Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 5 of 161
Found at i:1414503 original size:32 final size:32
Alignment explanation
Indices: 1414467--1414528 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1414457 CTAATTTAAT
1414467 TCTTAATAGTTTGTTATATCAAAATATTTTCA
1 TCTTAATAGTTTGTTATATCAAAATATTTTCA
*
1414499 TCTTAATAGTTTGTTATATCAAACTATTTT
1 TCTTAATAGTTTGTTATATCAAAATATTTT
1414529 GAAAATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (32 bp):
TCTTAATAGTTTGTTATATCAAAATATTTTCA
Found at i:1417489 original size:6 final size:6
Alignment explanation
Indices: 1417473--1417504 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1417463 ATTACTTGGT
1417473 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA T
1417505 GGTCTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:1423160 original size:19 final size:20
Alignment explanation
Indices: 1423131--1423190 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
1423121 TTGATTATAT
1423131 TATTGTTTTATCATTT-TAAA
1 TATT-TTTTATCATTTATAAA
*
1423151 TATTTTTTATTATTTATAAA
1 TATTTTTTATCATTTATAAA
* *
1423171 -ATTTATCAT-ATTTATAAA
1 TATTTTTTATCATTTATAAA
1423189 TA
1 TA
1423191 AGAATCCTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 9 0.26
19 18 0.51
20 8 0.23
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTTTATCATTTATAAA
Found at i:1423683 original size:281 final size:276
Alignment explanation
Indices: 1423154--1423695 Score: 666
Period size: 275 Copynumber: 1.9 Consensus size: 276
1423144 TTTTAAATAT
* ** *
1423154 TTTTTATTATTTATAAAATTTATCATATTTATAAATAAGAATCCTGATTCTTTTAAAACACTTCT
1 TTTTTATTATTTATAAAATTTATCACAGGTATAAAAAAGAATCCTGATTCTTTTAAAACACTTCT
* * *
1423219 GTTAAATGAATTTATATAATAATTTAAAAAAGGTTAAAATTAATGTAGAAATATTTTATCTTTAA
66 GTTAAATGAATTTATATAATAATATAAAAAAGGTTAAAATTAATGTACAAATACTTTATCTTTAA
* * * *
1423284 AGTATTATGTTTCATTAATAAAATAGTGAAAAAATATTACTTTAGTTTTAAATATTAAAATTTAA
131 AGTATTATGTTTCATTAACAAAAAAGTAAAAAAATATTACTTTAGTTTTAAATATCAAAATTTAA
* *
1423349 TTATTTATATAATAAATAACTTTATATTTCATGTGTATAATTTTATAAATAATAC-TTTATATAA
196 TTATTTATATAATAAATAACTTTATATTTCATATATATAATTTTATAAATAATACATTTATATAA
1423413 TTTATTATATAAATGG
261 TTTATTATATAAATGG
* ** *
1423429 TTTTTATTATTTACT-AGATTTATCACAGGTATAAAAAAGAATTTTGATTCTTTTAAAACACTTT
1 TTTTTATTATTTA-TAAAATTTATCACAGGTATAAAAAAGAATCCTGATTCTTTTAAAACACTTC
* * * ** *
1423493 TGTTTAATGCATTTATATGACAATAA-ATAAAAAA-GTT-AATTTTTTTTATCAAATTACTTTAT
65 TGTTAAATGAATTTATAT---AATAATATAAAAAAGGTTAAAATTAATGTA-CAAA-TACTTTAT
* * *
1423555 -TTTAAAGTATTTTTTTTCCATTAACCAAAAAAGTAAAAAAAATAATTCTGCTTTAGTTTTAAA-
125 CTTTAAAGTATTATGTTT-CATTAA-CAAAAAAGT-AAAAAAAT-A-T-TACTTTAGTTTTAAAT
* *
1423618 ATCAAAATTTAATTATTTATATAATAAATATCTTTATATTTCATATATATGATTTTATAAATAAT
184 ATCAAAATTTAATTATTTATATAATAAATAACTTTATATTTCATATATATAATTTTATAAATAAT
*
1423683 ACATTTATGTAAT
249 ACATTTATATAAT
1423696 ATAACAATTA
Statistics
Matches: 225, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
275 77 0.34
276 22 0.10
277 20 0.09
278 12 0.05
279 7 0.03
280 1 0.00
281 63 0.28
282 23 0.10
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (276 bp):
TTTTTATTATTTATAAAATTTATCACAGGTATAAAAAAGAATCCTGATTCTTTTAAAACACTTCT
GTTAAATGAATTTATATAATAATATAAAAAAGGTTAAAATTAATGTACAAATACTTTATCTTTAA
AGTATTATGTTTCATTAACAAAAAAGTAAAAAAATATTACTTTAGTTTTAAATATCAAAATTTAA
TTATTTATATAATAAATAACTTTATATTTCATATATATAATTTTATAAATAATACATTTATATAA
TTTATTATATAAATGG
Found at i:1427861 original size:17 final size:17
Alignment explanation
Indices: 1427835--1427871 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1427825 TGAATTAGTA
1427835 AACCACCATATTACTGC
1 AACCACCATATTACTGC
*
1427852 AACCATCATATTACTGC
1 AACCACCATATTACTGC
1427869 AAC
1 AAC
1427872 ATTCTCCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.32, G:0.05, T:0.24
Consensus pattern (17 bp):
AACCACCATATTACTGC
Found at i:1430814 original size:23 final size:22
Alignment explanation
Indices: 1430762--1430814 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1430752 TCCACGTCTT
*
1430762 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
1430784 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
1430807 TTTCTTTT
1 TTTCTTTT
1430815 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:1439246 original size:25 final size:26
Alignment explanation
Indices: 1439211--1439267 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1439201 GAAGCTCCGG
*
1439211 AGAGCCGTTAA-CGGGAAGCTCACAA
1 AGAGCCGTTAATCGAGAAGCTCACAA
*
1439236 AGAGCCTTTAATCGAGAAGCTCACAA
1 AGAGCCGTTAATCGAGAAGCTCACAA
1439262 AGAGCC
1 AGAGCC
1439268 ATATATCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.14
Consensus pattern (26 bp):
AGAGCCGTTAATCGAGAAGCTCACAA
Found at i:1439363 original size:24 final size:24
Alignment explanation
Indices: 1439330--1439406 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
1439320 CACAATCGAT
*
1439330 CGGGATGCTCCGAAGAGCTATTAA
1 CGGGAAGCTCCGAAGAGCTATTAA
* *
1439354 CGGGAAGCT-CGCAAGAACCATATAA
1 CGGGAAGCTCCG-AAGAGCTAT-TAA
* *
1439379 CGGGAAGCTCATG-AGAGCTAATAA
1 CGGGAAGCTC-CGAAGAGCTATTAA
1439403 CGGG
1 CGGG
1439407 GCGCTCTCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.05
24 22 0.52
25 17 0.40
27 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.16
Consensus pattern (24 bp):
CGGGAAGCTCCGAAGAGCTATTAA
Found at i:1439743 original size:21 final size:20
Alignment explanation
Indices: 1439719--1439770 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1439709 TATACGAATG
*
1439719 AATTTAACATAAATTTAATAC
1 AATTT-ACATAAATTCAATAC
* *
1439740 AATTTACATTCAATTCAATCC
1 AATTTACA-TAAATTCAATAC
1439761 AATTTACATA
1 AATTTACATA
1439771 TTAGGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTACATAAATTCAATAC
Found at i:1441335 original size:74 final size:74
Alignment explanation
Indices: 1441257--1441426 Score: 216
Period size: 74 Copynumber: 2.3 Consensus size: 74
1441247 TGCGTGTTTG
* * *
1441257 GCTAACCTCACTAGATTATGCCTTAAAGGTTGATCTGGTGAAACTCCCTAGATCATGCCATAT-G
1 GCTAACCTCCCTAGATTATGCCTTAAAGATGGATCTGGTGAAACTCCCTAGATCATGCCATATAG
1441321 AGCGAGTCAA
66 -GCGAGTCAA
* * * * *
1441331 GCTAACCTCCCTGGATTATGCCTTAAAGATGGATCTGGTGAACCTCCCTGGGTTATGCCATATAG
1 GCTAACCTCCCTAGATTATGCCTTAAAGATGGATCTGGTGAAACTCCCTAGATCATGCCATATAG
**
1441396 GCGAGTTTA
66 GCGAGTCAA
* *
1441405 GCTGACCTCCCTAGATCATGCC
1 GCTAACCTCCCTAGATTATGCC
1441427 ATATAGGTGA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 81 0.99
75 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (74 bp):
GCTAACCTCCCTAGATTATGCCTTAAAGATGGATCTGGTGAAACTCCCTAGATCATGCCATATAG
GCGAGTCAA
Found at i:1441457 original size:111 final size:111
Alignment explanation
Indices: 1441300--1441550 Score: 292
Period size: 111 Copynumber: 2.3 Consensus size: 111
1441290 TCTGGTGAAA
* *
1441300 CTCCCTAGATCATGCCATAT-GAGCGAGTC-AAGCTAACCTCCCTGGATTATGCCTTAAAGATGG
1 CTCCCTAGATCATGCCATATAG-GTGAGTCTAAGCTAACCTCACTGGATTATGCCTTAAAGATGG
* * * ** **
1441363 ATCTGGTGAACCTCCCTGGGTTATGCCATATAGGCGAGTTTAGCTGAC
65 ATCTGGCGAACCTCCCTGGATCAT-CCATATAAACGAGTCCAGCTGAC
* * * *
1441411 CTCCCTAGATCATGCCATATAGGTGAGTCTTA-CTGACCTCATTGGATTATGCCTTAAAGGTGGA
1 CTCCCTAGATCATGCCATATAGGTGAGTCTAAGCTAACCTCACTGGATTATGCCTTAAAGATGGA
* * * *
1441475 TCTGGCGAACCTCCCTGGATCATCCTTGTAAATGAGTCCGGCTGAC
66 TCTGGCGAACCTCCCTGGATCATCCATATAAACGAGTCCAGCTGAC
* *
1441521 CTCCCTGGACCATGCCATATAGGTGAGTCT
1 CTCCCTAGATCATGCCATATAGGTGAGTCT
1441551 GGCAGACTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
110 43 0.36
111 74 0.62
112 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (111 bp):
CTCCCTAGATCATGCCATATAGGTGAGTCTAAGCTAACCTCACTGGATTATGCCTTAAAGATGGA
TCTGGCGAACCTCCCTGGATCATCCATATAAACGAGTCCAGCTGAC
Found at i:1441494 original size:37 final size:38
Alignment explanation
Indices: 1441255--1441494 Score: 120
Period size: 37 Copynumber: 6.5 Consensus size: 38
1441245 CATGCGTGTT
* * * * *
1441255 TGGCTAACCTCACTAGATTATGCCTTAAAGGTTGA-TC
1 TGGCGAACCTCCCTGGATTATGCCATAAAGGTCGAGTC
* * * * *
1441292 TGGTGAAACTCCCTAGATCATGCCAT-ATGAG-CGAGTC
1 TGGCGAACCTCCCTGGATTATGCCATAAAG-GTCGAGTC
** * * * *
1441329 AAGCTAACCTCCCTGGATTATGCCTTAAAGATGGA-TC
1 TGGCGAACCTCCCTGGATTATGCCATAAAGGTCGAGTC
* * * *
1441366 TGGTGAACCTCCCTGGGTTATGCCATATAGG-CGAGTT
1 TGGCGAACCTCCCTGGATTATGCCATAAAGGTCGAGTC
* * * *
1441403 TAGCTG-ACCTCCCTAGATCATGCCATATAGGT-GAGTC
1 TGGC-GAACCTCCCTGGATTATGCCATAAAGGTCGAGTC
** ** * *
1441440 TTACTG-ACCTCATTGGATTATGCCTTAAAGGTGGA-TC
1 TGGC-GAACCTCCCTGGATTATGCCATAAAGGTCGAGTC
1441477 TGGCGAACCTCCCTGGAT
1 TGGCGAACCTCCCTGGAT
1441495 CATCCTTGTA
Statistics
Matches: 147, Mismatches: 47, Indels: 18
0.69 0.22 0.08
Matches are distributed among these distances:
36 7 0.05
37 133 0.90
38 7 0.05
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (38 bp):
TGGCGAACCTCCCTGGATTATGCCATAAAGGTCGAGTC
Found at i:1441573 original size:110 final size:111
Alignment explanation
Indices: 1441342--1441557 Score: 272
Period size: 110 Copynumber: 2.0 Consensus size: 111
1441332 CTAACCTCCC
* * * ** **
1441342 TGGATTATGCCTTAAAGATGGATCTGGTGAACCTCCCTGGGTTATGCCATATAGGCGAGTTTAGC
1 TGGATTATGCCTTAAAGATGGATCTGGCGAACCTCCCTGGATCATGCCATATAAACGAGTCCAGC
* * *
1441407 TGACCTCCCTAGATCATGCCATATAGGTGAGTCTTACTGACCTCAT
66 TGACCTCCCTAGACCATGCCATATAGGTGAGTCTGACAGACCTCAT
* * * * *
1441453 TGGATTATGCCTTAAAGGTGGATCTGGCGAACCTCCCTGGATCAT-CCTTGTAAATGAGTCCGGC
1 TGGATTATGCCTTAAAGATGGATCTGGCGAACCTCCCTGGATCATGCCATATAAACGAGTCCAGC
* *
1441517 TGACCTCCCTGGACCATGCCATATAGGTGAGTCTGGCAGAC
66 TGACCTCCCTAGACCATGCCATATAGGTGAGTCTGACAGAC
1441558 TTTCTTGGAT
Statistics
Matches: 88, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
110 47 0.53
111 41 0.47
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (111 bp):
TGGATTATGCCTTAAAGATGGATCTGGCGAACCTCCCTGGATCATGCCATATAAACGAGTCCAGC
TGACCTCCCTAGACCATGCCATATAGGTGAGTCTGACAGACCTCAT
Found at i:1441653 original size:21 final size:23
Alignment explanation
Indices: 1441629--1441677 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1441619 CCGCAAAGTC
1441629 TCATACTAC-CCT-AAAGGGCTT
1 TCATACTACTCCTAAAAGGGCTT
* *
1441650 TCATACTACTCGTAAAAGGGTTT
1 TCATACTACTCCTAAAAGGGCTT
1441673 TCATA
1 TCATA
1441678 ACTATGTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 2 0.08
23 13 0.54
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (23 bp):
TCATACTACTCCTAAAAGGGCTT
Found at i:1444268 original size:27 final size:27
Alignment explanation
Indices: 1444230--1444299 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1444220 AAATCATTTT
1444230 TTCAGAGTTCGCCATATGTACTATTCC
1 TTCAGAGTTCGCCATATGTACTATTCC
* *
1444257 TTCAGAGTTCGCTATATGTATTATTCC
1 TTCAGAGTTCGCCATATGTACTATTCC
*
1444284 TTTAGAGTTCGCCATA
1 TTCAGAGTTCGCCATA
1444300 CATATTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (27 bp):
TTCAGAGTTCGCCATATGTACTATTCC
Found at i:1444305 original size:27 final size:27
Alignment explanation
Indices: 1444233--1444336 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
1444223 TCATTTTTTC
** * *
1444233 AGAGTTCGCCATATGTACTATTCCTTC
1 AGAGTTCGCCATACATATTATTCCTTT
* **
1444260 AGAGTTCGCTATATGTATTATTCCTTT
1 AGAGTTCGCCATACATATTATTCCTTT
*
1444287 AGAGTTCGCCATACATATTATTTCTTT
1 AGAGTTCGCCATACATATTATTCCTTT
* *
1444314 AGAGTTTAG-CACACATATTATTC
1 AGAG-TTCGCCATACATATTATTC
1444337 TCTCAATGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
27 63 0.95
28 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (27 bp):
AGAGTTCGCCATACATATTATTCCTTT
Found at i:1444538 original size:27 final size:27
Alignment explanation
Indices: 1444488--1444559 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
1444478 TTAGAACGCA
*
1444488 CCATGAAGGCATTCCTTTCTATAGATCG
1 CCATAAAGGC-TTCCTTTCTATAGATCG
*
1444516 CCATAAAGGCTTCCATTTC-ATAGATGG
1 CCATAAAGGCTTCC-TTTCTATAGATCG
* *
1444543 CCACAAAGACTTCCTTT
1 CCATAAAGGCTTCCTTT
1444560 TTCCGATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 23 0.59
28 13 0.33
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (27 bp):
CCATAAAGGCTTCCTTTCTATAGATCG
Found at i:1450696 original size:9 final size:9
Alignment explanation
Indices: 1450682--1450715 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
1450672 GATAGAGGAC
1450682 TAAAATGAA
1 TAAAATGAA
1450691 TAAAATGAA
1 TAAAATGAA
1450700 TAAAATGAA
1 TAAAATGAA
1450709 TAAAATG
1 TAAAATG
1450716 GAAAATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
TAAAATGAA
Found at i:1459164 original size:12 final size:12
Alignment explanation
Indices: 1459147--1459186 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
1459137 AAAATGGTGA
1459147 AAATGGTTATTG
1 AAATGGTTATTG
1459159 AAATGGTTATTG
1 AAATGGTTATTG
1459171 AAATGGTTATTG
1 AAATGGTTATTG
1459183 AAAT
1 AAAT
1459187 TTTTGAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (12 bp):
AAATGGTTATTG
Found at i:1460321 original size:21 final size:21
Alignment explanation
Indices: 1460297--1460338 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1460287 AATTTGAATA
1460297 AGATCTCCAAAGGTGCTGCCT
1 AGATCTCCAAAGGTGCTGCCT
*
1460318 AGATCTCCAAAGGTGTTGCCT
1 AGATCTCCAAAGGTGCTGCCT
1460339 TGCTGGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
AGATCTCCAAAGGTGCTGCCT
Found at i:1463062 original size:101 final size:102
Alignment explanation
Indices: 1462946--1463130 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
1462936 AAAGTGATGG
* *
1462946 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-C-CAGAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTCAGAATAAT-GGTCACATGTGTAGT
1463009 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* *
1463047 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTCATAGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTCAGAATAATGGTCACATGTGTAGTA
*
1463112 CTATGTGTAGGCTACTATG
66 CTATGTGCAGGCTACTATG
1463131 TGAAGCGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 37 0.48
102 34 0.44
103 6 0.08
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTCAGAATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:1463076 original size:51 final size:49
Alignment explanation
Indices: 1462943--1463128 Score: 203
Period size: 51 Copynumber: 3.7 Consensus size: 49
1462933 GTGAAAGTGA
*
1462943 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-G-T
* * * * *
1462993 AGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-T
* * * **
1463043 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTCATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT
*
1463093 AATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1463129 TGTGAAGCGG
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 42 0.37
51 70 0.62
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT
Found at i:1463377 original size:16 final size:16
Alignment explanation
Indices: 1463356--1463387 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1463346 TGATTGAAAG
*
1463356 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
1463372 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
1463388 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:1470541 original size:21 final size:21
Alignment explanation
Indices: 1470515--1470578 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
1470505 TACTCCGATA
1470515 CCCCTAAATTGCACATACGTG
1 CCCCTAAATTGCACATACGTG
* * * ** *
1470536 CCCCT-ATTTGTACTTTGGTA
1 CCCCTAAATTGCACATACGTG
*
1470556 CCCCTAAATTACACATACGTG
1 CCCCTAAATTGCACATACGTG
1470577 CC
1 CC
1470579 ACTGTTTGTA
Statistics
Matches: 29, Mismatches: 13, Indels: 2
0.66 0.30 0.05
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (21 bp):
CCCCTAAATTGCACATACGTG
Found at i:1470574 original size:123 final size:124
Alignment explanation
Indices: 1470312--1470741 Score: 417
Period size: 123 Copynumber: 3.5 Consensus size: 124
1470302 GTTAATTATT
* * * * * * * * *
1470312 CCCTGAATCGCACATACATG-CCTTTTTTATACTTCGAAACCCCTAAAATT-CACATATGTACCC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCT-GAATTGCACATACGTGCCC
* * * * * * *
1470375 -CTATTTGTATTTCAATACCCCTGAATTGCACATATGTGCCCCTATTTGTATTTTAGTAC
65 ACTATTTGTACTCCGATACCCCTAAATTGCACATACGTGCCCCTATTTGTACTTTGGTAC
* *
1470434 CCTTGAATTGGGA-ATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGTGCCC
1 CCCTGAATT-GCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGTGCCC
*
1470498 A-TATTTTTACTCCGATACCCCTAAATTGCACATACGTGCCCCTATTTGTACTTTGGTAC
65 ACTATTTGTACTCCGATACCCCTAAATTGCACATACGTGCCCCTATTTGTACTTTGGTAC
* * * *
1470557 CCCTAAATTACACATACGTGCCACTGTTTGTACTT-TAGTACCCCTGAATTGCACATACGTG-CC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGA-TACCCCTGAATTGCACATACGTGCCC
* ** * * * * * * *
1470620 ACTGTTTGTACTTTGGTACCCTTTAATTGCACATACATGACACT-GTTGTACTTTGGTAC
65 ACTATTTGTACTCCGATACCCCTAAATTGCACATACGTGCCCCTATTTGTACTTTGGTAC
* * * * * * *
1470679 CCCTGAATTGCACATATGTTCCCCTATTTGTATTTCGGTACTCTTGAATTGCACATACGTGCC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGTGCC
1470742 TCTGTTTAGA
Statistics
Matches: 252, Mismatches: 47, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
122 85 0.34
123 167 0.66
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (124 bp):
CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGTGCCCA
CTATTTGTACTCCGATACCCCTAAATTGCACATACGTGCCCCTATTTGTACTTTGGTAC
Found at i:1470727 original size:41 final size:40
Alignment explanation
Indices: 1470358--1470741 Score: 351
Period size: 41 Copynumber: 9.4 Consensus size: 40
1470348 AAACCCCTAA
* * **
1470358 AATT-CACATATGTACCCCTATTTGTATTTCAATACCCCTG
1 AATTGCACATACGTGCCCCTATTTGTATTT-GGTACCCCTG
* * *
1470398 AATTGCACATATGTGCCCCTATTTGTATTTTAGTACCCTTG
1 AATTGCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
* * * *
1470439 AATTGGGA-ATACGTGCCCCTGTTTGTACTTCGATACCCCTG
1 AATT-GCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
* * ** * *
1470480 AATTGCACATACGTGCCCATATTTTTACTCCGATACCCCTA
1 AATTGCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
*
1470521 AATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCCTA
1 AATTGCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
* * * *
1470562 AATTACACATACGTGCCACTGTTTGTACTTTAGTACCCCTG
1 AATTGCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
* * * *
1470603 AATTGCACATACGTGCCACTGTTTGTACTTTGGTACCCTTT
1 AATTGCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
* * * *
1470644 AATTGCACATACATGACACT-GTTGTACTTTGGTACCCCTG
1 AATTGCACATACGTGCCCCTATTTGTA-TTTGGTACCCCTG
* * * *
1470684 AATTGCACATATGTTCCCCTATTTGTATTTCGGTACTCTTG
1 AATTGCACATACGTGCCCCTATTTGTATTT-GGTACCCCTG
1470725 AATTGCACATACGTGCC
1 AATTGCACATACGTGCC
1470742 TCTGTTTAGA
Statistics
Matches: 292, Mismatches: 46, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
40 41 0.14
41 246 0.84
42 5 0.02
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (40 bp):
AATTGCACATACGTGCCCCTATTTGTATTTGGTACCCCTG
Found at i:1474317 original size:19 final size:19
Alignment explanation
Indices: 1474293--1474403 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
1474283 AATCTTCAGG
1474293 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1474312 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
1474331 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1474350 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
1474369 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1474388 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
1474404 AGATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:1474343 original size:38 final size:38
Alignment explanation
Indices: 1474300--1474403 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
1474290 AGGGATATGC
1474300 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
1474338 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1474376 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
1474404 AGATATGATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:1474429 original size:22 final size:21
Alignment explanation
Indices: 1474293--1474429 Score: 114
Period size: 19 Copynumber: 6.9 Consensus size: 21
1474283 AATCTTCAGG
*
1474293 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
1474312 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
1474331 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
1474350 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
1474369 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
1474388 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
1474410 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
1474430 TTAATTTGTA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
19 79 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:1480040 original size:14 final size:15
Alignment explanation
Indices: 1480021--1480049 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1480011 AAAATAATAG
1480021 CAAAGAAAAA-AAAA
1 CAAAGAAAAAGAAAA
1480035 CAAAGAAAAAGAAAA
1 CAAAGAAAAAGAAAA
1480050 AGGAGAGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
CAAAGAAAAAGAAAA
Found at i:1481331 original size:44 final size:44
Alignment explanation
Indices: 1481281--1481514 Score: 202
Period size: 44 Copynumber: 5.3 Consensus size: 44
1481271 AATAGTAGAT
* *
1481281 CTTGCCTTCCTGCACCGACAGCGAAGCAGATTAAAGACACCAGC
1 CTTGCCTCCCTGCGCCGACAGCGAAGCAGATTAAAGACACCAGC
* ** * * * * *
1481325 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAAATAGCAGAT
1 CTTGCCTCCCTGCGCCGACAGCGAAGCAGATT-AAAGACACCAG-C
* **
1481370 CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCGCCGACAGCGAAGCAGATTAAAGACACCAGC
* ** * * * * *
1481414 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAAATAGCAGAT
1 CTTGCCTCCCTGCGCCGACAGCGAAGCAGATT-AAAGACACCAG-C
* **
1481459 CTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCGCCGACAGCGAAGCAGATTAAAGACACCAGC
1481503 CTTGCCTCCCTG
1 CTTGCCTCCCTG
1481515 GGTTGCAGTG
Statistics
Matches: 140, Mismatches: 44, Indels: 12
0.71 0.22 0.06
Matches are distributed among these distances:
43 25 0.18
44 51 0.36
45 40 0.29
46 24 0.17
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.18
Consensus pattern (44 bp):
CTTGCCTCCCTGCGCCGACAGCGAAGCAGATTAAAGACACCAGC
Found at i:1481420 original size:89 final size:89
Alignment explanation
Indices: 1481269--1481592 Score: 504
Period size: 89 Copynumber: 3.6 Consensus size: 89
1481259 CAGATCAGTG
* * **
1481269 AAAATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATTAAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1481334 CTGGGTTGCAGCGAAGCAGGTTAA
66 CTGGGTTGCAGCGAAGCAGGTTAA
1481358 AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1481423 CTGGGTTGCAGCGAAGCAGGTTAA
66 CTGGGTTGCAGCGAAGCAGGTTAA
1481447 AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* *
1481512 CTGGGTTGCAGTGGAGCAGGTTAAACAAAAAA
66 CTGGGTTGCAGCGAAGCAGGTT--------AA
* *
1481544 AAAATAGCAGATCTTGCCTTCCTGCGCCAACAGTGAAGCAGATCGAAGA
1 AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGA
1481593 TGGCGGATTT
Statistics
Matches: 219, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
89 170 0.78
97 49 0.22
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (89 bp):
AAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
CTGGGTTGCAGCGAAGCAGGTTAA
Found at i:1482354 original size:132 final size:132
Alignment explanation
Indices: 1481580--1482340 Score: 1249
Period size: 132 Copynumber: 5.8 Consensus size: 132
1481570 CCAACAGTGA
1481580 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
1481645 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTGCAAATCTTATCTCTCTAAGCAGTAGC
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGC
1481710 GG
131 GG
1481712 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG-CAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
1481776 TCTACTTACCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGC
1481841 GG
131 GG
* * * *
1481843 AGCAGAT-AAAAATGGCGGATTTTACCTCCCTGTGGTTACAGTGAAGTACATTGAATCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
1481907 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCCCCCTAAGCAGTAAC
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGC
1481972 GG
131 GG
* *
1481974 AGCAGATCCAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
1482039 TCTACTTCCCTAGG-CAACAGTGTAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
66 TCTACTTCCCT-GGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
1482103 CGG
130 CGG
* *
1482106 AGCAGATCGAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
1482171 TCTACTTCCCTGGACAACAGTGGGATAGATTAAAAATTTCAGATCTTATCTCTCTAAGCAGTAGC
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGC
1482236 GG
131 GG
* * * *
1482238 AGCAGATCGAAGATAGCCGATTTTACCTCCCTGTGGTTACAGCGGAGTACATTGAATCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
1482303 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATT
1482341 GAAAATCCTA
Statistics
Matches: 586, Mismatches: 39, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
130 45 0.08
131 154 0.26
132 385 0.66
133 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGC
GG
Found at i:1482936 original size:22 final size:22
Alignment explanation
Indices: 1482876--1482919 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
1482866 AATCTTCAGG
1482876 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAAAAGATAT
1482895 GATATGCAATCTTAAAAGATAT
1 GATATGCAATCTTAAAAGATAT
1482917 GAT
1 GAT
1482920 TTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
22 9 0.41
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
GATATGCAATCTTAAAAGATAT
Found at i:1483112 original size:44 final size:43
Alignment explanation
Indices: 1483050--1483136 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 43
1483040 AAAAAAAAAG
1483050 AAAAAAAAAGGGAGGAATAAAAAAAGAGAACGATTGGCAGTTT
1 AAAAAAAAAGGGAGGAATAAAAAAAGAGAACGATTGGCAGTTT
1483093 AAAAAAAAAGAGGAGGAATAAAAAAAGAGAACGATTGGCAGTTT
1 AAAAAAAAAG-GGAGGAATAAAAAAAGAGAACGATTGGCAGTTT
1483137 TTTAAAGGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 10 0.23
44 33 0.77
ACGTcount: A:0.56, C:0.05, G:0.25, T:0.14
Consensus pattern (43 bp):
AAAAAAAAAGGGAGGAATAAAAAAAGAGAACGATTGGCAGTTT
Found at i:1488682 original size:20 final size:20
Alignment explanation
Indices: 1488657--1488695 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1488647 TTACTTCTTC
1488657 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
1488677 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
1488696 AAGTAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:1489025 original size:50 final size:49
Alignment explanation
Indices: 1488897--1489082 Score: 155
Period size: 50 Copynumber: 3.8 Consensus size: 49
1488887 GATAAAAACA
* * * * *
1488897 TGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTTCCCGTA--C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-G-TTCTCATATGG
* * *
1488946 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATA-TGG
* ** *
1488996 TGACC-ATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGG-AGTTCTCATAT-GG
* * *
1489046 TGCCAACGCCATGTCCCAGACATGCTCTTACGTGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1489083 CCTTTCATAA
Statistics
Matches: 111, Mismatches: 18, Indels: 15
0.77 0.12 0.10
Matches are distributed among these distances:
47 6 0.05
48 1 0.01
49 38 0.34
50 61 0.55
51 5 0.05
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATGG
Found at i:1496413 original size:50 final size:51
Alignment explanation
Indices: 1496359--1496465 Score: 164
Period size: 50 Copynumber: 2.1 Consensus size: 51
1496349 ACATGGGAGT
* *
1496359 TCTCATAC-CGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATACTCGATGCCCACGCCATGTCCCAGACATGGTCTTACGGGGGACC
* *
1496409 TCTCAT-CTCGATGCCGACGCCATGTCCCAGACATGGTCTTACGTGGGACC
1 TCTCATACTCGATGCCCACGCCATGTCCCAGACATGGTCTTACGGGGGACC
1496459 TCTCATA
1 TCTCATA
1496466 ACCTCAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.19, C:0.34, G:0.23, T:0.24
Consensus pattern (51 bp):
TCTCATACTCGATGCCCACGCCATGTCCCAGACATGGTCTTACGGGGGACC
Found at i:1526163 original size:17 final size:17
Alignment explanation
Indices: 1526141--1526173 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1526131 CACTAACATG
1526141 AAAATGTAATGACAATA
1 AAAATGTAATGACAATA
1526158 AAAATGTAATGACAAT
1 AAAATGTAATGACAAT
1526174 GTGTACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAATGTAATGACAATA
Found at i:1526308 original size:17 final size:18
Alignment explanation
Indices: 1526281--1526314 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1526271 CTGTACGATG
1526281 TTTCTTCCTCCTCCTTTT
1 TTTCTTCCTCCTCCTTTT
*
1526299 TTTC-TCCTCCTTCTTT
1 TTTCTTCCTCCTCCTTT
1526315 AATTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCTTCCTCCTCCTTTT
Found at i:1539248 original size:13 final size:13
Alignment explanation
Indices: 1539230--1539283 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
1539220 GGAAATGTAT
*
1539230 GTTTTTATGTTAC
1 GTTTTTACGTTAC
*
1539243 GTTTTTACGTTAATAT
1 GTTTTTACG-T--TAC
*
1539259 GTTTTTATGTTAC
1 GTTTTTACGTTAC
1539272 GTTTTTACGTTA
1 GTTTTTACGTTA
1539284 ATGCTCTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 21 0.64
14 1 0.03
15 1 0.03
16 10 0.30
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (13 bp):
GTTTTTACGTTAC
Found at i:1539260 original size:29 final size:29
Alignment explanation
Indices: 1539227--1539285 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1539217 TTTGGAAATG
1539227 TATGTTTTTATGTTACGTTTTTACGTTAA
1 TATGTTTTTATGTTACGTTTTTACGTTAA
1539256 TATGTTTTTATGTTACGTTTTTACGTTAA
1 TATGTTTTTATGTTACGTTTTTACGTTAA
1539285 T
1 T
1539286 GCTCTGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (29 bp):
TATGTTTTTATGTTACGTTTTTACGTTAA
Found at i:1541071 original size:3 final size:3
Alignment explanation
Indices: 1541063--1541102 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1541053 TAAATTAAAG
1541063 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1541103 GTGAAGATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1541948 original size:36 final size:35
Alignment explanation
Indices: 1541882--1541954 Score: 110
Period size: 36 Copynumber: 2.1 Consensus size: 35
1541872 ACAAGTTAAA
1541882 AAAATTATAAAAATTATTTTAAAAAATAAAAAAATT
1 AAAATTATAAAAATTATTTTAAAAAAT-AAAAAATT
***
1541918 AAAATTATAAAAATTATTTTAAATTTTAAAAAATT
1 AAAATTATAAAAATTATTTTAAAAAATAAAAAATT
1541953 AA
1 AA
1541955 TTAAATACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 10 0.29
36 24 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (35 bp):
AAAATTATAAAAATTATTTTAAAAAATAAAAAATT
Found at i:1544335 original size:22 final size:22
Alignment explanation
Indices: 1544307--1544352 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1544297 GTTTGTTCTT
1544307 TTTTTTTAAATTAATTTGGTCA
1 TTTTTTTAAATTAATTTGGTCA
* *
1544329 TTTTTTTAATTTAATTTTGTCA
1 TTTTTTTAAATTAATTTGGTCA
1544351 TT
1 TT
1544353 AATTTTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (22 bp):
TTTTTTTAAATTAATTTGGTCA
Found at i:1545546 original size:19 final size:19
Alignment explanation
Indices: 1545513--1545559 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
1545503 TTAAACGTGG
1545513 TTATAAAAAATCATAAAATAT
1 TTAT-AAAAATCATAAAA-AT
1545534 TTATAAAAA-CATAAAAAT
1 TTATAAAAATCATAAAAAT
*
1545552 TAATAAAA
1 TTATAAAA
1545560 TTGTAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 7 0.28
20 5 0.20
21 4 0.16
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
TTATAAAAATCATAAAAAT
Found at i:1545550 original size:20 final size:21
Alignment explanation
Indices: 1545513--1545559 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1545503 TTAAACGTGG
1545513 TTATAAAAAATCATAAAATAT
1 TTATAAAAAATCATAAAATAT
1545534 TTAT-AAAAA-CATAAAA-AT
1 TTATAAAAAATCATAAAATAT
*
1545552 TAATAAAA
1 TTATAAAA
1545560 TTGTAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 5 0.21
21 4 0.17
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
TTATAAAAAATCATAAAATAT
Found at i:1545559 original size:18 final size:20
Alignment explanation
Indices: 1545518--1545559 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
1545508 CGTGGTTATA
*
1545518 AAAAATCATAAAATATTTAT
1 AAAAATCATAAAATATTAAT
1545538 AAAAA-CATAAAA-ATTAAT
1 AAAAATCATAAAATATTAAT
1545556 AAAA
1 AAAA
1545560 TTGTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATCATAAAATATTAAT
Found at i:1546670 original size:20 final size:20
Alignment explanation
Indices: 1546645--1546691 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1546635 GGTTCTTGAG
*
1546645 AGAGAAAAATGAAGCTAGAT
1 AGAGAAAAATGAAGCTAGAC
** *
1546665 AGAGAAAGTTGGAGCTAGAC
1 AGAGAAAAATGAAGCTAGAC
1546685 AGAGAAA
1 AGAGAAA
1546692 GCTTTCATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.30, T:0.13
Consensus pattern (20 bp):
AGAGAAAAATGAAGCTAGAC
Found at i:1547798 original size:18 final size:18
Alignment explanation
Indices: 1547772--1547837 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
1547762 ATTTTAATTG
*
1547772 TGATGTGGAGTTTTGTTC
1 TGATATGGAGTTTTGTTC
* *
1547790 TGATATGGAATTCTGTTC
1 TGATATGGAGTTTTGTTC
* * *
1547808 TAATATGGATTTTTGTTG
1 TGATATGGAGTTTTGTTC
*
1547826 TGATCTGGAGTT
1 TGATATGGAGTT
1547838 CTATTTCCTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.48
Consensus pattern (18 bp):
TGATATGGAGTTTTGTTC
Found at i:1558473 original size:21 final size:21
Alignment explanation
Indices: 1558447--1558500 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
1558437 TTGGTATTTG
1558447 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
1558468 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
1558489 GGTATTTGGTAC
1 GG-AATTGGTAC
1558501 CAATTTGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:1558478 original size:11 final size:11
Alignment explanation
Indices: 1558458--1558490 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1558448 GAATTGGTAC
1558458 GAAATGGTATG
1 GAAATGGTATG
*
1558469 GAATTGGTAT-
1 GAAATGGTATG
1558479 GAAATGGTATG
1 GAAATGGTATG
1558490 G
1 G
1558491 TATTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:1559745 original size:18 final size:18
Alignment explanation
Indices: 1559722--1559756 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1559712 TCTGTAGCTT
*
1559722 CTTCCTCCTCTTCACTTC
1 CTTCCTCCTCCTCACTTC
*
1559740 CTTCCTCGTCCTCACTT
1 CTTCCTCCTCCTCACTT
1559757 ACATTCTCCT
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:0.06, C:0.49, G:0.03, T:0.43
Consensus pattern (18 bp):
CTTCCTCCTCCTCACTTC
Found at i:1566990 original size:21 final size:21
Alignment explanation
Indices: 1566940--1566993 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1566930 TGGTCGTATA
*
1566940 TGCCTTTTCTTCCAGGTCTTC
1 TGCCTCTTCTTCCAGGTCTTC
* **
1566961 T-TCTACTTCTTCGGGGTCTTC
1 TGCCT-CTTCTTCCAGGTCTTC
1566982 TGCCTCTTCTTC
1 TGCCTCTTCTTC
1566994 TTGATCCTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.04, C:0.33, G:0.15, T:0.48
Consensus pattern (21 bp):
TGCCTCTTCTTCCAGGTCTTC
Found at i:1574164 original size:50 final size:50
Alignment explanation
Indices: 1574036--1574282 Score: 248
Period size: 50 Copynumber: 4.8 Consensus size: 50
1574026 GATAATAACA
* ** * *
1574036 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTC-TGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATAT-CGG
* * * **
1574085 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
1574135 TGCCTATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
1574185 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
1574241 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1574283 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 23, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
48 6 0.04
49 35 0.21
50 82 0.49
53 2 0.01
56 41 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:1577836 original size:68 final size:69
Alignment explanation
Indices: 1577743--1577870 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 69
1577733 TTAAAACAAT
1577743 AGAGTTGTTCACACACTACCATTTGACTTATCTATCGATAGACTGAT-GCATCAAAAACTAAACA
1 AGAGTTGTTCACACACTACCATTTGACTTATCTATCGATAGACTGATAG-ATCAAAAACTAAACA
1577807 ACACC
65 ACACC
* * * * *
1577812 AGAGTTGTT-TCACACTAGCATTTGACTTATCTTTCTATAGATTGATAGATCAAAAACTA
1 AGAGTTGTTCACACACTACCATTTGACTTATCTATCGATAGACTGATAGATCAAAAACTA
1577871 TTACTTTTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
68 43 0.81
69 10 0.19
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (69 bp):
AGAGTTGTTCACACACTACCATTTGACTTATCTATCGATAGACTGATAGATCAAAAACTAAACAA
CACC
Found at i:1586862 original size:3 final size:3
Alignment explanation
Indices: 1586854--1586894 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1586844 CCTGAAATTA
1586854 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1586895 AGAAAGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1597792 original size:11 final size:11
Alignment explanation
Indices: 1597776--1597805 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1597766 AATCTTTTCT
1597776 AGAGAATTTTG
1 AGAGAATTTTG
1597787 AGAGAATTTTG
1 AGAGAATTTTG
*
1597798 AGAAAATT
1 AGAGAATT
1597806 AAAGATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (11 bp):
AGAGAATTTTG
Found at i:1599970 original size:25 final size:25
Alignment explanation
Indices: 1599922--1599970 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1599912 CATAATTGAA
* * *
1599922 ATGAAATCGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
1599947 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
1599971 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:1600415 original size:43 final size:43
Alignment explanation
Indices: 1600367--1600452 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
1600357 TATGTGATTG
1600367 ATATTGAAATGAC-AATGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGACAAAT-ATGAGAAATGAATATGAGATGAGAAA
* *
1600410 ATATTGAAATGGCAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
1600453 TGAGATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 37 0.93
44 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.23, T:0.24
Consensus pattern (43 bp):
ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
Found at i:1601793 original size:49 final size:49
Alignment explanation
Indices: 1601716--1601812 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
1601706 TCTAGAAGGG
* *
1601716 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATGT
*
1601765 ATAAATAGTGATAAGAGTGTAGATAATGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATG
1601813 CATAGCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.44, C:0.05, G:0.25, T:0.26
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATGT
Found at i:1604866 original size:141 final size:140
Alignment explanation
Indices: 1604492--1605444 Score: 1015
Period size: 141 Copynumber: 7.0 Consensus size: 140
1604482 TACAACAAAA
* *
1604492 TAGTCCTAAGATGACACTTTTGGGGCTACACTTTCCTAAGTGTTGGGATAGA-TTGATCAACATA
1 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTG-CCAACATA
*
1604556 CGCTTTGACCAACTCTTTGTATTAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAG
65 CGCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAG
* *
1604621 TTAGCTCTGTC
130 TTGGCTTTGTC
* * *
1604632 TAGTCCTAAGACGACACTTTTGGGGTGACACTTTCCTAAGTGTTGGGATAGACTTACCAACATAC
1 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
** * *
1604697 GCTTTGGTCAACTCTTTGTATAAGGGTTGGGATATGTATGCCTAAGGCAACACTTAAATAAGAGT
66 GCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
*
1604762 TGGCTTTTGTG
131 TGGC-TTTGTC
*
1604773 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTTCTAAGTGTTGGGATAGACTTGCCAACATAC
1 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * * * * *
1604838 GTTTTGACCAAATTTTTGCATAAAGGTTGAGG-TATGCATGCCTAAGACAACGCTTAAATAAGAG
66 GCTTTGACCAACTCTTTGTATAAGGGTTG-GGATATGCATGCCTAAGGCAACGCTTAAATAAGAG
* *
1604902 TTGGCTTTTATG
130 TTGGC-TTTGTC
* * * * * *
1604914 TAGTCCTAAGACGACATTTTTGGGGCGACACCTTCCTAAGTGTTGAGATAGACTTGTCAATATAC
1 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * *
1604979 GCTCTGGCCAACTCTTTGTATAAGGGTTGGGGTATGCATGCCTAAGGCAACGCTTAAATAAGAGT
66 GCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
*
1605044 TCGCTTTGTC
131 TGGCTTTGTC
* **
1605054 CAGTCCTAAGATG--AC--TT----------TTTCCTAAGTGTTGGG-TAGACTTGCTGACATAC
1 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* ** * *
1605104 GTTTTGGTCAACTTTTTGTATAAGGGTTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGA-T
66 GCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
*
1605168 TCGACTTTGTC
131 T-GGCTTTGTC
* * ** * *
1605179 CA-ACACTGTGCCT-ACACTTTT-GGGCTGACACTTTCCTAAGTGTTGGGATATACTTGCCAACA
1 TAGTC-CTAAG-ATGACACTTTTGGGGC-GACACTTTCCTAAGTGTTGGGATAGACTTGCCAACA
* ** * * *
1605241 TACACTTTGGTCAACTCTTTGTGTAAGGGTTGGGATATGCATGCCTAAGGCAATGCTTCAATAAG
63 TACGCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAG
1605306 A-TTCGGC--T-T-
128 AGTT-GGCTTTGTC
* * * * *
1605315 T-GTCC----A--ACAC-TAT--GCCAACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATAT
1 TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * **
1605370 GCTTTGGCCAACTCTTTGTATAAGGGTTGGTATATGCATGCCTAAGGCAATACTTAAATAAGAGT
66 GCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
1605435 TGGCTTTGTC
131 TGGCTTTGTC
1605445 CAATAGTATG
Statistics
Matches: 692, Mismatches: 93, Indels: 66
0.81 0.11 0.08
Matches are distributed among these distances:
124 3 0.00
125 82 0.12
126 110 0.16
127 6 0.01
128 3 0.00
129 7 0.01
135 1 0.00
136 3 0.00
137 1 0.00
138 2 0.00
139 16 0.02
140 212 0.31
141 244 0.35
142 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (140 bp):
TAGTCCTAAGATGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
GCTTTGACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
TGGCTTTGTC
Found at i:1605431 original size:126 final size:126
Alignment explanation
Indices: 1605206--1605447 Score: 387
Period size: 126 Copynumber: 1.9 Consensus size: 126
1605196 TTTTGGGCTG
* * *
1605206 ACACTTTCCTAAGTGTTGGGATATACTTGCCAACATACACTTTGGTCAACTCTTTGTGTAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAAGGGT
* *
1605271 TGGGATATGCATGCCTAAGGCAATGCTTCAATAAGA-TTCGGCTTTGTCCAACACTATGCCA
66 TGGGATATGCATGCCTAAGGCAATACTTAAATAAGAGTT-GGCTTTGTCCAACACTATGCCA
* **
1605332 ACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAAGGGT
*
1605397 TGGTATATGCATGCCTAAGGCAATACTTAAATAAGAGTTGGCTTTGTCCAA
66 TGGGATATGCATGCCTAAGGCAATACTTAAATAAGAGTTGGCTTTGTCCAA
1605448 TAGTATGTCT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
126 104 0.98
127 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (126 bp):
ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAAGGGT
TGGGATATGCATGCCTAAGGCAATACTTAAATAAGAGTTGGCTTTGTCCAACACTATGCCA
Found at i:1606232 original size:10 final size:10
Alignment explanation
Indices: 1606217--1606241 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1606207 GGAATCCAAT
1606217 TATTTCTGTG
1 TATTTCTGTG
1606227 TATTTCTGTG
1 TATTTCTGTG
1606237 TATTT
1 TATTT
1606242 ACTTGAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (10 bp):
TATTTCTGTG
Found at i:1606356 original size:39 final size:39
Alignment explanation
Indices: 1606312--1606391 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
1606302 TCTAATTCTT
1606312 AATCATTATTATTTTAATGAAAAACTAATGAAAATGTGA
1 AATCATTATTATTTTAATGAAAAACTAATGAAAATGTGA
1606351 AATCATTATTATTTTAATGAAAAACTAATGAAAATGTGA
1 AATCATTATTATTTTAATGAAAAACTAATGAAAATGTGA
1606390 AA
1 AA
1606392 AATTTAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (39 bp):
AATCATTATTATTTTAATGAAAAACTAATGAAAATGTGA
Found at i:1606453 original size:22 final size:21
Alignment explanation
Indices: 1606428--1606468 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1606418 AATCTTATTA
*
1606428 ATTTTTAAAATTTTTATGAACT
1 ATTTGTAAAATTTTT-TGAACT
*
1606450 ATTTGTATAATTTTTTGAA
1 ATTTGTAAAATTTTTTGAA
1606469 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTTGTAAAATTTTTTGAACT
Found at i:1609885 original size:43 final size:42
Alignment explanation
Indices: 1609835--1610175 Score: 328
Period size: 43 Copynumber: 8.0 Consensus size: 42
1609825 GGGTTATCGA
* * * *
1609835 TATGTGATAACATGTAAGACCATGTCTAGGACATTGGCATTG
1 TATGTGATTACGTATAAGACCATGTCTGGGACATTGGCATTG
* * **
1609877 TACTGTGATTATGTATAAAACCATGTCTGGGACATTGGCACCG
1 TA-TGTGATTACGTATAAGACCATGTCTGGGACATTGGCATTG
* ** *
1609920 TTATATGATTTTGTATAAGAACC-TGTCTGGGACAGTGGCATTG
1 -TATGTGATTACGTATAAG-ACCATGTCTGGGACATTGGCATTG
* * *
1609963 ATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTG
1 -TATGTGATTACGTATAAGACCATGTCTGGGACATTGGCATTG
* *
1610006 TATTGTGATTACGTATAAGACCATGTCTAGGACATTGACATCAT-
1 TA-TGTGATTACGTATAAGACCATGTCTGGGACATTGGCAT--TG
* * * * *
1610050 TATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCG
1 TATGTGATTACGTATAAGACCATGTCTGGGACATTGGCATTG
* * * *
1610092 ATATGTGATAACATGTAAGACCATGTCTGGGGCATTGGCATTG
1 -TATGTGATTACGTATAAGACCATGTCTGGGACATTGGCATTG
*
1610135 TACTGTGATTACGCT-TAAGTCCATGTCTGGGACATTGGCAT
1 TA-TGTGATTACG-TATAAGACCATGTCTGGGACATTGGCAT
1610176 CATTATATGA
Statistics
Matches: 241, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
42 9 0.04
43 223 0.93
44 8 0.03
45 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
TATGTGATTACGTATAAGACCATGTCTGGGACATTGGCATTG
Found at i:1610201 original size:129 final size:129
Alignment explanation
Indices: 1609830--1610201 Score: 593
Period size: 129 Copynumber: 2.9 Consensus size: 129
1609820 CATTAGGGTT
* *
1609830 ATCGATATGTGATAACATGTAAGACCATGTCTAGGACATTGGCATTGTACTGTGATTATGTATAA
1 ATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTGTGATTACGTATAA
* * * * *
1609895 AACCATGTCTGGGACATTGGCACCGTTATATGATTTTGTATAAGAACCTGTCTGGGACAGTGGC
66 GACCATGTCTGGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGC
* *
1609959 ATTGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACGTATAA
1 ATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTGTGATTACGTATAA
* *
1610024 GACCATGTCTAGGACATTGACATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGC
66 GACCATGTCTGGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGC
*
1610088 ATCGATATGTGATAACATGTAAGACCATGTCTGGGGCATTGGCATTGTACTGTGATTACGCT-TA
1 ATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTGTGATTACG-TATA
* * *
1610152 AGTCCATGTCTGGGACATTGGCATCATTATATGATTTCGTGTAACACCCT
65 AGACCATGTCTGGGACATTGGCATCATTATATGATTTCGTATAAGACCCT
1610202 ATAAGACCCT
Statistics
Matches: 223, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 222 1.00
130 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (129 bp):
ATCGATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTACTGTGATTACGTATAA
GACCATGTCTGGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGC
Found at i:1613820 original size:43 final size:43
Alignment explanation
Indices: 1613772--1614144 Score: 381
Period size: 43 Copynumber: 8.7 Consensus size: 43
1613762 TGATAACATG
*
1613772 TAAGACCATGTCTAGGACATTGGCATTGTAT-TGTAATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGT-ATTACGTA
* **
1613815 TAAGACCATGTCTGGGACATTGGCATCGTTATATG-ATTTTGTA
1 TAAGACCATGTCTGGGACATTGGCATTG-TATATGTATTACGTA
* * * * * *
1613858 TAAGACCCTGTCTGGGACAGTGGCATCG-ATATGTGATAACATG
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGT-ATTACGTA
1613901 TAAGACCATGTCTGGGACATTGGCATTGTAT-TGTAATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGT-ATTACGTA
* *
1613944 TAAGACCATGTCTAGGACATTGGCATCAT-TATATG-ATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCAT--TGTATATGTATTACGTA
* * * * * *
1613987 TAAGACCCTGTCTGGGACAGTGGCATCG-ATATGTGATAACATG
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGT-ATTACGTA
1614030 TAAGACCATGTCTGGGACATTGGCATTGTAT-TGTAATTACGTA
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGT-ATTACGTA
* *
1614073 TAAGACCATGTCTAGGACATTGGCATCAT-TATATG-ATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCAT--TGTATATGTATTACGTA
* *
1614116 TAAGACCCTGTCTGGGATA-TGGCATTGTA
1 TAAGACCATGTCTGGGACATTGGCATTGTA
1614145 CGAGCTATTA
Statistics
Matches: 274, Mismatches: 40, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.00
41 12 0.04
42 6 0.02
43 234 0.85
44 13 0.05
45 8 0.03
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATTGTATATGTATTACGTA
Found at i:1613876 original size:86 final size:87
Alignment explanation
Indices: 1613772--1614144 Score: 422
Period size: 86 Copynumber: 4.3 Consensus size: 87
1613762 TGATAACATG
*
1613772 TAAGACCATGTCTAGGACATTGGCATTGTAT-TGTAATTACGTATAAGACCATGTCTGGGACATT
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGTAATTACGTATAAGACCATGTCTGGGACATT
**
1613836 GGCATCGTTATATGATTTTGTA
66 GGCATCGTTATATGATTACGTA
* * * * * * *
1613858 TAAGACCCTGTCTGGGACAGTGGCATCG-ATATGTGATAACATGTAAGACCATGTCTGGGACATT
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGTAATTACGTATAAGACCATGTCTGGGACATT
*
1613922 GGCATTG-TAT-TGTAATTACGTA
66 GGCATCGTTATATG--ATTACGTA
* * *
1613944 TAAGACCATGTCTAGGACATTGGCATCAT-TATATG--ATTTCGTATAAGACCCTGTCTGGGACA
1 TAAGACCATGTCTGGGACATTGGCAT--TGTATATGTAATTACGTATAAGACCATGTCTGGGACA
* * * * * *
1614006 GTGGCATCGATATGTGATAACATG
64 TTGGCATCGTTATATGATTACGTA
*
1614030 TAAGACCATGTCTGGGACATTGGCATTGTAT-TGTAATTACGTATAAGACCATGTCTAGGACATT
1 TAAGACCATGTCTGGGACATTGGCATTGTATATGTAATTACGTATAAGACCATGTCTGGGACATT
* *
1614094 GGCATCATTATATGATTTCGTA
66 GGCATCGTTATATGATTACGTA
* *
1614116 TAAGACCCTGTCTGGGATA-TGGCATTGTA
1 TAAGACCATGTCTGGGACATTGGCATTGTA
1614145 CGAGCTATTA
Statistics
Matches: 237, Mismatches: 39, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
84 5 0.02
85 18 0.08
86 204 0.86
87 3 0.01
88 7 0.03
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (87 bp):
TAAGACCATGTCTGGGACATTGGCATTGTATATGTAATTACGTATAAGACCATGTCTGGGACATT
GGCATCGTTATATGATTACGTA
Found at i:1613988 original size:129 final size:129
Alignment explanation
Indices: 1613756--1614140 Score: 718
Period size: 129 Copynumber: 3.0 Consensus size: 129
1613746 TAGGGTTACT
*
1613756 GATATGTGATAACATGTAAGACCATGTCTAGGACATTGGCATTGTATTGTAATTACGTATAAGAC
1 GATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTAATTACGTATAAGAC
* * *
1613821 CATGTCTGGGACATTGGCATCGTTATATGATTTTGTATAAGACCCTGTCTGGGACAGTGGCATC
66 CATGTCTAGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATC
1613885 GATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTAATTACGTATAAGAC
1 GATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTAATTACGTATAAGAC
1613950 CATGTCTAGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATC
66 CATGTCTAGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATC
1614014 GATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTAATTACGTATAAGAC
1 GATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTAATTACGTATAAGAC
*
1614079 CATGTCTAGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGATA-TGGCAT
66 CATGTCTAGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCAT
1614141 TGTACGAGCT
Statistics
Matches: 251, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
128 6 0.02
129 245 0.98
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (129 bp):
GATATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTAATTACGTATAAGAC
CATGTCTAGGACATTGGCATCATTATATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATC
Found at i:1615816 original size:44 final size:44
Alignment explanation
Indices: 1615768--1615880 Score: 190
Period size: 44 Copynumber: 2.6 Consensus size: 44
1615758 AGTTTTAGAA
1615768 TAATGAGGCCCAAAGGACTACGGAGTTTTAATGGAGTATGATGT
1 TAATGAGGCCCAAAGGACTACGGAGTTTTAATGGAGTATGATGT
*
1615812 TAATGAGGCCCAAAGGACTACGGAGTTTTGATGGAGTATGATGT
1 TAATGAGGCCCAAAGGACTACGGAGTTTTAATGGAGTATGATGT
* * *
1615856 TAATAAGGCCCAAGGGACTAAGGAG
1 TAATGAGGCCCAAAGGACTACGGAG
1615881 AGAGCAACTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (44 bp):
TAATGAGGCCCAAAGGACTACGGAGTTTTAATGGAGTATGATGT
Found at i:1619742 original size:21 final size:22
Alignment explanation
Indices: 1619705--1619748 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1619695 ATTCATTTGA
* *
1619705 AATATATATTTTCTAAATTTAT
1 AATATATATTTTATAAACTTAT
1619727 AATATAT-TTTTATAAACTTAT
1 AATATATATTTTATAAACTTAT
1619748 A
1 A
1619749 TATTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATATATTTTATAAACTTAT
Found at i:1619803 original size:8 final size:8
Alignment explanation
Indices: 1619790--1619852 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
1619780 ATTAGACACT
1619790 TTTATATA
1 TTTATATA
1619798 TTTATATA
1 TTTATATA
*
1619806 TTTTTGCATA
1 TTTAT--ATA
*
1619816 TGTTATAGGA
1 T-TTATA-TA
1619826 TTTTATATA
1 -TTTATATA
1619835 TTTATAT-
1 TTTATATA
1619842 TTTATATA
1 TTTATATA
1619850 TTT
1 TTT
1619853 TCAAAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
7 7 0.16
8 22 0.49
9 2 0.04
10 10 0.22
11 4 0.09
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (8 bp):
TTTATATA
Found at i:1624073 original size:75 final size:75
Alignment explanation
Indices: 1623988--1624140 Score: 243
Period size: 75 Copynumber: 2.0 Consensus size: 75
1623978 CTGTTGTCCC
* *
1623988 ATAATTTTTTGATGTCATGGGAAACAAGTTGACAACATGTTTGCAACGTGTTGACTGCTTCTATT
1 ATAATTTTTTGATGTCATGGGAAACAAGTTGACAACATGTTCGCAACGTGTTGACTCCTTCTATT
1624053 AGGATTTTGT
66 AGGATTTTGT
* * * * *
1624063 ATAATTTTTTGATGTCATGTGAAATAGGTTGACAATATGTTCGCAACTTGTTGACTCCTTCTATT
1 ATAATTTTTTGATGTCATGGGAAACAAGTTGACAACATGTTCGCAACGTGTTGACTCCTTCTATT
1624128 AGGATTTTGT
66 AGGATTTTGT
1624138 ATA
1 ATA
1624141 TAAATTACTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (75 bp):
ATAATTTTTTGATGTCATGGGAAACAAGTTGACAACATGTTCGCAACGTGTTGACTCCTTCTATT
AGGATTTTGT
Found at i:1624556 original size:38 final size:37
Alignment explanation
Indices: 1624322--1625109 Score: 611
Period size: 37 Copynumber: 21.5 Consensus size: 37
1624312 ATTAGACATG
* * *
1624322 AGACAAAGATCTATCCTAACCTTTTT-AAGTTTGCCTT
1 AGAC-AAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
* * *
1624359 AGACGA-GTTTA-CCTTAACCTTTTT-AAGGTTGCCTT
1 AGACAAGGTCTATCC-CAACCTTTTTAAAGGTTGCCTT
* ** * *
1624394 CGA-TGGGTTTATCCCAA-CTTTCTTTAA-GTTGCCTT
1 AGACAAGGTCTATCCCAACCTTT-TTAAAGGTTGCCTT
* * * *
1624429 GGAAAAGGTCTATCCCAACCTTTTT-AAGGTTTCTTT
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
* * * ** * *
1624465 AAAC-GGGTCTATTCTGACATTTTT-AAGGTTGTCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
* *
1624500 AGAC-AGGTCAATCCCAACCTTTTCTAAAAGTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTT-TAAAGGTTGCCTT
* * * *
1624537 AGACAAGGTCTATCTCAACCTGTTT-AAGGTTACTTT
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
* *
1624573 AGATCAA--TCTATCCCAACCTTTTT-AATGTTGCTTT
1 AGA-CAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
* *
1624608 AGACAA-GTCTATCCCAACCTTTTTTGAAGATTGCCTT
1 AGACAAGGTCTATCCCAACC-TTTTTAAAGGTTGCCTT
* *
1624645 AGACAA-GTTTATCCCAACCTTTTTTTAAGGTTGCCTT
1 AGACAAGGTCTATCCCAACC-TTTTTAAAGGTTGCCTT
* *
1624682 AGACAAGATCTATCCCAACATTTTTAAAAGGTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTT-AAAGGTTGCCTT
* * *
1624720 AGAC-TGGTCTATCCCAACATTTTTAAAAGATTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTT-AAAGGTTGCCTT
*
1624757 AGAC-AGGTCTATCCCAACTTTTTTTAAAGGTTGCCTT
1 AGACAAGGTCTATCCCAAC-CTTTTTAAAGGTTGCCTT
** * * *
1624794 AGACAAGGTCTGCCCCAACTTTTTTTTAAGGTTACCTT
1 AGACAAGGTCTATCCCAAC-CTTTTTAAAGGTTGCCTT
* * * *
1624832 AAAC-TGGTCTATCTCAACCTTTCTTAAAGTTTGCCTT
1 AGACAAGGTCTATCCCAACCTTT-TTAAAGGTTGCCTT
* * *
1624869 AGACACGGTCTATACCAACCTATTT-AAGGTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
* * * * *
1624905 AGACGA-TTCTATTCCAATCTTTTTTAAAGGTTGTCTT
1 AGACAAGGTCTATCCCAA-CCTTTTTAAAGGTTGCCTT
* * *
1624942 AGACAAGATCTATCCCAACTTTTTTTAAATGTTGCCTT
1 AGACAAGGTCTATCCCAAC-CTTTTTAAAGGTTGCCTT
* * * **
1624980 AGATAAGGTCTATCCCAACTTTTTTAAACAGTTATCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAA-GGTTGCCTT
* *
1625018 AGAC-TGGGCTATCCCAACCTTTTT-AAGGTTGCCTT
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
*
1625053 AGACAA-GTCTATCACAACCTTTTTCAAAGGTTGGCCTT
1 AGACAAGGTCTATCCCAACCTTTTT-AAAGGTT-GCCTT
* *
1625091 -GACTAGGTCTTTCCCAACC
1 AGACAAGGTCTATCCCAACC
1625110 CTTCAATGAG
Statistics
Matches: 611, Mismatches: 109, Indels: 61
0.78 0.14 0.08
Matches are distributed among these distances:
34 9 0.01
35 159 0.26
36 66 0.11
37 218 0.36
38 159 0.26
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (37 bp):
AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
Found at i:1624722 original size:75 final size:72
Alignment explanation
Indices: 1624322--1625109 Score: 598
Period size: 75 Copynumber: 10.8 Consensus size: 72
1624312 ATTAGACATG
* * * * * *
1624322 AGACAAAGATCTATCCTAACCTTTTT-AAGTTTGCCTTAGACGAGTTTA-CCTTAACCTTTTTAA
1 AGAC-AAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGTCTATCC-CAACCTTTTTAA
1624385 GGTTGCCTT
64 GGTTGCCTT
* ** * * * *
1624394 CGA-TGGGTTTATCCCAA-CTTTCTTTAA-GTTGCCTTGGAAAAGGTCTATCCCAACCTTTTTAA
1 AGACAAGGTCTATCCCAACCTTT-TTAAAGGTTGCCTTAGACAA-GTCTATCCCAACCTTTTTAA
* *
1624456 GGTTTCTTT
64 GGTTGCCTT
* * * ** * * * *
1624465 AAAC-GGGTCTATTCTGACATTTTT-AAGGTTGTCTTAGACAGGTCAATCCCAACCTTTTCTAAA
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTT-T-AA
*
1624528 AGTTGCCTT
64 GGTTGCCTT
* * * * *
1624537 AGACAAGGTCTATCTCAACCTGTTT-AAGGTTACTTTAGATCAA-TCTATCCCAACCTTTTTAAT
1 AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGA-CAAGTCTATCCCAACCTTTTTAAG
*
1624600 GTTGCTTT
65 GTTGCCTT
* * *
1624608 AGACAA-GTCTATCCCAACCTTTTTTGAAGATTGCCTTAGACAAGTTTATCCCAACCTTTTTTTA
1 AGACAAGGTCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGTCTATCCCAACC--TTTTTA
1624672 AGGTTGCCTT
63 AGGTTGCCTT
* * ** *
1624682 AGACAAGATCTATCCCAACATTTTTAAAAGGTTGCCTTAGACTGGTCTATCCCAACATTTTTAAA
1 AGACAAGGTCTATCCCAACCTTTTT-AAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTTT--A
*
1624747 AGATTGCCTT
63 AGGTTGCCTT
* ** *
1624757 AGAC-AGGTCTATCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTGCCCCAACTTTTTTTT
1 AGACAAGGTCTATCCCAAC-CTTTTTAAAGGTTGCCTTAGACAA-GTCTATCCCAAC--CTTTTT
*
1624821 AAGGTTACCTT
62 AAGGTTGCCTT
* * * * * * *
1624832 AAAC-TGGTCTATCTCAACCTTTCTTAAAGTTTGCCTTAGACACGGTCTATACCAACCTATTTAA
1 AGACAAGGTCTATCCCAACCTTT-TTAAAGGTTGCCTTAGACA-AGTCTATCCCAACCTTTTTAA
1624896 GGTTGCCTT
64 GGTTGCCTT
* * * * * *
1624905 AGACGA-TTCTATTCCAATCTTTTTTAAAGGTTGTCTTAGACAAGATCTATCCCAACTTTTTTTA
1 AGACAAGGTCTATCCCAA-CCTTTTTAAAGGTTGCCTTAGACAAG-TCTATCCCAAC-CTTTTT-
*
1624969 AATGTTGCCTT
62 AAGGTTGCCTT
* * * ** ** *
1624980 AGATAAGGTCTATCCCAACTTTTTTAAACAGTTATCTTAGACTGGGCTATCCCAACCTTTTTAAG
1 AGACAAGGTCTATCCCAACCTTTTTAAA-GGTTGCCTTAGACAAGTCTATCCCAACCTTTTTAAG
1625045 GTTGCCTT
65 GTTGCCTT
* * *
1625053 AGACAA-GTCTATCACAACCTTTTTCAAAGGTTGGCCTT-GACTAGGTCTTTCCCAACC
1 AGACAAGGTCTATCCCAACCTTTTT-AAAGGTT-GCCTTAGAC-AAGTCTATCCCAACC
1625110 CTTCAATGAG
Statistics
Matches: 565, Mismatches: 115, Indels: 71
0.75 0.15 0.09
Matches are distributed among these distances:
69 4 0.01
70 51 0.09
71 69 0.12
72 64 0.11
73 129 0.23
74 72 0.13
75 150 0.27
76 21 0.04
77 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (72 bp):
AGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTTTAAGG
TTGCCTT
Found at i:1626025 original size:17 final size:19
Alignment explanation
Indices: 1625986--1626030 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1625976 GAATTTGTCT
*
1625986 CAAAAGTATTTTTTTAATCC
1 CAAAAGTGTTTTTTT-ATCC
1626006 CAAAAGTGTTTTTTT-T-C
1 CAAAAGTGTTTTTTTATCC
1626023 CAAAAGTG
1 CAAAAGTG
1626031 ATTATTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 9 0.38
18 1 0.04
20 14 0.58
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (19 bp):
CAAAAGTGTTTTTTTATCC
Found at i:1626733 original size:11 final size:11
Alignment explanation
Indices: 1626719--1626745 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1626709 TCTTTTTAGC
1626719 CATTGAATTTG
1 CATTGAATTTG
1626730 CATTGAATTTG
1 CATTGAATTTG
1626741 CATTG
1 CATTG
1626746 TTTATCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (11 bp):
CATTGAATTTG
Found at i:1629840 original size:15 final size:15
Alignment explanation
Indices: 1629820--1629848 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1629810 ATTAATTTTA
1629820 GAGTTAATTTTAAAT
1 GAGTTAATTTTAAAT
1629835 GAGTTAATTTTAAA
1 GAGTTAATTTTAAA
1629849 ATATATATAA
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:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
GAGTTAATTTTAAAT
Found at i:1630646 original size:29 final size:29
Alignment explanation
Indices: 1630614--1630676 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
1630604 TGGTAGGTCA
1630614 TGTGCAACACACGGCCATGTGACAGACCG
1 TGTGCAACACACGGCCATGTGACAGACCG
* * *
1630643 TGTGCGACACATGGCTATGTGACAGACCG
1 TGTGCAACACACGGCCATGTGACAGACCG
1630672 TGTGC
1 TGTGC
1630677 TGAACCGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (29 bp):
TGTGCAACACACGGCCATGTGACAGACCG
Found at i:1631167 original size:36 final size:36
Alignment explanation
Indices: 1631116--1631204 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
1631106 GGACACTAAG
* *
1631116 TGGTGTGTAGAGATGGATGGGTGTTTTATACTCATA
1 TGGTGTGTAGGGATGGATGGGTGCTTTATACTCATA
1631152 TGGTGTGTAGGGATGGATGGGTGCTTTATACTCATA
1 TGGTGTGTAGGGATGGATGGGTGCTTTATACTCATA
*
1631188 TGGTGTGTTGGGATGGA
1 TGGTGTGTAGGGATGGA
1631205 CGAAGTTGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.19, C:0.06, G:0.38, T:0.37
Consensus pattern (36 bp):
TGGTGTGTAGGGATGGATGGGTGCTTTATACTCATA
Found at i:1634311 original size:367 final size:367
Alignment explanation
Indices: 1633638--1634372 Score: 1470
Period size: 367 Copynumber: 2.0 Consensus size: 367
1633628 TCACAAAAAC
1633638 TCCTCTTTTCTTGCCGTCTAATCCCTAGAATTAGTTTCAATTGATTTCGTAATCTGTTTTAATTT
1 TCCTCTTTTCTTGCCGTCTAATCCCTAGAATTAGTTTCAATTGATTTCGTAATCTGTTTTAATTT
1633703 ATTTGCTGTTTTGTGTTCTTTGATAGATTCGGCTGATTGGAAGTTAATCTTGGGGCTTAATTCCG
66 ATTTGCTGTTTTGTGTTCTTTGATAGATTCGGCTGATTGGAAGTTAATCTTGGGGCTTAATTCCG
1633768 CATTCTTGGTTTCCAAGATTGGATATCTATAAGTGTTTTTGATTCTTAGCTGTTCTTTATTGATT
131 CATTCTTGGTTTCCAAGATTGGATATCTATAAGTGTTTTTGATTCTTAGCTGTTCTTTATTGATT
1633833 TGGGGATTTTTAGTTTCCAGATCTAATTGATTCTAATTAAGTTTTGTTGTTTCGTTTCAGATCCA
196 TGGGGATTTTTAGTTTCCAGATCTAATTGATTCTAATTAAGTTTTGTTGTTTCGTTTCAGATCCA
1633898 AACGTTTAGAGTTTTTGTAGGAATTTCTCGTGACTTGACAACTTGATCTTCATCCACGCGCAACC
261 AACGTTTAGAGTTTTTGTAGGAATTTCTCGTGACTTGACAACTTGATCTTCATCCACGCGCAACC
1633963 CTCTATCATTTGGTATCATATTTTGGGCGTTTTGGGTGTTCT
326 CTCTATCATTTGGTATCATATTTTGGGCGTTTTGGGTGTTCT
1634005 TCCTCTTTTCTTGCCGTCTAATCCCTAGAATTAGTTTCAATTGATTTCGTAATCTGTTTTAATTT
1 TCCTCTTTTCTTGCCGTCTAATCCCTAGAATTAGTTTCAATTGATTTCGTAATCTGTTTTAATTT
1634070 ATTTGCTGTTTTGTGTTCTTTGATAGATTCGGCTGATTGGAAGTTAATCTTGGGGCTTAATTCCG
66 ATTTGCTGTTTTGTGTTCTTTGATAGATTCGGCTGATTGGAAGTTAATCTTGGGGCTTAATTCCG
1634135 CATTCTTGGTTTCCAAGATTGGATATCTATAAGTGTTTTTGATTCTTAGCTGTTCTTTATTGATT
131 CATTCTTGGTTTCCAAGATTGGATATCTATAAGTGTTTTTGATTCTTAGCTGTTCTTTATTGATT
1634200 TGGGGATTTTTAGTTTCCAGATCTAATTGATTCTAATTAAGTTTTGTTGTTTCGTTTCAGATCCA
196 TGGGGATTTTTAGTTTCCAGATCTAATTGATTCTAATTAAGTTTTGTTGTTTCGTTTCAGATCCA
1634265 AACGTTTAGAGTTTTTGTAGGAATTTCTCGTGACTTGACAACTTGATCTTCATCCACGCGCAACC
261 AACGTTTAGAGTTTTTGTAGGAATTTCTCGTGACTTGACAACTTGATCTTCATCCACGCGCAACC
1634330 CTCTATCATTTGGTATCATATTTTGGGCGTTTTGGGTGTTCT
326 CTCTATCATTTGGTATCATATTTTGGGCGTTTTGGGTGTTCT
1634372 T
1 T
1634373 GGTTGATTTC
Statistics
Matches: 368, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
367 368 1.00
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.46
Consensus pattern (367 bp):
TCCTCTTTTCTTGCCGTCTAATCCCTAGAATTAGTTTCAATTGATTTCGTAATCTGTTTTAATTT
ATTTGCTGTTTTGTGTTCTTTGATAGATTCGGCTGATTGGAAGTTAATCTTGGGGCTTAATTCCG
CATTCTTGGTTTCCAAGATTGGATATCTATAAGTGTTTTTGATTCTTAGCTGTTCTTTATTGATT
TGGGGATTTTTAGTTTCCAGATCTAATTGATTCTAATTAAGTTTTGTTGTTTCGTTTCAGATCCA
AACGTTTAGAGTTTTTGTAGGAATTTCTCGTGACTTGACAACTTGATCTTCATCCACGCGCAACC
CTCTATCATTTGGTATCATATTTTGGGCGTTTTGGGTGTTCT
Found at i:1647078 original size:3 final size:3
Alignment explanation
Indices: 1647070--1647113 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1647060 AGAAGTAAAA
1647070 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1647114 TGAGTGATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1651880 original size:18 final size:18
Alignment explanation
Indices: 1651857--1651893 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1651847 ATTAAATGGA
1651857 TTTAATATTA-TAATATTT
1 TTTAATATTAGT-ATATTT
1651875 TTTAATATTAGTATATTT
1 TTTAATATTAGTATATTT
1651893 T
1 T
1651894 ATATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAATATTAGTATATTT
Found at i:1651941 original size:20 final size:19
Alignment explanation
Indices: 1651926--1651964 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1651916 AAATTTTATT
1651926 TAAATATAAAACATTTGTAA
1 TAAATATAAAACATTT-TAA
*
1651946 TAAATATAATACATTTTAA
1 TAAATATAAAACATTTTAA
1651965 AATTTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAATATAAAACATTTTAA
Found at i:1654564 original size:24 final size:23
Alignment explanation
Indices: 1654501--1654565 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
1654491 TTATTTTTAT
1654501 TTTATTTTTATTTATATGTAATTA
1 TTTA-TTTTATTTATATGTAATTA
*
1654525 TTT-TTTATAATCTATATGT-ATATA
1 TTTATTT-T-ATTTATATGTAAT-TA
1654549 TTTATTTTATTATATAT
1 TTTATTTTATT-TATAT
1654566 ACGTATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
22 3 0.09
23 5 0.15
24 23 0.68
25 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (23 bp):
TTTATTTTATTTATATGTAATTA
Found at i:1667995 original size:44 final size:44
Alignment explanation
Indices: 1667815--1667999 Score: 113
Period size: 44 Copynumber: 4.2 Consensus size: 44
1667805 AAAATTGTAG
* *
1667815 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
* * ** * **
1667859 ATCTTATCTTTCCAAG-A-TAGTGGGAAGCAGATTTAAGTCACCAA
1 ATCTTATCTCTCTAAGCAGTAGT-GG-AGCAGATCGAAGACGGCAA
** * * * * ** * * * ** * *
1667903 GCCTTGTCTCTCTGAGCAGCAGCGGAGTGGTTTGAAAATTGTAG
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
*
1667947 ATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGAAGACGGCAA
1 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1667991 ATCTTATCT
1 ATCTTATCT
1668000 TTCCAAGATA
Statistics
Matches: 96, Mismatches: 41, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
42 4 0.04
43 3 0.03
44 84 0.88
45 3 0.03
46 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
Found at i:1668087 original size:132 final size:132
Alignment explanation
Indices: 1666446--1668049 Score: 2688
Period size: 132 Copynumber: 12.2 Consensus size: 132
1666436 ACCGGTGAAA
* * * *
1666446 CACCAAACCTTGTCCCCCTGAGCAACAGCGGAGTAGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
** * *
1666511 GCAGTAGTGGAGCAGATCGAAGACAACAAATCTTATTTTTCCAAGATAGTGGGAAGCAGATTGAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1666576 GT
131 GT
*
1666578 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTGCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
* * *
1666643 GCAGTAGTAGAGCAGATCGAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
*
1666708 CT
131 GT
* *
1666710 CACCAAGCCTTATCTCCCTGAGTAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
* * *
1666775 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTACCTTTCCAAGATAGGGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
*
1666840 GC
131 GT
* * *
1666842 CACCAAGCCTTGTCTCCTTGAGCAACAGCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
* * *
1666907 GTAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1666972 GT
131 GT
** *
1666974 CACCAAGTATTGTTTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
*
1667039 GCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1667104 GT
131 GT
*
1667106 CACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
*
1667171 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1667236 GT
131 GT
*
1667238 CACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
*
1667303 GCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAG-GGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
*
1667367 GC
131 GT
** * *
1667369 CATAAAGCCTTGTCTCCCTGAGCTGTAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
* *
1667434 GCAGTAGTTGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1667499 GT
131 GT
* * *
1667501 CACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTAGGTTAAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
* * *
1667566 GTAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1667631 GT
131 GT
*
1667633 CACCAAGCCTTGTCTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
* * *
1667698 GTAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1667763 GT
131 GT
*
1667765 CACCAAGCCTTGTCTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
*
1667830 GTAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
1667895 GT
131 GT
* * *
1667897 CACCAAGCCTTGTCTCTCTGAGCAGCAGCGGAGTGGTTTGAAAATTGTAGATCTTATCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
*
1667962 GCAGTAGTGGAGTAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
*
1668027 GC
131 GT
1668029 CACCAAGCCTTGTCTCCCTGA
1 CACCAAGCCTTGTCTCCCTGA
1668050 AGTTACAGCG
Statistics
Matches: 1385, Mismatches: 86, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
131 122 0.09
132 1263 0.91
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GT
Found at i:1669693 original size:22 final size:20
Alignment explanation
Indices: 1669665--1669706 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1669655 TATTTTTTAA
*
1669665 ATATATGTATATATATATTTTT
1 ATATATGCATAT-T-TATTTTT
1669687 ATATATGCATATTTATTTTT
1 ATATATGCATATTTATTTTT
1669707 GTAGTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
ATATATGCATATTTATTTTT
Found at i:1684658 original size:14 final size:14
Alignment explanation
Indices: 1684639--1684665 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1684629 TGTTAAAACT
1684639 AAATATTTTGGAAA
1 AAATATTTTGGAAA
1684653 AAATATTTTGGAA
1 AAATATTTTGGAA
1684666 GAGCAGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
AAATATTTTGGAAA
Found at i:1688386 original size:80 final size:80
Alignment explanation
Indices: 1688253--1688414 Score: 306
Period size: 80 Copynumber: 2.0 Consensus size: 80
1688243 TCAAACAAAT
1688253 AGTCAGTCAGCACAAGCCATGGATAACTTTGACTATATGTGTTCCCATGAACACTTTGATTATAA
1 AGTCAGTCAGCACAAGCCATGGATAACTTTGACTATATGTGTTCCCATGAACACTTTGATTATAA
* *
1688318 CAAAGATATTTATGA
66 AAAAGATACTTATGA
1688333 AGTCAGTCAGCACAAGCCATGGATAACTTTGACTATATGTGTTCCCATGAACACTTTGATTATAA
1 AGTCAGTCAGCACAAGCCATGGATAACTTTGACTATATGTGTTCCCATGAACACTTTGATTATAA
1688398 AAAAGATACTTATGA
66 AAAAGATACTTATGA
1688413 AG
1 AG
1688415 GAGTCTATAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (80 bp):
AGTCAGTCAGCACAAGCCATGGATAACTTTGACTATATGTGTTCCCATGAACACTTTGATTATAA
AAAAGATACTTATGA
Found at i:1693546 original size:22 final size:22
Alignment explanation
Indices: 1693515--1693570 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1693505 ATTGAACGTT
* *
1693515 ATGTCACAACATGGGGGGTTTG
1 ATGTCGCAACATGGGGGGTTCG
1693537 ATGTCGCAACATGGGGGGTTCG
1 ATGTCGCAACATGGGGGGTTCG
*
1693559 ATGTTGCAACAT
1 ATGTCGCAACAT
1693571 AAAGAGCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (22 bp):
ATGTCGCAACATGGGGGGTTCG
Found at i:1695255 original size:21 final size:22
Alignment explanation
Indices: 1695216--1695259 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1695206 ACCACAAACA
1695216 AAAATGCAAACCAAACATGACC
1 AAAATGCAAACCAAACATGACC
* *
1695238 AAAA-GCAAATCAATCATGACC
1 AAAATGCAAACCAAACATGACC
1695259 A
1 A
1695260 TTTTGACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.25, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAATGCAAACCAAACATGACC
Found at i:1699805 original size:36 final size:36
Alignment explanation
Indices: 1699758--1699832 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1699748 AAATTAAAAT
1699758 TTTGGCCTACACACAGTGGTATGACGATACCAAACC
1 TTTGGCCTACACACAGTGGTATGACGATACCAAACC
*
1699794 TTTGGCCTACACACAGTGGTATGACGATACCAGACC
1 TTTGGCCTACACACAGTGGTATGACGATACCAAACC
1699830 TTT
1 TTT
1699833 AGTATCGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (36 bp):
TTTGGCCTACACACAGTGGTATGACGATACCAAACC
Found at i:1701544 original size:130 final size:127
Alignment explanation
Indices: 1701313--1701643 Score: 490
Period size: 130 Copynumber: 2.6 Consensus size: 127
1701303 AGATCAAACT
* * *
1701313 TAATCACTTTAATATTAAATTAATCTAATGCTTAT--TATAAGTATTATATTAAA-TTAATATTA
1 TAATCACTTTAATATTAAATTAAT-AAATACTTATAAGATAAGTATTA-ATTAAATTTAATATTA
1701375 AATCTATTAAATTAATAGAATATTTATATATAAGATAAATATTAAATTTAATTTAATATTAAGG
64 AATCTATTAAATTAATAGAATATTTATATATAAGATAAATATTAAATTTAATTTAATATTAAGG
*
1701439 TGATCACTTTAATATTAAATTAATAAGATACTTATAAGAATAAGTATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAA-ATACTTATAAG-ATAAGTATTA-ATTAAATTTAATATT
* *
1701504 AAATCTATTAAATTAATAGAATATTTATCTATAAGATAAATTTTAAATTTAATTTAATATTAAGG
63 AAATCTATTAAATTAATAGAATATTTATATATAAGATAAATATTAAATTTAATTTAATATTAAGG
* *
1701569 TAATCACTTTAATATTAAATTAATAAATA-TTATCAAGATAAATATTTAATTTAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAATACTTAT-AAGATAAGTA-TTAATTAAATTTAATATTA
*
1701633 AATTTATTAAA
64 AATCTATTAAA
1701644 ATATTATTAT
Statistics
Matches: 187, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
125 1 0.01
126 30 0.16
128 35 0.19
129 25 0.13
130 96 0.51
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (127 bp):
TAATCACTTTAATATTAAATTAATAAATACTTATAAGATAAGTATTAATTAAATTTAATATTAAA
TCTATTAAATTAATAGAATATTTATATATAAGATAAATATTAAATTTAATTTAATATTAAGG
Found at i:1701646 original size:17 final size:17
Alignment explanation
Indices: 1701607--1701649 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1701597 ATTATCAAGA
*
1701607 TAAATATTTAATTTAAT
1 TAAATATTAAATTTAAT
*
1701624 TTAATATTAAATTT-AT
1 TAAATATTAAATTTAAT
1701640 TAAAATATTA
1 T-AAATATTA
1701650 TTATTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAATATTAAATTTAAT
Found at i:1701652 original size:67 final size:70
Alignment explanation
Indices: 1701509--1701652 Score: 161
Period size: 67 Copynumber: 2.1 Consensus size: 70
1701499 ATATTAAATC
*
1701509 TATTAAATTAATAGAATATTTATCTATAAGATAAATTTTAAATTTAATTTAATATTAAGGTAATC
1 TATTAAATTAATAGAATATTTATC--TAAGATAAATTTTAAATTTAATTTAATATTAAAGTAATC
***
1701574 ACTTTAA
64 AAAATAA
* * *
1701581 TATTAAATTAATA-AATA-TTATC-AAGATAAATATTT-AATTTAATTTAATATTAAATTTATTA
1 TATTAAATTAATAGAATATTTATCTAAGATAAAT-TTTAAATTTAATTTAATATTAAAGTAATCA
*
1701642 AAATAT
65 AAATAA
1701648 TATTA
1 TATTA
1701653 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
67 38 0.60
68 3 0.05
70 5 0.08
71 4 0.06
72 13 0.21
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (70 bp):
TATTAAATTAATAGAATATTTATCTAAGATAAATTTTAAATTTAATTTAATATTAAAGTAATCAA
AATAA
Found at i:1708726 original size:25 final size:25
Alignment explanation
Indices: 1708698--1708776 Score: 122
Period size: 25 Copynumber: 3.2 Consensus size: 25
1708688 TGTAGTGGCA
* *
1708698 AGGTGGCGACACAGGTGTGGCAAGG
1 AGGTGGTGTCACAGGTGTGGCAAGG
*
1708723 AGGTCGTGTCACAGGTGTGGCAAGG
1 AGGTGGTGTCACAGGTGTGGCAAGG
*
1708748 AGGTGGTGTCACAGGTGTGGTAAGG
1 AGGTGGTGTCACAGGTGTGGCAAGG
1708773 AGGT
1 AGGT
1708777 CAGAGGTTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.22, C:0.13, G:0.47, T:0.19
Consensus pattern (25 bp):
AGGTGGTGTCACAGGTGTGGCAAGG
Found at i:1710748 original size:37 final size:37
Alignment explanation
Indices: 1710699--1710804 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 37
1710689 CGAATGCAGT
* *
1710699 TATATATATAATTATTCAAATGCATATGCCAAAAGCA
1 TATATTTATAATTATTCAAATACATATGCCAAAAGCA
1710736 TATATTTATAATTATTATTCAAATACATATGCCAAAAGCA
1 TATATTTAT-A--ATTATTCAAATACATATGCCAAAAGCA
* * *
1710776 TATATTTATACTTA-TCAATTACATGTGCC
1 TATATTTATAATTATTCAAATACATATGCC
1710805 GAATGCACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
36 13 0.21
37 11 0.18
38 1 0.02
39 1 0.02
40 35 0.57
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (37 bp):
TATATTTATAATTATTCAAATACATATGCCAAAAGCA
Found at i:1710765 original size:40 final size:40
Alignment explanation
Indices: 1710709--1710790 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
1710699 TATATATATA
*
1710709 ATTATTCAAATGCATATGCCAAAAGCATATATTTATAATT
1 ATTATTCAAATACATATGCCAAAAGCATATATTTATAATT
*
1710749 ATTATTCAAATACATATGCCAAAAGCATATATTTATACTT
1 ATTATTCAAATACATATGCCAAAAGCATATATTTATAATT
1710789 AT
1 AT
1710791 CAATTACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (40 bp):
ATTATTCAAATACATATGCCAAAAGCATATATTTATAATT
Found at i:1710822 original size:34 final size:35
Alignment explanation
Indices: 1710782--1710855 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
1710772 AGCATATATT
* *
1710782 TATACTTATCAAT-TACATGTGCCGAATGC-ACATA
1 TATACTTAT-AATCCACATATGCCGAATGCAACATA
*
1710816 TATACTTATAATCCACATATGCTGAATGCATACATA
1 TATACTTATAATCCACATATGCCGAATGCA-ACATA
1710852 TATA
1 TATA
1710856 TATCCAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.09
34 22 0.65
36 9 0.26
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAACATA
Found at i:1711072 original size:41 final size:40
Alignment explanation
Indices: 1711022--1711231 Score: 285
Period size: 41 Copynumber: 5.1 Consensus size: 40
1711012 TTAATTTAAA
* *
1711022 CAGATTCACTGGCACTTAGCCTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAA-CCTGATT
*
1711064 CAGATCACTGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTA-AACCTGATT
* * *
1711105 TAGATCACCGGCACTTATCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTA-AACCTGATT
*
1711146 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTA-AACCTGATT
*
1711187 CAGATCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGG-CTT-AAACCTGATT
1711229 CAG
1 CAG
1711232 TACACCAGCT
Statistics
Matches: 154, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
41 134 0.87
42 19 0.12
43 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (40 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAACCTGATT
Found at i:1711149 original size:82 final size:82
Alignment explanation
Indices: 1711022--1711261 Score: 322
Period size: 82 Copynumber: 2.9 Consensus size: 82
1711012 TTAATTTAAA
* * *
1711022 CAGATTCACTGGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACTGGCACTTAGCCTGC
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGC
1711087 TAGGCTTATAACCTGATT
65 TAGGCTTATAACCTGATT
* * *
1711105 TAGATCACCGGCACTTATCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCT
*
1711170 AGGCTTATAACCTGGTT
66 AGGCTTATAACCTGATT
* * * **
1711187 CAGATCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATTCAG-TACACCAGCTTTTAGCCTG
1 CAGATCACCGGCACTTAGCCTGCTAGG-CTTAAAGCCTGATTCAGAT-CACCGGCACTTAGCCTG
1711251 CT-GGACTTATA
64 CTAGG-CTTATA
1711262 GTCTGAAAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
82 100 0.72
83 39 0.28
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (82 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCT
AGGCTTATAACCTGATT
Found at i:1711821 original size:78 final size:76
Alignment explanation
Indices: 1711598--1711822 Score: 199
Period size: 78 Copynumber: 2.9 Consensus size: 76
1711588 TACATTTAAC
* * ** *
1711598 ATTCGAATCTCACATATACCTATATAATTTCATACCCCAT-TTCAATACAAAAACTTATACATGT
1 ATTCGAATCTAACATATACATATATAATTTCATA-CTTATATTCAATATAAAAA-TTATACAT-T
* *
1711662 ACAT--ATATACAT
63 ATATACACATACAT
* * * *
1711674 ATTCGAATCTAACATATATACATATATAATTTTATACTTACATTCGAA-ATAAGTACTTATAC-T
1 ATTCGAATCTAAC--ATATACATATATAATTTCATACTTATATTC-AATATAA-AAATTATACAT
*
1711737 TGTATACACATACAT
62 TATATACACATACAT
* * *
1711752 TTTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAACAATTATACATATA
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATATAAA-AATTATACAT-TA
1711817 TATACA
64 TATACA
1711823 TGCTTATTTG
Statistics
Matches: 118, Mismatches: 20, Indels: 20
0.75 0.13 0.13
Matches are distributed among these distances:
75 2 0.02
76 53 0.45
77 4 0.03
78 56 0.47
79 3 0.03
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.37
Consensus pattern (76 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATATAAAAATTATACATTATA
TACACATACAT
Found at i:1712078 original size:78 final size:78
Alignment explanation
Indices: 1711961--1712316 Score: 624
Period size: 78 Copynumber: 4.6 Consensus size: 78
1711951 ACATTCAACA
* *
1711961 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1712025 AACATACATACTT
66 AACATACATACTT
1712038 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1712103 AACATACATACTT
66 AACATACATACTT
*
1712116 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATTTCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1712181 AACATACATACTT
66 AACATACATACTT
* *
1712194 TTAACTAAATTCAAGAATTTATTCATGAATATACATATATATCCGAACCTTATATATATAAATAT
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
1712259 AACATACAGACTT
66 AACATACATACTT
* *
1712272 TTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAATTTATTCATGTATATACATATA-TATCC
1712317 ACTATTAGTT
Statistics
Matches: 267, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
77 14 0.05
78 248 0.93
79 5 0.02
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (78 bp):
TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:1715046 original size:27 final size:27
Alignment explanation
Indices: 1715016--1715069 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1715006 AAAATTTTTT
1715016 ATTACCGAAATACCCCCGATA-GGTAAA
1 ATTACCGAAATACCCCC-ATAGGGTAAA
*
1715043 ATTATCGAAATACCCCCATAGGGTAAA
1 ATTACCGAAATACCCCCATAGGGTAAA
1715070 CTGACTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (27 bp):
ATTACCGAAATACCCCCATAGGGTAAA
Found at i:1717774 original size:41 final size:40
Alignment explanation
Indices: 1717714--1717968 Score: 262
Period size: 41 Copynumber: 6.3 Consensus size: 40
1717704 AATAATATTG
* *
1717714 CTGAATTGCATATACGTGCCCCTGTTTGTACTTCTGTACCA
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTT-TGTACCC
* * * *
1717755 CTGAATTGCACATATGTGCCCC-ATTTGTACTTCGGTACCT
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTT-TGTACCC
* * * *
1717795 TTGAATTGCACATGCGTGTCCCTTTTTGTACTTTAGTACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTT-GTACCC
* * * * *
1717836 CTAAATTGAATATATGTTCCCCTGTTTGTACTTTGGTACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTT-GTACCC
*
1717877 CTGAATTGCACATACGTGCCCCTGTTAGTACTTTGATACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTTG-TACCC
* * *
1717918 CTGAATTGCACATATGTTCCCCTATTTGTACTTTGATACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTTG-TACCC
*
1717959 ATGAA-TGCAC
1 CTGAATTGCAC
1717969 TTTTGTACCA
Statistics
Matches: 178, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
40 39 0.22
41 139 0.78
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (40 bp):
CTGAATTGCACATACGTGCCCCTGTTTGTACTTTGTACCC
Found at i:1717879 original size:20 final size:20
Alignment explanation
Indices: 1717854--1717920 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
1717844 AATATATGTT
1717854 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
* * * ** *
1717874 CCCCTGAATTGCACATACGTG
1 CCCCTG-TTTGTACTTTGGTA
* *
1717895 CCCCTGTTAGTACTTTGATA
1 CCCCTGTTTGTACTTTGGTA
1717915 CCCCTG
1 CCCCTG
1717921 AATTGCACAT
Statistics
Matches: 32, Mismatches: 14, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.34
Consensus pattern (20 bp):
CCCCTGTTTGTACTTTGGTA
Found at i:1717887 original size:82 final size:81
Alignment explanation
Indices: 1717714--1717968 Score: 325
Period size: 82 Copynumber: 3.1 Consensus size: 81
1717704 AATAATATTG
* * *
1717714 CTGAATTGCATATACGTGCCCCTGTTTGTACTTCTGTACCACTGAATTGCACATATGTGCCCC-A
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTT-TGTACCCCTGAATTGCACATATGTTCCCCTA
* *
1717778 TTTGTACTTCGGTACCT
65 TTTGTACTTTGGTACCC
* * * * * * * *
1717795 TTGAATTGCACATGCGTGTCCCTTTTTGTACTTTAGTACCCCTAAATTGAATATATGTTCCCCTG
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTT-GTACCCCTGAATTGCACATATGTTCCCCTA
1717860 TTTGTACTTTGGTACCC
65 TTTGTACTTTGGTACCC
*
1717877 CTGAATTGCACATACGTGCCCCTGTTAGTACTTTGATACCCCTGAATTGCACATATGTTCCCCTA
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTTG-TACCCCTGAATTGCACATATGTTCCCCTA
*
1717942 TTTGTACTTTGATACCC
65 TTTGTACTTTGGTACCC
*
1717959 ATGAA-TGCAC
1 CTGAATTGCAC
1717969 TTTTGTACCA
Statistics
Matches: 147, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 57 0.39
82 89 0.61
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (81 bp):
CTGAATTGCACATACGTGCCCCTGTTTGTACTTTGTACCCCTGAATTGCACATATGTTCCCCTAT
TTGTACTTTGGTACCC
Found at i:1727088 original size:21 final size:21
Alignment explanation
Indices: 1727059--1727110 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1727049 TCTCTCTCGC
*
1727059 TTTCCTTTTTGCCTTTTTCA-T
1 TTTCATTTTTGCC-TTTTCACT
*
1727080 TTTCATTTTCTTCCTTTTCACT
1 TTTCATTTT-TGCCTTTTCACT
1727102 TTT-ATTTTT
1 TTTCATTTTT
1727111 CTCTTCTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 19 0.70
22 7 0.26
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTCATTTTTGCCTTTTCACT
Found at i:1731191 original size:21 final size:21
Alignment explanation
Indices: 1731144--1731185 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1731134 GCAATTTTGT
*
1731144 AATTAAAGTGAAATTAAAACA
1 AATTAAAGTGAAAGTAAAACA
1731165 AATTAAAGTGAAAGTAAAACA
1 AATTAAAGTGAAAGTAAAACA
1731186 CTTTAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (21 bp):
AATTAAAGTGAAAGTAAAACA
Found at i:1734388 original size:12 final size:12
Alignment explanation
Indices: 1734371--1734400 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1734361 TTAGAGAGTT
1734371 ACACGGGTGAGG
1 ACACGGGTGAGG
*
1734383 ACACGGGTTAGG
1 ACACGGGTGAGG
1734395 ACACGG
1 ACACGG
1734401 CCGTGTGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.43, T:0.10
Consensus pattern (12 bp):
ACACGGGTGAGG
Found at i:1735813 original size:42 final size:42
Alignment explanation
Indices: 1735675--1735901 Score: 300
Period size: 42 Copynumber: 5.5 Consensus size: 42
1735665 TTTAAACAGA
* * * *
1735675 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGAT-TCAG-
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATAT-TGT
* * * * * *
1735716 TACACTGGCATTTAGCCTGCTAGACATATAGTCTGA-AATGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1735757 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* *
1735799 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1735841 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1735883 TTCACCGGCATTAAGCCTG
1 TTCACCGGCATTAAGCCTG
1735902 ATAGGCACTG
Statistics
Matches: 166, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
40 3 0.02
41 60 0.36
42 103 0.62
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
Found at i:1736507 original size:23 final size:23
Alignment explanation
Indices: 1736477--1736521 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1736467 TACTTGTATA
*
1736477 TACATGTATAAAT-TCAAAACTTG
1 TACATGTAAAAATAT-AAAACTTG
1736500 TACATGTAAAAATATAAAACTT
1 TACATGTAAAAATATAAAACTT
1736522 TTATGCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (23 bp):
TACATGTAAAAATATAAAACTTG
Found at i:1737325 original size:26 final size:26
Alignment explanation
Indices: 1737289--1737342 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1737279 CGATCTCAAA
1737289 AACGTAAAAATTTTCAAAAACCGAAC
1 AACGTAAAAATTTTCAAAAACCGAAC
*
1737315 AACGTAAAAATTTTCAAAAACTGAAC
1 AACGTAAAAATTTTCAAAAACCGAAC
1737341 AA
1 AA
1737343 AAACGAACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.20
Consensus pattern (26 bp):
AACGTAAAAATTTTCAAAAACCGAAC
Found at i:1739617 original size:50 final size:50
Alignment explanation
Indices: 1739492--1739638 Score: 213
Period size: 50 Copynumber: 2.9 Consensus size: 50
1739482 GATAATAACA
** * **
1739492 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTCTTGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCAG
* *
1739543 TGCCAACGCCGTGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
1739593 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
1739639 CCAAATGTCA
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 52 0.60
51 35 0.40
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:1739750 original size:13 final size:13
Alignment explanation
Indices: 1739729--1739760 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1739719 GCTTGGATCA
*
1739729 TCATCAAATAAAT
1 TCATAAAATAAAT
1739742 TCATAAAATAAAT
1 TCATAAAATAAAT
1739755 TCATAA
1 TCATAA
1739761 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1743540 original size:3 final size:3
Alignment explanation
Indices: 1743532--1743563 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1743522 GTGGAATGGA
1743532 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1743564 ATAACAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:1744203 original size:117 final size:118
Alignment explanation
Indices: 1743911--1744279 Score: 460
Period size: 114 Copynumber: 3.2 Consensus size: 118
1743901 ATGAGTACTA
* * * * *
1743911 GGCACAACATTTACTTCGGTTATATCGATGAGCGCTAGACACAAACTAATTACTTCAGACATTCC
1 GGCACAATATTTACTTCGGTTATACCGATGAGCGCTAGGCGCAAACTAATTACTTCAGACGTTCC
* * * *
1743976 GATGAGGCACTAGCTGCCAAATGGTTACTTCGACTACGTCTC---GA-TGCTA
66 GATGAGGCACTAGGTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTG
* * *
1744025 GGCACAATTTTTACTTTGGTTATACCGATGAGCGCTAGGTGCAAACTAATTACTTCAGACGTTCC
1 GGCACAATATTTACTTCGGTTATACCGATGAGCGCTAGGCGCAAACTAATTACTTCAGACGTTCC
* *
1744090 GATGAGGCACTAGGTGTCAAATGGTTAC-TCAACTACGTGTCGATGAGTGTTG
66 GATGAGGCACTAGGTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTG
** * * * *
1744142 GGCGTAATATTTACTTCAGTTATACCAATGAGCGCTAGGCGCAAACTAATTACTTCGGACGTTCT
1 GGCACAATATTTACTTCGGTTATACCGATGAGCGCTAGGCGCAAACTAATTACTTCAGACGTTCC
* * * * *
1744207 AATGAGGCATTGGGTGCCAAATGGTTACTTTGACTACATGTCGATGAGTGTTG
66 GATGAGGCACTAGGTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTG
* *
1744260 GGCACATTTTTTACTTCGGT
1 GGCACAATATTTACTTCGGT
1744280 CATATTGATG
Statistics
Matches: 215, Mismatches: 35, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
113 11 0.05
114 83 0.39
116 2 0.01
117 83 0.39
118 36 0.17
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (118 bp):
GGCACAATATTTACTTCGGTTATACCGATGAGCGCTAGGCGCAAACTAATTACTTCAGACGTTCC
GATGAGGCACTAGGTGCCAAATGGTTACTTCGACTACGTGTCGATGAGTGTTG
Done.