Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, whole genome shotgun sequence
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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:2333618 original size:15 final size:15
Alignment explanation
Indices: 2333598--2333626 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2333588 CATGTGATAG
2333598 TCATGCAACTAGCCC
1 TCATGCAACTAGCCC
2333613 TCATGCAACTAGCC
1 TCATGCAACTAGCC
2333627 TTTAGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (15 bp):
TCATGCAACTAGCCC
Found at i:2348411 original size:15 final size:15
Alignment explanation
Indices: 2348382--2348414 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2348372 AATTTGCTTA
2348382 ATTTAATTTATTTTC
1 ATTTAATTTATTTTC
2348397 ATTT-ATTTATGTTTC
1 ATTTAATTTAT-TTTC
2348412 ATT
1 ATT
2348415 ATGGGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (15 bp):
ATTTAATTTATTTTC
Found at i:2353791 original size:75 final size:75
Alignment explanation
Indices: 2353678--2353818 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
2353668 ACAACATGGT
* * * *
2353678 GTCTCAAGTCTAGGGAGTACTTACACAACTTACACATGAGAAGTGTTGCATAGTCACTGAAGTGT
1 GTCTCAAGTCTAAGGAGTACTTACACAACTAACACATGAAAAGTGTTGCATAGACACTGAAGTGT
2353743 ACAACCTAAC
66 ACAACCTAAC
* * * *
2353753 GTCTCAAGTTTAAGGAGTATTTACCCAACTAACACATGAAAAGTGTTGCATAGACACTGGAGTGT
1 GTCTCAAGTCTAAGGAGTACTTACACAACTAACACATGAAAAGTGTTGCATAGACACTGAAGTGT
2353818 A
66 A
2353819 TTACCAAATG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (75 bp):
GTCTCAAGTCTAAGGAGTACTTACACAACTAACACATGAAAAGTGTTGCATAGACACTGAAGTGT
ACAACCTAAC
Found at i:2354812 original size:22 final size:22
Alignment explanation
Indices: 2354787--2354856 Score: 59
Period size: 27 Copynumber: 3.0 Consensus size: 22
2354777 TTATTTTTGT
2354787 TTTATTTTTTAAATATTAATAA
1 TTTATTTTTTAAATATTAATAA
*
2354809 TTTATAATTTAATTATACTATTAATAA
1 TTTAT--TTT--TTA-AATATTAATAA
** *
2354836 TTTATAATTTGAATATTAATA
1 TTTATTTTTTAAATATTAATA
2354857 TTTTTAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 14 0.37
23 2 0.05
24 3 0.08
25 1 0.03
26 3 0.08
27 15 0.39
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
TTTATTTTTTAAATATTAATAA
Found at i:2354882 original size:41 final size:41
Alignment explanation
Indices: 2354835--2354934 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
2354825 ACTATTAATA
* *
2354835 ATTTATAATTTGAATATTAATATTTTTAAATATTATTATTTT
1 ATTTATAATTTGAATATTAATATTTTT-AATACTAATATTTT
2354877 A-TTATAATTTG-ATCATTAATATTTTTAATACTAATATTTT
1 ATTTATAATTTGAAT-ATTAATATTTTTAATACTAATATTTT
*
2354917 ATTTTTAATTT-AATATTA
1 ATTTATAATTTGAATATTA
2354935 TTATGATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
40 19 0.37
41 32 0.62
42 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (41 bp):
ATTTATAATTTGAATATTAATATTTTTAATACTAATATTTT
Found at i:2354921 original size:20 final size:20
Alignment explanation
Indices: 2354847--2354938 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
2354837 TTATAATTTG
* *
2354847 AATATTAATATTTTTAA-AT
1 AATATTATTATTTTTAATCT
* *
2354866 ATTATTATT-TTATTATAATTT
1 AATATTATTATT-TT-TAATCT
* *
2354887 GATCATTAATATTTTTAATACT
1 AAT-ATTATTATTTTTAAT-CT
*
2354909 AATATT-TTATTTTTAATTT
1 AATATTATTATTTTTAATCT
2354928 AATATTATTAT
1 AATATTATTAT
2354939 GATTAAAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.04
19 16 0.29
20 17 0.30
21 9 0.16
22 10 0.18
23 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (20 bp):
AATATTATTATTTTTAATCT
Found at i:2355166 original size:14 final size:15
Alignment explanation
Indices: 2355147--2355176 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2355137 ATTTTCATTA
2355147 AAATTTTAA-AATTT
1 AAATTTTAATAATTT
2355161 AAATTTTAATAATTT
1 AAATTTTAATAATTT
2355176 A
1 A
2355177 TTATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTTAATAATTT
Found at i:2355270 original size:16 final size:16
Alignment explanation
Indices: 2355245--2355275 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2355235 TTATACTTTC
2355245 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
2355261 ATTAATAATTTAATA
1 ATTAAAAATTTAATA
2355276 ACGTAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:2355372 original size:16 final size:16
Alignment explanation
Indices: 2355344--2355378 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2355334 GATTAAAATA
*
2355344 TTAAAATGTTAATATT
1 TTAAAATATTAATATT
*
2355360 TTAAAATATTAATTTT
1 TTAAAATATTAATATT
2355376 TTA
1 TTA
2355379 TAATTTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTAAAATATTAATATT
Found at i:2361337 original size:21 final size:21
Alignment explanation
Indices: 2361313--2361364 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2361303 TTGAATAACA
*
2361313 TAGTTGATCCTAAAAGCTTTG
1 TAGTCGATCCTAAAAGCTTTG
* *
2361334 TAGTCGATCTTAGAAGCTTTG
1 TAGTCGATCCTAAAAGCTTTG
*
2361355 TAGTCTATCC
1 TAGTCGATCC
2361365 CAAAGACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (21 bp):
TAGTCGATCCTAAAAGCTTTG
Found at i:2362081 original size:52 final size:50
Alignment explanation
Indices: 2361968--2362088 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 50
2361958 GAACAAGTAA
* **
2361968 CAAGTAAAATATGTTTCCTAAGTTAAATGCAAGAAAGCATAAACAATGAAT
1 CAAGTAAAATAT-TTTCCTAAGCTAAATGCAAGAAAGCATAAACAACAAAT
* * *
2362019 TAAATCAAAATATTTTCCTTAGCTAAATGCAAGTAAAGCATAAACAACAAAT
1 CAAGT-AAAATATTTTCCTAAGCTAAATGCAAG-AAAGCATAAACAACAAAT
*
2362071 CAAGGTAAAATAATTTCC
1 CAA-GTAAAATATTTTCC
2362089 AAAGGCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
51 21 0.36
52 36 0.62
53 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (50 bp):
CAAGTAAAATATTTTCCTAAGCTAAATGCAAGAAAGCATAAACAACAAAT
Found at i:2364457 original size:2 final size:2
Alignment explanation
Indices: 2364450--2364488 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
2364440 TCACATACGC
*
2364450 AT AT AT AT AT AT AT AT AT AT AT -T CAA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT A
2364489 AACACACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2368889 original size:26 final size:26
Alignment explanation
Indices: 2368837--2368889 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2368827 AAATAAATTG
* *
2368837 TTATTATTTTATTATGTTTAATCAAA
1 TTATTATTTTATTATCTTAAATCAAA
*
2368863 TTATTATATTT-TTATCTTAAATTAAA
1 TTATTAT-TTTATTATCTTAAATCAAA
2368889 T
1 T
2368890 AAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATTATTTTATTATCTTAAATCAAA
Found at i:2400553 original size:30 final size:30
Alignment explanation
Indices: 2400489--2400553 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
2400479 TTGATTAAGG
* *
2400489 ATGAAGAAGATGACATGCAAAGAGTTGAAG
1 ATGAAGAAGATGACATGCAAAGAGATGAAA
* * *
2400519 ATGAAGAAGATGAGATGGAAGGAGATGAAA
1 ATGAAGAAGATGACATGCAAAGAGATGAAA
2400549 ATGAA
1 ATGAA
2400554 AATGAAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.32, T:0.15
Consensus pattern (30 bp):
ATGAAGAAGATGACATGCAAAGAGATGAAA
Found at i:2403033 original size:54 final size:54
Alignment explanation
Indices: 2402971--2403076 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 54
2402961 AACAATTTCT
* * *
2402971 GTTGGAAATGTTTTTTCAACGAAAAA-TTCCACTGGAAAATTTCAACGAAATTCA
1 GTTGGAAATGCTTTTTCAACAAAAAAGTT-CACTGGAAAATTTCAACAAAATTCA
* ** *
2403025 GTTGGAAATGCTTTTTGAACAAAAAAGTTCGTTGGAAATTTTCAACAAAATT
1 GTTGGAAATGCTTTTTCAACAAAAAAGTTCACTGGAAAATTTCAACAAAATT
2403077 TTTCCGTTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (54 bp):
GTTGGAAATGCTTTTTCAACAAAAAAGTTCACTGGAAAATTTCAACAAAATTCA
Found at i:2413142 original size:2 final size:2
Alignment explanation
Indices: 2413135--2413162 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2413125 TGTTGCTATC
2413135 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
2413163 GTTGTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2426298 original size:6 final size:6
Alignment explanation
Indices: 2426287--2426311 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2426277 TTTCATTATC
2426287 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
2426312 TCTTAATTGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:2426298 original size:126 final size:130
Alignment explanation
Indices: 2426142--2426397 Score: 412
Period size: 132 Copynumber: 2.0 Consensus size: 130
2426132 NNATGTATTG
2426142 CTAGATGCCGCTCATTATCTATAAATATAAATAT-AA-AT-TT-TTAATTGAATTAATTTATATT
1 CTAGATGCCGCTCATTATCTATAAATATAAATATAAATATATTCTTAATTGAATTAATTTATATT
* *
2426203 TATTGTCAACATGTTGAAAACCTAATGGGTCACACACATAAGGTAAATTGTCGAAATTAATTTAC
66 TATTGCCAACATGTTGAAAACCTAATGGGTCACACACATAAGGTAAATTATCGAAATTAATTTAC
**
2426268 CTAGATGCCTTTCATTATCTATAAATATAAATATAAATATAAATTCTTAATTGAATTAATTTATA
1 CTAGATGCCGCTCATTATCTATAAATATAAATATAAATAT--ATTCTTAATTGAATTAATTTATA
**
2426333 TTTATTGCCAACATGTTGGGAACCTAATGGGTCACACACATAAGGTAAATTATCGAAATTAATTT
64 TTTATTGCCAACATGTTGAAAACCTAATGGGTCACACACATAAGGTAAATTATCGAAATTAATTT
2426398 GAGTTCAATT
Statistics
Matches: 118, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
126 32 0.27
127 2 0.02
128 2 0.02
131 2 0.02
132 80 0.68
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (130 bp):
CTAGATGCCGCTCATTATCTATAAATATAAATATAAATATATTCTTAATTGAATTAATTTATATT
TATTGCCAACATGTTGAAAACCTAATGGGTCACACACATAAGGTAAATTATCGAAATTAATTTAC
Found at i:2446819 original size:15 final size:14
Alignment explanation
Indices: 2446782--2446821 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
2446772 TAAGTCGAAC
2446782 CTTCCTTTCTCTTT
1 CTTCCTTTCTCTTT
*
2446796 CTCTTCTTTCTCCTTT
1 CT-TCCTTTCT-CTTT
2446812 CTTCCTTTCT
1 CTTCCTTTCT
2446822 TATCATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 14 0.64
16 6 0.27
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTCCTTTCTCTTT
Found at i:2456170 original size:13 final size:13
Alignment explanation
Indices: 2456138--2456180 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2456128 CCAAGCCGAA
*
2456138 CCTTCCTTCCTTT
1 CCTTCTTTCCTTT
*
2456151 -CTCTCTTTTCTTT
1 CCT-TCTTTCCTTT
2456164 CCTTCTTTCCTTT
1 CCTTCTTTCCTTT
2456177 CCTT
1 CCTT
2456181 TCTCTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
CCTTCTTTCCTTT
Found at i:2460255 original size:77 final size:78
Alignment explanation
Indices: 2460174--2460324 Score: 207
Period size: 77 Copynumber: 1.9 Consensus size: 78
2460164 TGAATTTTCT
* * *
2460174 AAATTAAAATACTATTCTTAATTTTA-AAATTTTCTTTTAAAGTAAGAAATAATTTCCTACTTTT
1 AAATTAAAATACTATCCTTAATTTTAGAAA-TTACTTTTAAAGTAAGAAACAATTTCCTACTTTT
2460238 T-ATGAATCATCCA
65 TGATGAATCATCCA
* * * *
2460251 AAATTCAAATTCTATCCTTAATTTTAGGAATTACTTTTAAAGTAAGAAACAATTTCCTATTTTTT
1 AAATTAAAATACTATCCTTAATTTTAGAAATTACTTTTAAAGTAAGAAACAATTTCCTACTTTTT
*
2460316 GGTGAATCA
66 GATGAATCA
2460325 CCCCAAATGA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 55 0.86
78 9 0.14
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (78 bp):
AAATTAAAATACTATCCTTAATTTTAGAAATTACTTTTAAAGTAAGAAACAATTTCCTACTTTTT
GATGAATCATCCA
Found at i:2461447 original size:51 final size:51
Alignment explanation
Indices: 2461392--2461493 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2461382 TCTTTTTTGT
2461392 CAAACAAAAAAACTATATTTCTTTTCTTATTTTTATGAAATGACTAAGAAG
1 CAAACAAAAAAACTATATTTCTTTTCTTATTTTTATGAAATGACTAAGAAG
2461443 CAAACAAAAAAACTATATTTCTTTTCTTATTTTTATGAAATGACTAAGAAG
1 CAAACAAAAAAACTATATTTCTTTTCTTATTTTTATGAAATGACTAAGAAG
2461494 TGGCTGAAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (51 bp):
CAAACAAAAAAACTATATTTCTTTTCTTATTTTTATGAAATGACTAAGAAG
Found at i:2476833 original size:107 final size:107
Alignment explanation
Indices: 2476647--2476859 Score: 381
Period size: 107 Copynumber: 2.0 Consensus size: 107
2476637 GCTTTTCAGG
* *
2476647 CAAGTACACACTCTAAAACCTCAACTCGGATTTGCTTTCTCCACATTTATAATATGCTAACTCAC
1 CAAGTACACACTCCAAAACCTCAACTCGGATGTGCTTTCTCCACATTTATAATATGCTAACTCAC
2476712 GTTTAGGCACATTCGACATCAAATGGTCTTACACCATCCTCA
66 GTTTAGGCACATTCGACATCAAATGGTCTTACACCATCCTCA
*
2476754 CAAGTACACACTCCACAACCTCAACTCGGATGTGCTTTCTCCACATTTATAATATGCTAACTCAC
1 CAAGTACACACTCCAAAACCTCAACTCGGATGTGCTTTCTCCACATTTATAATATGCTAACTCAC
* *
2476819 TTTTAGGCACATTCGATATCAAATGGTCTTACACCATCCTC
66 GTTTAGGCACATTCGACATCAAATGGTCTTACACCATCCTC
2476860 GCAATATCTT
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (107 bp):
CAAGTACACACTCCAAAACCTCAACTCGGATGTGCTTTCTCCACATTTATAATATGCTAACTCAC
GTTTAGGCACATTCGACATCAAATGGTCTTACACCATCCTCA
Found at i:2478771 original size:35 final size:35
Alignment explanation
Indices: 2478725--2478801 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
2478715 GAAAAGAAAT
* * * * *
2478725 AGATCAGGCATGTGCCGAAGTAACGAGTGGAGAAC
1 AGATCACGCATGTGCCAAAGCAACGAGCGAAGAAC
*
2478760 AGATCACGCATGTGCCAAAGCAATGAGCGAAGAAC
1 AGATCACGCATGTGCCAAAGCAACGAGCGAAGAAC
2478795 AGATCAC
1 AGATCAC
2478802 ACACAACGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.13
Consensus pattern (35 bp):
AGATCACGCATGTGCCAAAGCAACGAGCGAAGAAC
Found at i:2482481 original size:16 final size:16
Alignment explanation
Indices: 2482460--2482561 Score: 167
Period size: 16 Copynumber: 6.6 Consensus size: 16
2482450 TAGATATGTG
2482460 TGTGTGTGTGTGTCTA
1 TGTGTGTGTGTGTCTA
2482476 TGTGTGTGTGTGTCTA
1 TGTGTGTGTGTGTCTA
2482492 TGTGTGTGTGT-T-TA
1 TGTGTGTGTGTGTCTA
*
2482506 TGTGTGTATGTGTCTA
1 TGTGTGTGTGTGTCTA
2482522 TGTGTGTGTGT-T-TA
1 TGTGTGTGTGTGTCTA
2482536 TGTGTGTGTGTGTCTA
1 TGTGTGTGTGTGTCTA
2482552 TGTGTGTGTG
1 TGTGTGTGTG
2482562 CATATCTATA
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
14 25 0.31
15 4 0.05
16 51 0.64
ACGTcount: A:0.07, C:0.04, G:0.37, T:0.52
Consensus pattern (16 bp):
TGTGTGTGTGTGTCTA
Found at i:2482498 original size:30 final size:30
Alignment explanation
Indices: 2482462--2482561 Score: 182
Period size: 30 Copynumber: 3.3 Consensus size: 30
2482452 GATATGTGTG
*
2482462 TGTGTGTGTGTCTATGTGTGTGTGTGTCTA
1 TGTGTGTGTGTTTATGTGTGTGTGTGTCTA
*
2482492 TGTGTGTGTGTTTATGTGTGTATGTGTCTA
1 TGTGTGTGTGTTTATGTGTGTGTGTGTCTA
2482522 TGTGTGTGTGTTTATGTGTGTGTGTGTCTA
1 TGTGTGTGTGTTTATGTGTGTGTGTGTCTA
2482552 TGTGTGTGTG
1 TGTGTGTGTG
2482562 CATATCTATA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.07, C:0.04, G:0.37, T:0.52
Consensus pattern (30 bp):
TGTGTGTGTGTTTATGTGTGTGTGTGTCTA
Found at i:2484111 original size:40 final size:40
Alignment explanation
Indices: 2484052--2484144 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
2484042 CAAAGGTAGA
* * * * * *
2484052 GTGCTCTAACCTTATAAAGGTATAGACTCTGTGAAAGGTT
1 GTGCTTTAACCTTAAAAAGGCAGAGACTCTGTAAAAAGTT
* *
2484092 GTGCTTTAACTTTAAAAAGGCAGAGACTTTGTAAAAAGTT
1 GTGCTTTAACCTTAAAAAGGCAGAGACTCTGTAAAAAGTT
2484132 GTGCTTTAACCTT
1 GTGCTTTAACCTT
2484145 GAAAGACAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (40 bp):
GTGCTTTAACCTTAAAAAGGCAGAGACTCTGTAAAAAGTT
Found at i:2487402 original size:60 final size:60
Alignment explanation
Indices: 2487330--2487445 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
2487320 CCGTTCTTTC
*
2487330 TCTTTTCTATCCTTATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATTTT
1 TCTTTTCTATCCTCATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATTTT
* * * * *
2487390 TCTTTTCTATCCTCATAAATTAAGAGTAACTGAACGCAAAAGGAAAGAGATCAAGA
1 TCTTTTCTATCCTCATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGA
2487446 GAAAAGCCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (60 bp):
TCTTTTCTATCCTCATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATTTT
Found at i:2487438 original size:160 final size:164
Alignment explanation
Indices: 2487163--2487488 Score: 498
Period size: 160 Copynumber: 2.0 Consensus size: 164
2487153 TTTTTTTTTT
* * *
2487163 TTCTCTCTCTTTTCTATCCTCATAAATTAAAAGTAACTAACCACCAAAAGAAAGAGATCAAGATT
1 TTCTCTCTCTTTTCTATCCTCATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATT
*
2487228 TTTCTTTTCTATCCTCATAAATTAAAAGTAACTGAACAC---AAAAAGA-AAGAGAAAAGTCTAA
66 TTTCTTTTCTATCCTCATAAATTAAAAGTAACTGAACACAAGAAAAAGACAAGAGAAAAGCCTAA
*
2487289 TATCTCTCAAAAAAATAAAAAGGGAAAAGAACCG
131 TATCTCCCAAAAAAATAAAAAGGGAAAAGAACCG
* *
2487323 TTCTTTCTCTTTTCTATCCTTATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATT
1 TTCTCTCTCTTTTCTATCCTCATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATT
* * *
2487388 TTTCTTTTCTATCCTCATAAATTAAGAGTAACTGAACGCAAAAGGAAAGAGATCAAGAGAAAAGC
66 TTTCTTTTCTATCCTCATAAATTAAAAGTAACTGAA--CACAA-GAAAAAGA-CAAGAGAAAAGC
2487453 CTAATATCTCCCAAAAAAATAAAAAGGGAAAAGAAC
127 CTAATATCTCCCAAAAAAATAAAAAGGGAAAAGAAC
2487489 TGAAAATAAA
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
160 95 0.64
162 2 0.01
166 6 0.04
168 45 0.30
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (164 bp):
TTCTCTCTCTTTTCTATCCTCATAAATTAAAAGTAACTAAACACAAAAAGAAAGAAATCAAGATT
TTTCTTTTCTATCCTCATAAATTAAAAGTAACTGAACACAAGAAAAAGACAAGAGAAAAGCCTAA
TATCTCCCAAAAAAATAAAAAGGGAAAAGAACCG
Found at i:2487735 original size:48 final size:48
Alignment explanation
Indices: 2487660--2487756 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
2487650 ATTCCACCAG
* *
2487660 CATCTCATGGAAGAAAGGATTAAAAGGATTGCTTAATGTTGGAATCAA
1 CATCTCATGGAAGAAAGGACTAAAAGGATTGCCTAATGTTGGAATCAA
*
2487708 CATCTCATGGAAGAAAGGACTAGAAGGATTGCCTAATGTTGGAATCAA
1 CATCTCATGGAAGAAAGGACTAAAAGGATTGCCTAATGTTGGAATCAA
2487756 C
1 C
2487757 TTAATTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (48 bp):
CATCTCATGGAAGAAAGGACTAAAAGGATTGCCTAATGTTGGAATCAA
Found at i:2493102 original size:42 final size:42
Alignment explanation
Indices: 2493041--2493120 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
2493031 GACTTAGTTT
* *
2493041 TATTTCCTAAGTCTATTGCCTGATATTTCTTAAACATTGGAA
1 TATTTCCTAAGTCTATTGCCTAATATGTCTTAAACATTGGAA
* *
2493083 TATTTCCTAAGTTTGTTGCCTAATATGTCTTAAACATT
1 TATTTCCTAAGTCTATTGCCTAATATGTCTTAAACATT
2493121 ATCTTACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (42 bp):
TATTTCCTAAGTCTATTGCCTAATATGTCTTAAACATTGGAA
Found at i:2498279 original size:1 final size:1
Alignment explanation
Indices: 2498273--2498298 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2498263 CAATGTAGAT
2498273 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
2498299 GCCTCTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2498471 original size:75 final size:75
Alignment explanation
Indices: 2498333--2498473 Score: 219
Period size: 75 Copynumber: 1.9 Consensus size: 75
2498323 AGTGAACTTT
* *
2498333 TTATACCTTGGCTTAATTACTTTTCTTTCTCCTCAACCTATAGTAATTGAAATAGTGCGAATGAC
1 TTATACCTTGGCTTAATTACTTTTCTTTCTCCTCAACCTATAATAATTGAAATAGTACGAATGAC
2498398 TGAGAAATTC
66 TGAGAAATTC
* * * **
2498408 TTATACCTTGGCTTAATTACTTTTCTTTCTCCTCAGCCTGTAATAGTTGAAATAGTATTAATGAC
1 TTATACCTTGGCTTAATTACTTTTCTTTCTCCTCAACCTATAATAATTGAAATAGTACGAATGAC
2498473 T
66 T
2498474 AAGTCTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (75 bp):
TTATACCTTGGCTTAATTACTTTTCTTTCTCCTCAACCTATAATAATTGAAATAGTACGAATGAC
TGAGAAATTC
Found at i:2499682 original size:22 final size:22
Alignment explanation
Indices: 2499657--2499698 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2499647 ATTGATAGGT
2499657 TCATTTTCAATTTTATTCTCGC
1 TCATTTTCAATTTTATTCTCGC
2499679 TCATTTTCAATTTTATTCTC
1 TCATTTTCAATTTTATTCTC
2499699 ATTAAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.57
Consensus pattern (22 bp):
TCATTTTCAATTTTATTCTCGC
Found at i:2508284 original size:22 final size:21
Alignment explanation
Indices: 2508241--2508284 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2508231 ATACAAAACA
* *
2508241 AAAAGTAAATATATTTATATT
1 AAAAGTAAATATATATACATT
*
2508262 AAAAGTATATAATATATACATT
1 AAAAGTAAAT-ATATATACATT
2508284 A
1 A
2508285 TTATACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAAGTAAATATATATACATT
Found at i:2521157 original size:17 final size:17
Alignment explanation
Indices: 2521127--2521159 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2521117 ATTATTTCGA
2521127 GTTTAAAATATTTAATG
1 GTTTAAAATATTTAATG
2521144 GTTTATAAAT-TTTAAT
1 GTTTA-AAATATTTAAT
2521160 TTATAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
GTTTAAAATATTTAATG
Found at i:2522034 original size:250 final size:250
Alignment explanation
Indices: 2520923--2522458 Score: 1506
Period size: 252 Copynumber: 6.1 Consensus size: 250
2520913 AGATGTGAGA
* * *
2520923 AATAAGAATAAAAATAATTATAGTAAAAATTAGTAGTTGAAAAACCTTGATC-TAAAGCAGTAAG
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGA-CGTAAAG-TGTAAG
** * * ** ** * *
2520987 AATTAACATAAAAAATTATAAAGGTAGAATAAACATCGTTAAAATATTGACGTAAACGTGTAAGA
64 AATTAATGTAAAAAATTATAAAAGTAGAACAAGTATTATCAAAATATTGATGTAAACGTGTAAGA
* * * ** * * *
2521052 TTTAAGATAAAAAGTCAATTATATTTAATAAATATAATTTTTTAGATAA-TTAAATATTTAAATT
129 TTTAACATAACAAGTCAATTATGTCAAATAAACATAATTTTTT-GA-AACATAAACATTTAAATT
*
2521116 TATTATT-TCGAGTTTAAAATATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
192 TA-TATTCTCGAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
* * * *
2521175 AGTAAGGATAAAAATAACTATAGTAAAAATTAGTAATTGAAAAATCTTGACGTAAATTTGTAAGA
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGACGTAAA-GTGTAAGA
* ** * * *
2521240 ATTAATGTTAAAAATTATAAAAGTAGAACAAACA-TAGTCAAAATATTGATATTAACATGTAAGA
65 ATTAATGTAAAAAATTATAAAAGTAGAACAAGTATTA-TCAAAATATTGATGTAAACGTGTAAGA
* ** * * * * *
2521304 TTTTATGTAACAAG-CTAATTATGTCAAAAAAACTTAACTTTTTGAAAC--AAATA-TTAAAATT
129 TTTAACATAACAAGTC-AATTATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATTT
* * *
2521365 ATATTCTCGAGTTTAAAGTATTTAAAGATTTACAAATTTTAATTTATAAATGAATAAT
193 ATATTCTCGAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
* * * * ** * *
2521423 AATAACGATAAAAATAATTATAGTAAAAATTAGTAACTCAAAAATCTTGATATAAACATGAAAGA
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGACGTAAA-GTGTAAGA
* * * * * *
2521488 ATTAATGTAAAAAATTA-AAAAGGTAGAAAAATTATTGTCGAAATATTTATGTAAACGTGTGAGA
65 ATTAATGTAAAAAATTATAAAA-GTAGAACAAGTATTATCAAAATATTGATGTAAACGTGTAAGA
** *** * * ** *
2521552 TTTAATGTAGTTAGTCAATTATGTCAAATAAATATAAATTTTTGAAACAATAAATGTTTAAATAT
129 TTTAACATAACAAGTCAATTATGTCAAATAAACATAATTTTTTGAAAC-ATAAACATTTAAATTT
** ** **
2521617 ATATT-TTTATGTTTAAAGTATTTAACAGTTTATAAATTTTAATTTATAAACAAATAAT
193 ATATTCTCGA-GTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
* * ** * *
2521675 AATAATGATAAAAATAATTATAGTTAAAA-TAGTAATTGAAAAACCTTGTTGTAAA-TCTATTGG
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGACGTAAAGTGTA--AG
* * *
2521738 AATTAATGTAAAAAATTATAAAAGT-GAAAAAAGTATTACCAAAATATTGATGTAAACGTGTTAG
64 AATTAATGTAAAAAATTATAAAAGTAG-AACAAGTATTATCAAAATATTGATGTAAACGTGTAAG
* * * *
2521802 ATTTAACATAACATGTCTATGATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATCT
128 ATTTAACATAACAAGTCAATTATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATTT
* * *
2521867 ATATTCTCGAGTTTAAAGTA-TTAATGGTTTACAAATTTTAATTTATGAAGGAATAAT
193 ATATTCTCGAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
* * * * * *
2521924 AATAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAATAACTTTGACATAAAGTGGTAAGA
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGACGTAAAGT-GTAAGA
* * * * * * *
2521989 ATGAATGTAAAAAATTATAAAAGTAGAGCAAGTATCATTAAAATATTGATATAAATGTGTAATAT
65 ATTAATGTAAAAAATTATAAAAGTAGAACAAGTATTATCAAAATATTGATGTAAACGTGTAAGAT
* * * * * *
2522054 TT-ACGTAACAAATCAATTATTTCAAATGAACATAATATTTTGAAAAATTAAACATTTAAATTTA
130 TTAACATAACAAGTCAATTATGTCAAATAAACATAATTTTTTGAAACA-TAAACATTTAAATTTA
* * **
2522118 TATTCTTGAGTTGAAAGTATTTAACAGTTTATAAATTTTAATTTATAAATG-ATAAT
194 TATTCTCGAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
* * * * * *
2522174 AGTAAAGATAAAAATAATTGTAGTGAAAATTTA-CAATTGAAAAACCTTGATGTAAAGTAGTAAG
1 AATAAGGATAAAAATAATTATAGT-AAAAATTAGTAATTGAAAAACCTTGACGTAAAGT-GTAAG
* * ** * * * * * *
2522238 AAATGACATAAGAAATTATAAAAGT-GAAACAAGTTTTTTCAAAATATTGACGTAAACATGTTAG
64 AATTAATGTAAAAAATTATAAAAGTAG-AACAAGTATTATCAAAATATTGATGTAAACGTGTAAG
* * * *
2522302 ATTTAACATAACAAATCAATTATATCAAATAAACATAATTTTTAGAAAAAATTAAACATTTAAAT
128 ATTTAACATAACAAGTCAATTATGTCAAATAAACATAATTTTTTG-AAACA-TAAACATTTAAAT
* *
2522367 TTATATTCTTGAGTTTAAAGTATTTAATGGTTTAAAAATTTTAATTTATAAATGAATAAT
191 TTATATTCTCGAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
** * *
2522427 TGTAAGGATAAAACTAATTATAGCAAAAATTA
1 AATAAGGATAAAAATAATTATAGTAAAAATTA
2522459 TTATCTCAAA
Statistics
Matches: 1060, Mismatches: 194, Indels: 60
0.81 0.15 0.05
Matches are distributed among these distances:
247 8 0.01
248 195 0.18
249 104 0.10
250 238 0.22
251 193 0.18
252 298 0.28
253 24 0.02
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (250 bp):
AATAAGGATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGACGTAAAGTGTAAGAA
TTAATGTAAAAAATTATAAAAGTAGAACAAGTATTATCAAAATATTGATGTAAACGTGTAAGATT
TAACATAACAAGTCAATTATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATTTATA
TTCTCGAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
Found at i:2522072 original size:500 final size:493
Alignment explanation
Indices: 2520923--2522458 Score: 1654
Period size: 500 Copynumber: 3.1 Consensus size: 493
2520913 AGATGTGAGA
* * *
2520923 AATAAGAATAAAAATAATTATAGTAAAAATTAGTAGTTGAAAAACCTTGATC-TAAAGCAGTAAG
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAGTTG-AAAACTTTGA-CATAAAG-TGTAAG
** * * * *
2520987 AATTAACATAAAAAATTATAAAGGTAGAATAAACATCGTTAAAATATTGACGTAAACGTGTAAGA
63 AATTAATGTAAAAAATTATAAAAGTAGAAAAAATATCGTTAAAATATTGATGTAAACGTGTAAGA
** * * *
2521052 TTTAAGATAAAAAGTCAATTATATTTAATAAATATAATTTTTTAGATAATTAAATATTTAAATTT
128 TTTAAG-TAAAAA-TCAATTATATCAAATAAATATAAATTTTT-GAAAAATAAATATTTAAATTT
* * ** * *
2521117 ATTATTTCGAGTTTAAAATATTTAATGGTTTATAAATTTTAATTTATAAATGAATAATAGTAAGG
190 A-TATTTTGAGTTTAAAGTATTTAACAGTTTATAAATTTTAATTTATAAA-AAATAATAGTAAAG
* * * * *
2521182 ATAAAAATAACTATAGTAAAAATTAGTAATTGAAAAATCTTGACGTAAATTTGTAAGAATTAATG
253 ATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGATGTAAATCTATAAGAATTAATG
* * * * * * **
2521247 TTAAAAATTATAAAAGTAGAACAAACA-TAGTCAAAATATTGATATTAACATGTAAGATTTTATG
318 TAAAAAATTATAAAAGT-GAA-AAA-AGTATTCAAAATATTGATGTAAACATGTTAGATTTAACA
* * * * *
2521311 TAACAAG-CTAATTATGTCAAAAAAACTTAACTTTTTGAAAC--AAATATTAAAATTATATTCTC
380 TAACAAGTCT-ATTATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATTATATTCTC
* *
2521373 GAGTTTAAAGTATTTAAAGATTTACAAATTTTAATTTATAAATGAATAAT
444 GAGTTTAAAGTATTTAATGGTTTACAAATTTTAATTTATAAATGAATAAT
* ** * * * * *
2521423 AATAACGATAAAAATAATTATAGTAAAAATTAGTAACTCAAAAATCTTGATATAAACATGAAAGA
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAGTTGAAAACT-TTGACATAAA-GTGTAAGA
* * ** * *
2521488 ATTAATGTAAAAAATTA-AAAAGGTAGAAAAATTATTGTCGAAATATTTATGTAAACGTGTGAGA
64 ATTAATGTAAAAAATTATAAAA-GTAGAAAAAATATCGTTAAAATATTGATGTAAACGTGTAAGA
** * * * *
2521552 TTTAATGTAGTTAGTCAATTATGTCAAATAAATATAAATTTTTGAAACAATAAATGTTTAAATAT
128 TTTAA-GTA-AAAATCAATTATATCAAATAAATATAAATTTTTGAAA-AATAAATATTTAAATTT
* * *
2521617 ATATTTTTATGTTTAAAGTATTTAACAGTTTATAAATTTTAATTTATAAACAAATAATAATAATG
190 ATATTTTGA-GTTTAAAGTATTTAACAGTTTATAAATTTTAATTTATAAA-AAATAATAGTAAAG
* * **
2521682 ATAAAAATAATTATAGTTAAAA-TAGTAATTGAAAAACCTTGTTGTAAATCTATTGGAATTAATG
253 ATAAAAATAATTATAGTAAAAATTAGTAATTGAAAAACCTTGATGTAAATCTATAAGAATTAATG
*
2521746 TAAAAAATTATAAAAGTGAAAAAAGTATTACCAAAATATTGATGTAAACGTGTTAGATTTAACAT
318 TAAAAAATTATAAAAGTGAAAAAAGTATT--CAAAATATTGATGTAAACATGTTAGATTTAACAT
* *
2521811 AACATGTCTATGATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATCTATATTCTCG
381 AACAAGTCTATTATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAAT-TATATTCTCG
* *
2521876 AGTTTAAAGTA-TTAATGGTTTACAAATTTTAATTTATGAAGGAATAAT
445 AGTTTAAAGTATTTAATGGTTTACAAATTTTAATTTATAAATGAATAAT
* *
2521924 AATAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAATAACTTTGACATAAAGTGGTAAGA
1 AATAAGGATAAAAATAATTATAGTAAAAATTAGTAGTTGAA-AACTTTGACATAAAGT-GTAAGA
* ** * * * * *
2521989 ATGAATGTAAAAAATTATAAAAGTAGAGCAAGTATCATTAAAATATTGATATAAATGTGTAATAT
64 ATTAATGTAAAAAATTATAAAAGTAGAAAAAATATCGTTAAAATATTGATGTAAACGTGTAAGAT
* * * * *
2522054 TTACGTAACAAATCAATTATTTCAAATGAACAT-AATATTTTGAAAAATTAAACATTTAAATTTA
129 TTAAGTAA-AAATCAATTATATCAAATAAATATAAAT-TTTTGAAAAA-TAAATATTTAAATTTA
* **
2522118 TATTCTTGAGTTGAAAGTATTTAACAGTTTATAAATTTTAATTTATAAATGATAATAGTAAAGAT
191 TATT-TTGAGTTTAAAGTATTTAACAGTTTATAAATTTTAATTTATAAAAAATAATAGTAAAGAT
* * * * * * **
2522183 AAAAATAATTGTAGTGAAAATTTA-CAATTGAAAAACCTTGATGTAAA-GTAGTAAGAAATGACA
255 AAAAATAATTATAGT-AAAAATTAGTAATTGAAAAACCTTGATGTAAATCTA-TAAGAATTAATG
* * * *
2522246 TAAGAAATTATAAAAGTGAAACAAGTTTTTTCAAAATATTGACGTAAACATGTTAGATTTAACAT
318 TAAAAAATTATAAAAGTGAAAAAAG--TATTCAAAATATTGATGTAAACATGTTAGATTTAACAT
* * * * *
2522311 AACAAATCAATTATATCAAATAAACATAATTTTTAGAAAAAATTAAACATTTAAATTTATATTCT
381 AACAAGTCTATTATGTCAAATAAACATAATTTTTTG-AAACA-TAAACATTTAAA-TTATATTCT
* *
2522376 TGAGTTTAAAGTATTTAATGGTTTAAAAATTTTAATTTATAAATGAATAAT
443 CGAGTTTAAAGTATTTAATGGTTTACAAATTTTAATTTATAAATGAATAAT
** * *
2522427 TGTAAGGATAAAACTAATTATAGCAAAAATTA
1 AATAAGGATAAAAATAATTATAGTAAAAATTA
2522459 TTATCTCAAA
Statistics
Matches: 861, Mismatches: 144, Indels: 59
0.81 0.14 0.06
Matches are distributed among these distances:
496 1 0.00
497 6 0.01
498 3 0.00
499 159 0.18
500 414 0.48
501 153 0.18
502 63 0.07
503 62 0.07
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (493 bp):
AATAAGGATAAAAATAATTATAGTAAAAATTAGTAGTTGAAAACTTTGACATAAAGTGTAAGAAT
TAATGTAAAAAATTATAAAAGTAGAAAAAATATCGTTAAAATATTGATGTAAACGTGTAAGATTT
AAGTAAAAATCAATTATATCAAATAAATATAAATTTTTGAAAAATAAATATTTAAATTTATATTT
TGAGTTTAAAGTATTTAACAGTTTATAAATTTTAATTTATAAAAAATAATAGTAAAGATAAAAAT
AATTATAGTAAAAATTAGTAATTGAAAAACCTTGATGTAAATCTATAAGAATTAATGTAAAAAAT
TATAAAAGTGAAAAAAGTATTCAAAATATTGATGTAAACATGTTAGATTTAACATAACAAGTCTA
TTATGTCAAATAAACATAATTTTTTGAAACATAAACATTTAAATTATATTCTCGAGTTTAAAGTA
TTTAATGGTTTACAAATTTTAATTTATAAATGAATAAT
Found at i:2530294 original size:54 final size:54
Alignment explanation
Indices: 2530227--2530412 Score: 219
Period size: 54 Copynumber: 3.4 Consensus size: 54
2530217 GAGTCTAATC
* * *
2530227 TTGATCACGAACTAAATTTGATATCTTCATTTCAAGAGTCTTGGCGACTTGATT
1 TTGATCACGAACTAAACTTGATATCTTCACTTCAAGAGTCTTGGCGACTTGATA
** * * ** * *
2530281 TTGATCATAAACTAAGCTTGATATCTTCACTTCAAGAATCTTAACGACTCGATC
1 TTGATCACGAACTAAACTTGATATCTTCACTTCAAGAGTCTTGGCGACTTGATA
* * * *
2530335 TTGATCACGAACTATACTTGATATCTTCACTTCAAGGGTCTTGGCAACATGATA
1 TTGATCACGAACTAAACTTGATATCTTCACTTCAAGAGTCTTGGCGACTTGATA
**
2530389 TTGATCACGAACTATTCTTGATAT
1 TTGATCACGAACTAAACTTGATAT
2530413 AAGTCTTGGC
Statistics
Matches: 109, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (54 bp):
TTGATCACGAACTAAACTTGATATCTTCACTTCAAGAGTCTTGGCGACTTGATA
Found at i:2531471 original size:3 final size:3
Alignment explanation
Indices: 2531463--2531497 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2531453 TTCCATGTCG
2531463 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2531498 CAACAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2533173 original size:12 final size:12
Alignment explanation
Indices: 2533156--2533197 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2533146 TGTTATTTCT
*
2533156 TTTTTTGTTTTG
1 TTTTTTATTTTG
*
2533168 TTTTTTATTTTA
1 TTTTTTATTTTG
2533180 TTTTTTATCTTT-
1 TTTTTTAT-TTTG
2533192 TTTTTT
1 TTTTTT
2533198 GCTTTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 24 0.89
13 3 0.11
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.86
Consensus pattern (12 bp):
TTTTTTATTTTG
Found at i:2533971 original size:15 final size:16
Alignment explanation
Indices: 2533947--2533976 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2533937 ACATTCATCT
2533947 TTTTTATTTGATTTAA
1 TTTTTATTTGATTTAA
2533963 TTTTT-TTTGATTTA
1 TTTTTATTTGATTTA
2533977 TTAAATACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTATTTGATTTAA
Found at i:2546524 original size:36 final size:36
Alignment explanation
Indices: 2546443--2546525 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
2546433 CAATAGGGTT
*
2546443 AGGCGTAACCTTTACAACATGCCTTTTAACAAGATC
1 AGGCGTAACCTTCACAACATGCCTTTTAACAAGATC
** * ** *
2546479 AATCATAACCTTCACAACATGCCTTTTCCCAGGATC
1 AGGCGTAACCTTCACAACATGCCTTTTAACAAGATC
2546515 AGGCGTAACCT
1 AGGCGTAACCT
2546526 CTACTAAGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (36 bp):
AGGCGTAACCTTCACAACATGCCTTTTAACAAGATC
Found at i:2548265 original size:19 final size:19
Alignment explanation
Indices: 2548237--2548277 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2548227 AATCATCAAC
* *
2548237 CAACACAGAGAATTATAAT
1 CAACACAGAGAACTACAAT
*
2548256 CAACATAGAGAACTACAAT
1 CAACACAGAGAACTACAAT
2548275 CAA
1 CAA
2548278 AAAAGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.17
Consensus pattern (19 bp):
CAACACAGAGAACTACAAT
Found at i:2549762 original size:27 final size:28
Alignment explanation
Indices: 2549717--2549857 Score: 103
Period size: 28 Copynumber: 5.1 Consensus size: 28
2549707 AACCTTTACA
*
2549717 ATGGCTTTTAATGGATTCAAC-CAAACGC
1 ATGG-TTTTAATGGATTCAACACAAACCC
*
2549745 ATGGTTTTAATTGG-TTCACCACAAACCC
1 ATGGTTTTAA-TGGATTCAACACAAACCC
* * *
2549773 ATGGTTTTAA-CGAGTT-AATA-AACCCC
1 ATGGTTTTAATGGA-TTCAACACAAACCC
* * * * *
2549799 ATGGCTTTAACGGGTTTACCACAAACCC
1 ATGGTTTTAATGGATTCAACACAAACCC
* *
2549827 ATGGTTTTTAATGGAATCACCACAAACCC
1 ATGG-TTTTAATGGATTCAACACAAACCC
2549856 AT
1 AT
2549858 ACTAACTTTT
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
26 17 0.19
27 16 0.18
28 34 0.39
29 21 0.24
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (28 bp):
ATGGTTTTAATGGATTCAACACAAACCC
Found at i:2549836 original size:29 final size:28
Alignment explanation
Indices: 2549738--2549857 Score: 111
Period size: 28 Copynumber: 4.3 Consensus size: 28
2549728 TGGATTCAAC
* **
2549738 CAAACGCATGGTTTTAATTGGTTCACCA
1 CAAACCCATGGTTTTAACGGGTTCACCA
*
2549766 CAAACCCATGGTTTTAACGAGTT-A--A
1 CAAACCCATGGTTTTAACGGGTTCACCA
* * *
2549791 TAAACCCCATGGCTTTAACGGGTTTACCA
1 CAAA-CCCATGGTTTTAACGGGTTCACCA
* **
2549820 CAAACCCATGGTTTTTAATGGAATCACCA
1 CAAACCCATGG-TTTTAACGGGTTCACCA
2549849 CAAACCCAT
1 CAAACCCAT
2549858 ACTAACTTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
25 4 0.05
26 17 0.23
27 2 0.03
28 26 0.35
29 25 0.34
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (28 bp):
CAAACCCATGGTTTTAACGGGTTCACCA
Found at i:2557570 original size:53 final size:53
Alignment explanation
Indices: 2557508--2557614 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
2557498 AAATTTACTC
2557508 AAATTAGATTGGCTCACTTAATTAACTAACTTAAAATATTTAAATTAAACCTA
1 AAATTAGATTGGCTCACTTAATTAACTAACTTAAAATATTTAAATTAAACCTA
2557561 AAATTAGATTGGCTCACTTAATTAACTAACTTAAAATATTTAAATTAAACCTA
1 AAATTAGATTGGCTCACTTAATTAACTAACTTAAAATATTTAAATTAAACCTA
2557614 A
1 A
2557615 TTGAATTCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.36
Consensus pattern (53 bp):
AAATTAGATTGGCTCACTTAATTAACTAACTTAAAATATTTAAATTAAACCTA
Found at i:2581508 original size:13 final size:14
Alignment explanation
Indices: 2581485--2581514 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2581475 AATTATCTAG
2581485 TAAATTTTTTTTTA
1 TAAATTTTTTTTTA
2581499 TAAA-TTTTTTTTA
1 TAAATTTTTTTTTA
2581512 TAA
1 TAA
2581515 GTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TAAATTTTTTTTTA
Found at i:2584301 original size:240 final size:241
Alignment explanation
Indices: 2583871--2584450 Score: 817
Period size: 240 Copynumber: 2.4 Consensus size: 241
2583861 NNNNNNNACC
* * * *
2583871 AGTCAATTAAGTAAAAATAATATAAATTTAATAAAAAGTAAATATTTAAATTTATATTCCCGAAC
1 AGTCAATTAAGTAAAAACAATGTAAATTTAATAAAAAGTAAATATTTAAATTTATATTCTCGGAC
*
2583936 TGAAAGGGTTTAACGATAT-AAAATTTTAATTTTTCAATAAAAGATAACTAATTATAATTCAAAA
66 TGAAAGTGTTTAACGATATAAAAATTTTAATTTTTCAATAAAAGATAACTAATTATAATTCAAAA
* * * * *
2584000 TTGATGTGAAAAAACCTTGATGTAAAACTGTAAGAATTAACGTAAAAGCTTGTAAAGGTGGAATA
131 TTGACGTGAAAAAACCTTGACGTAAAAATGTAAGAATTAACATAAAAGCTTATAAAGGTGGAATA
*
2584065 ACTAAAAT-TTAAATATTAACGTAAGCGTGTGAGAGTTAACGTAAAA
196 AAT-AAATCTTAAATATTAACGTAAGCGTGTGAGAGTTAACGTAAAA
* * * *
2584111 AGTCAACTAAGTAAAAACAATGTAAATTTAAT-GAAAGCAAATATTTAAATTTATATTATCGGAC
1 AGTCAATTAAGTAAAAACAATGTAAATTTAATAAAAAGTAAATATTTAAATTTATATTCTCGGAC
**********
2584175 TGAAAGTGTTTAACGATATAAAAATTTTAATTTTNNNNNNNNNNATAACTAATTATAATTCAAAA
66 TGAAAGTGTTTAACGATATAAAAATTTTAATTTTTCAATAAAAGATAACTAATTATAATTCAAAA
**
2584240 TTGACGTGAAAAAGTCTTGACGTAAAAATGTAAGAATTAACATAAAAGCTTATAAAGGTGGAATA
131 TTGACGTGAAAAAACCTTGACGTAAAAATGTAAGAATTAACATAAAAGCTTATAAAGGTGGAATA
* * *
2584305 AATAAATCTTAAATCTTAATGTAAGCGTGTGAGAGTTAACGTAAGA
196 AATAAATCTTAAATATTAACGTAAGCGTGTGAGAGTTAACGTAAAA
* * *
2584351 AGTTAATTAAGTGAAAACAATGTAAATTTAATCAAAAGTAAATATTTAAATTTATATTCTC-GAG
1 AGTCAATTAAGTAAAAACAATGTAAATTTAATAAAAAGTAAATATTTAAATTTATATTCTCGGA-
2584415 CTGAAAGTGTTTAACGATATAAAAATTTTAATTTTT
65 CTGAAAGTGTTTAACGATATAAAAATTTTAATTTTT
2584451 NNNNNNNNNN
Statistics
Matches: 299, Mismatches: 37, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
239 49 0.16
240 190 0.64
241 60 0.20
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.32
Consensus pattern (241 bp):
AGTCAATTAAGTAAAAACAATGTAAATTTAATAAAAAGTAAATATTTAAATTTATATTCTCGGAC
TGAAAGTGTTTAACGATATAAAAATTTTAATTTTTCAATAAAAGATAACTAATTATAATTCAAAA
TTGACGTGAAAAAACCTTGACGTAAAAATGTAAGAATTAACATAAAAGCTTATAAAGGTGGAATA
AATAAATCTTAAATATTAACGTAAGCGTGTGAGAGTTAACGTAAAA
Found at i:2584920 original size:240 final size:241
Alignment explanation
Indices: 2584605--2585380 Score: 1016
Period size: 239 Copynumber: 3.2 Consensus size: 241
2584595 NNNNNNNNNN
*
2584605 TAAAAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCCCGGGCTGAAAGTGTTT
1 TAAAAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTT
*
2584670 AACGATATAAAAGTTTTAATTTTTCAATAAAGGATAACTAATTATATTTCAAAATTGACGTGAAA
66 AACGATATAAAAATTTTAATTTTTCAATAAAGGATAACTAATTATATTTCAAAATTGACGTGAAA
*
2584735 AAACTTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTTTAAAGGTAGAATAACTAAATTTTA
131 AAACTTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTTTAAAGGTGGAATAACTAAATTTTA
* *
2584800 AATCTTAACGTAAGTGTATAAGAGTTAACTTAACAAGTCAATTAAG
196 AATCTTAACGTAAGTGTGTAAGAGTTAACATAACAAGTCAATTAAG
* * *
2584846 TAAAAACAATGTAAATTTAATG-AAAGCAAATATTTAAATTTTTATTCTCGGGTTGAAAGTGTTT
1 TAAAAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTT
*
2584910 AACGATATAAAAATTTTAA-TTTTCAATAAAAGATAACTAATTATAATTT-AAAATTGACGTGAA
66 AACGATATAAAAATTTTAATTTTTCAATAAAGGATAACTAATTAT-ATTTCAAAATTGACGTGAA
* * * *
2584973 AAAATCTTT-ACGTAAAACTGTAAGTATTGACATAAAAGCTTGTGAAA-GTGGAGTAACTAAATT
130 AAAA-CTTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTT-TTAAAGGTGGAATAACTAAATT
* ** *
2585036 TTAGATCTTAACGTAAGCATGTAAGAGTTAACATAAGAAGTCAATTAAG
193 TTAAATCTTAACGTAAGTGTGTAAGAGTTAACATAACAAGTCAATTAAG
* * *
2585085 TAAAAATAATATAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTAAAAGTGTTT
1 TAAAAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTT
* *
2585150 AACGATATAAAAATTTTAATTTTTAAATAAATGATAATAAGGATTAAACTAATTATAATTCAAAA
66 AACGATATAAAAATTTTAA-TTTT---T-CA--AT-A-AAGGA-T-AACTAATTATATTTCAAAA
* * * * *
2585215 TTGACGTG-AAAAAGTATTGATGTAAAATTGTAAGAATTGACGTAAAAACTTATAAAGGTGGAAT
120 TTGACGTGAAAAAACT-TTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTTTAAAGGTGGAAT
** * * * *
2585279 AACTAAATTTTAAATCTTAACAAAAATGTGTGAGAGTTAACGTAATAAGTCAATTAAG
184 AACTAAATTTTAAATCTTAACGTAAGTGTGTAAGAGTTAACATAACAAGTCAATTAAG
* * *
2585337 T-AAAA-AATTTAATTTTATTG-AAA--AAATATTTAAATTTATATTCT
1 TAAAAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCT
2585381 TAGATAAATT
Statistics
Matches: 468, Mismatches: 47, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
239 149 0.32
240 125 0.27
241 22 0.05
242 3 0.01
245 1 0.00
246 1 0.00
247 21 0.04
248 2 0.00
249 4 0.01
250 17 0.04
251 18 0.04
252 105 0.22
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (241 bp):
TAAAAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTT
AACGATATAAAAATTTTAATTTTTCAATAAAGGATAACTAATTATATTTCAAAATTGACGTGAAA
AAACTTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTTTAAAGGTGGAATAACTAAATTTTA
AATCTTAACGTAAGTGTGTAAGAGTTAACATAACAAGTCAATTAAG
Found at i:2585877 original size:242 final size:243
Alignment explanation
Indices: 2585400--2586080 Score: 851
Period size: 242 Copynumber: 2.8 Consensus size: 243
2585390 TTTAATTTTT
2585400 AAATAAAAATAATTATAGTTTAAAATTGA-AATAGATAAG-CGTTGACGTAAAACTGTAAGAATT
1 AAATAAAAATAATTATAGTTTAAAATTGATAA-AGATAAGTC-TTGACGTAAAACTGTAAGAATT
*
2585463 GACGTAAAAACTTAT-AAAGATGGAATAACTAAATTTTAAATCTTAACGTAAATATGTGAGAGTT
64 GACGTAAAAACTTATAAAAG-T-GAATAAATAAATTTTAAATCTTAACGTAAATATGTGAGAGTT
* * * * * *
2585527 AACGTAATAAGT-TAATTAAGT-ACAAAAGTCTAATTTTAATGAAAAATAAATATTTATATTTAT
127 AACGTAACAAGTCT-ATTAAGTAAAAAAAATTTAATTTTAATGAAAAATAAATATTTAAATATAT
2585590 ATTATAGAGCTAAAAGTATGTAACGATATATAAATTTTAATTTTTTAAAT-AA
191 ATTATAGAGCTAAAAGTATGTAACGATATATAAATTTTAATTTTTTAAATAAA
* * * *
2585642 AAATAAAAATAATTATAGTATAAAATTGATAAAAATAAGTTTTAACGTAAAACTGTAAGAATTGA
1 AAATAAAAATAATTATAGTTTAAAATTGATAAAGATAAGTCTTGACGTAAAACTGTAAGAATTGA
* * ** * * *
2585707 CATAAAAATTTATAAAAGTAGAATAAATAAATTTTAAATCTTAACGTAAACGTATAAGAATTAAC
66 CGTAAAAACTTATAAAAGT-GAATAAATAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAAC
*
2585772 GTAACAAGTCTATTAAGTAAAAAAAATTTAATTTTACTGAAAAATAAATATTTAAATATATATTA
130 GTAACAAGTCTATTAAGTAAAAAAAATTTAATTTTAATGAAAAATAAATATTTAAATATATATTA
*
2585837 TCAGA-CTAAAAGT-GGTTAACGATATATAAATTTT-ATTTTTTAAATAAAAA
195 T-AGAGCTAAAAGTATG-TAACGATATATAAATTTTAATTTTTTAAAT--AAA
* * * * * *
2585887 ATAATAAAAATAATTATAGTTTAAAATTGACT-TAGATAAATCTTGACGTAAAAGTATAACAGTT
1 A-AATAAAAATAATTATAGTTTAAAATTGA-TAAAGATAAGTCTTGACGTAAAACTGTAAGAATT
* * *
2585951 GATGTAAAAACTTATAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAATATGTGAGAGTTA
64 GACGTAAAAACTTATAAAAGTG-AATAAATAAATTTTAAATCTTAACGTAAATATGTGAGAGTTA
* ** * *
2586016 ACGCAACAAACCAATTGAGTAAAAAAAAATTCTAATTTTAATGAAAAATAAATATTTAAATATAT
128 ACGTAACAAGTCTATTAAGT-AAAAAAAATT-TAATTTTAATGAAAAATAAATATTTAAATATAT
2586081 TTTCTTCTGC
Statistics
Matches: 377, Mismatches: 47, Indels: 24
0.84 0.10 0.05
Matches are distributed among these distances:
242 135 0.36
243 74 0.20
244 3 0.01
245 4 0.01
246 118 0.31
247 11 0.03
248 32 0.08
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (243 bp):
AAATAAAAATAATTATAGTTTAAAATTGATAAAGATAAGTCTTGACGTAAAACTGTAAGAATTGA
CGTAAAAACTTATAAAAGTGAATAAATAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAACG
TAACAAGTCTATTAAGTAAAAAAAATTTAATTTTAATGAAAAATAAATATTTAAATATATATTAT
AGAGCTAAAAGTATGTAACGATATATAAATTTTAATTTTTTAAATAAA
Found at i:2586291 original size:251 final size:233
Alignment explanation
Indices: 2585401--2586223 Score: 585
Period size: 242 Copynumber: 3.4 Consensus size: 233
2585391 TTAATTTTTA
* * * * * * *
2585401 AATAAAAATAATTATAGTTTAAAATTGAAATAGAT-AAGCGTTGACGTAAAACTGTAAGAATTGA
1 AATAAAAATAATTATAGCTCAAAATTGACATAGATAAATC-TTGACGTAAAAGTATAACAATTGA
* * * *
2585465 CGTAAAAACTTATAAAGATGGAATAACTAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAAC
65 CGTAAAAACTTATAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAATATATGAGAGTTAAC
* * *** * * * *
2585530 GTAATAAGTTAATTAAGTACAAAAGTCTAATTTTAATGAAAAATAAATATTTATATTTATATTAT
130 GCAACAAACCAATTAAGTA-AAAAGTCTAATTTTAAT-AAAAATAAATATTTAAATATATTTTCT
*** * * * * *
2585595 AGAGCTAAAAGTATGTAACGATATATAAATTTTAATTTTTTAAATAAA-
193 TCTGCTAAATGTATATAA--AT-TTTAATTTTTAA----ATAAA-AAAT
* * * * * * * * * *
2585643 AATAAAAATAATTATAG-TATAAAATTGATAAAAATAAGTTTTAACGTAAAACTGTAAGAATTGA
1 AATAAAAATAATTATAGCT-CAAAATTGACATAGATAAATCTTGACGTAAAAGTATAACAATTGA
* * * * ** * *
2585707 CATAAAAATTTATAAAAGT-AGAATAAATAAATTTTAAATCTTAACGTAAACGTATAAGAATTAA
65 CGTAAAAACTTATAAAGGTGA-AATAATTAAATTTTAAATCTTAACGTAAATATATGAGAGTTAA
* ** * * * * *
2585771 CGTAACAAGTCTATTAAGTAAAAAAAATTTAATTTTACTGAAAAATAAATATTTAAATATATATT
129 CGCAACAAACCAATTAAGT--AAAAAGTCTAATTTTAAT-AAAAATAAATATTTAAATATATTTT
* * *
2585836 -ATCAGACTAAAAGTGGTTAACGATATATAAATTTTATTTTTTAAATAAAAAAT
191 CTTCTG-CT-AAA-----T---G-TATATAAATTTTAATTTTTAAATAAAAAAT
* * * * *
2585889 AATAAAAATAATTATAGTTTAAAATTGACTTAGATAAATCTTGACGTAAAAGTATAACAGTTGAT
1 AATAAAAATAATTATAGCTCAAAATTGACATAGATAAATCTTGACGTAAAAGTATAACAATTGAC
*
2585954 GTAAAAACTTATAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAATATGTGAGAGTTAACG
66 GTAAAAACTTATAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAATATATGAGAGTTAACG
* *
2586019 CAACAAACCAATTGAGTAAAAAAAAATTCTAATTTTAATGAAAAATAAATATTTAAATATATTTT
131 CAACAAACCAATTAAGT----AAAAAGTCTAATTTTAAT-AAAAATAAATATTTAAATATATTTT
2586084 CTTCTGCTAAATGTANNNNNNNNNNTATAAATTTTAATTTTTAAATAAAAAAT
191 CTTCTGCTAAATGTA----------TATAAATTTTAATTTTTAAATAAAAAAT
* * * *
2586137 AATAATAACAATTATTATAGCTCAAAATTGTCATAGATAAATCTTGACGTAAAATTGTAACAATT
1 AAT-A-AA-AATAATTATAGCTCAAAATTGACATAGATAAATCTTGACGTAAAAGTATAACAATT
2586202 GACGTAAAAACTTATAAAGGTG
63 GACGTAAAAACTTATAAAGGTG
2586224 GAANNNNNNN
Statistics
Matches: 469, Mismatches: 77, Indels: 61
0.77 0.13 0.10
Matches are distributed among these distances:
238 2 0.00
239 1 0.00
241 1 0.00
242 124 0.26
243 41 0.09
244 4 0.01
245 3 0.01
246 121 0.26
247 5 0.01
248 74 0.16
249 4 0.01
250 11 0.02
251 71 0.15
252 1 0.00
253 6 0.01
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.34
Consensus pattern (233 bp):
AATAAAAATAATTATAGCTCAAAATTGACATAGATAAATCTTGACGTAAAAGTATAACAATTGAC
GTAAAAACTTATAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAATATATGAGAGTTAACG
CAACAAACCAATTAAGTAAAAAGTCTAATTTTAATAAAAATAAATATTTAAATATATTTTCTTCT
GCTAAATGTATATAAATTTTAATTTTTAAATAAAAAAT
Found at i:2586618 original size:17 final size:17
Alignment explanation
Indices: 2586598--2586663 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
2586588 TTTTATAATT
2586598 TAAAATTAAAAATAAAA
1 TAAAATTAAAAATAAAA
* *
2586615 TAAAATTAAAACTTAAA
1 TAAAATTAAAAATAAAA
** *
2586632 TAACTTTAAATAAAATAAA
1 TAAAATTAAA-AATA-AAA
*
2586651 TAAATTTAAAAAT
1 TAAAATTAAAAAT
2586664 TATTTATATT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 23 0.61
18 3 0.08
19 12 0.32
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATTAAAAATAAAA
Found at i:2589674 original size:27 final size:28
Alignment explanation
Indices: 2589625--2589679 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2589615 ATAAATAATA
* *
2589625 TTTTAATTAAAAATAATTAATTAATTAT
1 TTTTAATAAAAAATAACTAATTAATTAT
*
2589653 TTTTAATAAAAAAT-ACTCATTAATTAT
1 TTTTAATAAAAAATAACTAATTAATTAT
2589680 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTAATAAAAAATAACTAATTAATTAT
Found at i:2601970 original size:83 final size:83
Alignment explanation
Indices: 2601844--2602007 Score: 235
Period size: 83 Copynumber: 2.0 Consensus size: 83
2601834 TACAAATCTG
*
2601844 TAACATATATAAAAAGGAGATCCAAAACTGTTTTCATGCTTGATCACGTCATACA-A-TATAATA
1 TAACATATATAAAAAGGAGATCCAAAACTGTTTTCATGCTTGATCACATCATACAGAGTAT--TA
*
2601907 AAGTCATTTTTTATATTTTA
64 AAGTCATTTTCTATATTTTA
* * *
2601927 TAACATATAT-AAAAGGAAGATCCAAAATTGTTTTCATGTTTGATCACATTATACAGAGTATTAA
1 TAACATATATAAAAAGG-AGATCCAAAACTGTTTTCATGCTTGATCACATCATACAGAGTATTAA
2601991 AGTCATTTTCTATATTT
65 AGTCATTTTCTATATTT
2602008 AAACATGAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
82 6 0.08
83 63 0.86
84 1 0.01
85 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (83 bp):
TAACATATATAAAAAGGAGATCCAAAACTGTTTTCATGCTTGATCACATCATACAGAGTATTAAA
GTCATTTTCTATATTTTA
Found at i:2603178 original size:43 final size:42
Alignment explanation
Indices: 2603109--2603191 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 42
2603099 TTATAATGCT
* * **
2603109 TAATATGCTTTATTTGTAGTCCTATGATTCCAAACATAATACC
1 TAATATCCTTGATTTGTAGTCCTATGACACC-AACATAATACC
*
2603152 TAATATCCTTGATTTGGT-GTCTTATGACACCAACATAATA
1 TAATATCCTTGATTT-GTAGTCCTATGACACCAACATAATA
2603192 GATGATGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 9 0.26
43 23 0.68
44 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (42 bp):
TAATATCCTTGATTTGTAGTCCTATGACACCAACATAATACC
Found at i:2603825 original size:43 final size:43
Alignment explanation
Indices: 2603733--2603830 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
2603723 TGCCAAGCTT
* * * * * *
2603733 CCAAGCTTAATGCTTGATATACTTGATCTGGGGTCTTATGATA
1 CCAAGCATAATACTTGATATACTTGAACTGAGGTATTACGATA
* *
2603776 CCAAGCATAATACTTGATGTACTTGAACTGAGGTATTACGATT
1 CCAAGCATAATACTTGATATACTTGAACTGAGGTATTACGATA
*
2603819 CTAAGCATAATA
1 CCAAGCATAATA
2603831 GATGATATCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (43 bp):
CCAAGCATAATACTTGATATACTTGAACTGAGGTATTACGATA
Found at i:2605342 original size:6 final size:7
Alignment explanation
Indices: 2605317--2605341 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2605307 TTTACTTTTT
2605317 TTTTTCA
1 TTTTTCA
2605324 TTTTTCA
1 TTTTTCA
2605331 TTTTTCA
1 TTTTTCA
2605338 TTTT
1 TTTT
2605342 CTCTTTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:2605976 original size:34 final size:34
Alignment explanation
Indices: 2605938--2606029 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
2605928 TAGGCTTAAC
* *
2605938 CACAACCCT-TACAATGCCTTTCTA-TGAAAGCAAG
1 CACAA-CCTATACAATGCCTTT-TACTAAAACCAAG
* *
2605972 CACAACCTACACAATGCCTTTTACTAAAACCTAG
1 CACAACCTATACAATGCCTTTTACTAAAACCAAG
*
2606006 CACAACATATACAATGCCTTTTAC
1 CACAACCTATACAATGCCTTTTAC
2606030 GAAGAGTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 5 0.10
34 45 0.90
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (34 bp):
CACAACCTATACAATGCCTTTTACTAAAACCAAG
Found at i:2608835 original size:25 final size:25
Alignment explanation
Indices: 2608783--2608855 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
2608773 AAATATTTCT
* * ***
2608783 TTATTAATTAACATAATTATAATAA
1 TTATGAATCAACATAATTATAGGGA
**
2608808 TTATGAATCATTATAATTATAGGGA
1 TTATGAATCAACATAATTATAGGGA
*
2608833 TTATGAATTAACATAATTATAGG
1 TTATGAATCAACATAATTATAGG
2608856 AATTTTATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (25 bp):
TTATGAATCAACATAATTATAGGGA
Found at i:2613086 original size:8 final size:8
Alignment explanation
Indices: 2613060--2613123 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 8
2613050 AAAGTGAGAA
2613060 AAGAAAGG
1 AAGAAAGG
2613068 -AG-AAGG
1 AAGAAAGG
2613074 AAAGAAAGG
1 -AAGAAAGG
2613083 AAGAAAGG
1 AAGAAAGG
2613091 AAGAAAGG
1 AAGAAAGG
* *
2613099 -AGGAAGA
1 AAGAAAGG
2613106 AGAGAAAGG
1 A-AGAAAGG
2613115 AAAGAAAGG
1 -AAGAAAGG
2613124 TTCGGCCTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
6 4 0.09
7 7 0.15
8 18 0.39
9 16 0.35
10 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (8 bp):
AAGAAAGG
Found at i:2618431 original size:3 final size:3
Alignment explanation
Indices: 2618423--2618452 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2618413 CTGGAGTCTT
2618423 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2618453 ATTCTTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2623367 original size:30 final size:30
Alignment explanation
Indices: 2623333--2623398 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
2623323 CTTGATTGAG
*
2623333 GATGAAGAAGATGACATGCAAAGAGATGAA
1 GATGAAGAAAATGACATGCAAAGAGATGAA
* *
2623363 GATGAAGAAAATGACATGGAATGAGATGAA
1 GATGAAGAAAATGACATGCAAAGAGATGAA
*
2623393 AATGAA
1 GATGAA
2623399 AATGAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.05, G:0.29, T:0.15
Consensus pattern (30 bp):
GATGAAGAAAATGACATGCAAAGAGATGAA
Found at i:2623415 original size:18 final size:18
Alignment explanation
Indices: 2623388--2623434 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2623378 ATGGAATGAG
* *
2623388 ATGAAAATGAAAATGAAA
1 ATGAAGATGAAAACGAAA
*
2623406 ATGAAGATGAAAACGAAG
1 ATGAAGATGAAAACGAAA
*
2623424 TTGAAGATGAA
1 ATGAAGATGAA
2623435 GACAAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGAAGATGAAAACGAAA
Found at i:2623423 original size:12 final size:12
Alignment explanation
Indices: 2623382--2623436 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
2623372 AATGACATGG
2623382 AATG-AGATGAA
1 AATGAAGATGAA
*
2623393 AATGAAAATGAA
1 AATGAAGATGAA
2623405 AATGAAGATGAA
1 AATGAAGATGAA
* *
2623417 AACGAAGTTGAA
1 AATGAAGATGAA
*
2623429 GATGAAGA
1 AATGAAGA
2623437 CAAATAAACA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 4 0.11
12 32 0.89
ACGTcount: A:0.56, C:0.02, G:0.25, T:0.16
Consensus pattern (12 bp):
AATGAAGATGAA
Found at i:2624428 original size:21 final size:21
Alignment explanation
Indices: 2624376--2624428 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2624366 TTTGTTTTTA
*
2624376 ATTAATTTGTATAAATTTGTTT
1 ATTAATTT-TATAAATTTGTAT
*
2624398 AGTT-ACTTTATAAATTTGTAT
1 A-TTAATTTTATAAATTTGTAT
2624419 ATTAATTTTA
1 ATTAATTTTA
2624429 GTTCCATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.08
21 18 0.69
22 4 0.15
23 2 0.08
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (21 bp):
ATTAATTTTATAAATTTGTAT
Found at i:2626131 original size:21 final size:21
Alignment explanation
Indices: 2626105--2626174 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2626095 TAGTGATTAT
2626105 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTGTTTAA
** * ** *
2626126 ATTTAAATAAAAATTAATTAC
1 ATTTAAATTTAATTTGTTTAA
*
2626147 ATTTAAATTTAGTTTGTTTAA
1 ATTTAAATTTAATTTGTTTAA
2626168 ATTTAAA
1 ATTTAAA
2626175 AGTAATATAC
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTAATTTGTTTAA
Found at i:2627320 original size:47 final size:47
Alignment explanation
Indices: 2627266--2627466 Score: 287
Period size: 47 Copynumber: 4.2 Consensus size: 47
2627256 TTTGTATGGT
2627266 TTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTTG
1 TTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTTG
** *
2627313 TTAGGTAAAATTTATATTATGAATGATGTAATTTATTTTACTTATTTG
1 TTAGGTAAAATTTATAAAATGCATGATGTAA-TTATTTTACTTATTTG
* *
2627361 TTAGGTAAAATTTAT-AAATCACATAATGTAATTATTTTACTTATTTG
1 TTAGGTAAAATTTATAAAAT-GCATGATGTAATTATTTTACTTATTTG
* * *
2627408 TTTGGTAAAATCTATAAAATGCATTATGTAATTATTTTAACTTATTTG
1 TTAGGTAAAATTTATAAAATGCATGATGTAATTATTTT-ACTTATTTG
*
2627456 TTAAGTAAAAT
1 TTAGGTAAAAT
2627467 GGTACGCAAA
Statistics
Matches: 136, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
47 75 0.55
48 61 0.45
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (47 bp):
TTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTTG
Found at i:2627327 original size:27 final size:27
Alignment explanation
Indices: 2627297--2627375 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
2627287 CATGATGTAA
2627297 TTATTTTACTTATTTGTTAGGTAAAAT
1 TTATTTTACTTATTTGTTAGGTAAAAT
* * * *
2627324 TTATATTA-TGA-ATG--ATGT--AAT
1 TTATTTTACTTATTTGTTAGGTAAAAT
2627345 TTATTTTACTTATTTGTTAGGTAAAAT
1 TTATTTTACTTATTTGTTAGGTAAAAT
2627372 TTAT
1 TTAT
2627376 AAATCACATA
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
21 10 0.26
22 2 0.05
23 5 0.13
25 5 0.13
26 2 0.05
27 14 0.37
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (27 bp):
TTATTTTACTTATTTGTTAGGTAAAAT
Found at i:2627367 original size:95 final size:95
Alignment explanation
Indices: 2627266--2627466 Score: 289
Period size: 95 Copynumber: 2.1 Consensus size: 95
2627256 TTTGTATGGT
* * * *
2627266 TTAGGTAAAATTTATAAAAT-GCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTATAT
1 TTAGGTAAAATTTAT-AAATCACATAATGTAATTATTTTACTTATTTGTTAGGTAAAATCTATAA
*
2627330 TATGAATGATGTAATTTATTTT-ACTTATTTG
65 AATGAATGATGTAA-TTATTTTAACTTATTTG
*
2627361 TTAGGTAAAATTTATAAATCACATAATGTAATTATTTTACTTATTTGTTTGGTAAAATCTATAAA
1 TTAGGTAAAATTTATAAATCACATAATGTAATTATTTTACTTATTTGTTAGGTAAAATCTATAAA
* *
2627426 ATGCATTATGTAATTATTTTAACTTATTTG
66 ATGAATGATGTAATTATTTTAACTTATTTG
*
2627456 TTAAGTAAAAT
1 TTAGGTAAAAT
2627467 GGTACGCAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 11 0.12
95 84 0.88
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (95 bp):
TTAGGTAAAATTTATAAATCACATAATGTAATTATTTTACTTATTTGTTAGGTAAAATCTATAAA
ATGAATGATGTAATTATTTTAACTTATTTG
Found at i:2631670 original size:25 final size:24
Alignment explanation
Indices: 2631637--2631683 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2631627 GATATACATA
*
2631637 TGGCAAGGCCATAGGGTGATATATG
1 TGGCAAGGCCATA-AGTGATATATG
*
2631662 TGGCTAGGCCATAAGTGATATA
1 TGGCAAGGCCATAAGTGATATA
2631684 CGTGATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.26
Consensus pattern (24 bp):
TGGCAAGGCCATAAGTGATATATG
Found at i:2638923 original size:11 final size:11
Alignment explanation
Indices: 2638907--2638932 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2638897 CTAATTACTA
2638907 TTTATAAATAT
1 TTTATAAATAT
2638918 TTTATAAATAT
1 TTTATAAATAT
2638929 TTTA
1 TTTA
2638933 ATAATTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTATAAATAT
Found at i:2642135 original size:169 final size:168
Alignment explanation
Indices: 2641834--2642166 Score: 632
Period size: 169 Copynumber: 2.0 Consensus size: 168
2641824 GAAATTACTC
2641834 CACAGTGAGTACATGAAAGCAAACCAAACATTAAGTATCTTGTCGGACTGTTGCTTTCATGTAAT
1 CACAGTGAGTACATGAAAGCAAACCAAACATTAAGTATCTTGTCGGACTGTTGCTTTCATGTAAT
2641899 CTTGATCCACTCCCAGAAGTAACTAATACAGATTCAGGTAACAACTAAGACATAAATGTTCACTT
66 CTTGATCCACTCCCAGAAGTAACTAATACAGATTCAGGTAACAACTAAGACATAAATGTTCACTT
2641964 TCCCTTCC-CTAGGATCACGTTTAAGATATATATATATA
131 TCCC-TCCTCTAGGATCACGTTTAAGATATATATATATA
*
2642002 CACAGTGAGTACATGAAAGCAAACCAAACATTAAGTATCTTGTCGGGCTGTTGCTTTCATGTAAT
1 CACAGTGAGTACATGAAAGCAAACCAAACATTAAGTATCTTGTCGGACTGTTGCTTTCATGTAAT
2642067 CTTTGATCCACTCCCAGAAGTAACTAATACAGATTCAGGTAACAACTAAGACATAAATGTTCACT
66 C-TTGATCCACTCCCAGAAGTAACTAATACAGATTCAGGTAACAACTAAGACATAAATGTTCACT
2642132 TTCCCTCCTCTAGGATCACGTTTAAGATATATATA
130 TTCCCTCCTCTAGGATCACGTTTAAGATATATATA
2642167 CACTTTTGTT
Statistics
Matches: 162, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
168 68 0.42
169 94 0.58
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (168 bp):
CACAGTGAGTACATGAAAGCAAACCAAACATTAAGTATCTTGTCGGACTGTTGCTTTCATGTAAT
CTTGATCCACTCCCAGAAGTAACTAATACAGATTCAGGTAACAACTAAGACATAAATGTTCACTT
TCCCTCCTCTAGGATCACGTTTAAGATATATATATATA
Found at i:2646126 original size:18 final size:18
Alignment explanation
Indices: 2646103--2646137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2646093 GATGTTCAAT
*
2646103 TTTGAAAATATAATTTTA
1 TTTGAAAATAGAATTTTA
*
2646121 TTTGAAAGTAGAATTTT
1 TTTGAAAATAGAATTTT
2646138 GAAGATACAA
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:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTGAAAATAGAATTTTA
Found at i:2653253 original size:18 final size:18
Alignment explanation
Indices: 2653230--2653264 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2653220 TTGTATCTTC
*
2653230 AAAATTCTACTTTCAAAT
1 AAAATTATACTTTCAAAT
*
2653248 AAAATTATATTTTCAAA
1 AAAATTATACTTTCAAA
2653265 ATTGAACATT
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:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTATACTTTCAAAT
Found at i:2653318 original size:10 final size:10
Alignment explanation
Indices: 2653303--2653329 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2653293 TTCTCCGGTG
2653303 TATATATGTA
1 TATATATGTA
2653313 TATATATGTA
1 TATATATGTA
2653323 TATATAT
1 TATATAT
2653330 AGCAGAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATGTA
Found at i:2655368 original size:48 final size:48
Alignment explanation
Indices: 2655297--2655388 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
2655287 TCTTACTAAA
*
2655297 GGTATGATCCTCAATATAAGTATAATCATATAATATGATTCAAGTTTT
1 GGTATGATCCTCAATATAAGTATAATAATATAATATGATTCAAGTTTT
*
2655345 GGTATGATGCTCAATATAAGTATAATAATATAATATGATTCAAG
1 GGTATGATCCTCAATATAAGTATAATAATATAATATGATTCAAG
2655389 CAGTTGGTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (48 bp):
GGTATGATCCTCAATATAAGTATAATAATATAATATGATTCAAGTTTT
Found at i:2658226 original size:15 final size:16
Alignment explanation
Indices: 2658206--2658238 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2658196 CAATCACCTG
2658206 TTATTTTATTT-TTTC
1 TTATTTTATTTATTTC
2658221 TTATTTTATTTATTTC
1 TTATTTTATTTATTTC
2658237 TT
1 TT
2658239 CAATTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTATTTATTTC
Found at i:2665835 original size:59 final size:60
Alignment explanation
Indices: 2665722--2665875 Score: 190
Period size: 59 Copynumber: 2.6 Consensus size: 60
2665712 CTAGCTAGTA
* *
2665722 AATTGATATATGGTGGCGTGGGGTGTCCCACGAG-AAGGCATGGATGGGGAAGAGGCCCT
1 AATTAATATATGGTGGCGTGGGGTGTCCCACGAGTAAGGCATGGATGGGGAAGAGGCCCC
* * * *
2665781 GATTAATATATGGTGGCATAGGGTGTCCCACAAGTAA-GCACT-GATTGGGG-AGAGGCCCC
1 AATTAATATATGGTGGCGTGGGGTGTCCCACGAGTAAGGCA-TGGA-TGGGGAAGAGGCCCC
* *
2665840 AATTGATCTATGGTGGCGTGGGGTGTCCCACGAGTA
1 AATTAATATATGGTGGCGTGGGGTGTCCCACGAGTA
2665876 GATGTTGATA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 72 0.90
60 8 0.10
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (60 bp):
AATTAATATATGGTGGCGTGGGGTGTCCCACGAGTAAGGCATGGATGGGGAAGAGGCCCC
Found at i:2667164 original size:69 final size:69
Alignment explanation
Indices: 2667053--2667191 Score: 181
Period size: 69 Copynumber: 2.0 Consensus size: 69
2667043 ACAATATCAG
* * * * * * * *
2667053 TTCAAGCCATACAAATATATTTCTTCAAGTCGCAACTAACTAAAGTGATCAACCAAAAAATTGAG
1 TTCAAGCCATAAAAATATACTTCTACAAGACACAACTAACTAAAATGATCAACCAAAAAACTAAG
2667118 CTTC
66 CTTC
*
2667122 TTCAAGCCATAAAAATATACTTCTACAA-ACAACAACTAACTAAAATGATTAACCAAAAAACTAA
1 TTCAAGCCATAAAAATATACTTCTACAAGAC-ACAACTAACTAAAATGATCAACCAAAAAACTAA
2667186 GCTTC
65 GCTTC
2667191 T
1 T
2667192 AATTGCTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (69 bp):
TTCAAGCCATAAAAATATACTTCTACAAGACACAACTAACTAAAATGATCAACCAAAAAACTAAG
CTTC
Found at i:2669582 original size:31 final size:30
Alignment explanation
Indices: 2669512--2669626 Score: 131
Period size: 31 Copynumber: 3.8 Consensus size: 30
2669502 TTGAGAGATG
* * *
2669512 AAATTGTAAATGATGAAAAGTTGAAGAATT
1 AAATTGTAAATAATGAAAAGTTTAAAAATT
* * *
2669542 AAATCGTAAAAAATGAAAAGTTTAAAAAACT
1 AAATTGTAAATAATGAAAAGTTT-AAAAATT
*
2669573 AAATTGTAAATAATGAAAAGATTTAAAGATT
1 AAATTGTAAATAATGAAAAG-TTTAAAAATT
* *
2669604 AAATTTTAAATAATAAAAAGTTT
1 AAATTGTAAATAATGAAAAGTTT
2669627 TAAGGACCAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
30 22 0.31
31 46 0.65
32 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (30 bp):
AAATTGTAAATAATGAAAAGTTTAAAAATT
Found at i:2671536 original size:39 final size:38
Alignment explanation
Indices: 2671503--2671627 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 38
2671493 AAGATCTACA
2671503 TATGAATGGTTTTGTTTATTCATATGATGAAGATTGATT
1 TATGAAT-GTTTTGTTTATTCATATGATGAAGATTGATT
* * *
2671542 TACGAATACTTTCGTTTATTCATATGATGAAGATTGATT
1 TATGAAT-GTTTTGTTTATTCATATGATGAAGATTGATT
** * *
2671581 TATGAATGTTTTGATTTATTCATATGACAAATAATGATT
1 TATGAATGTTTTG-TTTATTCATATGATGAAGATTGATT
2671620 TATGAATG
1 TATGAATG
2671628 AGATAAGATC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 4 0.05
39 70 0.95
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.46
Consensus pattern (38 bp):
TATGAATGTTTTGTTTATTCATATGATGAAGATTGATT
Found at i:2671777 original size:33 final size:33
Alignment explanation
Indices: 2671740--2671837 Score: 101
Period size: 33 Copynumber: 3.0 Consensus size: 33
2671730 CGAGTTATAA
2671740 TAGTTAGCATATGACCCTGCTAATAGGTTACAC
1 TAGTTAGCATATGACCCTGCTAATAGGTTACAC
* * * *
2671773 TAGTTAGCATACG-CCTCCGCTAACAGGTTACAG
1 TAGTTAGCATATGACC-CTGCTAATAGGTTACAC
* * *
2671806 TAGTTAGTATATGACTCTACT-ATGAGGTTACA
1 TAGTTAGCATATGACCCTGCTAAT-AGGTTACA
2671838 ATAATTAGTA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
32 3 0.06
33 48 0.92
34 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (33 bp):
TAGTTAGCATATGACCCTGCTAATAGGTTACAC
Found at i:2679980 original size:31 final size:31
Alignment explanation
Indices: 2679940--2679999 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2679930 ATAGATGGAG
*
2679940 AAGACGGTCATAGAGAAAATAGCATATTGAC
1 AAGAAGGTCATAGAGAAAATAGCATATTGAC
2679971 AAGAAGGTCATAGAGAAAATAGCATATTG
1 AAGAAGGTCATAGAGAAAATAGCATATTG
2680000 GCATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (31 bp):
AAGAAGGTCATAGAGAAAATAGCATATTGAC
Found at i:2685730 original size:57 final size:58
Alignment explanation
Indices: 2685619--2685732 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 58
2685609 GGGCATTTAA
* *
2685619 GTGATGTTTTGAACTAGGCTTTAAAGTCTTTGGTGCGAGCTATATGCTCAAATCATTG
1 GTGATGTTTTGAACTAGGCTTTAAAGTCTTTGGTGCGAGCTACATGCCCAAATCATTG
* * * * * *
2685677 GTGATGTTTT-AAGTAGGCTTTAAGGTCTTTGGTGTGGGTTACATGCCCGAATCATT
1 GTGATGTTTTGAACTAGGCTTTAAAGTCTTTGGTGCGAGCTACATGCCCAAATCATT
2685733 TTAATGGATA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
57 38 0.79
58 10 0.21
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (58 bp):
GTGATGTTTTGAACTAGGCTTTAAAGTCTTTGGTGCGAGCTACATGCCCAAATCATTG
Found at i:2686900 original size:59 final size:59
Alignment explanation
Indices: 2686828--2686946 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
2686818 AAAATAAATC
* *
2686828 TGTCATATATTTTCTAAAGAATAAT-ACCCAAGCTTTGGATAAATGTATCTAACTTCTAT
1 TGTCATATATTTTCCAAAGAAT-ATCACCCAAACTTTGGATAAATGTATCTAACTTCTAT
* *
2686887 TGTCATATATTTTCCAAAGAATATCACTCAAACTTTGGATAAATGTATTTAACTTCTAT
1 TGTCATATATTTTCCAAAGAATATCACCCAAACTTTGGATAAATGTATCTAACTTCTAT
2686946 T
1 T
2686947 TTTACTTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 2 0.04
59 53 0.96
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (59 bp):
TGTCATATATTTTCCAAAGAATATCACCCAAACTTTGGATAAATGTATCTAACTTCTAT
Found at i:2693774 original size:23 final size:23
Alignment explanation
Indices: 2693744--2693790 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2693734 TTAATATATC
2693744 TTGCTTAGCTATTGTGGATATTG
1 TTGCTTAGCTATTGTGGATATTG
2693767 TTGCTTAGCTATTGTGGATATTG
1 TTGCTTAGCTATTGTGGATATTG
2693790 T
1 T
2693791 ATATCTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.49
Consensus pattern (23 bp):
TTGCTTAGCTATTGTGGATATTG
Found at i:2695790 original size:36 final size:35
Alignment explanation
Indices: 2695743--2695828 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 35
2695733 AAATTTGATG
2695743 AATATTAATATTTAAC-TTAAAAT-ATTAAAAAATAAA
1 AATATTAATATTTAACTTTAAAATAATT---AAATAAA
* *
2695779 AATATTAATATTTAACTTTAAAATAATTAATTTAA
1 AATATTAATATTTAACTTTAAAATAATTAAATAAA
2695814 AATATTAATATTTAA
1 AATATTAATATTTAA
2695829 ATTATACAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 20 0.43
36 16 0.35
37 7 0.15
38 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (35 bp):
AATATTAATATTTAACTTTAAAATAATTAAATAAA
Found at i:2695799 original size:29 final size:33
Alignment explanation
Indices: 2695743--2695828 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 33
2695733 AAATTTGATG
* **
2695743 AATATTAATATTTAACTTAAAATATTAAAAAATAAA
1 AATATTAATATTTAACTTTAAA-A-TAATTAAT-AA
2695779 AATATTAATATTTAACTTTAAAATAATTAATTTAA
1 AATATTAATATTTAACTTTAAAATAATTAA--TAA
2695814 AATATTAATATTTAA
1 AATATTAATATTTAA
2695829 ATTATACAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
34 5 0.11
35 18 0.40
36 22 0.49
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATTAATATTTAACTTTAAAATAATTAATAA
Found at i:2695830 original size:14 final size:14
Alignment explanation
Indices: 2695785--2695822 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2695775 TAAAAATATT
*
2695785 AATATTTAACTTTAA
1 AATAATTAA-TTTAA
2695800 AATAATTAATTTAA
1 AATAATTAATTTAA
2695814 AAT-ATTAAT
1 AATAATTAAT
2695823 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATTAATTTAA
Found at i:2696391 original size:32 final size:33
Alignment explanation
Indices: 2696325--2696395 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
2696315 CCACCATGAT
*
2696325 AGAAAATATTTTTCATAAAGTGATCCAAACAAC
1 AGAAAATATTTTTCATAAACTGATCCAAACAAC
* *
2696358 AGAAAATATTTTT-A-ACAACTTATCCAAATAAC
1 AGAAAATATTTTTCATA-AACTGATCCAAACAAC
2696390 AGAAAA
1 AGAAAA
2696396 CATTGAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 20 0.59
33 13 0.38
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (33 bp):
AGAAAATATTTTTCATAAACTGATCCAAACAAC
Found at i:2696443 original size:30 final size:30
Alignment explanation
Indices: 2696404--2696466 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2696394 AACATTGAAT
*
2696404 TTTCTTGTAAAATATTTTACATAGAAAAAA
1 TTTCCTGTAAAATATTTTACATAGAAAAAA
*
2696434 TTTCCTGTAAAATATTTTATATAGAAAAAA
1 TTTCCTGTAAAATATTTTACATAGAAAAAA
2696464 TTT
1 TTT
2696467 TCTGCCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (30 bp):
TTTCCTGTAAAATATTTTACATAGAAAAAA
Found at i:2706025 original size:20 final size:21
Alignment explanation
Indices: 2706000--2706038 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2705990 CAACACCTCA
2706000 TTTAACTAACTAA-ACCTTGG
1 TTTAACTAACTAAGACCTTGG
*
2706020 TTTAACTAATTAAGACCTT
1 TTTAACTAACTAAGACCTT
2706039 TTTGTCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTAACTAACTAAGACCTTGG
Found at i:2706459 original size:29 final size:29
Alignment explanation
Indices: 2706423--2706479 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2706413 AAATATTTAT
2706423 AATATCCATAGTAACTAAACAAGATATAC
1 AATATCCATAGTAACTAAACAAGATATAC
* *
2706452 AATATCCATAGTAGCTAAGCAAGATATA
1 AATATCCATAGTAACTAAACAAGATATA
2706480 TTGAATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.25
Consensus pattern (29 bp):
AATATCCATAGTAACTAAACAAGATATAC
Found at i:2716833 original size:36 final size:36
Alignment explanation
Indices: 2716768--2716841 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
2716758 GATGTGGGTA
* ** *
2716768 GACTCTGTTGTTTGTCGTGGCAATGGGGCATGATAT
1 GACTCTGTTGTTTGTCGTAGCAACAGGGCATGACAT
* *
2716804 GACTCTGTTGTTTGTTGTAGCACCAGGGCATGACAT
1 GACTCTGTTGTTTGTCGTAGCAACAGGGCATGACAT
2716840 GA
1 GA
2716842 TATTTTATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (36 bp):
GACTCTGTTGTTTGTCGTAGCAACAGGGCATGACAT
Found at i:2718386 original size:19 final size:18
Alignment explanation
Indices: 2718347--2718401 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
2718337 TTGAAACCAA
*
2718347 AAAGAAGG-AAGAAAGGAG
1 AAAGAAGGAAAGAAA-AAG
2718365 AAAGAAGGAAAGAAAAATG
1 AAAGAAGGAAAGAAAAA-G
*
2718384 AAAGAGAAGAAAGAAAAA
1 AAAGA-AGGAAAGAAAAA
2718402 AAGCTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.28
19 12 0.38
20 11 0.34
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (18 bp):
AAAGAAGGAAAGAAAAAG
Found at i:2719828 original size:25 final size:25
Alignment explanation
Indices: 2719794--2719848 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2719784 TCTGTGATAT
* *
2719794 ATATATGTGGCAAGGCCATGGGTTG
1 ATATATGTGGCAAGGCCAAGAGTTG
*
2719819 ATATATGTGGCTAGGCCAAGAGTTG
1 ATATATGTGGCAAGGCCAAGAGTTG
2719844 ATATA
1 ATATA
2719849 CATGGTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (25 bp):
ATATATGTGGCAAGGCCAAGAGTTG
Found at i:2725431 original size:26 final size:26
Alignment explanation
Indices: 2725395--2725445 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2725385 GGATTGAGAG
*
2725395 AAGGATCACAGAGAGTTAAGTGACTC
1 AAGGATCACAGAGAGTCAAGTGACTC
2725421 AAGGATCACAGAGAGTCAAGTGACT
1 AAGGATCACAGAGAGTCAAGTGACT
2725446 TGAGATAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (26 bp):
AAGGATCACAGAGAGTCAAGTGACTC
Found at i:2726505 original size:21 final size:21
Alignment explanation
Indices: 2726476--2726518 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2726466 AAGTGATTAA
2726476 TTTAAGTTATTTTAGTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
* *
2726497 TTTAGGTTATTTTATTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
2726518 T
1 T
2726519 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTAAGTTATTTTAGTTAAAT
Found at i:2727075 original size:21 final size:22
Alignment explanation
Indices: 2727042--2727099 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
2727032 CAGAGAGCTC
*
2727042 AGCGCTGCAGCGCTGGAGAAGT
1 AGCGCCGCAGCGCTGGAGAAGT
* *
2727064 AGCG-CGTAGCGCTAGAGAAGT
1 AGCGCCGCAGCGCTGGAGAAGT
2727085 AGCGCCGCAGCGCTG
1 AGCGCCGCAGCGCTG
2727100 CGCGACTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.22, C:0.26, G:0.40, T:0.12
Consensus pattern (22 bp):
AGCGCCGCAGCGCTGGAGAAGT
Found at i:2727236 original size:10 final size:12
Alignment explanation
Indices: 2727194--2727230 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2727184 AGAGATTTTT
2727194 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2727206 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2727218 GAGGCAGCAAGA
1 GAGGCAGCAAGA
2727230 G
1 G
2727231 GCAGCAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:2728784 original size:30 final size:31
Alignment explanation
Indices: 2728726--2728784 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
2728716 GAATTGGAAC
* *
2728726 TTGATATTTGTTTTGAACTTTGGATTTGGTG
1 TTGATATTTATTTTGAACTTTAGATTTGGTG
2728757 TTGATA-TTATTTTG-ACTTTAGACTTTGG
1 TTGATATTTATTTTGAACTTTAGA-TTTGG
2728785 ATTTGGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 12 0.48
31 6 0.24
ACGTcount: A:0.19, C:0.05, G:0.22, T:0.54
Consensus pattern (31 bp):
TTGATATTTATTTTGAACTTTAGATTTGGTG
Found at i:2735811 original size:155 final size:155
Alignment explanation
Indices: 2735568--2735887 Score: 502
Period size: 155 Copynumber: 2.1 Consensus size: 155
2735558 AATAGTGGAG
2735568 AATCCTAAGCTCAGCATTCTTAATCTCACTAACATAGCTCTTAAAGGGAAACTTCTCCTTTTTCC
1 AATCCTAAGCTCAGCATTCTTAATCTCACTAACATAGCTCTTAAAGGGAAACTTCTCCTTTTTCC
2735633 TAGTTACAATCTCCCAAAAATGGTTTGGATTATATTTCTC-AGTCATTTTGTACTT-TCTTATTT
66 TAGTTACAATCTCCCAAAAATGGTTTGGATTATATTTCTCAAG-CATTTTGTA-TTCTCTTATTT
* *
2735696 CAAATTCTGTTTTTAAAAATTCTCCTA
129 CAAATTCTATATTTAAAAATTCTCCTA
* * * *
2735723 AATCCTAAGCTGAGCATTCTTAATCTCACTAGCATAGCTCTTAAAGGGAACCTTTTCCCTTTTTC
1 AATCCTAAGCTCAGCATTCTTAATCTCACTAACATAGCTCTTAAAGGGAAACTTCT-CCTTTTTC
*
2735788 C-AGTTACAATCTCCCAAAGATGGTTTGGATTATATTTCTCAAGCATTTTGTATTCTCTTATTTC
65 CTAGTTACAATCTCCCAAAAATGGTTTGGATTATATTTCTCAAGCATTTTGTATTCTCTTATTTC
** *
2735852 AAATTCTATATTTAGGAATTCTCTTA
130 AAATTCTATATTTAAAAATTCTCCTA
2735878 AATCCTAAGC
1 AATCCTAAGC
2735888 ATTAATTTGA
Statistics
Matches: 152, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
154 2 0.01
155 139 0.91
156 11 0.07
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (155 bp):
AATCCTAAGCTCAGCATTCTTAATCTCACTAACATAGCTCTTAAAGGGAAACTTCTCCTTTTTCC
TAGTTACAATCTCCCAAAAATGGTTTGGATTATATTTCTCAAGCATTTTGTATTCTCTTATTTCA
AATTCTATATTTAAAAATTCTCCTA
Found at i:2736127 original size:16 final size:18
Alignment explanation
Indices: 2736098--2736130 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2736088 TCCCGATGAA
2736098 TCAATAAAACTTTCCCAG
1 TCAATAAAACTTTCCCAG
2736116 TCAA-AAAA-TTTCCCA
1 TCAATAAAACTTTCCCA
2736131 CAAGATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.27
Consensus pattern (18 bp):
TCAATAAAACTTTCCCAG
Found at i:2736309 original size:21 final size:21
Alignment explanation
Indices: 2736283--2736325 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2736273 TTACTTTTTT
2736283 TTTTCTGCTGAAGAGTCCTTG
1 TTTTCTGCTGAAGAGTCCTTG
2736304 TTTTCTGCTGAAGAGTCCTTG
1 TTTTCTGCTGAAGAGTCCTTG
2736325 T
1 T
2736326 ATCTATCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (21 bp):
TTTTCTGCTGAAGAGTCCTTG
Found at i:2746137 original size:261 final size:261
Alignment explanation
Indices: 2745673--2746202 Score: 1015
Period size: 261 Copynumber: 2.0 Consensus size: 261
2745663 GAATGAGGAA
2745673 TGTCTTGTTATCATCAAAATTATATGAAGTCAACACATACATGTTCTAAGTTAATAACACAAGAA
1 TGTCTTGTTATCATCAAAATTATATGAAGTCAACACATACATGTTCTAAGTTAATAACACAAGAA
2745738 AAAGGTAAATTAAATTATTCATTGGTGATGAAAATCATTGAAGGGAGTTGATCATTGACCTTGTC
66 AAAGGTAAATTAAATTATTCATTGGTGATGAAAATCATTGAAGGGAGTTGATCATTGACCTTGTC
2745803 TTATGATTCATGGGAAAATTGAAATCTTCAATAGCAATGAGCTTGATGAAAATTCAACAAAGGGT
131 TTATGATTCATGGGAAAATTGAAATCTTCAATAGCAATGAGCTTGATGAAAATTCAACAAAGGGT
*
2745868 GTTCCTTTTGAATGGTAATATTTTTCAAACACCATATTGGTCATGTTGTTGATTATGTCTAGCAA
196 GTTCCTTTTGAATGGTAATATTTTTCAAACACCATATTGATCATGTTGTTGATTATGTCTAGCAA
2745933 T
261 T
*
2745934 TGTCTTGTTATCATCAAAATTATATGAAGTCAACACATACATGTTCTAAGTTAATAGCACAAGAA
1 TGTCTTGTTATCATCAAAATTATATGAAGTCAACACATACATGTTCTAAGTTAATAACACAAGAA
*
2745999 AAAGGTAATTTAAATTATTCATTGGTGATGAAAATCATTGAAGGGAGTTGATCATTGACCTTGTC
66 AAAGGTAAATTAAATTATTCATTGGTGATGAAAATCATTGAAGGGAGTTGATCATTGACCTTGTC
*
2746064 TTATGATTCATGGGAAAATTGAAATCTTCAATAGCAATGAGCTTGATGAAAATTCAACAAATGGT
131 TTATGATTCATGGGAAAATTGAAATCTTCAATAGCAATGAGCTTGATGAAAATTCAACAAAGGGT
2746129 GTTCCTTTTGAATGGTAATATTTTTCAAACACCATATTGATCATGTTGTTGATTATGTCTAGCAA
196 GTTCCTTTTGAATGGTAATATTTTTCAAACACCATATTGATCATGTTGTTGATTATGTCTAGCAA
2746194 T
261 T
2746195 TGTGCTTG
1 TGT-CTTG
2746203 AATGATGAAT
Statistics
Matches: 264, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
261 260 0.98
262 4 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (261 bp):
TGTCTTGTTATCATCAAAATTATATGAAGTCAACACATACATGTTCTAAGTTAATAACACAAGAA
AAAGGTAAATTAAATTATTCATTGGTGATGAAAATCATTGAAGGGAGTTGATCATTGACCTTGTC
TTATGATTCATGGGAAAATTGAAATCTTCAATAGCAATGAGCTTGATGAAAATTCAACAAAGGGT
GTTCCTTTTGAATGGTAATATTTTTCAAACACCATATTGATCATGTTGTTGATTATGTCTAGCAA
T
Found at i:2765133 original size:58 final size:58
Alignment explanation
Indices: 2765043--2765161 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
2765033 GGAGTGGTGA
2765043 TGCTCCCTTGGGCACTATGGCCTTTAGTCTTGCAAGGTCACGGTGTTACTCGTTATGC
1 TGCTCCCTTGGGCACTATGGCCTTTAGTCTTGCAAGGTCACGGTGTTACTCGTTATGC
*
2765101 TGCTCCCTTGGGCACTATGGCCTTTAGTCTTGCAAGGTCGCGGTGTTACTCGTTATGC
1 TGCTCCCTTGGGCACTATGGCCTTTAGTCTTGCAAGGTCACGGTGTTACTCGTTATGC
2765159 TGC
1 TGC
2765162 CTTTGTGCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.13, C:0.26, G:0.27, T:0.34
Consensus pattern (58 bp):
TGCTCCCTTGGGCACTATGGCCTTTAGTCTTGCAAGGTCACGGTGTTACTCGTTATGC
Found at i:2783237 original size:21 final size:22
Alignment explanation
Indices: 2783202--2783245 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2783192 CTCTTAAAGT
2783202 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
2783224 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
2783245 A
1 A
2783246 TTAATCGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:2783458 original size:19 final size:20
Alignment explanation
Indices: 2783434--2783477 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2783424 TAGTTTGAAA
2783434 GTTAAAAATGAC-TTAATCG
1 GTTAAAAATGACTTTAATCG
* *
2783453 GTTAAAGATGCCTTTAATCG
1 GTTAAAAATGACTTTAATCG
2783473 GTTAA
1 GTTAA
2783478 TGAAGCACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
GTTAAAAATGACTTTAATCG
Found at i:2787153 original size:22 final size:21
Alignment explanation
Indices: 2787139--2787183 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2787129 TTTATTCTTC
2787139 TCATTTTTCTTTTTTCATTTT
1 TCATTTTTCTTTTTTCATTTT
* *
2787160 TCCTTTTTACTTTTTTCACTTT
1 TCATTTTT-CTTTTTTCATTTT
2787182 TC
1 TC
2787184 TTCATGACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
TCATTTTTCTTTTTTCATTTT
Found at i:2787156 original size:14 final size:15
Alignment explanation
Indices: 2787139--2787188 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2787129 TTTATTCTTC
2787139 TCATTTTT-CTTTTT
1 TCATTTTTCCTTTTT
2787153 TCATTTTTCCTTTTT
1 TCATTTTTCCTTTTT
* *
2787168 ACTTTTTTCACTTTTCT
1 TCATTTTTC-CTTTT-T
2787185 TCAT
1 TCAT
2787189 GACTGCAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 13 0.45
16 5 0.17
17 3 0.10
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTTCCTTTTT
Found at i:2790738 original size:28 final size:28
Alignment explanation
Indices: 2790690--2790743 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2790680 GATTGAAACT
2790690 TTATCTATTTTTAGTGCAATTTATTTTC
1 TTATCTATTTTTAGTGCAATTTATTTTC
* *
2790718 TTATTTATGTTTT-GTGTAATTTATTT
1 TTATCTAT-TTTTAGTGCAATTTATTT
2790744 GTTTTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.20, C:0.06, G:0.09, T:0.65
Consensus pattern (28 bp):
TTATCTATTTTTAGTGCAATTTATTTTC
Found at i:2800459 original size:25 final size:25
Alignment explanation
Indices: 2800431--2800490 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2800421 GTGATCACAA
*
2800431 CCACATATATCAACTTA-TGGCCTAG
1 CCACATATATCAAC-CAGTGGCCTAG
* *
2800456 CCACAAATATCAACCAGTGGCCTTG
1 CCACATATATCAACCAGTGGCCTAG
2800481 CCACATATAT
1 CCACATATAT
2800491 ATCACAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCAGTGGCCTAG
Found at i:2809324 original size:23 final size:22
Alignment explanation
Indices: 2809268--2809324 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2809258 AATGAATATA
*
2809268 TATATATATATATATATATTTGTT
1 TATATACAT-TAT-TATATTTGTT
*
2809292 TATCTACATTATTATATTTGGTT
1 TATATACATTATTATATTT-GTT
*
2809315 TATATGCATT
1 TATATACATT
2809325 CCCTCATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 7 0.25
23 14 0.50
24 7 0.25
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (22 bp):
TATATACATTATTATATTTGTT
Found at i:2821024 original size:74 final size:74
Alignment explanation
Indices: 2820891--2821073 Score: 262
Period size: 74 Copynumber: 2.5 Consensus size: 74
2820881 AGAAAACACA
* * * *
2820891 TAATCAACTATGAAGCATGGTTAGTCAACTAAGAGCTCATTGCTAGAGACTTCAATTACAAGAGA
1 TAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTGCTAGAGAATTCAATTACAAGACA
*
2820956 GAG-AGAACT
66 AAGAAG-ACT
**
2820965 TAATTGACTGAA-AAGCATGGTTAGTCAACTAAGAGCTCACTGCTAGAGAATTCAATTACAAGAC
1 TAATCAACT-AAGAAGCATGGTTAGTCAACTAAGAGCTCACTGCTAGAGAATTCAATTACAAGAC
2821029 AAAGAAGACT
65 AAAGAAGACT
*
2821039 TAATCAACTAAGAAGTATGGTTAGTCAACTAAGAG
1 TAATCAACTAAGAAGCATGGTTAGTCAACTAAGAG
2821074 TACTCTGTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
73 2 0.02
74 91 0.95
75 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (74 bp):
TAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTGCTAGAGAATTCAATTACAAGACA
AAGAAGACT
Found at i:2829945 original size:74 final size:74
Alignment explanation
Indices: 2829760--2829937 Score: 232
Period size: 74 Copynumber: 2.4 Consensus size: 74
2829750 GACGTAGTGC
* ** ** *
2829760 ACTAAGAAGTGTGGTTAGTCAACTAAGAGCTCACTACCAGAGACCTCAATTACAAGACAAAAAGA
1 ACTAAGAAGTATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAATTTAATTACAAGACAAAAAGA
*
2829825 ACTTAATCG
66 ACTTAATCA
* * * *
2829834 ACTAAAAAGTATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAATTTAATTACTAGGCAGAGAAG
1 ACTAAGAAGTATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAATTTAATTACAAGACA-AAAAG
2829899 -ACTTAATCA
65 AACTTAATCA
*
2829908 ACTAAGAAGTATGATTAGTCAACTAAGAGC
1 ACTAAGAAGTATGGTTAGTCAACTAAGAGC
2829938 ACTCTGTCCG
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 86 0.96
75 4 0.04
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (74 bp):
ACTAAGAAGTATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAATTTAATTACAAGACAAAAAGA
ACTTAATCA
Found at i:2834843 original size:22 final size:22
Alignment explanation
Indices: 2834805--2834847 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2834795 GAGTTATTTG
2834805 AGCTTAATTTTGATAATAATGT
1 AGCTTAATTTTGATAATAATGT
*
2834827 AGCTTAGTTCTTG-TAATAATG
1 AGCTTAATT-TTGATAATAATG
2834848 CATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (22 bp):
AGCTTAATTTTGATAATAATGT
Found at i:2845301 original size:2 final size:2
Alignment explanation
Indices: 2845296--2845320 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2845286 TGTATATATA
2845296 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2845321 TTGCTTTAAG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2849098 original size:20 final size:22
Alignment explanation
Indices: 2849062--2849119 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
2849052 CAGTAACACC
* *
2849062 TTTCTTTTTTATGTC-A-ACTT
1 TTTCTTTTTTTTTTCAACACTT
2849082 TTTCTTTTTTTTTTCAACACTT
1 TTTCTTTTTTTTTTCAACACTT
2849104 TATTCTTTTTCTTTTT
1 T-TTCTTTTT-TTTTT
2849120 TTTTCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.41
21 1 0.03
22 5 0.16
23 8 0.25
24 5 0.16
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTTTTTTTCAACACTT
Found at i:2851901 original size:26 final size:27
Alignment explanation
Indices: 2851865--2851920 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2851855 GAAAGGGTTG
2851865 AGTTATT-AAAAAATTCAATTATGCTT
1 AGTTATTAAAAAAATTCAATTATGCTT
2851891 AGTTATTAAAAAAATTCAATTATGCTT
1 AGTTATTAAAAAAATTCAATTATGCTT
2851918 AGT
1 AGT
2851921 GTTCACTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (27 bp):
AGTTATTAAAAAAATTCAATTATGCTT
Done.