Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 183 of 199
Found at i:58476707 original size:18 final size:17
Alignment explanation
Indices: 58476679--58476713 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58476669 ATTATTAAGA
*
58476679 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58476696 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58476714 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58476944 original size:16 final size:17
Alignment explanation
Indices: 58476910--58476946 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
58476900 GATTAGCTAT
58476910 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
58476927 TACACCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
58476943 TACA
1 TACA
58476947 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (17 bp):
TACACCTCTAATCCCAA
Found at i:58479429 original size:26 final size:26
Alignment explanation
Indices: 58479381--58479430 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
58479371 AAAGATATTT
**
58479381 TTGAAATAATAAATGTTTTTTTTAAA
1 TTGAAATAATAAATGTTAATTTTAAA
58479407 TTGAAATAATAAATGTTAATTTTA
1 TTGAAATAATAAATGTTAATTTTA
58479431 TTCTAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (26 bp):
TTGAAATAATAAATGTTAATTTTAAA
Found at i:58485345 original size:43 final size:43
Alignment explanation
Indices: 58485246--58485529 Score: 320
Period size: 43 Copynumber: 6.6 Consensus size: 43
58485236 TTTTAGAAAT
* * * *
58485246 AAACGCCGCTATAGAACAAGACCTTTAGCGACGC-TTTCCCAA
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
* *
58485288 AAACGCCGCTATAGAACATGAGCTTTAGCGGTGCTTTTTCCA-
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
* *
58485330 AAATCGCCGCTATAGAACATTAACTTTAGCGGCGCTTTTTCCAC
1 AAA-CGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
* * * * * *
58485374 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCACCTTTTCTAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
* * ** *
58485417 AAACGCCACTAAAGAGTAAGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
* * * *
58485460 AAACGCCACTATAGAACATGACCTTTTGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
* *
58485503 AAACGCCGCTAAAGAACATGACTTTTA
1 AAACGCCGCTATAGAACATGACCTTTA
58485530 AAAAATATTT
Statistics
Matches: 205, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 33 0.16
43 169 0.82
44 3 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTTCCAC
Found at i:58485453 original size:129 final size:128
Alignment explanation
Indices: 58485246--58485529 Score: 356
Period size: 129 Copynumber: 2.2 Consensus size: 128
58485236 TTTTAGAAAT
* * * * *
58485246 AAACGCCGCTATAGAACAAGACCTTTAGCGACGCTTTCCCAAAAACGCCGCTATAGAACATGAGC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGACGCTTTCCCAAAAACGCCACTAAAGAACAAGACC
* * * * *
58485311 TTTAGCGGTGCTTTTTCCA-AAATCGCCGCTATAGAACATTAACTTTAGCGGCGCTTTTTCCAC
66 TTTAGCGGCGCTTTTTCCACAAA-CGCCACTATAGAACATGAACTTTAGCGACGCTTTTCCCAC
* * * **
58485374 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCAC-CTTTTCTACAAACGCCACTAAAGAGTAAGA
1 AAACGCCGCTAAAGAACAAGACCTTTAGC-G-ACGCTTTCCCAAAAACGCCACTAAAGAACAAGA
* *
58485438 CCTTTAGCGGCGCTTTTTCCACAAACGCCACTATAGAACATGACCTTTTGCGACGCTTTTCCCAC
64 CCTTTAGCGGCGCTTTTTCCACAAACGCCACTATAGAACATGAACTTTAGCGACGCTTTTCCCAC
* *
58485503 AAACGCCGCTAAAGAACATGACTTTTA
1 AAACGCCGCTAAAGAACAAGACCTTTA
58485530 AAAAATATTT
Statistics
Matches: 134, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
128 28 0.21
129 101 0.75
130 5 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCGACGCTTTCCCAAAAACGCCACTAAAGAACAAGACC
TTTAGCGGCGCTTTTTCCACAAACGCCACTATAGAACATGAACTTTAGCGACGCTTTTCCCAC
Found at i:58488427 original size:57 final size:57
Alignment explanation
Indices: 58488314--58488427 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 57
58488304 CTCCACTCCA
* * **
58488314 ACATTTACAGTTTCACCTCCATTTATTTGAATAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
58488371 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
58488428 TCGTCAACGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 47 0.94
58 3 0.06
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Found at i:58489283 original size:149 final size:149
Alignment explanation
Indices: 58488926--58489884 Score: 1349
Period size: 149 Copynumber: 6.4 Consensus size: 149
58488916 CTGTCAATTA
* * * * *
58488926 TCATAAAAACGCCACAAAAAAATTTTCATTTTGAATAAAACTACGCCGTTTTGCTAAGCTATGCT
1 TCATAAAAACGCCGCAAAAAAA-TTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCT
* * *
58488991 AAAAGAGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTC
65 AAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTG
*
58489056 CTTACTTTTAGCGGCGTTTT
130 CTTACCTTTAGCGGCGTTTT
**
58489076 T-ATGCAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
1 TCATAAAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
*
58489140 AAAGGGGGCTATTTTTTTAAAGTACAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
66 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
58489205 TTACCTTTAGCGGCGTTTT
131 TTACCTTTAGCGGCGTTTT
*
58489224 TCATAAAAACGTCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
1 TCATAAAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
* * *
58489289 AAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTTC
66 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
58489354 TTACCTTTAGCGGCGTTTT
131 TTACCTTTAGCGGCGTTTT
*** * *
58489373 T-ACGCAAACGCCGC-AAAAAATTTTATTTTTAACAAAACTACGCCGTTTTGCTATGCCATTCTA
1 TCATAAAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
58489436 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
66 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
*
58489501 TTACCTTTAGCGGCATTTT
131 TTACCTTTAGCGGCGTTTT
* *
58489520 TCATAAAAACGCCACAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCTATGCTA
1 TCATAAAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
*
58489585 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGC-ATTTTTATAAAAACGCCGCAATTGC
66 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
58489649 TTACCTTTAGCGGCGTTTT
131 TTACCTTTAGCGGCGTTTT
* * * * *
58489668 T-ATGAAAAATGCCGCAAAAAAAAATTCATTTTGAATAAAACTACGCCGTTTTGCTATGCTATGC
1 TCAT-AAAAACGCCGC-AAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGC
** * *
58489732 TAAAAGGGGGCTATTTTGTTTTTTA-TAAATTGATTTATTTTTTGCGGCCTTTTTT-TAGAAAAC
64 TAAAAGGGGGCTA-TTT-TTTTAAAGTAAA---A-TTA--TTTTGTGGCGTTTTTTATA-AAAAC
* * * *
58489795 GCCGCTATTGCTTATCTTTTGCAGCGTTTT
120 GCCGCAATTGCTTACCTTTAGCGGCGTTTT
* * * *
58489825 CCATTAAAACGCCGCAAAATATTATTTCATTTTGAACAAAA-TGACGCCGTTTTGCTATGC
1 TCATAAAAACGCCGCAAAA-A-AATTTCATTTTTAACAAAACT-ACGCCGTTTTGCTATGC
58489885 TAAAAAAATT
Statistics
Matches: 733, Mismatches: 57, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
147 130 0.18
148 189 0.26
149 301 0.41
150 8 0.01
151 5 0.01
153 1 0.00
154 3 0.00
156 14 0.02
157 47 0.06
158 35 0.05
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (149 bp):
TCATAAAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCAATTGC
TTACCTTTAGCGGCGTTTT
Found at i:58489509 original size:296 final size:297
Alignment explanation
Indices: 58488926--58489886 Score: 1419
Period size: 296 Copynumber: 3.2 Consensus size: 297
58488916 CTGTCAATTA
* *
58488926 TCATAAAAACGCCACAAAAAAATTTTCATTTTGAATAAAACTACGCCGTTTTGCTAAGCTATGCT
1 TCATAAAAACGCCACAAAAAAA-TTTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCT
*
58488991 AAAAGAGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTC
65 AAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTC
*
58489056 CTTACTTTTAGCGGCGTTTTTATGCAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCC
130 CTTACCTTTAGCGGCGTTTTTATGCAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCC
*
58489121 GTTTTGCTATGCCATGCTAAAAGGGGGCTATTTTTTTAAAGTACAATTATTTTGTGGCGTTTTTT
195 GTTTTGCTATGCCATGCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTT
58489186 ATAAAAACGCCGCAATTGCTTACCTTTAGCGGCGTTTT
260 ATAAAAACGCCGCAATTGCTTACCTTTAGCGGCGTTTT
* * * *
58489224 TCATAAAAACGTCGCAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCCATGCTA
1 TCATAAAAACGCCACAAAAAAATTTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTA
* *
58489289 AAAGGGGGCTATTTTTTAAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTTC
66 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTCC
* *
58489354 TTACCTTTAGCGGCGTTTTTACGCAAACGCCGC-AAAAAATTTTATTTTTAACAAAACTACGCCG
131 TTACCTTTAGCGGCGTTTTTATGCAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCG
*
58489418 TTTTGCTATGCCATTCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTA
196 TTTTGCTATGCCATGCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTA
*
58489483 TAAAAACGCCGCAATTGCTTACCTTTAGCGGCATTTT
261 TAAAAACGCCGCAATTGCTTACCTTTAGCGGCGTTTT
*
58489520 TCATAAAAACGCCACAAAAAAATTTCATTTTTAACAAAACTACGCCGTTTTGCTATGCTATGCTA
1 TCATAAAAACGCCACAAAAAAATTTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTA
* * *
58489585 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGC-ATTTTTATAAAAACGCCGCAATTGC
66 AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTCC
* * * * *
58489649 TTACCTTTAGCGGCGTTTTTATGAAAAATGCCGCAAAAAAAAATTCATTTTGAATAAAACTACGC
131 TTACCTTTAGCGGCGTTTTTATG-CAAACGCCGC-AAAAAAATTTCATTTTTAACAAAACTACGC
* ** *
58489714 CGTTTTGCTATGCTATGCTAAAAGGGGGCTATTTTGTTTTTTA-TAAATTGATTTATTTTTTGCG
194 CGTTTTGCTATGCCATGCTAAAAGGGGGCTA-TTT-TTTTAAAGTAAA---A-TTA--TTTTGTG
* * * * *
58489778 GCCTTTTTT-TAGAAAACGCCGCTATTGCTTATCTTTTGCAGCGTTTT
251 GCGTTTTTTATA-AAAACGCCGCAATTGCTTACCTTTAGCGGCGTTTT
* * * *
58489825 CCATTAAAACGCCGCAAAATATTATTTCATTTTGAACAAAA-TGACGCCGTTTTGCTATGCTA
1 TCATAAAAACGCCACAAAA-A-AATTTCATTTTGAACAAAACT-ACGCCGTTTTGCTATGCTA
58489887 AAAAAATTTT
Statistics
Matches: 603, Mismatches: 45, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
295 44 0.07
296 237 0.39
297 132 0.22
298 74 0.12
299 7 0.01
300 5 0.01
302 1 0.00
303 3 0.00
304 2 0.00
305 60 0.10
306 2 0.00
307 36 0.06
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (297 bp):
TCATAAAAACGCCACAAAAAAATTTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTATGCTA
AAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTCC
TTACCTTTAGCGGCGTTTTTATGCAAACGCCGCAAAAAAATTTCATTTTTAACAAAACTACGCCG
TTTTGCTATGCCATGCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTA
TAAAAACGCCGCAATTGCTTACCTTTAGCGGCGTTTT
Found at i:58489919 original size:15 final size:15
Alignment explanation
Indices: 58489899--58489927 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58489889 AAAATTTTAT
58489899 TTTATTTTTTATAAA
1 TTTATTTTTTATAAA
58489914 TTTATTTTTTATAA
1 TTTATTTTTTATAA
58489928 TAAAAAAAAC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTTTTATAAA
Found at i:58490497 original size:14 final size:14
Alignment explanation
Indices: 58490478--58490539 Score: 90
Period size: 14 Copynumber: 4.4 Consensus size: 14
58490468 AACCTTAAAT
58490478 CCCTAAC-TCTTAAC
1 CCCTAACATC-TAAC
58490492 CCCTAACATCTAAC
1 CCCTAACATCTAAC
58490506 CCCTAACATCTAAC
1 CCCTAACATCTAAC
**
58490520 CCCTAACCCCTAAC
1 CCCTAACATCTAAC
58490534 CCCTAA
1 CCCTAA
58490540 ACCTTAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 43 0.96
15 2 0.04
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (14 bp):
CCCTAACATCTAAC
Found at i:58490498 original size:7 final size:7
Alignment explanation
Indices: 58490478--58490539 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
58490468 AACCTTAAAT
58490478 CCCTAAC
1 CCCTAAC
* *
58490485 TCTTAAC
1 CCCTAAC
58490492 CCCTAAC
1 CCCTAAC
**
58490499 ATCTAAC
1 CCCTAAC
58490506 CCCTAAC
1 CCCTAAC
**
58490513 ATCTAAC
1 CCCTAAC
58490520 CCCTAAC
1 CCCTAAC
58490527 CCCTAAC
1 CCCTAAC
58490534 CCCTAA
1 CCCTAA
58490540 ACCTTAAATC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:58490580 original size:14 final size:14
Alignment explanation
Indices: 58490562--58490603 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
58490552 AACACTTAAA
58490562 CCATAATCCCTAAT
1 CCATAATCCCTAAT
*
58490576 TCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
58490591 CCATACTCCCTAA
1 CCATAATCCCTAA
58490604 ACCTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:58490600 original size:15 final size:15
Alignment explanation
Indices: 58490558--58490604 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
58490548 TCCAAACACT
58490558 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
58490572 T-AATTCATAATCCC
1 TAAATCCATAATCCC
*
58490586 TAAATCCATACTCCC
1 TAAATCCATAATCCC
58490601 TAAA
1 TAAA
58490605 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:58490825 original size:7 final size:7
Alignment explanation
Indices: 58490805--58490887 Score: 60
Period size: 7 Copynumber: 11.6 Consensus size: 7
58490795 CCTAGCACAT
58490805 CTAACCC
1 CTAACCC
58490812 CTAAACCC
1 CT-AACCC
58490820 CTAACCC
1 CTAACCC
58490827 TCTAACCC
1 -CTAACCC
58490835 CTAACCC
1 CTAACCC
* *
58490842 TTAAATCC
1 CT-AACCC
58490850 C-AACCC
1 CTAACCC
*
58490856 CTAATCC
1 CTAACCC
* *
58490863 ATAATCC
1 CTAACCC
*
58490870 CTAATCC
1 CTAACCC
* *
58490877 ATAATCC
1 CTAACCC
58490884 CTAA
1 CTAA
58490888 ACCCATACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
6 5 0.08
7 40 0.63
8 18 0.29
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAACCC
Found at i:58490825 original size:15 final size:15
Alignment explanation
Indices: 58490805--58490859 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
58490795 CCTAGCACAT
58490805 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
58490820 CTAACCCTCT-AACCC
1 CTAACCC-CTAAACCC
* *
58490835 CTAACCCTTAAATCC
1 CTAACCCCTAAACCC
58490850 C-AACCCCTAA
1 CTAACCCCTAA
58490860 TCCATAATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 9 0.26
15 24 0.69
16 2 0.06
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:58490871 original size:14 final size:14
Alignment explanation
Indices: 58490854--58490902 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
58490844 AAATCCCAAC
58490854 CCCTAATCCATAAT
1 CCCTAATCCATAAT
58490868 CCCTAATCCATAAT
1 CCCTAATCCATAAT
* *
58490882 CCCTAAACCCATACT
1 CCCT-AATCCATAAT
58490897 CCCTAA
1 CCCTAA
58490903 ACCGGCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAATCCATAAT
Found at i:58490899 original size:15 final size:15
Alignment explanation
Indices: 58490861--58490905 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
58490851 AACCCCTAAT
*
58490861 CCATAATCCCT-AAT
1 CCATAATCCCTAAAC
58490875 CCATAATCCCTAAAC
1 CCATAATCCCTAAAC
*
58490890 CCATACTCCCTAAAC
1 CCATAATCCCTAAAC
58490905 C
1 C
58490906 GGCCTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (15 bp):
CCATAATCCCTAAAC
Found at i:58491206 original size:73 final size:73
Alignment explanation
Indices: 58491055--58491280 Score: 323
Period size: 73 Copynumber: 3.1 Consensus size: 73
58491045 TATTTTTTTT
* * *
58491055 GCCGCTAAATCCCCGAAAGCTCACAAAACAGCGTCATTTGGCTTA--TTTTTTTGCGGCACTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
*
58491118 TTAAAAAT
66 TTAAAAAC
* * *
58491126 GCCGCTAAATACCCAAAAGCTCACAAAACGGCGTGGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
58491191 TTAAAAAC
66 TTAAAAAC
* * *
58491199 GCCGCTAAATCCCCGAAAGCCCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGC-TTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
*
58491263 TTCCAAAAC
66 TT-AAAAAC
58491272 GCCGCTAAA
1 GCCGCTAAA
58491281 GCCCTGACCA
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
71 40 0.29
72 5 0.04
73 93 0.67
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (73 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
TTAAAAAC
Found at i:58491433 original size:113 final size:113
Alignment explanation
Indices: 58491180--58491487 Score: 492
Period size: 113 Copynumber: 2.7 Consensus size: 113
58491170 ATGTTTTTTT
*
58491180 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCCCACAAAACGACGTCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGCTTAT
* *
58491245 GTTTTTTTGCGGCGCTTCTTCCAAAACGCCGCTAAAGCCCTGACCATTA
66 G-TTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGACCATTA
* **
58491294 GCGGCGCTTTCTTAAAAACGCTGCTAAATCCCCAAAAGCCCACAAAACGGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGCTTAT
58491359 GTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGACCATTA
66 GTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGACCATTA
* *
58491407 GCGGCGC-TTCATTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTCGTTGGGCTTA
1 GCGGCGCTTTC-TTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGCTTA
* * *
58491471 GGTTGTTTGTGGCGCTT
65 TGTTTTTTGCGGCGCTT
58491488 TTTGGAAAAT
Statistics
Matches: 179, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
112 3 0.02
113 114 0.64
114 62 0.35
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (113 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGCTTAT
GTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGACCATTA
Found at i:58492565 original size:101 final size:101
Alignment explanation
Indices: 58492390--58492591 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 101
58492380 TAACTAAGTG
*
58492390 TCAGTTGCTGACTCAGTCTCGAACAACTAATTTCTTATCCTATTTGATATCCAAGAGGCAACTCA
1 TCAGTTGCTGACTCAGTCTCGAACAACTAATTTCTTATCCTATTCGATATCCAAGAGGCAACTCA
58492455 TTTGAAATTACTTCTCTAACTGATAAATAATCTTGT
66 TTTGAAATTACTTCTCTAACTGATAAATAATCTTGT
*
58492491 TCAGTTGCTGACTCAGTCTCGAACAACTAATTTCTTATCCTATTCGATATCCAAGAGGCAGCTCA
1 TCAGTTGCTGACTCAGTCTCGAACAACTAATTTCTTATCCTATTCGATATCCAAGAGGCAACTCA
58492556 TTTGAAATTACTTCTCTAACTGATAAATAATCTTGT
66 TTTGAAATTACTTCTCTAACTGATAAATAATCTTGT
58492592 AACTCAACGC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (101 bp):
TCAGTTGCTGACTCAGTCTCGAACAACTAATTTCTTATCCTATTCGATATCCAAGAGGCAACTCA
TTTGAAATTACTTCTCTAACTGATAAATAATCTTGT
Found at i:58495986 original size:50 final size:50
Alignment explanation
Indices: 58495871--58496119 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
58495861 GATAATAACA
* * ** * *
58495871 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
58495922 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
58495972 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
58496022 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
58496077 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
58496120 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
50 90 0.54
51 33 0.20
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:58496057 original size:100 final size:104
Alignment explanation
Indices: 58495870--58496119 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 104
58495860 TGATAATAAC
** * *
58495870 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
58495935 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* * *
58495972 -TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
58496036 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
58496077 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
58496120 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
100 48 0.37
101 35 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:58496235 original size:13 final size:13
Alignment explanation
Indices: 58496214--58496244 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58496204 GCTTAGATCA
*
58496214 TCATCAAATAAAT
1 TCATAAAATAAAT
58496227 TCATAAAATAAAT
1 TCATAAAATAAAT
58496240 TCATA
1 TCATA
58496245 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:58496492 original size:30 final size:29
Alignment explanation
Indices: 58496456--58496512 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
58496446 CCTCGACTCT
*
58496456 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTACAAAATTAC-ATTTTACCCCTA
* *
58496486 AACTTTTACATAATTACATTTTGCCCC
1 AACTTTTACAAAATTACATTTTACCCC
58496513 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTACCCCTA
Found at i:58502514 original size:26 final size:26
Alignment explanation
Indices: 58502485--58502552 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
58502475 CTAGTTTGGC
58502485 AATGCTTTTGAAAAGTACTTTTGAAA
1 AATGCTTTTGAAAAGTACTTTTGAAA
* * * *
58502511 AATGC-TATGAAAAAATGCTTTTGAGA
1 AATGCTTTTG-AAAAGTACTTTTGAAA
* *
58502537 AGTGTTTTTGAAAAGT
1 AATGCTTTTGAAAAGT
58502553 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 3 0.09
26 26 0.81
27 3 0.09
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (26 bp):
AATGCTTTTGAAAAGTACTTTTGAAA
Found at i:58502781 original size:24 final size:24
Alignment explanation
Indices: 58502747--58502792 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
58502737 TATATGAAAT
* *
58502747 ATAAATTTTAAATATTTTTAAGCA
1 ATAAATATTAAATATTTATAAGCA
*
58502771 ATAAATATTAATTATTTATAAG
1 ATAAATATTAAATATTTATAAG
58502793 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAGCA
Found at i:58502891 original size:19 final size:20
Alignment explanation
Indices: 58502859--58502896 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
58502849 TTGTAATTAG
58502859 TATTTTAAAAAAT-ATTTTT
1 TATTTTAAAAAATAATTTTT
**
58502878 TATTTTAATTAATAATTTT
1 TATTTTAAAAAATAATTTT
58502897 AACACATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTAAAAAATAATTTTT
Found at i:58504261 original size:22 final size:22
Alignment explanation
Indices: 58504236--58504282 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
58504226 GTTACAGAAA
58504236 GAAGATAGGTCTTCGCCTAAAG
1 GAAGATAGGTCTTCGCCTAAAG
58504258 GAAGATAGGTCTTCGCCTAAAG
1 GAAGATAGGTCTTCGCCTAAAG
58504280 GAA
1 GAA
58504283 AATCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (22 bp):
GAAGATAGGTCTTCGCCTAAAG
Found at i:58504474 original size:83 final size:83
Alignment explanation
Indices: 58504331--58504506 Score: 345
Period size: 83 Copynumber: 2.1 Consensus size: 83
58504321 ATTTAAGTCC
58504331 TTTA-AAACAATTTATTTGATAAATTTAAGACTTAAAACGCAAAAGAAAAAAATAAATAAATAAC
1 TTTATAAACAATTTATTTGATAAATTTAAGACTTAAAACGCAAAAGAAAAAAATAAATAAATAAC
58504395 CTTTGAGCCTTAGCTATT
66 CTTTGAGCCTTAGCTATT
58504413 TTTATAAACAATTTATTTGATAAATTTAAGACTTAAAACGCAAAAGAAAAAAATAAATAAATAAC
1 TTTATAAACAATTTATTTGATAAATTTAAGACTTAAAACGCAAAAGAAAAAAATAAATAAATAAC
58504478 CTTTGAGCCTTAGCTATT
66 CTTTGAGCCTTAGCTATT
58504496 TTTATAAACAA
1 TTTATAAACAA
58504507 GTTCTCATCT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 4 0.04
83 89 0.96
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (83 bp):
TTTATAAACAATTTATTTGATAAATTTAAGACTTAAAACGCAAAAGAAAAAAATAAATAAATAAC
CTTTGAGCCTTAGCTATT
Found at i:58526098 original size:18 final size:18
Alignment explanation
Indices: 58526075--58526164 Score: 144
Period size: 18 Copynumber: 5.0 Consensus size: 18
58526065 CCCAACTACT
*
58526075 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
58526093 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
58526111 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
58526129 GTATATGTGAATAGTGCC
1 GTATACGTGAATAGTACC
58526147 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
58526165 ATAAACGGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:58531036 original size:44 final size:44
Alignment explanation
Indices: 58530962--58531089 Score: 154
Period size: 44 Copynumber: 2.9 Consensus size: 44
58530952 CCACTCTTTG
* * *
58530962 TTTTTTGCTTTC-TAATTCTCG-AATCCGTGTTTCTGATCATTTCC
1 TTTTTTGCTTCCAT-ATTCT-GAAATCTGTGTTTGTGATCATTTCC
*
58531006 TTTTTTGCTTCCATATTC-GCAAATCTGTGTTTGTGGTCATTTCC
1 TTTTTTGCTTCCATATTCTG-AAATCTGTGTTTGTGATCATTTCC
* *
58531050 TTTTTTGCTTCCATATTCTGAGATCTGTGTCTGTGATCAT
1 TTTTTTGCTTCCATATTCTGAAATCTGTGTTTGTGATCAT
58531090 CACCAAAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
42 1 0.01
44 70 0.96
45 2 0.03
ACGTcount: A:0.14, C:0.20, G:0.15, T:0.51
Consensus pattern (44 bp):
TTTTTTGCTTCCATATTCTGAAATCTGTGTTTGTGATCATTTCC
Found at i:58533688 original size:17 final size:15
Alignment explanation
Indices: 58533666--58533713 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 15
58533656 TTCATGCTAT
58533666 ATTTTTTTAATTTTA
1 ATTTTTTTAATTTTA
*
58533681 TGATTTTTTTTAATTTCA
1 --A-TTTTTTTAATTTTA
58533699 ATTTTTTTATATTTT
1 ATTTTTTTA-ATTTT
58533714 TGAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 1 0.04
18 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
ATTTTTTTAATTTTA
Found at i:58533874 original size:28 final size:28
Alignment explanation
Indices: 58533843--58533896 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
58533833 AATTAAGTGT
*
58533843 TATATAT-ATATTAAAGTAAATATTAAAA
1 TATATATAATATTAAA-TAAAAATTAAAA
*
58533871 TATATATAATATTCAATAAAAATTAA
1 TATATATAATATTAAATAAAAATTAA
58533897 TTAAGAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TATATATAATATTAAATAAAAATTAAAA
Found at i:58545783 original size:16 final size:17
Alignment explanation
Indices: 58545746--58545785 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
58545736 TGTAATATTC
58545746 ATATTATAAATAGTAAA
1 ATATTATAAATAGTAAA
58545763 A-ATTA-AAATAG-AGAA
1 ATATTATAAATAGTA-AA
58545778 ATATTATA
1 ATATTATA
58545786 TATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.05
15 9 0.45
16 8 0.40
17 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATTATAAATAGTAAA
Found at i:58554047 original size:16 final size:17
Alignment explanation
Indices: 58554010--58554049 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
58554000 TGTAATATTC
58554010 ATATTATAAATAGTAAA
1 ATATTATAAATAGTAAA
58554027 A-ATTA-AAATAG-AGAA
1 ATATTATAAATAGTA-AA
58554042 ATATTATA
1 ATATTATA
58554050 TATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.05
15 9 0.45
16 8 0.40
17 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATTATAAATAGTAAA
Found at i:58562309 original size:16 final size:17
Alignment explanation
Indices: 58562272--58562311 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
58562262 TGTAATATTC
58562272 ATATTATAAATAGTAAA
1 ATATTATAAATAGTAAA
58562289 A-ATTA-AAATAG-AGAA
1 ATATTATAAATAGTA-AA
58562304 ATATTATA
1 ATATTATA
58562312 TATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.05
15 9 0.45
16 8 0.40
17 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATTATAAATAGTAAA
Found at i:58570575 original size:16 final size:17
Alignment explanation
Indices: 58570538--58570577 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
58570528 TGTAATATTC
58570538 ATATTATAAATAGTAAA
1 ATATTATAAATAGTAAA
58570555 A-ATTA-AAATAG-AGAA
1 ATATTATAAATAGTA-AA
58570570 ATATTATA
1 ATATTATA
58570578 TATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.05
15 9 0.45
16 8 0.40
17 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
ATATTATAAATAGTAAA
Found at i:58578291 original size:90 final size:90
Alignment explanation
Indices: 58578139--58578309 Score: 238
Period size: 90 Copynumber: 1.9 Consensus size: 90
58578129 ACATCTACAT
*
58578139 ATTATCTGGCAGCTTTATCTTAAAAAATGTTGTATATTCACAACCATCTGGTAGCGTATTAACTT
1 ATTATCTGGCAGCTTTATCTTAAAAAATGTTGTATATTCACAACCATCTAGTAGCGTATTAACTT
* *
58578204 GTAACCTTTGGTGGTTTGCCCACCC
66 GCAACATTTGGTGGTTTGCCCACCC
* ** * *
58578229 ATTATCTGGCAGCTTTTAT-TTGCAATTATGTTGTGTATTCACAACCGTCTAGTAGC-TATTAAC
1 ATTATCTGGCAGC-TTTATCTT-AAAAAATGTTGTATATTCACAACCATCTAGTAGCGTATTAAC
58578292 TTGCAACATTTGGTGGTT
64 TTGCAACATTTGGTGGTT
58578310 CATCTACAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
90 38 0.54
91 33 0.46
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (90 bp):
ATTATCTGGCAGCTTTATCTTAAAAAATGTTGTATATTCACAACCATCTAGTAGCGTATTAACTT
GCAACATTTGGTGGTTTGCCCACCC
Found at i:58579320 original size:154 final size:154
Alignment explanation
Indices: 58579130--58579410 Score: 411
Period size: 154 Copynumber: 1.8 Consensus size: 154
58579120 CAATTGTGGA
* * *
58579130 GCTTTTTGAAAAACGCCGCTATAGGTCGAGCATTAGCAGCGCTCTTCCAAAAACGCCGCAAAAAA
1 GCTTGTTGAAAAACGCCACTATAGGTCGAGCATTAGCAGCACTCTTCCAAAAACGCCGCAAAAAA
* * **
58579195 TTAAGCACAA-GGCGGTCATTTTATGTTGAGCTTTAGTGGCATTTGCGGTGCTTTTTGAAAAAAG
66 TTAAGCACAACGGC-ATCATTTTATGTTGAGCTTTAGTGGCATTAGCGGCACTTTTTGAAAAAAG
58579259 CCGCTATAGGTCGATCATTAGCGAC
130 CCGCTATAGGTCGATCATTAGCGAC
* * * ** *
58579284 GCTTGTTGAAAAACGCCATTATAGGTCGAGCATTAGCGGCATTCTTTGAAAAACGCTGCAAAAAA
1 GCTTGTTGAAAAACGCCACTATAGGTCGAGCATTAGCAGCACTCTTCCAAAAACGCCGCAAAAAA
* *
58579349 TTAAGCACAACGTCATCATTTTATGTTGAGCTTTAGTGGCATTAGCGGCATTTTTTGAAAAA
66 TTAAGCACAACGGCATCATTTTATGTTGAGCTTTAGTGGCATTAGCGGCACTTTTTGAAAAA
58579411 CACCGCAAAT
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
154 109 0.98
155 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (154 bp):
GCTTGTTGAAAAACGCCACTATAGGTCGAGCATTAGCAGCACTCTTCCAAAAACGCCGCAAAAAA
TTAAGCACAACGGCATCATTTTATGTTGAGCTTTAGTGGCATTAGCGGCACTTTTTGAAAAAAGC
CGCTATAGGTCGATCATTAGCGAC
Found at i:58579333 original size:40 final size:39
Alignment explanation
Indices: 58579244--58579339 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
58579234 CATTTGCGGT
* * *
58579244 GCTTTTTGAAAAAAGCCGCTATAGGTCGATCATTAGCGA
1 GCTTTTTGAAAAACGCCACTATAGGTCGAGCATTAGCGA
* *
58579283 CGCTTGTTGAAAAACGCCATTATAGGTCGAGCATTAGCG-
1 -GCTTTTTGAAAAACGCCACTATAGGTCGAGCATTAGCGA
58579322 GCATTCTTTGAAAAACGC
1 GC-TT-TTTGAAAAACGC
58579340 TGCAAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
40 44 0.92
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (39 bp):
GCTTTTTGAAAAACGCCACTATAGGTCGAGCATTAGCGA
Found at i:58579722 original size:7 final size:7
Alignment explanation
Indices: 58579701--58579900 Score: 143
Period size: 7 Copynumber: 28.3 Consensus size: 7
58579691 TTAATTATCA
*
58579701 TTATAGT
1 TTATGGT
*
58579708 TTAGGGT
1 TTATGGT
58579715 TTATGGT
1 TTATGGT
*
58579722 TTAGGGT
1 TTATGGT
*
58579729 ATATGGT
1 TTATGGT
58579736 TTATGGT
1 TTATGGT
*
58579743 TTAAT-AT
1 TT-ATGGT
*
58579750 TTAGGGT
1 TTATGGT
* *
58579757 TTAGGGA
1 TTATGGT
*
58579764 TTATAGT
1 TTATGGT
58579771 TTATGGT
1 TTATGGT
58579778 TTATGGT
1 TTATGGT
*
58579785 TTAAGGT
1 TTATGGT
*
58579792 TTATGGA
1 TTATGGT
58579799 TTATGGGT
1 TTAT-GGT
* *
58579807 TTAGGGA
1 TTATGGT
58579814 TTATGGT
1 TTATGGT
*
58579821 TTACGGT
1 TTATGGT
*
58579828 TTAGGGT
1 TTATGGT
* *
58579835 TTAAGGG
1 TTATGGT
*
58579842 TTGTGGT
1 TTATGGT
58579849 TTATGGT
1 TTATGGT
* *
58579856 TTAGGGG
1 TTATGGT
*
58579863 TT-GGTGT
1 TTATG-GT
*
58579870 TTAAGGT
1 TTATGGT
*
58579877 TTAGGGGT
1 TTA-TGGT
58579885 TTATGGT
1 TTATGGT
58579892 TTATGGT
1 TTATGGT
58579899 TT
1 TT
58579901 TGGGTTTTGG
Statistics
Matches: 150, Mismatches: 37, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
6 3 0.02
7 133 0.89
8 14 0.09
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (7 bp):
TTATGGT
Found at i:58579843 original size:8 final size:7
Alignment explanation
Indices: 58579706--58579947 Score: 139
Period size: 7 Copynumber: 33.9 Consensus size: 7
58579696 TATCATTATA
58579706 GTTTAGG
1 GTTTAGG
*
58579713 GTTTATG
1 GTTTAGG
58579720 GTTTAGG
1 GTTTAGG
* *
58579727 GTATATG
1 GTTTAGG
*
58579734 GTTTATG
1 GTTTAGG
**
58579741 GTTTAAT
1 GTTTAGG
*
58579748 ATTTAGG
1 GTTTAGG
58579755 GTTTAGG
1 GTTTAGG
* **
58579762 GATTATA
1 GTTTAGG
*
58579769 GTTTATG
1 GTTTAGG
*
58579776 GTTTATG
1 GTTTAGG
*
58579783 GTTTAAG
1 GTTTAGG
*
58579790 GTTTATG
1 GTTTAGG
*
58579797 GATTATGG
1 GTTTA-GG
58579805 GTTTAGG
1 GTTTAGG
* *
58579812 GATTATG
1 GTTTAGG
*
58579819 GTTTACG
1 GTTTAGG
58579826 GTTTAGG
1 GTTTAGG
58579833 GTTTAAGG
1 GTTT-AGG
58579841 G-TT-GTG
1 GTTTAG-G
*
58579847 GTTTATG
1 GTTTAGG
58579854 GTTTAGG
1 GTTTAGG
*
58579861 GGTT-GG
1 GTTTAGG
*
58579867 TGTTTAAG
1 -GTTTAGG
58579875 GTTTAGGG
1 GTTTA-GG
*
58579883 GTTTATG
1 GTTTAGG
*
58579890 GTTTATG
1 GTTTAGG
*
58579897 GTTTTGG
1 GTTTAGG
*
58579904 GTTTTGG
1 GTTTAGG
*
58579911 GTTTGGGG
1 GTTT-AGG
58579919 GATTTAGGG
1 G-TTTA-GG
*
58579928 GTTAAGG
1 GTTTAGG
*
58579935 GTTTAAG
1 GTTTAGG
58579942 GTTTAG
1 GTTTAG
58579948 ATTAATCAGT
Statistics
Matches: 183, Mismatches: 41, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
5 1 0.01
6 4 0.02
7 150 0.82
8 22 0.12
9 6 0.03
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:58580710 original size:12 final size:12
Alignment explanation
Indices: 58580693--58580720 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
58580683 AGGGACTGTC
58580693 GTTAATCAAAAT
1 GTTAATCAAAAT
58580705 GTTAATCAAAAT
1 GTTAATCAAAAT
58580717 GTTA
1 GTTA
58580721 TTTTGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (12 bp):
GTTAATCAAAAT
Found at i:58580766 original size:15 final size:15
Alignment explanation
Indices: 58580742--58580775 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
58580732 TCAAAATAGA
58580742 AATTACTGTAAGAAT
1 AATTACTGTAAGAAT
*
58580757 AATTATTGTAAGAAT
1 AATTACTGTAAGAAT
58580772 AATT
1 AATT
58580776 TGAATTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (15 bp):
AATTACTGTAAGAAT
Found at i:58581058 original size:43 final size:43
Alignment explanation
Indices: 58581004--58581139 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 43
58580994 AGGTCATGTT
*
58581004 CTTTAGC-GCATTTTTTATAAAGGAACCGCTAAAGATAATGAC
1 CTTTAGCGGCATTTTCTATAAAGGAACCGCTAAAGATAATGAC
* * *
58581046 TTTTAGCGGCATTTGCTATAACAGCG--CCGCTAAAGATCATGAC
1 CTTTAGCGGCATTTTCTATAA-AG-GAACCGCTAAAGATAATGAC
* *
58581089 CTTTAGCGGCGTTTTCTATAAA-AACACCGCTAAAGA-ATATGAC
1 CTTTAGCGGCATTTTCTATAAAGGA-ACCGCTAAAGATA-ATGAC
58581132 CTTTAGCG
1 CTTTAGCG
58581140 CGTTTGTGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
42 7 0.09
43 68 0.87
44 2 0.03
45 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCATTTTCTATAAAGGAACCGCTAAAGATAATGAC
Found at i:58581096 original size:85 final size:84
Alignment explanation
Indices: 58580919--58581139 Score: 220
Period size: 86 Copynumber: 2.6 Consensus size: 84
58580909 ATCTGCCAAA
* *
58580919 TTTAGTGGCATTTT-TAGT-AAAATACCGCTAAAG-AATGGTACTTTTAGCGGCATTTGTAAAAT
1 TTTAGCGGCATTTTCTA-TAAAAACACCGCTAAAGAAAT-G-ACTTTTAGCGGCATTTGT--AAT
* * **
58580981 AAAGTGCCGCTAAAGGTCATGTTC
61 AAAGCGCCGCTAAAGATCATGACC
* *
58581005 TTTAGC-GCATTTTTTATAAAGGA-ACCGCTAAAGATAATGACTTTTAGCGGCATTTGCT-ATAA
1 TTTAGCGGCATTTTCTATAAA-AACACCGCTAAAGA-AATGACTTTTAGCGGCATTTG-TAATAA
58581067 CAGCGCCGCTAAAGATCATGACC
63 -AGCGCCGCTAAAGATCATGACC
* *
58581090 TTTAGCGGCGTTTTCTATAAAAACACCGCTAAAGAATATGACCTTTAGCG
1 TTTAGCGGCATTTTCTATAAAAACACCGCTAAAGAA-ATGACTTTTAGCG
58581140 CGTTTGTGAA
Statistics
Matches: 115, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
84 4 0.03
85 34 0.30
86 71 0.62
87 3 0.03
88 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (84 bp):
TTTAGCGGCATTTTCTATAAAAACACCGCTAAAGAAATGACTTTTAGCGGCATTTGTAATAAAGC
GCCGCTAAAGATCATGACC
Found at i:58583309 original size:22 final size:23
Alignment explanation
Indices: 58583272--58583314 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
58583262 ACTTCTATAT
58583272 TTAATTTTTATACTTTAATTTAA
1 TTAATTTTTATACTTTAATTTAA
*
58583295 TTAATTTTTGT-CTTTAATTT
1 TTAATTTTTATACTTTAATTT
58583315 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (23 bp):
TTAATTTTTATACTTTAATTTAA
Found at i:58584063 original size:24 final size:24
Alignment explanation
Indices: 58584011--58584065 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
58584001 TTTCTTCGTA
*
58584011 TTATATATTAAATTTTCCAAATAT
1 TTATATATTAAATTTTACAAATAT
*
58584035 ATATAT-TTAAAGTTTCTACAAAT-T
1 TTATATATTAAA-TTT-TACAAATAT
58584059 TTATATA
1 TTATATA
58584066 ATTTTCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATATATTAAATTTTACAAATAT
Found at i:58584591 original size:16 final size:16
Alignment explanation
Indices: 58584572--58584604 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
58584562 TTTATTTTAG
58584572 AGCATATAAATTTGAA
1 AGCATATAAATTTGAA
*
58584588 AGCATATATATTTGAA
1 AGCATATAAATTTGAA
58584604 A
1 A
58584605 CTCTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (16 bp):
AGCATATAAATTTGAA
Found at i:58588600 original size:13 final size:14
Alignment explanation
Indices: 58588582--58588613 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
58588572 ACAACCACAG
58588582 TAATAAAATAA-AA
1 TAATAAAATAATAA
58588595 TAAT-AAATAATAA
1 TAATAAAATAATAA
58588608 TAATAA
1 TAATAA
58588614 TAAATTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 10 0.59
14 1 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAATAAAATAATAA
Found at i:58588614 original size:16 final size:15
Alignment explanation
Indices: 58588588--58588618 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
58588578 ACAGTAATAA
58588588 AATAAAATAATAAAT
1 AATAAAATAATAAAT
58588603 AATAATAATAATAAAT
1 AATAA-AATAATAAAT
58588619 TGACATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:58588865 original size:28 final size:29
Alignment explanation
Indices: 58588809--58588871 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
58588799 CAAAAGATAT
58588809 AAACAAATACATAATGATAACATATAATA
1 AAACAAATACATAATGATAACATATAATA
58588838 AAACAAATACATAATGAT-A-ATATCAATA
1 AAACAAATACATAATGATAACATAT-AATA
58588866 AAACAA
1 AAACAA
58588872 TATCAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 4 0.12
28 11 0.33
29 18 0.55
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.22
Consensus pattern (29 bp):
AAACAAATACATAATGATAACATATAATA
Found at i:58588887 original size:28 final size:27
Alignment explanation
Indices: 58588809--58588887 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 27
58588799 CAAAAGATAT
*
58588809 AAACAAATACATAATGATAACATATAATA
1 AAACAAATAAATAATGAT-A-ATATAATA
*
58588838 AAACAAATACATAATGATAATATCAATA
1 AAACAAATAAATAATGATAATAT-AATA
58588866 AAACAATATCAAAT-ATGA-AATA
1 AAACAA-AT-AAATAATGATAATA
58588888 AAGATAACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 4 0.09
28 15 0.33
29 24 0.52
30 3 0.07
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.24
Consensus pattern (27 bp):
AAACAAATAAATAATGATAATATAATA
Found at i:58590926 original size:132 final size:129
Alignment explanation
Indices: 58590489--58591024 Score: 520
Period size: 129 Copynumber: 4.0 Consensus size: 129
58590479 ATCGTTAGTG
* * * * *
58590489 TTGA-CTGCTCCACTACTGCTTAGGGGGAACAGAATCTACAAGTCTTTGACCTACTCCACTTATT
1 TTGATCTGATCCACTA-TGCTTAGGGTG-ACAGAATCTGCAA---TTTAACCTACTCCACTTACT
* *
58590553 GCTTTAGGGTGATTAGGCGAACCTAATGGCTTTATAATCTGCTTTTCCACTATATTGGGAAGATA
61 GC-TTAGGGTGA-TA-G-G-A-CTAATGGC-TTA-AATCTGC-TCTCCACTGTATT-GGAAGATA
*
58590618 TGATTCACC-TCATCT
116 AGATTCACCATC-T-T
*
58590633 TTGATCTGCA-CCACTACTGCTTAGGGTGACAGGAATCTGCATTTTAACCTACTCCAC-TACTGC
1 TTGATCTG-ATCCACTA-TGCTTAGGGTGACA-GAATCTGCAATTTAACCTACTCCACTTACTGC
* * *
58590696 TTAGGGTGATAGGCCTAATGGCTTAAATCTGCTCTCCCCTGTATTGGAACCATAAGA-TCACCAT
63 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTCTCCACTGTATTGGAA-GATAAGATTCACCAT
58590760 C-T
127 CTT
* *
58590762 TTGATCTGATTCCACTACGCTTAGGGTG-CAGAATCTGCAATCCTCAACCTACTCCAC-TACCTG
1 TTGATCTGA-TCCACTATGCTTAGGGTGACAGAATCTGCAAT--TTAACCTACTCCACTTA-CTG
* * * *
58590825 CTTA-GGTGATAGGGAACTAAAGGCTCTAAATTTGCTTTCCACTGTATTGGGAAAATAAGATTCA
62 CTTAGGGTGATA-GG-ACTAATGGCT-TAAATCTGCTCTCCACTGTATT-GGAAGATAAGATTCA
58590889 CCATCTT
123 CCATCTT
*
58590896 TTGATCTGATCCAC-ATG-TTAGGGTGACAGAATCTGGCAATTTAACCTACTGCCACTTACTGGT
1 TTGATCTGATCCACTATGCTTAGGGTGACAGAATCT-GCAATTTAACCTACT-CCACTTACTGCT
*
58590959 TAGGGTGATAGGACT-ATGGCTTAAATCTGCTCTCCACTGTATTAGAAGATACAGATTCACCATC
64 TAGGGTGATAGGACTAATGGCTTAAATCTGCTCTCCACTGTATTGGAAGATA-AGATTCACCATC
58591023 TT
128 TT
58591025 CGATCTACTC
Statistics
Matches: 341, Mismatches: 29, Indels: 59
0.79 0.07 0.14
Matches are distributed among these distances:
127 10 0.03
128 9 0.03
129 75 0.22
130 20 0.06
131 37 0.11
132 64 0.19
133 38 0.11
134 13 0.04
135 8 0.02
137 1 0.00
138 1 0.00
139 2 0.01
140 9 0.03
141 5 0.01
142 14 0.04
144 7 0.02
145 28 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (129 bp):
TTGATCTGATCCACTATGCTTAGGGTGACAGAATCTGCAATTTAACCTACTCCACTTACTGCTTA
GGGTGATAGGACTAATGGCTTAAATCTGCTCTCCACTGTATTGGAAGATAAGATTCACCATCTT
Found at i:58591068 original size:44 final size:45
Alignment explanation
Indices: 58591020--58591247 Score: 168
Period size: 46 Copynumber: 5.0 Consensus size: 45
58591010 CAGATTCACC
* *
58591020 ATCTTCGATCTACT-C-CTGCAGAATACAGGAAGATAAGATTTGCT
1 ATCTTCGATCT-CTCCGCTGCAGAATACAGGAAGAAAAGATCTGCT
* *
58591064 ATCTTCGATCTCTCTCCGCTGC-CAATAC-GGAAGACAAGATCTGC-
1 ATCTTCGA--TCTCTCCGCTGCAGAATACAGGAAGAAAAGATCTGCT
* *
58591108 ATCTTTGATCTCTCCGCTGCAGTAATACAGGAAGACAAAGATCTGTT
1 ATCTTCGATCTCTCCGCTGCAG-AATACAGGAAGA-AAAGATCTGCT
* *
58591155 ATATTCGATCTCCAGTCCGCTGC--CATACAGG-AGAACAAGATCTGCT
1 ATCTTCGATCT-C--TCCGCTGCAGAATACAGGAAGAA-AAGATCTGCT
* ** * *
58591201 ATCTTTGATCTCCTCTACTGCA-AACGTACAAGAAGACAAGATCTGCT
1 ATCTTCGATCT-CTCCGCTGCAGAA--TACAGGAAGAAAAGATCTGCT
58591248 TCTATTGATC
Statistics
Matches: 149, Mismatches: 18, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
42 12 0.08
44 26 0.17
45 24 0.16
46 40 0.27
47 35 0.23
48 4 0.03
50 8 0.05
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
ATCTTCGATCTCTCCGCTGCAGAATACAGGAAGAAAAGATCTGCT
Found at i:58591258 original size:93 final size:91
Alignment explanation
Indices: 58591019--58591289 Score: 240
Period size: 94 Copynumber: 3.0 Consensus size: 91
58591009 ACAGATTCAC
* * * * * *
58591019 CATCTTCGATCTACT-C-CTGCAGAATACAGGAAGA-TAAGATTTGCTATCTTCGATCTCTC--T
1 CATCTTTGATCT-CTCCACTGCAGAATACAAGAAGACAAAGATCTGTTATATTCGATCTC-CAGT
58591079 CCGCTGCCAATACGGAAGACAAGATCTG
64 CCGCTGCCAATACGGAAGACAAGATCTG
* *
58591107 CATCTTTGATCTCTCCGCTGCAGTAATACAGGAAGACAAAGATCTGTTATATTCGATCTCCAGTC
1 CATCTTTGATCTCTCCACTGCAG-AATACAAGAAGACAAAGATCTGTTATATTCGATCTCCAGTC
58591172 CGCTGCC-ATACAGG-AGAACAAGATCTG
65 CGCTGCCAATAC-GGAAG-ACAAGATCTG
* *
58591199 CTATCTTTGATCTCCTCTACTGCA-AACGTACAAGAAGAC-AAGATCTGCTTCTATT-GATCTCC
1 C-ATCTTTGATCT-CTCCACTGCAGAA--TACAAGAAGACAAAGATCTG-TTATATTCGATCTCC
* * *
58591261 -CTCCGCTACCAAATATAGGAAGACAAGAT
61 AGTCCGCTGCC-AATA-CGGAAGACAAGAT
58591290 GCTTGCTAAT
Statistics
Matches: 154, Mismatches: 12, Indels: 28
0.79 0.06 0.14
Matches are distributed among these distances:
87 2 0.01
88 12 0.08
89 6 0.04
90 13 0.08
91 25 0.16
92 32 0.21
93 26 0.17
94 36 0.23
95 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (91 bp):
CATCTTTGATCTCTCCACTGCAGAATACAAGAAGACAAAGATCTGTTATATTCGATCTCCAGTCC
GCTGCCAATACGGAAGACAAGATCTG
Found at i:58591283 original size:47 final size:45
Alignment explanation
Indices: 58591041--58591289 Score: 183
Period size: 47 Copynumber: 5.4 Consensus size: 45
58591031 ACTCCTGCAG
* * * *
58591041 AATACAGGAAGATAAGATTTGCTATCTTCGATCTCTCTCCGCTGCC-
1 AATACAGGAAGACAAGATCTGCT-TCTTTGATCTCCCTCCGCT-CCA
* *
58591087 AATAC-GGAAGACAAGATCTGCATCTTTGATCT--CTCCGCTGCA
1 AATACAGGAAGACAAGATCTGCTTCTTTGATCTCCCTCCGCTCCA
* *
58591129 GTAATACAGGAAGACAAAGATCTG-TTATATTCGATCTCCAGTCCGCTGCC-
1 --AATACAGGAAGAC-AAGATCTGCTTCT-TT-GATCTCC-CTCCGCT-CCA
** *
58591179 -ATACAGG-AGAACAAGATCTGCTATCTTTGATCT-CCTCTACTGCA
1 AATACAGGAAG-ACAAGATCTGCT-TCTTTGATCTCCCTCCGCTCCA
*
58591223 AACGTACAAGAAGACAAGATCTGCTTCTATTGATCTCCCTCCGCTACCA
1 AA--TACAGGAAGACAAGATCTGCTTCT-TTGATCTCCCTCCGCT-CCA
*
58591272 AATATAGGAAGACAAGAT
1 AATACAGGAAGACAAGAT
58591290 GCTTGCTAAT
Statistics
Matches: 161, Mismatches: 20, Indels: 43
0.72 0.09 0.19
Matches are distributed among these distances:
41 1 0.01
42 7 0.04
43 1 0.01
44 18 0.11
45 25 0.16
46 33 0.20
47 55 0.34
48 10 0.06
49 4 0.02
50 6 0.04
51 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
AATACAGGAAGACAAGATCTGCTTCTTTGATCTCCCTCCGCTCCA
Found at i:58593299 original size:6 final size:6
Alignment explanation
Indices: 58593288--58593321 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
58593278 CCTTGACCTC
*
58593288 TCTTTT TCTTTT TTTTTT TCTTTTT TCTTTT TCT
1 TCTTTT TCTTTT TCTTTT TC-TTTT TCTTTT TCT
58593322 CCTATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TCTTTT
Found at i:58593351 original size:21 final size:21
Alignment explanation
Indices: 58593326--58593382 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 21
58593316 TTTTCTCCTA
*
58593326 TTTTTGATTGATTTTTTTTATG
1 TTTTTGATTGATTTTTTTT-GG
58593348 TTTTTGATT--TTTTTTTTGG
1 TTTTTGATTGATTTTTTTTGG
*
58593367 -ATTTG-TTGATTTTTTT
1 TTTTTGATTGATTTTTTT
58593383 AAGCTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 2 0.06
18 4 0.13
19 8 0.26
20 8 0.26
22 9 0.29
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.75
Consensus pattern (21 bp):
TTTTTGATTGATTTTTTTTGG
Found at i:58593356 original size:18 final size:21
Alignment explanation
Indices: 58593328--58593382 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 21
58593318 TTCTCCTATT
58593328 TTTGATTGATTTTTTTTAT-G-
1 TTTG-TTGATTTTTTTTATGGA
*
58593348 TTT-TTGATTTTTTTTTTGGA
1 TTTGTTGATTTTTTTTATGGA
58593368 TTTGTTGATTTTTTT
1 TTTGTTGATTTTTTT
58593383 AAGCTTGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 13 0.42
19 1 0.03
20 6 0.19
21 11 0.35
ACGTcount: A:0.11, C:0.00, G:0.15, T:0.75
Consensus pattern (21 bp):
TTTGTTGATTTTTTTTATGGA
Found at i:58601277 original size:26 final size:28
Alignment explanation
Indices: 58601242--58601294 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
58601232 GGTAATTTTC
58601242 TTTCATTTGCTTCATTCATGAC-ATGCT
1 TTTCATTTGCTTCATTCATGACTATGCT
58601269 TTTC-TTTGCTTCATTCATGACTATGC
1 TTTCATTTGCTTCATTCATGACTATGC
58601295 AATGATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTCATTTGCTTCATTCATGACTATGCT
Found at i:58610458 original size:14 final size:14
Alignment explanation
Indices: 58610439--58610467 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58610429 TCATGCATAA
58610439 ATGAAAATGTTCCG
1 ATGAAAATGTTCCG
58610453 ATGAAAATGTTCCG
1 ATGAAAATGTTCCG
58610467 A
1 A
58610468 CATGGTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (14 bp):
ATGAAAATGTTCCG
Found at i:58613036 original size:21 final size:23
Alignment explanation
Indices: 58613004--58613046 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
58612994 TATTTATTTC
58613004 TTTTAAATATTAA-A-AAAATTA
1 TTTTAAATATTAATATAAAATTA
58613025 TTTT-AATAATTAATATAAAATT
1 TTTTAAAT-ATTAATATAAAATT
58613047 TTGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 1 0.05
23 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTAAATATTAATATAAAATTA
Found at i:58613577 original size:3 final size:3
Alignment explanation
Indices: 58613569--58613605 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
58613559 TGTTTAAAAT
58613569 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
58613606 TAGGGCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58615286 original size:31 final size:30
Alignment explanation
Indices: 58615245--58615303 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
58615235 TACAAAACGA
*
58615245 TTACTAAACTATTCGAAAGTTTTCATTTAAG
1 TTACTAAACTATTCGAAAATTTT-ATTTAAG
* *
58615276 TTACTTAACTATTTGAAAATTTTATTTA
1 TTACTAAACTATTCGAAAATTTTATTTA
58615304 GGTCATTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (30 bp):
TTACTAAACTATTCGAAAATTTTATTTAAG
Found at i:58617110 original size:60 final size:60
Alignment explanation
Indices: 58616984--58617102 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
58616974 TATATTTTTT
* ** * * * *
58616984 AATTTTTAGAGTTAGGACTAAATTAATAGATTTTGTAAACATTGAGGGTTAAATTTATTA
1 AATTTTTAGAATTAAAACTAAAATAATAAATTTTGTAAACATTGAGAGATAAATTTATTA
* *
58617044 AATTTTTAGAATTAAAACTAAAATGATAAATTTTGTAAACATTTAGAGATAAATTTATT
1 AATTTTTAGAATTAAAACTAAAATAATAAATTTTGTAAACATTGAGAGATAAATTTATT
58617103 GATTTTTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (60 bp):
AATTTTTAGAATTAAAACTAAAATAATAAATTTTGTAAACATTGAGAGATAAATTTATTA
Found at i:58618059 original size:61 final size:60
Alignment explanation
Indices: 58617992--58618140 Score: 149
Period size: 61 Copynumber: 2.4 Consensus size: 60
58617982 ATATATTTAA
* ** * *
58617992 AATTTTTTAGAGTTAGGACTAAATTGACAGGTTTTGTAAATATTGAAGG-TCATATTTATTG
1 AATTTTTTA-AATTAGGACTAAATTGACAACTTTTGTAAACATTGAAGGCT-AAATTTATTG
* * *
58618053 AATTTTTTAAATCTAGAACTAAAATAACAACTTTTGTAAACATTGAAGGCTAAATTTATTG
1 AATTTTTTAAAT-TAGGACTAAATTGACAACTTTTGTAAACATTGAAGGCTAAATTTATTG
* *
58618114 ATTTTTTTATATTTAGGA-TCAAATTGA
1 AATTTTTTA-AATTAGGACT-AAATTGA
58618141 TAGAATATGT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
60 3 0.04
61 65 0.92
62 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (60 bp):
AATTTTTTAAATTAGGACTAAATTGACAACTTTTGTAAACATTGAAGGCTAAATTTATTG
Found at i:58620359 original size:26 final size:26
Alignment explanation
Indices: 58620328--58620430 Score: 102
Period size: 26 Copynumber: 4.0 Consensus size: 26
58620318 TTTTATCATC
*
58620328 ATTTATTTTAAGTTTTTATATATATT
1 ATTTATTTTAAATTTTTATATATATT
* * *
58620354 ATTTATTTTAAGCTATTT-TACATATT
1 ATTTATTTTAA-ATTTTTATATATATT
* *
58620380 ATTTA-TTTAAATTTCTTTTATGTATT
1 ATTTATTTTAAATTT-TTATATATATT
* *
58620406 ATTTATTTTAAACTATTATATATAT
1 ATTTATTTTAAATTTTTATATATAT
58620431 CTTTCAAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
24 2 0.03
25 7 0.11
26 42 0.68
27 11 0.18
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (26 bp):
ATTTATTTTAAATTTTTATATATATT
Found at i:58620445 original size:21 final size:24
Alignment explanation
Indices: 58620421--58620471 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
58620411 TTTTAAACTA
*
58620421 TTATATATA-TCTTTCAAA-T-TT
1 TTATATATATTCTTTAAAACTGTT
*
58620442 TTATATTTATTCTTTAAAACTGTT
1 TTATATATATTCTTTAAAACTGTT
58620466 TTATAT
1 TTATAT
58620472 GTTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 8 0.32
23 1 0.04
24 8 0.32
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATATATATTCTTTAAAACTGTT
Found at i:58620489 original size:37 final size:38
Alignment explanation
Indices: 58620439--58620515 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
58620429 ATCTTTCAAA
*
58620439 TTTTTATATTTA-TTCTTTAAAACTGTTTTATATGTTAT
1 TTTTTATATTTATTTATTTAAAACTGTTTTAT-TGTTAT
* *
58620477 TTTTTATA-TTATTTATTTTAAATTGTTTTATTGTTAT
1 TTTTTATATTTATTTATTTAAAACTGTTTTATTGTTAT
58620514 TT
1 TT
58620516 ATTTTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (38 bp):
TTTTTATATTTATTTATTTAAAACTGTTTTATTGTTAT
Found at i:58620538 original size:25 final size:24
Alignment explanation
Indices: 58620475--58620543 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
58620465 TTTATATGTT
58620475 ATTTTTTATA-TTATTTATTTTAA
1 ATTTTTTATATTTATTTATTTTAA
**
58620498 ATTGTTTTAT-TGTTATTTATTTTTC
1 ATT-TTTTATAT-TTATTTATTTTAA
*
58620523 ATTTTTTATATTT-TATATTTT
1 ATTTTTTATATTTATTTATTTT
58620544 GTTTATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 10 0.26
24 14 0.36
25 15 0.38
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (24 bp):
ATTTTTTATATTTATTTATTTTAA
Found at i:58620543 original size:14 final size:14
Alignment explanation
Indices: 58620464--58620543 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
58620454 TTTAAAACTG
* *
58620464 TTTTATATGTTATT
1 TTTTATATTTTATA
58620478 TTTTATATTATT-TA
1 TTTTATATT-TTATA
* *
58620492 TTTTAAATTGTTTTA
1 TTTTATATT-TTATA
*
58620507 TTGT-TA-TTTAT-
1 TTTTATATTTTATA
*
58620518 TTTTCATTTTTTATA
1 TTTT-ATATTTTATA
58620533 TTTTATATTTT
1 TTTTATATTTT
58620544 GTTTATTTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
11 3 0.06
12 3 0.06
13 2 0.04
14 31 0.62
15 11 0.22
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (14 bp):
TTTTATATTTTATA
Found at i:58621162 original size:30 final size:30
Alignment explanation
Indices: 58621126--58621186 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
58621116 AAAAGGATCA
58621126 TATTTTAAAATCTTTTTCAAAATTTCAACT
1 TATTTTAAAATCTTTTTCAAAATTTCAACT
58621156 TATTTTAAAATCTTTTTCAAAATTTCAACT
1 TATTTTAAAATCTTTTTCAAAATTTCAACT
58621186 T
1 T
58621187 TCGGCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTAAAATCTTTTTCAAAATTTCAACT
Found at i:58624538 original size:32 final size:33
Alignment explanation
Indices: 58624456--58624539 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 33
58624446 AGAATAGCAT
58624456 ATGTTGGAATCCCTATAATTAAAGATAGAAATC
1 ATGTTGGAATCCCTATAATTAAAGATAGAAATC
*
58624489 TGATGGTATTGGAATCCCTATAATTAAGGATAGAAATC
1 --AT-G--TTGGAATCCCTATAATTAAAGATAGAAATC
58624527 -TGTTGGAATCCCT
1 ATGTTGGAATCCCT
58624540 TGTAAATAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
32 11 0.24
34 1 0.02
35 3 0.07
36 1 0.02
38 29 0.64
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (33 bp):
ATGTTGGAATCCCTATAATTAAAGATAGAAATC
Found at i:58628379 original size:32 final size:33
Alignment explanation
Indices: 58628298--58628380 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 33
58628288 TGAGGGGGAG
58628298 TGTTGGAATCCCTATAATTAAGGATAGAAATCTGA
1 TGTTGGAATCCCTATAATTAAGGATAGAAATC--A
58628333 TGGTATTGGAATCCCTATAATTAAGGATAGAAATC-
1 T-G--TTGGAATCCCTATAATTAAGGATAGAAATCA
58628368 TGTTGGAATCCCT
1 TGTTGGAATCCCT
58628381 TGTAAATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
32 11 0.24
34 1 0.02
35 2 0.04
36 1 0.02
38 30 0.67
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (33 bp):
TGTTGGAATCCCTATAATTAAGGATAGAAATCA
Found at i:58631018 original size:13 final size:13
Alignment explanation
Indices: 58631000--58631025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58630990 CTTTTGTAAC
58631000 TTAGTGAAGATGG
1 TTAGTGAAGATGG
58631013 TTAGTGAAGATGG
1 TTAGTGAAGATGG
58631026 CCTCCGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
TTAGTGAAGATGG
Found at i:58632508 original size:16 final size:16
Alignment explanation
Indices: 58632476--58632509 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58632466 CAAGAGCGTT
**
58632476 TGCAAAGAAGATTACA
1 TGCAAAGAAGAAGACA
58632492 TGCAAAGAAGAAGACA
1 TGCAAAGAAGAAGACA
58632508 TG
1 TG
58632510 TTTCAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.24, T:0.15
Consensus pattern (16 bp):
TGCAAAGAAGAAGACA
Found at i:58634073 original size:16 final size:17
Alignment explanation
Indices: 58634052--58634084 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58634042 TTCAATGGTA
58634052 ATTTTGAATTT-ATTTG
1 ATTTTGAATTTAATTTG
*
58634068 ATTTTGCATTTAATTTG
1 ATTTTGAATTTAATTTG
58634085 TCAAATACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.61
Consensus pattern (17 bp):
ATTTTGAATTTAATTTG
Found at i:58638679 original size:20 final size:21
Alignment explanation
Indices: 58638654--58638705 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
58638644 AAATATAAAA
*
58638654 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTTAAAAATTAT
*
58638674 TTTG-AATTTTAAAAAATTAT
1 TTTGAAATTTTTAAAAATTAT
*
58638694 TTTGATATTTTT
1 TTTGAAATTTTT
58638706 TTTTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTGAAATTTTTAAAAATTAT
Found at i:58640821 original size:20 final size:20
Alignment explanation
Indices: 58640796--58640845 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
58640786 TGATGAAATT
*
58640796 ACTTCATTGTGCTTAGTGGC
1 ACTTCATTGTGCTTAGTGAC
*
58640816 ACTTCATTATGCTTAGTGAC
1 ACTTCATTGTGCTTAGTGAC
*
58640836 ACTTCCTTGT
1 ACTTCATTGT
58640846 TCTTCTGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
ACTTCATTGTGCTTAGTGAC
Found at i:58642403 original size:17 final size:17
Alignment explanation
Indices: 58642373--58642407 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
58642363 AATCAAGCAC
*
58642373 CCTTAATGCTAGAATGG
1 CCTTAATGCAAGAATGG
*
58642390 CCTTAGTGCAAGAATGG
1 CCTTAATGCAAGAATGG
58642407 C
1 C
58642408 ATCCTGGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (17 bp):
CCTTAATGCAAGAATGG
Found at i:58646790 original size:18 final size:18
Alignment explanation
Indices: 58646764--58646799 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58646754 TTTTATATAT
* *
58646764 TTTTTAAAACATTATAAA
1 TTTTAAAAAAATTATAAA
58646782 TTTTAAAAAAATTATAAA
1 TTTTAAAAAAATTATAAA
58646800 GAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTATAAA
Found at i:58647520 original size:19 final size:17
Alignment explanation
Indices: 58647500--58647534 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
58647490 TAGATATAAT
58647500 TTTTATATATAAATATGA
1 TTTTAT-TATAAATATGA
*
58647518 TTTTATTTTAAATATGA
1 TTTTATTATAAATATGA
58647535 AAATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTTATTATAAATATGA
Found at i:58649998 original size:16 final size:16
Alignment explanation
Indices: 58649977--58650009 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58649967 CATTTGACCG
58649977 ATTAATACATAAATAT
1 ATTAATACATAAATAT
58649993 ATTAATACATAAATAT
1 ATTAATACATAAATAT
58650009 A
1 A
58650010 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAATACATAAATAT
Found at i:58650068 original size:42 final size:38
Alignment explanation
Indices: 58649985--58650069 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 38
58649975 CGATTAATAC
* * *
58649985 ATAAATATATTAATACATAAATATAAATTTTTTATGTT
1 ATAAATATATTAATACATAAAAATAAATTTTATATATT
58650023 ATAAAT-TATATAATACATAAAAATAACATAATTTAATATATT
1 ATAAATATAT-TAATACATAAAAATAA-AT--TTT-ATATATT
58650065 ATAAA
1 ATAAA
58650070 ATTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 3 0.08
38 21 0.54
39 2 0.05
41 3 0.08
42 10 0.26
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (38 bp):
ATAAATATATTAATACATAAAAATAAATTTTATATATT
Found at i:58662590 original size:18 final size:18
Alignment explanation
Indices: 58662569--58662617 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
58662559 AAGAATCTGT
58662569 GATAGATGAGGAATTTCA
1 GATAGATGAGGAATTTCA
*
58662587 GATAGATGAGGAATTTCC
1 GATAGATGAGGAATTTCA
* *
58662605 GGTAGATTAGGAA
1 GATAGATGAGGAA
58662618 GAACAATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.27
Consensus pattern (18 bp):
GATAGATGAGGAATTTCA
Found at i:58662881 original size:64 final size:64
Alignment explanation
Indices: 58662780--58662903 Score: 239
Period size: 64 Copynumber: 1.9 Consensus size: 64
58662770 ATATATGTCC
*
58662780 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATGTATCCAACATGTTTA
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAACATGTATCCAACATGTTTA
58662844 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAACATGTATCCAACATG
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAACATGTATCCAACATG
58662904 GATACAAAGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (64 bp):
AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAACATGTATCCAACATGTTTA
Found at i:58677431 original size:18 final size:18
Alignment explanation
Indices: 58677403--58677438 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58677393 AAATTTATAT
*
58677403 TTTTTAAAAAATTATAAA
1 TTTTAAAAAAATTATAAA
*
58677421 TTTTAAAAAAATTCTAAA
1 TTTTAAAAAAATTATAAA
58677439 GAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTATAAA
Found at i:58689494 original size:32 final size:32
Alignment explanation
Indices: 58689453--58689518 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
58689443 GAAGGTTTCA
58689453 AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
1 AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
*
58689485 AGTTTCTGATTTTAAGTCATGTCAGCTGTTGT
1 AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
58689517 AG
1 AG
58689519 GACCTGCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (32 bp):
AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
Found at i:58691231 original size:26 final size:27
Alignment explanation
Indices: 58691185--58691241 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 27
58691175 GAATGAAAAG
58691185 AAATTTTATAATTAATATA-TTAATTA
1 AAATTTTATAATTAATATATTTAATTA
*
58691211 AAATTTTAT-A-TAATGAGTATTTAATTG
1 AAATTTTATAATTAAT-A-TATTTAATTA
58691238 AAAT
1 AAAT
58691242 CATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.15
25 2 0.07
26 11 0.41
27 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTTATAATTAATATATTTAATTA
Found at i:58691512 original size:52 final size:52
Alignment explanation
Indices: 58691450--58691554 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
58691440 CAGCTGCTGG
* *
58691450 ACCTGCCAGGAAAAGTCTTTTGTTTGGACCCAAAATCTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
58691502 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
58691554 A
1 A
58691555 TCTCCAATGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (52 bp):
ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
Found at i:58695156 original size:112 final size:113
Alignment explanation
Indices: 58695016--58695378 Score: 497
Period size: 112 Copynumber: 3.2 Consensus size: 113
58695006 AAAAAAATTT
* *
58695016 ATTTATTTTTA-TTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTT
1 ATTTTTTTTTATTTTTTTTCTTA-TTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTT
*
58695080 TCTTTCTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
65 TCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
58695129 ATTTTTTTTTATTTTTTTTCTTATTTTTTATCTGATTCTGACAC-AAAAAAATAA-AATTTTTTT
1 ATTTTTTTTTATTTTTTTTCTTATTTTTTATCTGATTCTGACACGAAAAAAA-AATAATTTTTTT
*
58695192 TCTTTGTACTGTGTACTGGGTGCCGGCTATTGACAGGCCAGCACCCAAAA
65 TCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAA
* * * *******
58695242 ATTTTTTTTTAATTTTTTTCGTATTTTTTATCTTATTCTGACACG-AAAAAAAATAAAAAAAAAT
1 ATTTTTTTTTATTTTTTTTCTTATTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTTT
58695306 -TTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAAA
66 CTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
* *
58695352 TTTTTTTTTTTGTTTTTTTTCTT-TTTT
1 -ATTTTTTTTTATTTTTTTTCTTATTTT
58695379 GTATATCCGT
Statistics
Matches: 225, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
110 7 0.03
111 20 0.09
112 102 0.45
113 86 0.38
114 10 0.04
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (113 bp):
ATTTTTTTTTATTTTTTTTCTTATTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTTT
CTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
Found at i:58695885 original size:22 final size:22
Alignment explanation
Indices: 58695860--58695902 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58695850 TCTTACTTTT
58695860 TTACTATCATTTCATTATTATG
1 TTACTATCATTTCATTATTATG
* **
58695882 TTACTATTATTTTGTTATTAT
1 TTACTATCATTTCATTATTAT
58695903 TATTTAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (22 bp):
TTACTATCATTTCATTATTATG
Found at i:58695907 original size:14 final size:14
Alignment explanation
Indices: 58695873--58695907 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
58695863 CTATCATTTC
*
58695873 ATTATTATGTTACT
1 ATTATTTTGTTACT
*
58695887 ATTATTTTGTTATT
1 ATTATTTTGTTACT
58695901 ATTATTT
1 ATTATTT
58695908 AGATATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (14 bp):
ATTATTTTGTTACT
Found at i:58696020 original size:13 final size:13
Alignment explanation
Indices: 58696002--58696026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58695992 TATTTAAGTA
58696002 TAAATTTATTTTT
1 TAAATTTATTTTT
58696015 TAAATTTATTTT
1 TAAATTTATTTT
58696027 CAATTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAAATTTATTTTT
Found at i:58696095 original size:16 final size:17
Alignment explanation
Indices: 58696056--58696097 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
58696046 TATTTTAATG
58696056 TTTTTTATA-TTTTAGA
1 TTTTTTATATTTTTAGA
* *
58696072 TGTATTATATTTTTA-A
1 TTTTTTATATTTTTAGA
58696088 TTTTTTATAT
1 TTTTTTATAT
58696098 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTTAGA
Found at i:58702919 original size:22 final size:22
Alignment explanation
Indices: 58702878--58702919 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58702868 AAAAAAAAAC
* *
58702878 TACTATTTTCTTGTTGTTTTGA
1 TACTATTTTCTTATTATTTTGA
58702900 TACTATTTTCTTATTATTTT
1 TACTATTTTCTTATTATTTT
58702920 CTTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (22 bp):
TACTATTTTCTTATTATTTTGA
Found at i:58702925 original size:22 final size:22
Alignment explanation
Indices: 58702878--58702930 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
58702868 AAAAAAAAAC
* * *
58702878 TACTATTTTCTTGTTGTTTTGA
1 TACTATTTTCTTATTATTTTCA
*
58702900 TACTATTTTCTTATTATTTTCT
1 TACTATTTTCTTATTATTTTCA
*
58702922 TACTTTTTT
1 TACTATTTT
58702931 ACTATCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (22 bp):
TACTATTTTCTTATTATTTTCA
Found at i:58703089 original size:13 final size:13
Alignment explanation
Indices: 58703071--58703095 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58703061 TATTTAAGTA
58703071 TAAATTTATTTTT
1 TAAATTTATTTTT
58703084 TAAATTTATTTT
1 TAAATTTATTTT
58703096 CAATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAAATTTATTTTT
Found at i:58703165 original size:16 final size:17
Alignment explanation
Indices: 58703126--58703167 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
58703116 ATTTTAATGT
58703126 TTTTTTATA-TTTTAGA
1 TTTTTTATATTTTTAGA
* *
58703142 TGTATTATATTTTTA-A
1 TTTTTTATATTTTTAGA
58703158 TTTTTTATAT
1 TTTTTTATAT
58703168 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTTAGA
Found at i:58709650 original size:3 final size:3
Alignment explanation
Indices: 58709642--58709682 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
58709632 CTATTTTTCG
*
58709642 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58709683 GTTCGTTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:58717394 original size:22 final size:22
Alignment explanation
Indices: 58717369--58717411 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58717359 TATCTTAATA
*
58717369 ATAACAACAAAATTGTAACAAC
1 ATAACAACAAAATAGTAACAAC
* *
58717391 ATAATAATAAAATAGTAACAA
1 ATAACAACAAAATAGTAACAA
58717412 AGTAGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAC
Found at i:58723221 original size:72 final size:71
Alignment explanation
Indices: 58723142--58723350 Score: 222
Period size: 72 Copynumber: 2.9 Consensus size: 71
58723132 GAATTCATCA
* * *
58723142 ACTCAATTGGTTTCTTGACAAGCCTAATTGAGTGAGTTGCAATAGGTTTCCCAATGATTTTGGAA
1 ACTCAATTGG-TTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
58723207 TCTGTCC
65 TCTGTCC
* * * * * **
58723214 ACTCAATTGGTTCTAATG-GAAGCTTAAATAAGTGAGTTGCAAGATGTTACCCAATGATCTTAAA
1 ACTCAATTGGTTCT--TGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGA
*
58723278 ATTTGTCC
64 ATCTGTCC
** * * * *
58723286 ACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGATTTTCCAGTGATCTTGGAA
1 ACTCAATTGGTTC-TTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
58723351 CCGTTGTTGA
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
71 5 0.05
72 102 0.94
73 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (71 bp):
ACTCAATTGGTTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAAT
CTGTCC
Found at i:58725710 original size:11 final size:11
Alignment explanation
Indices: 58725673--58725763 Score: 59
Period size: 11 Copynumber: 8.5 Consensus size: 11
58725663 ATATTTTTTA
*
58725673 TTTTTAAAAAT
1 TTTTTAAAATT
*
58725684 ATTTTAAAATACT
1 TTTTTAAAAT--T
58725697 TTTTTAAAATT
1 TTTTTAAAATT
58725708 TTTTT---A--
1 TTTTTAAAATT
*
58725714 TTTTTAAAATA
1 TTTTTAAAATT
58725725 TTTTTAAAATACT
1 TTTTTAAAAT--T
*
58725738 TTTTTAAAAAT
1 TTTTTAAAATT
*
58725749 TTTCT-AAATT
1 TTTTTAAAATT
58725759 TTTTT
1 TTTTT
58725764 GTGTTTATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
6 5 0.08
8 1 0.02
9 1 0.02
10 8 0.13
11 29 0.46
13 19 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:58725719 original size:17 final size:17
Alignment explanation
Indices: 58725697--58725730 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58725687 TTAAAATACT
*
58725697 TTTTTAAAATTTTTTTA
1 TTTTTAAAATATTTTTA
58725714 TTTTTAAAATATTTTTA
1 TTTTTAAAATATTTTTA
58725731 AAATACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAAAATATTTTTA
Found at i:58725721 original size:41 final size:41
Alignment explanation
Indices: 58725665--58725751 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
58725655 ATAAATATAT
58725665 ATTTTTTATTTTTAAAA-ATATTTTAAAATACTTTTTTAAAA
1 ATTTTTTATTTTTAAAATAT-TTTTAAAATACTTTTTTAAAA
*
58725706 TTTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
1 ATTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
58725747 ATTTT
1 ATTTT
58725752 CTAAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 41 0.95
42 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (41 bp):
ATTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
Found at i:58725763 original size:23 final size:24
Alignment explanation
Indices: 58725685--58725763 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 24
58725675 TTTAAAAATA
58725685 TTTTAAAATACTTTTTTAAAATTTTTTTAT
1 TTTTAAAATA--TTTTTAAAA---TTTT-T
**
58725715 TTTTAAAATATTTTTAAAATACTT
1 TTTTAAAATATTTTTAAAATTTTT
58725739 TTTTAAAA-ATTTTCT-AAATTTTT
1 TTTTAAAATATTTT-TAAAATTTTT
58725762 TT
1 TT
58725764 GTGTTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 13 0.30
24 10 0.23
25 2 0.05
28 9 0.20
30 10 0.23
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTAAAATATTTTTAAAATTTTT
Found at i:58732249 original size:31 final size:29
Alignment explanation
Indices: 58732179--58732252 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
58732169 GGTTCAAGTT
* *
58732179 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* *
58732208 ACGTTTTAGTCACTTATGTTATCATGATGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
58732239 ACATTTTAGTCACT
1 ACATTTTAGTCACT
58732253 GAGCCGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 17 0.45
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:58734053 original size:21 final size:21
Alignment explanation
Indices: 58733999--58734054 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
58733989 TAATTTATAA
58733999 TTTTTTTTATATTTTGAAGAAT
1 TTTTTTTTA-ATTTTGAAGAAT
* * *
58734021 TTTTCTTGAATTTT-AAGATTT
1 TTTTTTTTAATTTTGAAGA-AT
58734042 TTTTTTTTAATTT
1 TTTTTTTTAATTT
58734055 CAAGTGCACA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 7 0.25
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTTTTAATTTTGAAGAAT
Found at i:58747848 original size:21 final size:21
Alignment explanation
Indices: 58747824--58747869 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58747814 TTCTGCTCTA
*
58747824 CTTCCCTCGCTACTGCCGCTG
1 CTTCCCTCGCCACTGCCGCTG
* *
58747845 CTTCCCTCGCCGCTGTCGCTG
1 CTTCCCTCGCCACTGCCGCTG
58747866 CTTC
1 CTTC
58747870 TCTTGCTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.48, G:0.20, T:0.30
Consensus pattern (21 bp):
CTTCCCTCGCCACTGCCGCTG
Found at i:58748298 original size:16 final size:16
Alignment explanation
Indices: 58748249--58748302 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
58748239 TTTGGTTCGC
*
58748249 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
58748265 TATATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
58748281 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
58748297 TGTAAT
1 TGTAAT
58748303 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:58748556 original size:18 final size:17
Alignment explanation
Indices: 58748535--58748569 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58748525 TTATTATTAA
*
58748535 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
58748553 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
58748570 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:58748708 original size:157 final size:157
Alignment explanation
Indices: 58748422--58748738 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
58748412 TAGAATACCC
*
58748422 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTACTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTACTGTTATTTAAATTTTAATAAGATTATTA
* *
58748487 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
58748552 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
58748579 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTACTGTTATTTAAATTTTAATAAGATTATTA
58748644 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
58748709 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
58748736 TTA
1 TTA
58748739 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTACTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:58748709 original size:16 final size:16
Alignment explanation
Indices: 58748672--58748713 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
58748662 TTAATCATAT
*
58748672 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
58748688 TT-AAATATATTATAA
1 TTAAAATATATTATAA
58748703 TTAAAATATAT
1 TTAAAATATAT
58748714 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:58748720 original size:14 final size:15
Alignment explanation
Indices: 58748681--58748722 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
58748671 TTTAAACATA
*
58748681 ATTATTATTAAATAT
1 ATTATAATTAAATAT
58748696 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
58748710 A-TATAATTTAATA
1 ATTATAATTAAATA
58748723 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:58748810 original size:120 final size:121
Alignment explanation
Indices: 58748670--58748967 Score: 512
Period size: 120 Copynumber: 2.5 Consensus size: 121
58748660 ATTTAATCAT
*
58748670 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
58748735 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
58748792 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
58748855 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * *
58748911 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
58748968 TAAAATAATT
Statistics
Matches: 169, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
119 3 0.02
120 161 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:58748840 original size:14 final size:15
Alignment explanation
Indices: 58748791--58748842 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
58748781 GTAAAATATA
58748791 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
58748806 TATTAAATATATTAT
1 AATTAAATATATTAT
58748821 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
58748834 AATTTAATA
1 AATTAAATA
58748843 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:58749053 original size:15 final size:15
Alignment explanation
Indices: 58749008--58749061 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
58748998 TATGAATTTG
58749008 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
58749022 -ATAA-TT-ATTACA
1 TATAATTTAATAATA
58749034 TATAATTTAATAATA
1 TATAATTTAATAATA
*
58749049 TATAATTTCATAA
1 TATAATTTAATAA
58749062 AATTCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
11 1 0.03
12 4 0.13
13 8 0.26
14 2 0.06
15 16 0.52
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:58749091 original size:88 final size:89
Alignment explanation
Indices: 58748983--58749187 Score: 279
Period size: 88 Copynumber: 2.3 Consensus size: 89
58748973 TAATTATAAC
* * * * * *
58748983 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATA-
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAG
* *
58749046 ATATATAATTTCATAAAATTCTTGA
65 ATATATAATTTCATAAAATTCGTAA
58749071 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATA--
58749136 GATATATAATTTCATAAAATTCGTAA
64 GATATATAATTTCATAAAATTCGTAA
*
58749162 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
58749188 CTAAAATCAA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
88 53 0.51
89 3 0.03
91 27 0.26
92 20 0.19
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (89 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGA
TATATAATTTCATAAAATTCGTAA
Found at i:58750131 original size:6 final size:6
Alignment explanation
Indices: 58750120--58750144 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58750110 GTTTGAACAT
58750120 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
58750145 ATAATTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Done.