
Alignment explanation
Indices: 55990821--55990850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55990811 TAAATTCATA
55990821 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
55990837 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
55990851 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:55990895 original size:26 final size:25
Alignment explanation
Indices: 55990857--55990917 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
55990847 ATTAAATTAT
*
55990857 ATATTTTTATTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
55990883 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
*
55990909 GTATTATTT
1 ATATTATTT
55990918 ATTATGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.23
26 19 0.61
27 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:55990969 original size:15 final size:16
Alignment explanation
Indices: 55990941--55990970 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55990931 TAAATTCATA
55990941 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
55990957 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
55990971 AATCATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:55990997 original size:16 final size:17
Alignment explanation
Indices: 55990963--55990998 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
55990953 TTATTAAGAA
55990963 TTTTATTAAATCATATAT
1 TTTTATTAAAT-ATATAT
55990981 TTTTATTAAAT-TATAT
1 TTTTATTAAATATATAT
55990997 TT
1 TT
55990999 AATAATAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
18 11 0.61
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTAAATATATAT
Found at i:55991089 original size:15 final size:16
Alignment explanation
Indices: 55991061--55991090 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55991051 TAAATTCATA
55991061 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
55991077 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
55991091 AATCATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:55991126 original size:18 final size:17
Alignment explanation
Indices: 55991083--55991118 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
55991073 TTATTAAGAA
55991083 TTTTATTAAATCATATAT
1 TTTTATTAAAT-ATATAT
55991101 TTTTATTAAAT-TATAT
1 TTTTATTAAATATATAT
55991117 TT
1 TT
55991119 AATTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
18 11 0.61
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTAAATATATAT
Found at i:55991209 original size:15 final size:16
Alignment explanation
Indices: 55991181--55991210 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55991171 TAAATTCATA
55991181 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
55991197 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
55991211 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:55991488 original size:16 final size:16
Alignment explanation
Indices: 55991463--55991518 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
55991453 AAGATTACAT
*
55991463 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
55991479 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
55991495 ATTACACTTCTATTCT
1 ATTACACCTCTATTCC
55991511 ATTACACC
1 ATTACACC
55991519 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:55993617 original size:162 final size:162
Alignment explanation
Indices: 55993376--55993722 Score: 595
Period size: 162 Copynumber: 2.1 Consensus size: 162
55993366 TTGGGAACAG
* **
55993376 CTCTTTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACATGTTGGGAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
* *
55993441 CAACTTATTGCATTCTGTGACTTGTACTTCTCTTAGGCATTGGAGGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
* *
55993506 AGTCTTGGATTATTTCTTCCATTCTAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
* * *
55993538 CTCTCTATCTTCAAAGTTTGCAATTTCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
*
55993603 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
55993668 AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
55993700 CTCTCTATCCTCAGAGTTTGCAA
1 CTCTCTATCCTCAGAGTTTGCAA
55993723 ATTGGGCGCA
Statistics
Matches: 172, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 172 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (162 bp):
CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
Found at i:56000800 original size:11 final size:11
Alignment explanation
Indices: 56000784--56000813 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
56000774 TCCAATTCAA
56000784 TCTCAAATTTC
1 TCTCAAATTTC
56000795 TCTCAAATTTC
1 TCTCAAATTTC
56000806 TCT-AAATT
1 TCTCAAATT
56000814 CCCTCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (11 bp):
TCTCAAATTTC
Found at i:56003991 original size:30 final size:30
Alignment explanation
Indices: 56003935--56004031 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
56003925 TACAGTAGCG
* *
56003935 GTGTGTGGCCATAGCCCAATATAGTAACAAA
1 GTGTG-GGCCTTAGCCCAATACAGTAACAAA
* *
56003966 GTGTGGGCCTTAGCCTAATACAGTAACAGA
1 GTGTGGGCCTTAGCCCAATACAGTAACAAA
* * *
56003996 GTGTGGGCCTTAACCCAATACAGTAATATA
1 GTGTGGGCCTTAGCCCAATACAGTAACAAA
56004026 GTGTGG
1 GTGTGG
56004032 TGCAAGTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 53 0.91
31 5 0.09
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (30 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAAA
Found at i:56004338 original size:64 final size:64
Alignment explanation
Indices: 56004234--56004359 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 64
56004224 CAGTAACATA
* * * * *
56004234 ATTGGCACAAAGCTATCAGTAGCAGTGATATGATTGGCACACAA-CCATCAGTAACGGTAATATG
1 ATTGGCACAAAGATATCAGTAACAGTAATATGATTAGCACA-AAGCCATCAGTAACGATAATATG
*
56004298 ATTGGCACAAAGATATCAGTAACGGTAATATG-TTCAGCACAAAGCCATCAGTAACGATAATA
1 ATTGGCACAAAGATATCAGTAACAGTAATATGATT-AGCACAAAGCCATCAGTAACGATAATA
56004360 AGATCGACAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
63 4 0.07
64 50 0.93
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (64 bp):
ATTGGCACAAAGATATCAGTAACAGTAATATGATTAGCACAAAGCCATCAGTAACGATAATATG
Found at i:56004353 original size:32 final size:32
Alignment explanation
Indices: 56004234--56004382 Score: 149
Period size: 32 Copynumber: 4.7 Consensus size: 32
56004224 CAGTAACATA
* * * *
56004234 ATTGGCACAAAGCTATCAGTAGCAGTGATATG
1 ATTGGCACAAAGCCATCAGTAACGGTAATATG
56004266 ATTGGCACACAA-CCATCAGTAACGGTAATATG
1 ATTGGCACA-AAGCCATCAGTAACGGTAATATG
**
56004298 ATTGGCACAAAGATATCAGTAACGGTAATATG
1 ATTGGCACAAAGCCATCAGTAACGGTAATATG
* * *
56004330 -TTCAGCACAAAGCCATCAGTAACGATAATAAG
1 ATT-GGCACAAAGCCATCAGTAACGGTAATATG
* * * *
56004362 ATCGACAGAAAGCCACCAGTA
1 ATTGGCACAAAGCCATCAGTA
56004383 GCATCGCAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
31 4 0.04
32 90 0.93
33 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (32 bp):
ATTGGCACAAAGCCATCAGTAACGGTAATATG
Found at i:56004438 original size:27 final size:27
Alignment explanation
Indices: 56004407--56004465 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
56004397 CTGCCAACAA
*
56004407 CAGTAATAGT-ATATGTGGCCA-AGCCAC
1 CAGTAACAGTGAT-TGTGG-CAGAGCCAC
56004434 CAGTAACAGTGATTGTGGCAGAGCCAC
1 CAGTAACAGTGATTGTGGCAGAGCCAC
*
56004461 TAGTA
1 CAGTA
56004466 CTGTACTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.07
27 24 0.86
28 2 0.07
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (27 bp):
CAGTAACAGTGATTGTGGCAGAGCCAC
Found at i:56004563 original size:24 final size:24
Alignment explanation
Indices: 56004531--56004582 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
56004521 GACATACTCG
*
56004531 AAATTAGTCATACAAATCACAGAC
1 AAATCAGTCATACAAATCACAGAC
*
56004555 AAATCAGTCATACCAATCACAGAC
1 AAATCAGTCATACAAATCACAGAC
56004579 AAAT
1 AAAT
56004583 TAACCATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (24 bp):
AAATCAGTCATACAAATCACAGAC
Found at i:56004596 original size:24 final size:24
Alignment explanation
Indices: 56004569--56004617 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
56004559 CAGTCATACC
* *
56004569 AATCACAGACAAATTAACCATTTA
1 AATCACAAACAAATCAACCATTTA
*
56004593 AATCACAAACAAATCAATCATTTA
1 AATCACAAACAAATCAACCATTTA
56004617 A
1 A
56004618 CCTCGATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.20, G:0.02, T:0.24
Consensus pattern (24 bp):
AATCACAAACAAATCAACCATTTA
Found at i:56004774 original size:26 final size:26
Alignment explanation
Indices: 56004698--56004789 Score: 112
Period size: 26 Copynumber: 3.5 Consensus size: 26
56004688 AGTAATTTTA
* * *
56004698 CCTATAGGGACATCACGGTCATTTTAC
1 CCTACAGGG-CATTACGGTCATTATAC
* *
56004725 CCTACAGGGGCATTACGATTATTATAC
1 CCTACA-GGGCATTACGGTCATTATAC
*
56004752 CCTACAGGGTATTACGGTCATTATAC
1 CCTACAGGGCATTACGGTCATTATAC
56004778 CCTACAGGGCAT
1 CCTACAGGGCAT
56004790 ACAGTCTCGA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
26 28 0.51
27 24 0.44
28 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (26 bp):
CCTACAGGGCATTACGGTCATTATAC
Found at i:56012061 original size:13 final size:14
Alignment explanation
Indices: 56012033--56012063 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56012023 TATGATAAAA
56012033 AAAACTTAAGTTTG
1 AAAACTTAAGTTTG
56012047 AAAACTTAA-TTTG
1 AAAACTTAAGTTTG
56012060 AAAA
1 AAAA
56012064 TTTGGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (14 bp):
AAAACTTAAGTTTG
Found at i:56012339 original size:34 final size:34
Alignment explanation
Indices: 56012301--56012443 Score: 196
Period size: 34 Copynumber: 4.2 Consensus size: 34
56012291 TCACTTGTCT
* *
56012301 TTTCTTGCAGGGAATCTTTACTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* * **
56012335 TTTCTTGCTGGGAATCTTTCTTGTTCATGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
*
56012369 TTTCTTGTAGGGAATCTTTCCTGTTCACACATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* * *
56012403 TTTCTTGCAGGGAATCTCTCCTATTCACACATAA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
56012437 TTTCTTG
1 TTTCTTG
56012444 TATCATTTCT
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 96 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
Found at i:56015268 original size:20 final size:22
Alignment explanation
Indices: 56015231--56015274 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
56015221 GAACAAATTG
56015231 TTGATTCTATTTCTTTTTG-AT
1 TTGATTCTATTTCTTTTTGTAT
56015252 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTC-TTTTTGTAT
56015273 TT
1 TT
56015275 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTGATTCTATTTCTTTTTGTAT
Found at i:56015330 original size:21 final size:23
Alignment explanation
Indices: 56015306--56015348 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
56015296 TTAATTTTTT
*
56015306 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
56015327 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
56015349 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:56015561 original size:39 final size:39
Alignment explanation
Indices: 56015447--56015580 Score: 94
Period size: 39 Copynumber: 3.4 Consensus size: 39
56015437 CGTTTGGACA
* * * * *
56015447 AAAATGCCGGTAAAAATCAAGCATTAGCGGCG-CTTTACG
1 AAAACGCCGCTAAAAA-AAAGCATTAGCGGCGTTTTTAAG
* ** * * *
56015486 AAAATCACCGCTAAAGATTATGCATT-GCAGCATTTTTAAG
1 AAAA-CGCCGCTAAA-AAAAAGCATTAGCGGCGTTTTTAAG
**
56015526 AAAACGCCGCTAAAAAAAAGCATTAGCGGCGTTTTTGGG
1 AAAACGCCGCTAAAAAAAAGCATTAGCGGCGTTTTTAAG
*
56015565 AAAACGCTGC-AAAAAA
1 AAAACGCCGCTAAAAAA
56015581 CCAAACCCAA
Statistics
Matches: 72, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
38 13 0.18
39 36 0.50
40 22 0.31
41 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.22
Consensus pattern (39 bp):
AAAACGCCGCTAAAAAAAAGCATTAGCGGCGTTTTTAAG
Found at i:56015703 original size:41 final size:41
Alignment explanation
Indices: 56015638--56015809 Score: 204
Period size: 41 Copynumber: 4.2 Consensus size: 41
56015628 TTTTTGGAGT
** * * * **
56015638 AGCGCCGCTAATGCTC-TAAGTTTTAGTGGCGTTTTTAAAAA
1 AGCGCCGCTAATGCTCGGGA-TTTTAGCGGCATTTTTGATGA
*
56015679 AGCGCCGCTAATGCTCGGGATTTTAGAGGCATTTTTGATGA
1 AGCGCCGCTAATGCTCGGGATTTTAGCGGCATTTTTGATGA
* **
56015720 AGTGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGATGA
1 AGCGCCGCTAATGCTCGGGATTTTAGCGGCATTTTTGATGA
*
56015761 AGCGCCGCTAATGCTCGGGTTTTTAGCGGCATTTTTG-TGAA
1 AGCGCCGCTAATGCTCGGGATTTTAGCGGCATTTTTGATG-A
56015802 AGCGCCGC
1 AGCGCCGC
56015810 AAAAAACATT
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.02
41 112 0.97
42 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (41 bp):
AGCGCCGCTAATGCTCGGGATTTTAGCGGCATTTTTGATGA
Found at i:56015950 original size:23 final size:25
Alignment explanation
Indices: 56015905--56015951 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
56015895 AGAAAAAAAT
* *
56015905 AACACGTAGAAATAATTTGAAATAA
1 AACACATAGAAATAATTTAAAATAA
56015930 AACACATAGAAA-AA-TTAAAATA
1 AACACATAGAAATAATTTAAAATA
56015952 CTATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 2 0.10
25 11 0.55
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (25 bp):
AACACATAGAAATAATTTAAAATAA
Found at i:56016262 original size:7 final size:7
Alignment explanation
Indices: 56016252--56016297 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
56016242 GATTTAATGT
56016252 TTAGGGG
1 TTAGGGG
56016259 TTA-GGG
1 TTAGGGG
56016265 TT-GGGG
1 TTAGGGG
**
56016271 TTAGACG
1 TTAGGGG
56016278 TTAGGGG
1 TTAGGGG
*
56016285 TTAGGAG
1 TTAGGGG
56016292 TTAGGG
1 TTAGGG
56016298 ATTTAGGGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
6 10 0.32
7 21 0.68
ACGTcount: A:0.17, C:0.02, G:0.50, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:56016286 original size:14 final size:13
Alignment explanation
Indices: 56016252--56016297 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
56016242 GATTTAATGT
*
56016252 TTAGGGGTTAGGG
1 TTAGGGGTTAGAG
56016265 TT-GGGGTTAGACG
1 TTAGGGGTTAGA-G
56016278 TTAGGGGTTAGGAG
1 TTAGGGGTTA-GAG
56016292 TTAGGG
1 TTAGGG
56016298 ATTTAGGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 8 0.28
13 5 0.17
14 14 0.48
15 2 0.07
ACGTcount: A:0.17, C:0.02, G:0.50, T:0.30
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:56016623 original size:29 final size:28
Alignment explanation
Indices: 56016590--56016654 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
56016580 TAATTAGTTT
*
56016590 AGAGTTAATGGGTTAAGGGTTAGGGGTTA
1 AGAGTTAAT-GATTAAGGGTTAGGGGTTA
* * *
56016619 AGAGTTAATGATTTAGGGTTTGGGGTTT
1 AGAGTTAATGATTAAGGGTTAGGGGTTA
56016647 AGA-TTAAT
1 AGAGTTAAT
56016655 TAGTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 5 0.16
28 18 0.56
29 9 0.28
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (28 bp):
AGAGTTAATGATTAAGGGTTAGGGGTTA
Found at i:56019909 original size:43 final size:43
Alignment explanation
Indices: 56019848--56019934 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
56019838 CAATGATGTA
* * * *
56019848 CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATCTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* *
56019891 CAAGATCTACTTGATTAAGAAAATGCATTGTATGTTTTATTAC
1 CAAGATCTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
56019934 C
1 C
56019935 TTGCATATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (43 bp):
CAAGATCTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:56020259 original size:43 final size:42
Alignment explanation
Indices: 56020211--56020426 Score: 306
Period size: 43 Copynumber: 5.0 Consensus size: 42
56020201 TTTAGTGGCA
* *
56020211 TTTGTGTGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGTG
1 TTTGTG-GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
* *
56020254 TTTGTGTGAAAAGCGCCGCTAAAGGTCCTGAGCTATAGCGGCG
1 TTTGTG-GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
** * *
56020297 TTTGTGGAAAAGCATCGCTAAAGGTTTTGATCTATAGTGGCG
1 TTTGTGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
*
56020339 TTTGTGGAAAAATCGCCGCTAAAGGTCTTGATCTATAGCGGCG
1 TTTGTGG-AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
*
56020382 TTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCG
1 TTTGT-GGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
56020425 TT
1 TT
56020427 AACAACAGCG
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 37 0.24
43 117 0.75
44 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (42 bp):
TTTGTGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
Found at i:56020356 original size:85 final size:85
Alignment explanation
Indices: 56020211--56020426 Score: 308
Period size: 85 Copynumber: 2.5 Consensus size: 85
56020201 TTTAGTGGCA
* *
56020211 TTTGTGTGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGTGTTTGTGTGAAAAGCGCCGCTAA
1 TTTGTG-GAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGTGAAAAGCGCCGCTAA
56020276 AGGTCCTGAGCTATAGCGGCG
65 AGGTCCTGAGCTATAGCGGCG
** * * *
56020297 TTTGTGGAAAAGCATCGCTAAAGGTTTTGATCTATAGTGGCGTTTGTG-GAAAAATCGCCGCTAA
1 TTTGTGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGTG-AAAAGCGCCGCTAA
* *
56020361 AGGTCTTGATCTATAGCGGCG
65 AGGTCCTGAGCTATAGCGGCG
*
56020382 TTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTT
1 TTTGT-GGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTT
56020427 AACAACAGCG
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
84 1 0.01
85 73 0.64
86 40 0.35
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (85 bp):
TTTGTGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGTGAAAAGCGCCGCTAAA
GGTCCTGAGCTATAGCGGCG
Found at i:56022394 original size:13 final size:13
Alignment explanation
Indices: 56022353--56022394 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
56022343 TAAACTAAGA
* *
56022353 ATATTGCATTCAG
1 ATATTCCATTCAT
56022366 ATATTCCA-TC-T
1 ATATTCCATTCAT
56022377 ATATTCCATTCAT
1 ATATTCCATTCAT
56022390 ATATT
1 ATATT
56022395 GTATTAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 8 0.32
12 4 0.16
13 13 0.52
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (13 bp):
ATATTCCATTCAT
Found at i:56024699 original size:13 final size:14
Alignment explanation
Indices: 56024671--56024701 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56024661 GTAATGATAA
56024671 AAAACTTAAGTTTG
1 AAAACTTAAGTTTG
56024685 AAAACTTAA-TTTG
1 AAAACTTAAGTTTG
56024698 AAAA
1 AAAA
56024702 TTTGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (14 bp):
AAAACTTAAGTTTG
Found at i:56024713 original size:22 final size:21
Alignment explanation
Indices: 56024681--56024748 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
56024671 AAAACTTAAG
56024681 TTTG-AAAACTTAATTTGAAAA
1 TTTGAAAAACTT-ATTTGAAAA
*
56024702 TTTGAAAAACTTAGTATT-AAAT
1 TTTGAAAAACTTA-T-TTGAAAA
*
56024724 TTTGAAGAAACTT-TTGGAAAA
1 TTTGAA-AAACTTATTTGAAAA
56024745 TTTG
1 TTTG
56024749 GAGAAACAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 1 0.03
21 13 0.33
22 17 0.44
23 8 0.21
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTGAAAAACTTATTTGAAAA
Found at i:56026069 original size:41 final size:41
Alignment explanation
Indices: 56026008--56026093 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
56025998 TGAGTCAAGT
*
56026008 CAATTAACGAAACCTTAAATGAAAAGCATAATCAAATTTCC
1 CAATTAACGAAACCTAAAATGAAAAGCATAATCAAATTTCC
56026049 CAATTAACGAAACCTAAAATGAAAAGCATAATCAAATTTCC
1 CAATTAACGAAACCTAAAATGAAAAGCATAATCAAATTTCC
56026090 CAAT
1 CAAT
56026094 ATTTGACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (41 bp):
CAATTAACGAAACCTAAAATGAAAAGCATAATCAAATTTCC
Found at i:56034117 original size:162 final size:162
Alignment explanation
Indices: 56033864--56034375 Score: 909
Period size: 162 Copynumber: 3.2 Consensus size: 162
56033854 TAATTGGGAA
*
56033864 CAACTCTCTATGC-TCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGGAGAGAA
1 CAACTCTCTAT-CTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAA
56033928 ATTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATCGGAAGCTTATGGTTGATACT
65 ATTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATCGGAAGCTTATGGTTGATACT
56033993 TGTGAGTCTTGAATTATTTCTTCCATTCCAAAG
130 TGTGAGTCTTGAATTATTTCTTCCATTCCAAAG
*
56034026 CAACTCACTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
1 CAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
* * *
56034091 TTTCAACTGATTGCATTCTCTGACTTGTAATTCCCTTAGGCATCGGAAGCTTATGGTTGATACTT
66 TTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATCGGAAGCTTATGGTTGATACTT
56034156 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
131 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
*
56034188 CAACTCTCTATCTTCAGAGTTTGCAATTGCCTAAGACTATTAGCAACACACATTGGGAAGAGAAA
1 CAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
* *
56034253 TTTCAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTT
66 TTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATCGGAAGCTTATGGTTGATACTT
*
56034318 GTGAGTCTTGGATTATTTCTTCCATTCCAAAG
131 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
* *
56034350 CACCTTTCTATCTTCAGAGTTTGCAA
1 CAACTCTCTATCTTCAGAGTTTGCAA
56034376 ATTGGGCACA
Statistics
Matches: 334, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
161 1 0.00
162 333 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (162 bp):
CAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
TTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATCGGAAGCTTATGGTTGATACTT
GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
Found at i:56039910 original size:21 final size:21
Alignment explanation
Indices: 56039878--56039918 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56039868 GAACATTTGG
56039878 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
56039899 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
56039919 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:56042488 original size:21 final size:21
Alignment explanation
Indices: 56042462--56042507 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
56042452 TAATCACAAC
* *
56042462 TTTATCAAACGAATTCAGTTT
1 TTTATCAAACAAATTCAGCTT
*
56042483 TTTATCAACCAAATTCAGCTT
1 TTTATCAAACAAATTCAGCTT
56042504 TTTA
1 TTTA
56042508 GCTAGACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (21 bp):
TTTATCAAACAAATTCAGCTT
Found at i:56043831 original size:16 final size:16
Alignment explanation
Indices: 56043797--56043846 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
56043787 AAAACTAGGG
* *
56043797 TTTTTAAAACATTTA-
1 TTTTTAAAATATTCAT
*
56043812 TTTTTACAATATTCAT
1 TTTTTAAAATATTCAT
*
56043828 TTTTTAAAATTTTCAT
1 TTTTTAAAATATTCAT
56043844 TTT
1 TTT
56043847 AAATTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTAAAATATTCAT
Found at i:56047841 original size:14 final size:14
Alignment explanation
Indices: 56047803--56047845 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
56047793 CAAAATGTAC
56047803 AATATAATTAAA-T
1 AATATAATTAAATT
56047816 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
56047831 AA-ATAATTTAATT
1 AATATAATTAAATT
56047844 AA
1 AA
56047846 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:56050327 original size:3 final size:3
Alignment explanation
Indices: 56050319--56050405 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
56050309 TAAAACAATT
** *
56050319 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * ** * *
56050367 TGA TGA TGA TGG TAT TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56050406 AAATCTTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:56050470 original size:17 final size:18
Alignment explanation
Indices: 56050428--56050468 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
56050418 TAAAAATTAT
*
56050428 ATAAAAGGATATAGATAA
1 ATAAAATGATATAGATAA
56050446 ATAAAATGATATA-ATAAA
1 ATAAAATGATATAGAT-AA
56050464 ATAAA
1 ATAAA
56050469 TGTATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (18 bp):
ATAAAATGATATAGATAA
Done.