Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1207447 original size:15 final size:15
Alignment explanation
Indices: 1207410--1207449 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1207400 GCTCAGGACA
*
1207410 ACGACGACGACAACG
1 ACGACGATGACAACG
*
1207425 ACGACGATGACGACG
1 ACGACGATGACAACG
1207440 ACGACGATGA
1 ACGACGATGA
1207450 TGATGGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.28, G:0.30, T:0.05
Consensus pattern (15 bp):
ACGACGATGACAACG
Found at i:1211406 original size:51 final size:51
Alignment explanation
Indices: 1211309--1211432 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 51
1211299 ATACACATAT
* * * * *
1211309 ATAGCGCGGTTCAGGGGGAGCGCTATACCCCACGTGTAACCCAATCATCAA
1 ATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGAACCAAATCAGCAA
* ** **
1211360 ATAGCGCGGTGCAGGGCGCGCGCTATACCCCACGTGGCGCCAAATCAGCGT
1 ATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGAACCAAATCAGCAA
1211411 ATAGCGCGG-GTCAGGGGGCGCG
1 ATAGCGCGGTG-CAGGGGGCGCG
1211433 TTTTACTGCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.02
51 60 0.98
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.15
Consensus pattern (51 bp):
ATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGAACCAAATCAGCAA
Found at i:1212397 original size:12 final size:12
Alignment explanation
Indices: 1212380--1212404 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1212370 TTTCTGAAAA
1212380 AAATAACATTTT
1 AAATAACATTTT
1212392 AAATAACATTTT
1 AAATAACATTTT
1212404 A
1 A
1212405 CTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAACATTTT
Found at i:1213219 original size:17 final size:18
Alignment explanation
Indices: 1213183--1213221 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1213173 ATTTAATTTC
1213183 ATTTTTTAATATTTGGAAT
1 ATTTTTTAATATTT-GAAT
*
1213202 ATTTTTTAATGTTT-AAT
1 ATTTTTTAATATTTGAAT
1213219 ATT
1 ATT
1213222 AAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
ATTTTTTAATATTTGAAT
Found at i:1215182 original size:14 final size:13
Alignment explanation
Indices: 1215153--1215197 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1215143 TTTTTTTAAG
*
1215153 TTTTGGAATATTT
1 TTTTGAAATATTT
1215166 TTTTGAAATATTT
1 TTTTGAAATATTT
*
1215179 TTTTCAAAATAATTT
1 TTTT-GAAAT-ATTT
1215194 TTTT
1 TTTT
1215198 CAAAATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
14 4 0.14
15 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTGAAATATTT
Found at i:1215193 original size:15 final size:15
Alignment explanation
Indices: 1215162--1215204 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1215152 GTTTTGGAAT
*
1215162 ATTTTTTT-GAAAT-
1 ATTTTTTTCAAAATA
1215175 ATTTTTTTCAAAATA
1 ATTTTTTTCAAAATA
1215190 ATTTTTTTCAAAATA
1 ATTTTTTTCAAAATA
1215205 TTGAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
15 15 0.56
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTTTTTCAAAATA
Found at i:1219089 original size:19 final size:19
Alignment explanation
Indices: 1219063--1219123 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
1219053 TCAAAAAACA
1219063 TAAATCAAAACAAATATAC
1 TAAATCAAAACAAATATAC
**
1219082 TATTTCAAAACAAATATAC
1 TAAATCAAAACAAATATAC
*
1219101 ATAAATCAAAACTAATATAC
1 -TAAATCAAAACAAATATAC
1219121 TAA
1 TAA
1219124 GCCAACTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAATCAAAACAAATATAC
Found at i:1219111 original size:20 final size:20
Alignment explanation
Indices: 1219060--1219120 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
1219050 GAATCAAAAA
1219060 ACATAAATCAAAACAAATAT
1 ACATAAATCAAAACAAATAT
**
1219080 AC-TATTTCAAAACAAATAT
1 ACATAAATCAAAACAAATAT
*
1219099 ACATAAATCAAAACTAATAT
1 ACATAAATCAAAACAAATAT
1219119 AC
1 AC
1219121 TAAGCCAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (20 bp):
ACATAAATCAAAACAAATAT
Found at i:1241641 original size:20 final size:18
Alignment explanation
Indices: 1241606--1241644 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1241596 GGGAAATGCT
1241606 TAACATTTTTTTAAAATA
1 TAACATTTTTTTAAAATA
1241624 TAACATTTTTATTAAAA-A
1 TAACATTTTT-TTAAAATA
1241642 TAA
1 TAA
1241645 TTAAAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAACATTTTTTTAAAATA
Found at i:1244992 original size:60 final size:59
Alignment explanation
Indices: 1244893--1245027 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
1244883 CATAACTATT
* *
1244893 CATTAAAAG-T-TAAAATATTCTTCGATTATAAAGTATTGTTTTATTAAGTTCT-TCAAC
1 CATTAAAAGTTATAAAATATTCTTCAATTATAAAGTATTGTTTTATT-AGTTATCTCAAC
* * *
1244950 TATTAAAAGTTATAAAATAGTT-TTCTAATTATAAAGTGTTGTTTTGTTAGTTATCTCAAC
1 CATTAAAAGTTATAAAATA-TTCTTC-AATTATAAAGTATTGTTTTATTAGTTATCTCAAC
1245010 CATTAAAAGTTATAAAAT
1 CATTAAAAGTTATAAAAT
1245028 GATCACCCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
57 8 0.12
58 1 0.01
59 15 0.22
60 43 0.64
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (59 bp):
CATTAAAAGTTATAAAATATTCTTCAATTATAAAGTATTGTTTTATTAGTTATCTCAAC
Found at i:1254254 original size:24 final size:24
Alignment explanation
Indices: 1254192--1254254 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
1254182 GGAGAAGAAT
* **
1254192 CTTCTTCATCGGATGGTGCTGATG
1 CTTCTTCATCGGAGGGTGCTGACA
** * *
1254216 CCCCTTTATCAGAGGGTGCTGACA
1 CTTCTTCATCGGAGGGTGCTGACA
1254240 CTTCTTCATCGGAGG
1 CTTCTTCATCGGAGG
1254255 ATTATAAAGG
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (24 bp):
CTTCTTCATCGGAGGGTGCTGACA
Found at i:1255840 original size:43 final size:43
Alignment explanation
Indices: 1255790--1255872 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
1255780 CTTCTCTGAT
1255790 GAAGGAGCATCGCTACTTCCCGATGAAGAAAATTCTTTACAGC
1 GAAGGAGCATCGCTACTTCCCGATGAAGAAAATTCTTTACAGC
*
1255833 GAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTAC
1 GAAGGAGCATCGCTACTTCCCGATGAAGAAAATTCTTTAC
1255873 CGCCCTCTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (43 bp):
GAAGGAGCATCGCTACTTCCCGATGAAGAAAATTCTTTACAGC
Found at i:1255895 original size:51 final size:51
Alignment explanation
Indices: 1255832--1255996 Score: 233
Period size: 51 Copynumber: 3.2 Consensus size: 51
1255822 TTCTTTACAG
1255832 CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCGCCCTCTG-
1 CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCGCCCTCTGA
* **
1255882 CTGAAGGAACATCGCTACTTATCGATGAAGAAGATTCTTTACCGCCCTCTGA
1 C-GAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCGCCCTCTGA
* * **
1255934 CGAAGGAGCATCGCTATTTCCCGATGAAGAAGATTTTTTACCATCCTCTGA
1 CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCGCCCTCTGA
* *
1255985 TGACGGAGCATC
1 CGAAGGAGCATC
1255997 ACCGCCCTCT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.01
51 99 0.98
52 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (51 bp):
CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCGCCCTCTGA
Found at i:1256012 original size:51 final size:51
Alignment explanation
Indices: 1255957--1256089 Score: 194
Period size: 51 Copynumber: 2.6 Consensus size: 51
1255947 CTATTTCCCG
* *
1255957 ATGAAGAAGATTTTTTACCATCCTCTGATGACGGAGCATCACCGCCCTCTA
1 ATGAAGAAGATTATTTACCATCCTCTGATGACGGAGCATCACCACCCTCTA
* * *
1256008 ATGAAGAAGATTATTTACTATCCTTTGATGACGGAGCATCACTACCCTCTA
1 ATGAAGAAGATTATTTACCATCCTCTGATGACGGAGCATCACCACCCTCTA
* * *
1256059 ATGAAGAAGATTCTTTCCCATCATCTGATGA
1 ATGAAGAAGATTATTTACCATCCTCTGATGA
1256090 AGGACCCTCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (51 bp):
ATGAAGAAGATTATTTACCATCCTCTGATGACGGAGCATCACCACCCTCTA
Found at i:1256012 original size:102 final size:102
Alignment explanation
Indices: 1255832--1256093 Score: 251
Period size: 102 Copynumber: 2.6 Consensus size: 102
1255822 TTCTTTACAG
* * *
1255832 CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCGCCCTCTGCTGAAGGAACATCGC
1 CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCACCCTCTGATGAAGGAACATCCC
* * * *
1255897 TACTTATCGATGAAGAAGATTCTTTACCGCCCTCTGA
66 GACCTATCAATGAAGAAGATTATTTACCGCCCTCTGA
* * * * *
1255934 CGAAGGAGCATCGCTATTTCCCGATGAAGAAGATTTTTTACCATCCTCTGATGACGGAGCATCAC
1 CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCACCCTCTGATGAAGGAACATC-C
* * *** *
1255999 CGCCCTCT-AATGAAGAAGATTATTTACTATCCTTTGA
65 CGACCTATCAATGAAGAAGATTATTTACCGCCCTCTGA
* * * * * * *
1256036 TGACGGAGCATCACTAC--CCTCTAATGAAGAAGATTCTTTCCCATCATCTGATGAAGGA
1 CGAAGGAGCATCGCTACTTCC-C-GATGAAGAAGATTCTTTACCACCCTCTGATGAAGGA
1256094 CCCTCACCAT
Statistics
Matches: 130, Mismatches: 27, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
100 2 0.02
101 1 0.01
102 123 0.95
103 4 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (102 bp):
CGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCACCCTCTGATGAAGGAACATCCC
GACCTATCAATGAAGAAGATTATTTACCGCCCTCTGA
Found at i:1266128 original size:2 final size:2
Alignment explanation
Indices: 1266121--1266146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1266111 TATCTTATGT
1266121 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1266147 ATTACAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1266702 original size:21 final size:23
Alignment explanation
Indices: 1266656--1266703 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
1266646 CGTATAATTA
1266656 TAAATTAGTTAAAAATTTAAAGG
1 TAAATTAGTTAAAAATTTAAAGG
* *
1266679 TAAATTA-TTGAAAA-TTATAGG
1 TAAATTAGTTAAAAATTTAAAGG
1266700 TAAA
1 TAAA
1266704 CTATATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (23 bp):
TAAATTAGTTAAAAATTTAAAGG
Found at i:1267462 original size:13 final size:13
Alignment explanation
Indices: 1267444--1267471 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1267434 ATATTTTTCA
1267444 AAAAAAAAATTGT
1 AAAAAAAAATTGT
1267457 AAAAAAAAATTGT
1 AAAAAAAAATTGT
1267470 AA
1 AA
1267472 GTTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAAAAAAATTGT
Found at i:1267819 original size:21 final size:23
Alignment explanation
Indices: 1267793--1267844 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1267783 GATCATTGGT
*
1267793 ATAATTTACCTTT-TATTTT-AA
1 ATAATTTACCTTTAAATTTTCAA
*
1267814 ATAATTTATCTTTAAATTTTCAA
1 ATAATTTACCTTTAAATTTTCAA
*
1267837 CTAATTTA
1 ATAATTTA
1267845 TAATCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 12 0.46
22 5 0.19
23 9 0.35
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (23 bp):
ATAATTTACCTTTAAATTTTCAA
Found at i:1268215 original size:11 final size:11
Alignment explanation
Indices: 1268199--1268228 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1268189 GTGTACGGTC
1268199 TAGATTAGTCT
1 TAGATTAGTCT
1268210 TAGATTAGTCT
1 TAGATTAGTCT
1268221 TAGATTAG
1 TAGATTAG
1268229 ATAGGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (11 bp):
TAGATTAGTCT
Found at i:1270358 original size:16 final size:17
Alignment explanation
Indices: 1270337--1270370 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1270327 TACTATTCAT
1270337 GTGAATAGTG-AATTTC
1 GTGAATAGTGAAATTTC
1270353 GTGAATAGTGAAATTTC
1 GTGAATAGTGAAATTTC
1270370 G
1 G
1270371 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (17 bp):
GTGAATAGTGAAATTTC
Found at i:1271138 original size:15 final size:16
Alignment explanation
Indices: 1271120--1271152 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1271110 GTGGCAGATC
1271120 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
1271135 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
1271151 AA
1 AA
1271153 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:1280669 original size:18 final size:17
Alignment explanation
Indices: 1280641--1280688 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
1280631 TATGAATATT
*
1280641 AATAAAATTTTAAAATA
1 AATAAAATTTTAAAAAA
1280658 AATAATAATTTTAAAAAA
1 AATAA-AATTTTAAAAAA
*
1280676 AATTCAAATTTTA
1 AA-TAAAATTTTA
1280689 GGATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 20 0.74
19 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAAATTTTAAAAAA
Found at i:1281742 original size:115 final size:115
Alignment explanation
Indices: 1281585--1281793 Score: 316
Period size: 117 Copynumber: 1.8 Consensus size: 115
1281575 GGATCTCTAA
* * *
1281585 ATTTTTATATTTATAGTCAGCCCCCAGTTTTTATAATTTCAT-AAAATTTTTAGTTTTTAACC-T
1 ATTTTTATATTTATAATCAGCCCCCAATTTTTATAATTTCATAAAAATGTTTAGTTTTTAACCTT
1281648 TTTTTCCATTTCTCTTATTTATTCATTCAATTTTGAATTGCATTTAACCG
66 TTTTTCCATTTCTCTTATTTATTCATTCAATTTTGAATTGCATTTAACCG
* * *
1281698 ATTTTTATATTTATAATTAGGGCCCCTAATTTTTAT-ATTGTCATAAAAATGTTTAGTTTTTAGC
1 ATTTTTATATTTATAATCA--GCCCCCAATTTTTATAATT-TCATAAAAATGTTTAGTTTTTAAC
1281762 CTTTTTTTCCATTTCTCTTATTTATTCATTCA
63 CTTTTTTTCCATTTCTCTTATTTATTCATTCA
1281794 TTAAATTTTG
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
113 17 0.20
114 3 0.04
115 17 0.20
116 18 0.21
117 30 0.35
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (115 bp):
ATTTTTATATTTATAATCAGCCCCCAATTTTTATAATTTCATAAAAATGTTTAGTTTTTAACCTT
TTTTTCCATTTCTCTTATTTATTCATTCAATTTTGAATTGCATTTAACCG
Found at i:1282037 original size:19 final size:19
Alignment explanation
Indices: 1282013--1282059 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1282003 TTAAGGTGTT
1282013 TTTTTAATAAAATAATAT-A
1 TTTTTAATAAAATAA-ATCA
* *
1282032 TTTTT-ACAAATTAAATCA
1 TTTTTAATAAAATAAATCA
1282050 TTTTTAATAA
1 TTTTTAATAA
1282060 TTTATTAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 8 0.35
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTAATAAAATAAATCA
Found at i:1282459 original size:32 final size:32
Alignment explanation
Indices: 1282417--1282477 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1282407 CATAAAATAG
1282417 TGATAAATTTAAAGATTGA-TTTATAATAGTT
1 TGATAAATTTAAAGATTGATTTTATAATAGTT
1282448 TGATACAATTTAAAGATTGATTTTATAATA
1 TGATA-AATTTAAAGATTGATTTTATAATA
1282478 ATTTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 5 0.18
32 14 0.50
33 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (32 bp):
TGATAAATTTAAAGATTGATTTTATAATAGTT
Found at i:1283469 original size:17 final size:18
Alignment explanation
Indices: 1283444--1283480 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1283434 TAGAGGGGTA
1283444 TTTCAGTTATTTTGTCAT
1 TTTCAGTTATTTTGTCAT
*
1283462 TTTC-GTTATTTTGTGAT
1 TTTCAGTTATTTTGTCAT
1283479 TT
1 TT
1283481 AAAAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.65
Consensus pattern (18 bp):
TTTCAGTTATTTTGTCAT
Found at i:1283954 original size:35 final size:36
Alignment explanation
Indices: 1283886--1283955 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
1283876 ACCAATTTAG
* *
1283886 GTTTCATAAGAAATTTGAGTATTTTTCTTATTAAAA
1 GTTTCATAAAAAAATTGAGTATTTTTCTTATTAAAA
*
1283922 GTTTCATAAAAAAATTGGGTA-TTTTCTTATTAAA
1 GTTTCATAAAAAAATTGAGTATTTTTCTTATTAAA
1283956 TATTAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (36 bp):
GTTTCATAAAAAAATTGAGTATTTTTCTTATTAAAA
Found at i:1288008 original size:22 final size:22
Alignment explanation
Indices: 1287980--1288028 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1287970 TAAACTCCCA
*
1287980 AAACCCAACTAAATAAA-AACCC
1 AAACCCAAATAAA-AAAGAACCC
*
1288002 AAACCCAAATAAAAAAGAACCG
1 AAACCCAAATAAAAAAGAACCC
1288024 AAACC
1 AAACC
1288029 GATTAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.61, C:0.29, G:0.04, T:0.06
Consensus pattern (22 bp):
AAACCCAAATAAAAAAGAACCC
Found at i:1293312 original size:11 final size:12
Alignment explanation
Indices: 1293288--1293313 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1293278 AAAATGAAAG
1293288 AAAGATTAAAAA
1 AAAGATTAAAAA
1293300 AAAGATTAAAAA
1 AAAGATTAAAAA
1293312 AA
1 AA
1293314 TACGAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAGATTAAAAA
Found at i:1293809 original size:24 final size:24
Alignment explanation
Indices: 1293781--1293826 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1293771 TGAGAATTTG
*
1293781 TTTTTATTTGTTT-TTTTCCTTTTA
1 TTTTTATTT-TTTGTTGTCCTTTTA
1293805 TTTTTATTTTTTGTTGTCCTTT
1 TTTTTATTTTTTGTTGTCCTTT
1293827 AAAAGACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTTATTTTTTGTTGTCCTTTTA
Found at i:1296260 original size:30 final size:29
Alignment explanation
Indices: 1296226--1296324 Score: 114
Period size: 30 Copynumber: 3.3 Consensus size: 29
1296216 GAATTTAGGG
1296226 AGTCAAATTGATATATTATCT-AAGTTTAGA
1 AGTCAAATTGATAT-TTATCTAAAGTTTA-A
1296256 AGTCAAA-TGATATTTCATCTAAAGTTTAA
1 AGTCAAATTGATATTT-ATCTAAAGTTTAA
*
1296285 CGTCAAATT-AGTATTCTATCTAAAGTTTAA
1 AGTCAAATTGA-TATT-TATCTAAAGTTTAA
1296315 AGGTCAAATT
1 A-GTCAAATT
1296325 AATAAGTATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
28 2 0.03
29 18 0.30
30 32 0.52
31 9 0.15
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (29 bp):
AGTCAAATTGATATTTATCTAAAGTTTAA
Found at i:1315911 original size:17 final size:16
Alignment explanation
Indices: 1315889--1315936 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1315879 AAATTTTAAA
1315889 TTTAAATCCATTAATATT
1 TTTAAATCCA--AATATT
* *
1315907 TTAAAACCCAAATATT
1 TTTAAATCCAAATATT
1315923 TTTAAATCCAAATA
1 TTTAAATCCAAATA
1315937 AAAATACTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 18 0.69
18 8 0.31
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAATCCAAATATT
Found at i:1327599 original size:107 final size:108
Alignment explanation
Indices: 1327464--1327660 Score: 333
Period size: 107 Copynumber: 1.8 Consensus size: 108
1327454 GTATGACTTA
* *
1327464 AAAATAAAAACGAGTTTAATATTTTTATTTAAATTATTTTTACAATTCTTTTAAAATAATAATAT
1 AAAATAAAAACGAGTTTAATATTGTTATTTAAATTATTTTTACAATTATTTTAAAATAATAATAT
*
1327529 ATAAATTATATTAAAATAAAATTATTTAGAGAATCCAAACCAC
66 ATAAATTATATAAAAATAAAATTATTTAGAGAATCCAAACCAC
* * *
1327572 AAAATAAAAA-TAGTTTAATATTGTTATTTGAATTATTTTTACAATTATTTTTAAATAATAATAT
1 AAAATAAAAACGAGTTTAATATTGTTATTTAAATTATTTTTACAATTATTTTAAAATAATAATAT
1327636 ATAAATTATATAAAAATAAAATTAT
66 ATAAATTATATAAAAATAAAATTAT
1327661 ATTAAAATTA
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
107 73 0.88
108 10 0.12
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (108 bp):
AAAATAAAAACGAGTTTAATATTGTTATTTAAATTATTTTTACAATTATTTTAAAATAATAATAT
ATAAATTATATAAAAATAAAATTATTTAGAGAATCCAAACCAC
Found at i:1327657 original size:16 final size:16
Alignment explanation
Indices: 1327638--1327668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1327628 AATAATATAT
1327638 AAATTATATAAAAATA
1 AAATTATATAAAAATA
*
1327654 AAATTATATTAAAAT
1 AAATTATATAAAAAT
1327669 TATTTAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATATAAAAATA
Found at i:1328505 original size:2 final size:2
Alignment explanation
Indices: 1328498--1328531 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1328488 CGAAGTGACT
*
1328498 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1328532 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1331781 original size:18 final size:19
Alignment explanation
Indices: 1331746--1331782 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1331736 CACGGAATGT
1331746 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1331766 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1331783 TGATTACAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1336526 original size:20 final size:20
Alignment explanation
Indices: 1336501--1336681 Score: 136
Period size: 20 Copynumber: 8.8 Consensus size: 20
1336491 ATGCGAAACA
1336501 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
1336521 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
1336541 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
1336561 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* *
1336582 AAGAATCGCAATGCGATTCA-
1 AA-AATCGCAACGCGATTTAG
*
1336602 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTTAG
**
1336623 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
1336644 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTTAG
1336665 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
1336682 CCAAGAATCG
Statistics
Matches: 130, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.01
20 87 0.67
21 14 0.11
22 28 0.22
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1336609 original size:42 final size:40
Alignment explanation
Indices: 1336585--1336694 Score: 184
Period size: 42 Copynumber: 2.7 Consensus size: 40
1336575 ATCTTCCAAG
* *
1336585 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
1336625 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTGAGAA
1336667 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
1336695 AACGGCAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
40 27 0.41
42 39 0.59
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:1336610 original size:62 final size:63
Alignment explanation
Indices: 1336539--1336680 Score: 195
Period size: 62 Copynumber: 2.3 Consensus size: 63
1336529 AATGTTGAAA
*
1336539 AGAAAATCGCAACGGTC-A-AAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGG-CGATAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
** *
1336601 A-AAGAATCGCAAC-GCGATTGAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTG
1 AGAA-AATCGCAACGGCGATAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1336663 AGAAAATCGCAAC-GCGAT
1 AGAAAATCGCAACGGCGAT
1336681 TCCAAGAATC
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
60 1 0.01
61 4 0.06
62 65 0.90
63 2 0.03
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (63 bp):
AGAAAATCGCAACGGCGATAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:1336681 original size:62 final size:62
Alignment explanation
Indices: 1336559--1336681 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
1336549 AACGGTCAAA
*
1336559 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
*
1336621 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCA-AAGAATCGCAACGCGATT
1336682 CCAAGAATCG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 56 0.97
63 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (62 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
Found at i:1336690 original size:20 final size:20
Alignment explanation
Indices: 1336563--1336694 Score: 142
Period size: 20 Copynumber: 6.4 Consensus size: 20
1336553 GTCAAAAGAA
1336563 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
1336585 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
1336605 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
1336625 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
1336647 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
1336667 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
1336687 AATCGCAA
1 AATCGCAA
1336695 AACGGCAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.02
20 61 0.66
21 1 0.01
22 28 0.30
23 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:1336816 original size:6 final size:6
Alignment explanation
Indices: 1336805--1336855 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
1336795 GACACGTATT
1336805 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1336853 ACC
1 ACC
1336856 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1337609 original size:6 final size:6
Alignment explanation
Indices: 1337598--1337642 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1337588 TCTCGTCTCG
1337598 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1337643 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1337778 original size:20 final size:20
Alignment explanation
Indices: 1337753--1337984 Score: 229
Period size: 20 Copynumber: 11.4 Consensus size: 20
1337743 TTTTGCCGTT
*
1337753 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
**
1337773 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
1337793 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
1337813 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
*
1337833 TTGCGATTATTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
1337853 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
1337873 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
* *
1337893 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTT-GGA-ATCGCG
*
1337915 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
* *
1337935 TTGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCG
1337955 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
1337977 TTGCGATT
1 TTGCGATT
1337985 TTCTTTTGAC
Statistics
Matches: 181, Mismatches: 19, Indels: 22
0.82 0.09 0.10
Matches are distributed among these distances:
19 10 0.06
20 129 0.71
21 13 0.07
22 29 0.16
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:1337800 original size:40 final size:40
Alignment explanation
Indices: 1337753--1337988 Score: 312
Period size: 40 Copynumber: 5.8 Consensus size: 40
1337743 TTTTGCCGTT
1337753 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
*
1337793 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
* *
1337833 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
* ** *
1337873 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCA-ATCGCG
*** *
1337915 TTGCGATTCTTGGAATCGCATTGCGATTCTT-TGGCTCGCA
1 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCAATCGCG
*
1337955 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 TTGCGATTCTTGG-A-ATCGCATTGCGATTTTCT
1337989 TTTGACCGTT
Statistics
Matches: 177, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
40 121 0.68
41 7 0.04
42 49 0.28
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
Found at i:1337940 original size:62 final size:61
Alignment explanation
Indices: 1337753--1337984 Score: 274
Period size: 60 Copynumber: 3.8 Consensus size: 61
1337743 TTTTGCCGTT
* **
1337753 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCAATCGCGTTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAAATCGCGTTGCGATTCTTGGAATCGCG
* * * * **
1337813 TTGCGATT-TTCTCAATCGCGTTGCGATTATT-GGAATCGCGTTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-TGAATCGCATTGCGATTCTTCGAAATCGCGTTGCGATTCTT-GGAATCGCG
* *
1337873 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAAGATCGCATTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAA-ATCGCGTTGCGATTCTTGGAATCGCG
** *
1337935 TTGCGATTCTTTGGCTCGCATTGCGATTCTTGGAAGATCGCGTTGCGATT
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAA-ATCGCGTTGCGATT
1337985 TTCTTTTGAC
Statistics
Matches: 146, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.03
60 69 0.47
61 6 0.04
62 65 0.45
63 2 0.01
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (61 bp):
TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAAATCGCGTTGCGATTCTTGGAATCGCG
Found at i:1338001 original size:62 final size:63
Alignment explanation
Indices: 1337753--1338045 Score: 249
Period size: 62 Copynumber: 4.8 Consensus size: 63
1337743 TTTTGCCGTT
* *** *
1337753 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCA-ATCGCGTTGCGA--TTCTTGGAATCGCG
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTCG-ATCGCG
* * * *
1337813 TTGCGATT-TTCTCAATCGCGTTGCGATTATTGG-A-ATCGCGTTGCGATTTTC-TCAATCGCG
1 TTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTCGATCGCG
* * * *
1337873 TTGCGATTCTTTGAATCGCATTGCGATTCTTCGAAGATCGCATTGCGA--TTCTTGGAATCGCA
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTCG-ATCGCG
** *
1337935 TTGCGATTCTTTGGCTCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTTTGA-C-CG
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTC-TTCGATCGCG
* * * *
1337997 TTGCGATT-TTCTAAATCGCGTTGCGATT-TT--TATATCGCGTTGCGATTTT
1 TTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTT
1338046 GTTGGTCATT
Statistics
Matches: 193, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
59 19 0.10
60 70 0.36
61 11 0.06
62 85 0.44
63 1 0.01
64 4 0.02
65 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (63 bp):
TTGCGATTCTTTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTCGATCGCG
Found at i:1338018 original size:20 final size:20
Alignment explanation
Indices: 1337995--1338043 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
1337985 TTCTTTTGAC
*
1337995 CGTTGCGATT-TTCTAAATCG
1 CGTTGCGATTCTT-TGAATCG
1338015 CGTTGCGATT-TTT-ATATCG
1 CGTTGCGATTCTTTGA-ATCG
1338034 CGTTGCGATT
1 CGTTGCGATT
1338044 TTGTTGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTTTGAATCG
Found at i:1339464 original size:2 final size:2
Alignment explanation
Indices: 1339457--1339487 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1339447 TCAAGGAAAC
1339457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1339488 AAAGTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1341589 original size:2 final size:2
Alignment explanation
Indices: 1341576--1341665 Score: 171
Period size: 2 Copynumber: 45.0 Consensus size: 2
1341566 CATTACTATG
*
1341576 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1341618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1341660 AT AT AT
1 AT AT AT
1341666 GATGTGTTCG
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1342721 original size:20 final size:20
Alignment explanation
Indices: 1342684--1342726 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1342674 CTAGTTTTTT
* *
1342684 TTTTTTAAATAACAAATCTA
1 TTTTTAAAATAACAAATCAA
1342704 TTTTTAAAATAA-ATAATCAA
1 TTTTTAAAATAACA-AATCAA
1342724 TTT
1 TTT
1342727 GATATAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTTAAAATAACAAATCAA
Found at i:1358888 original size:5 final size:5
Alignment explanation
Indices: 1358875--1358983 Score: 174
Period size: 5 Copynumber: 22.8 Consensus size: 5
1358865 GTCGTTCTGG
*
1358875 TGATT TGATC TGAT- TGAT- TGATC TGAT- TGAT- TGATC TGAT- TGATC
1 TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC
1358920 TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC
1 TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC TGATC
1358970 TGATC TGATC TGAT
1 TGATC TGATC TGAT
1358984 TTAATATGAG
Statistics
Matches: 100, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
4 20 0.20
5 80 0.80
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (5 bp):
TGATC
Found at i:1367671 original size:20 final size:22
Alignment explanation
Indices: 1367640--1367682 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1367630 TTAATTTAAT
1367640 ACATATTAAAAAATTTAT-TTA
1 ACATATTAAAAAATTTATATTA
*
1367661 ACATA-TAAAAATTTTATATTA
1 ACATATTAAAAAATTTATATTA
1367682 A
1 A
1367683 AATTAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
ACATATTAAAAAATTTATATTA
Found at i:1367881 original size:24 final size:24
Alignment explanation
Indices: 1367854--1367911 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1367844 CTTGTAATTT
1367854 ATAATTAT-TTATGAAAA-TAAATAA
1 ATAATTATATT-T-AAAATTAAATAA
*
1367878 ATAATTTATATTTAAAATTAATTAA
1 ATAA-TTATATTTAAAATTAAATAA
1367903 ATAATTATA
1 ATAATTATA
1367912 AGGATAGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 13 0.43
25 15 0.50
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAATTATATTTAAAATTAAATAA
Found at i:1371176 original size:31 final size:31
Alignment explanation
Indices: 1371131--1371222 Score: 157
Period size: 31 Copynumber: 3.0 Consensus size: 31
1371121 AAAACATAAG
*
1371131 ATATGATAACTTTCGTTTTTATTTAATTAAA
1 ATATGATAATTTTCGTTTTTATTTAATTAAA
*
1371162 ATATGATCATTTTCGTTTTTATTTAATTAAA
1 ATATGATAATTTTCGTTTTTATTTAATTAAA
*
1371193 ATATGATTATTTTCGTTTTTATTTAATTAA
1 ATATGATAATTTTCGTTTTTATTTAATTAA
1371223 GATGTGGTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (31 bp):
ATATGATAATTTTCGTTTTTATTTAATTAAA
Found at i:1372260 original size:31 final size:31
Alignment explanation
Indices: 1372189--1372263 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 31
1372179 TTAACTCGGG
*
1372189 GTGATCACATCTTAATTAAATAAAAACAAAA
1 GTGATCATATCTTAATTAAATAAAAACAAAA
**
1372220 GT-ATCATATCTTAATTAAATAAAAATGAAA
1 GTGATCATATCTTAATTAAATAAAAACAAAA
1372250 GTGATCATATCTTA
1 GTGATCATATCTTA
1372264 TGTTTTCTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 27 0.68
31 13 0.32
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (31 bp):
GTGATCATATCTTAATTAAATAAAAACAAAA
Found at i:1387343 original size:2 final size:2
Alignment explanation
Indices: 1387336--1387361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1387326 ATAAAACTAG
1387336 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1387362 ACTAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1389643 original size:36 final size:36
Alignment explanation
Indices: 1389596--1389667 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1389586 TGTCATAGCT
*
1389596 TACATGGGCTATTCCACAAGCCGTCGATACTAAGGA
1 TACATGGGCTATTCCACAAGCCGCCGATACTAAGGA
1389632 TACATGGGCTATTCCACAAGCCGCCGATACTAAGGA
1 TACATGGGCTATTCCACAAGCCGCCGATACTAAGGA
1389668 CGGTGAGGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (36 bp):
TACATGGGCTATTCCACAAGCCGCCGATACTAAGGA
Found at i:1392033 original size:112 final size:113
Alignment explanation
Indices: 1391864--1392087 Score: 260
Period size: 112 Copynumber: 2.0 Consensus size: 113
1391854 ATAATATATT
** * ** *
1391864 TTTTTATATTTATAATTAGGATCCCTAATTTTTATAATTTCTTAAATTTTTAGTTTTTA-TAT-T
1 TTTTTATATTTATAATTAGGA-CCCTAAACTTTATAATTTCTAAAATAATTAGTTTTTACCATCT
1391927 TTTTCTCATTTCTCTTGT-TAATTCATTCAATTTT-AATTAAATTTAATCA
65 TTTT-TCATTTCTCTTGTCT-ATTCATTCAATTTTGAATTAAATTTAATCA
* * *
1391976 TTTTTATATTTATAATTAGG-GCCTATAACTTTATAATTTCATAAAATAATTATTTTTTACCCTC
1 TTTTTATATTTATAATTAGGACCCTA-AACTTTATAATTTC-TAAAATAATTAGTTTTTACCATC
* * *
1392040 TTTTTTCGTTTCTTTTGTCTGTTCATTCAATTTTGAATTAAATTTAAT
64 TTTTTTCATTTCTCTTGTCTATTCATTCAATTTTGAATTAAATTTAAT
1392088 TATGTTTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
110 4 0.04
111 12 0.13
112 34 0.36
113 25 0.27
114 19 0.20
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (113 bp):
TTTTTATATTTATAATTAGGACCCTAAACTTTATAATTTCTAAAATAATTAGTTTTTACCATCTT
TTTTCATTTCTCTTGTCTATTCATTCAATTTTGAATTAAATTTAATCA
Found at i:1405393 original size:23 final size:23
Alignment explanation
Indices: 1405362--1405406 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1405352 GCCAATCAAA
*
1405362 CGGGGGAATGTGAATTTCATTCC
1 CGGGAGAATGTGAATTTCATTCC
*
1405385 CGGGAGAATGTGGATTTCATTC
1 CGGGAGAATGTGAATTTCATTC
1405407 TTATGGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (23 bp):
CGGGAGAATGTGAATTTCATTCC
Found at i:1406814 original size:21 final size:20
Alignment explanation
Indices: 1406790--1406831 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1406780 TTTTAATATG
1406790 TTTTGGCATATTTTTTCGATTT
1 TTTTGGC-TATTTTTTC-ATTT
1406812 TTTTGGCTATTTTTTCATTT
1 TTTTGGCTATTTTTTCATTT
1406832 ATCTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTTGGCTATTTTTTCATTT
Found at i:1407699 original size:30 final size:31
Alignment explanation
Indices: 1407645--1407717 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
1407635 ATTTGTACAC
*
1407645 TTTTGGTCACTTAAGTTATCGTTTTATTAAA
1 TTTTGGTCACTTAAGTTATAGTTTTATTAAA
* * *
1407676 TTTTGGTTAC-TATGTTATAGTTTTATTAAG
1 TTTTGGTCACTTAAGTTATAGTTTTATTAAA
1407706 TTTTGGTCACTT
1 TTTTGGTCACTT
1407718 TGACGTTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (31 bp):
TTTTGGTCACTTAAGTTATAGTTTTATTAAA
Found at i:1413331 original size:38 final size:37
Alignment explanation
Indices: 1413257--1413344 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 37
1413247 CCCGACCCGA
*
1413257 TCGGGTCGGATTTTTTTAAAAAAATTTCGGGTTCGGG
1 TCGGGTCGGGTTTTTTTAAAAAAATTTCGGGTTCGGG
** *
1413294 TCGGGTCGGGTTTTTTTAAATGTACTATTCGGG-TCGGG
1 TCGGGTCGGGTTTTTTTAAA-AAAAT-TTCGGGTTCGGG
1413332 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
1413345 AGGGTGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
37 19 0.42
38 20 0.44
39 6 0.13
ACGTcount: A:0.15, C:0.12, G:0.34, T:0.39
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTTAAAAAAATTTCGGGTTCGGG
Found at i:1413504 original size:5 final size:5
Alignment explanation
Indices: 1413494--1413524 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1413484 TATTATTATT
1413494 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
1413525 TTCTAAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1414507 original size:28 final size:28
Alignment explanation
Indices: 1414435--1414524 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
1414425 AATTGCTCAT
* * * *
1414435 GGGCCCGCTCTTTTAATTTTCACAATTA
1 GGGCCCCCTTTTTTAATTTTTACAACTA
*
1414463 GGGCCCCCTTCTTTTAATTTTTATAACTA
1 GGGCCCCCTT-TTTTAATTTTTACAACTA
* *
1414492 GGGCCCCCTTTTTTAATCTTTACATCTA
1 GGGCCCCCTTTTTTAATTTTTACAACTA
1414520 GGGCC
1 GGGCC
1414525 TTATTCTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 28 0.53
29 25 0.47
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.40
Consensus pattern (28 bp):
GGGCCCCCTTTTTTAATTTTTACAACTA
Found at i:1416575 original size:20 final size:20
Alignment explanation
Indices: 1416550--1416596 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1416540 TACGGAATGT
* *
1416550 AAGATTATCAGTGGAAATAA
1 AAGATTATCACTAGAAATAA
1416570 AAGATTATCACTAGAAATAA
1 AAGATTATCACTAGAAATAA
1416590 AAGATTA
1 AAGATTA
1416597 CCAGGGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (20 bp):
AAGATTATCACTAGAAATAA
Found at i:1421785 original size:11 final size:10
Alignment explanation
Indices: 1421751--1421781 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1421741 ATTATATTTT
*
1421751 ATTAAATTAA
1 ATTAGATTAA
1421761 ATTAGATTAA
1 ATTAGATTAA
1421771 ATTAGATTAA
1 ATTAGATTAA
1421781 A
1 A
1421782 ATTAAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (10 bp):
ATTAGATTAA
Found at i:1423923 original size:15 final size:15
Alignment explanation
Indices: 1423903--1423950 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1423893 TATTTAGTGT
*
1423903 GCGGGCAGATGTGGG
1 GCGGGCGGATGTGGG
1423918 GCGGGCGGATGTGGG
1 GCGGGCGGATGTGGG
* *
1423933 GCGAGCGGATGCGGG
1 GCGGGCGGATGTGGG
1423948 GCG
1 GCG
1423951 AGTAAGGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.10, C:0.17, G:0.62, T:0.10
Consensus pattern (15 bp):
GCGGGCGGATGTGGG
Found at i:1425110 original size:25 final size:26
Alignment explanation
Indices: 1425082--1425137 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1425072 AAAATAAAAG
1425082 ATTATT-GGAATGTATATTTGACCAA
1 ATTATTCGGAATGTATATTTGACCAA
** *
1425107 ATTATTCTTATTGTATATTTGACCAA
1 ATTATTCGGAATGTATATTTGACCAA
1425133 ATTAT
1 ATTAT
1425138 CCTTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (26 bp):
ATTATTCGGAATGTATATTTGACCAA
Found at i:1425123 original size:26 final size:26
Alignment explanation
Indices: 1425092--1425153 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1425082 ATTATTGGAA
*
1425092 TGTATATTTGACCAAATTATTCTTAT
1 TGTATATTTGACCAAATTATCCTTAT
1425118 TGTATATTTGACCAAATTATCCTTAT
1 TGTATATTTGACCAAATTATCCTTAT
*
1425144 TATATATTTG
1 TGTATATTTG
1425154 TATAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (26 bp):
TGTATATTTGACCAAATTATCCTTAT
Found at i:1429822 original size:16 final size:17
Alignment explanation
Indices: 1429801--1429834 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1429791 ATTTATTATT
*
1429801 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
1429817 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
1429834 A
1 A
1429835 AAATAGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:1430567 original size:2 final size:2
Alignment explanation
Indices: 1430560--1430591 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1430550 AATAAAAGCT
1430560 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1430592 CCACTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1438012 original size:27 final size:26
Alignment explanation
Indices: 1437972--1438057 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
1437962 ATTTTTAAAA
*
1437972 TATATTTATTAATAATTTTAATCATAT
1 TATATTTATTAAT-ATTATAATCATAT
1437999 TATATTT-TTCAATATTATAATCATA-
1 TATATTTATT-AATATTATAATCATAT
* *
1438024 TATTCAGTTATATAATA--ATAATGATAT
1 TA-T-ATTTAT-TAATATTATAATCATAT
1438051 TATATTT
1 TATATTT
1438058 TAGTTTAGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
25 5 0.10
26 23 0.47
27 15 0.31
28 5 0.10
29 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (26 bp):
TATATTTATTAATATTATAATCATAT
Found at i:1438287 original size:29 final size:27
Alignment explanation
Indices: 1438217--1438290 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 27
1438207 ATATTAGCTT
* *
1438217 ATATTACTATAATACTTT-TAAAAATA
1 ATATTAATATAATATTTTATAAAAATA
1438243 ATATT-AT-TGAA-ATTTTATAATAAATA
1 ATATTAATAT-AATATTTTATAA-AAATA
1438269 ATATTAATATCAATATTTTATA
1 ATATTAATAT-AATATTTTATA
1438291 TTTATAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 5 0.13
25 6 0.15
26 15 0.38
27 2 0.05
28 3 0.08
29 8 0.21
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATTAATATAATATTTTATAAAAATA
Found at i:1443305 original size:19 final size:19
Alignment explanation
Indices: 1443283--1443321 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1443273 CATATGTCCC
*
1443283 TAAATTATAT-CTTTAACTT
1 TAAATTA-ATCCTTAAACTT
1443302 TAAATTAATCCTTAAACTT
1 TAAATTAATCCTTAAACTT
1443321 T
1 T
1443322 TGAATATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTAATCCTTAAACTT
Found at i:1443426 original size:60 final size:59
Alignment explanation
Indices: 1443302--1443461 Score: 178
Period size: 60 Copynumber: 2.7 Consensus size: 59
1443292 TCTTTAACTT
* * * * * *
1443302 TAAATTAATCCTTAAACTTTTGAATATTCTAGTTTCATCTCTAAACCGTGACTCTCATTC
1 TAAATT-ATCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAACCATGACCCTCATTA
* * *
1443362 TAAATTGATCCTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACCCTCTTTA
1 TAAATT-ATCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAACCATGACCCTCATTA
** *
1443422 TAAATTAGTCCCCAAAC-TTTGAATATTTCAATTTCATCCC
1 TAAATTA-TCCTTAAACTTTTGAATATTTTAATTTCATCCC
1443462 CAAATTCATC
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 22 0.26
60 63 0.74
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (59 bp):
TAAATTATCCTTAAACTTTTGAATATTTTAATTTCATCCCTAAACCATGACCCTCATTA
Found at i:1457605 original size:30 final size:30
Alignment explanation
Indices: 1457569--1457628 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1457559 CTGGCCTCAA
1457569 TACTTCCTTGAATTGCATGCGCTATTCGTT
1 TACTTCCTTGAATTGCATGCGCTATTCGTT
1457599 TACTTCCTTGAATTGCATGCGCTATTCGTT
1 TACTTCCTTGAATTGCATGCGCTATTCGTT
1457629 CCATACATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (30 bp):
TACTTCCTTGAATTGCATGCGCTATTCGTT
Found at i:1466811 original size:12 final size:12
Alignment explanation
Indices: 1466794--1466822 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1466784 TTGTTGTGCT
1466794 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1466806 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1466818 TGCTC
1 TGCTC
1466823 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:1468292 original size:20 final size:20
Alignment explanation
Indices: 1468255--1468293 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1468245 AGATTGAGTG
* *
1468255 GATTTTAATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1468275 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1468294 AGTTTAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1468899 original size:21 final size:22
Alignment explanation
Indices: 1468859--1468899 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1468849 CTAAGGGTTT
* *
1468859 TGTAAAGATATCTACTAATTGG
1 TGTAAAGATATCAACAAATTGG
1468881 TGTAAAG-TATCAACAAATT
1 TGTAAAGATATCAACAAATT
1468900 CTAGAACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TGTAAAGATATCAACAAATTGG
Found at i:1477620 original size:60 final size:59
Alignment explanation
Indices: 1477556--1477669 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
1477546 ATAGTCGGAT
* * * * *
1477556 GATCATTTTATAA-TCTTTAATAGTTGAGGGACTTAATAAAATAATATTCTATAATTCATA
1 GATCATTTTATAACT-TTTAATAATAGA-AGACTTAATAAAACAATACTCTATAATTCATA
*
1477616 GATCATTTTATAACTTTTAATAATAGAAGATTTAATAAAACAATACTCTATAAT
1 GATCATTTTATAACTTTTAATAATAGAAGACTTAATAAAACAATACTCTATAAT
1477670 GAGAGAACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 23 0.49
60 23 0.49
61 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (59 bp):
GATCATTTTATAACTTTTAATAATAGAAGACTTAATAAAACAATACTCTATAATTCATA
Found at i:1481205 original size:174 final size:171
Alignment explanation
Indices: 1480820--1481223 Score: 562
Period size: 171 Copynumber: 2.3 Consensus size: 171
1480810 AGGTCCAAGT
* * * *
1480820 CCCGGCGTAGGGAACAAGTTTACCGAGTCCGGTCCGAGTCCTGGTGTGGGAAATAAATTTACTGA
1 CCCGGTGTAGGGAACAAGTTTACCGACTCCGGTCCGAGTCCTGGTGTGGGAAATAAGTTTACTAA
* * * *
1480885 TAGCTTCACTCTAGGTGGCATTAAAACCTCCAGTTCAAGTTCTGGTGATGGAAATAAGTTAACTG
66 TAGCTTCACTCTAGGTGGAATTAAAAACTCCAGTTCAAGTCCTGGTGATGAAAATAAGTTAACTG
* *
1480950 ATAGTCAGGTCATTGGAGGCATAAAGAATGGGGGGCCGAGC
131 ATAGTCAGATCATTGGAGGCATAAAGAATGGAGGGCCGAGC
* *
1480991 CCAGGTGTAGGGAACAAGTTTACCGACTCCGGTCCGAGTCCTGGCGTGGGAAATAAGTTTACTAA
1 CCCGGTGTAGGGAACAAGTTTACCGACTCCGGTCCGAGTCCTGGTGTGGGAAATAAGTTTACTAA
* *
1481056 TAGCTTCACTCTAGGTGGAATTAAAAACTTC-GTTTCAAGTCCTGGT-TTCGAAAATAAGTTAA-
66 TAGCTTCACTCTAGGTGGAATTAAAAACTCCAG-TTCAAGTCCTGGTGAT-GAAAATAAGTTAAC
* *
1481118 TCGATAGTCGTCAGATTATTGGAGGCATTAAGAATGGAGGGCCGAGC
129 T-GATA---GTCAGATCATTGGAGGCATAAAGAATGGAGGGCCGAGC
* * *
1481165 CCCGGTGTAGGGAACAAGTTTACTGACTCCGGTCCGAGTCCTGGTGTTGGAAACAAGTT
1 CCCGGTGTAGGGAACAAGTTTACCGACTCCGGTCCGAGTCCTGGTGTGGGAAATAAGTT
1481224 AACCGACGGC
Statistics
Matches: 206, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
170 3 0.01
171 115 0.56
174 88 0.43
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (171 bp):
CCCGGTGTAGGGAACAAGTTTACCGACTCCGGTCCGAGTCCTGGTGTGGGAAATAAGTTTACTAA
TAGCTTCACTCTAGGTGGAATTAAAAACTCCAGTTCAAGTCCTGGTGATGAAAATAAGTTAACTG
ATAGTCAGATCATTGGAGGCATAAAGAATGGAGGGCCGAGC
Found at i:1485882 original size:22 final size:23
Alignment explanation
Indices: 1485839--1485885 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1485829 TCATTTAAAT
1485839 AATAAACGAACATAAACAAACAC
1 AATAAACGAACATAAACAAACAC
*
1485862 AATAAACGAACA-ACACAAACAC
1 AATAAACGAACATAAACAAACAC
1485884 AA
1 AA
1485886 AAAAACTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.66, C:0.23, G:0.04, T:0.06
Consensus pattern (23 bp):
AATAAACGAACATAAACAAACAC
Found at i:1485891 original size:23 final size:23
Alignment explanation
Indices: 1485842--1485889 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1485832 TTTAAATAAT
*
1485842 AAACGAACATAAACAAACACAAT
1 AAACGAACATAAACAAACACAAA
*
1485865 AAACGAACA-ACACAAACACAAA
1 AAACGAACATAAACAAACACAAA
1485887 AAA
1 AAA
1485890 ACTTATTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.69, C:0.23, G:0.04, T:0.04
Consensus pattern (23 bp):
AAACGAACATAAACAAACACAAA
Found at i:1486737 original size:6 final size:6
Alignment explanation
Indices: 1486726--1486754 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1486716 TTTATTTTAA
1486726 ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
1486755 TTTGGTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.66, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:1486836 original size:2 final size:2
Alignment explanation
Indices: 1486829--1486870 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1486819 AATAATTATT
1486829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1486870 T
1 T
1486871 TAATAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1486874 original size:6 final size:7
Alignment explanation
Indices: 1486829--1486875 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 7
1486819 AATAATTATT
1486829 TATATATA
1 TATATA-A
1486837 TATATATA
1 TATATA-A
1486845 TATATATA
1 TATATA-A
1486853 TATATATA
1 TATATA-A
1486861 TATATAA
1 TATATAA
1486868 TAT-TAA
1 TATATAA
1486874 TA
1 TA
1486876 AATTTAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 5 0.13
7 4 0.10
8 30 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TATATAA
Found at i:1486965 original size:12 final size:12
Alignment explanation
Indices: 1486950--1486984 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1486940 CGATTCTCGG
1486950 CCCAATACCCGA
1 CCCAATACCCGA
*
1486962 CCCAATACCCGG
1 CCCAATACCCGA
1486974 CCCAATACCCG
1 CCCAATACCCG
1486985 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1490279 original size:30 final size:31
Alignment explanation
Indices: 1490224--1490288 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1490214 CCAAGTGATC
*
1490224 AAAACTTAATAAAAAAATAACGTAAGAGACT
1 AAAACTTAATAAAAAAATAACGTAAGAGACA
* * *
1490255 AAAACTTAAT-AAACAATAATGTAAGCGACA
1 AAAACTTAATAAAAAAATAACGTAAGAGACA
1490285 AAAA
1 AAAA
1490289 GTGTACACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.18
Consensus pattern (31 bp):
AAAACTTAATAAAAAAATAACGTAAGAGACA
Found at i:1490963 original size:29 final size:28
Alignment explanation
Indices: 1490916--1491094 Score: 93
Period size: 29 Copynumber: 6.2 Consensus size: 28
1490906 TATTCTACGT
* *
1490916 TAAAATAT-TTTGAAGTTAAAATAAAAA
1 TAAAATATATTTAAAATTAAAATAAAAA
* *
1490943 TAAAATATATTTAAAATTTAAAGTAATAA
1 TAAAATATATTTAAAA-TTAAAATAAAAA
* *
1490972 TATAAA-ATATTT---AGT-AAATAAAGA
1 TA-AAATATATTTAAAATTAAAATAAAAA
* *
1490996 TAAAATGTATACTTTGAAAAGTAAAAATAATAA
1 TAAAA--TATA-TTT-AAAA-TTAAAATAAAAA
** *
1491029 TAAAATATATTCTTAAAATTTTAGTAAAAA
1 TAAAATATA-T-TTAAAATTAAAATAAAAA
* *
1491059 TAAAATATTTTTTTAAA-TAATAATAAAAA
1 TAAAATA-TATTTAAAATTAA-AATAAAAA
1491088 TAAAATA
1 TAAAATA
1491095 CTTTAAATTT
Statistics
Matches: 113, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
23 3 0.03
24 8 0.07
25 1 0.01
26 4 0.04
27 11 0.10
28 6 0.05
29 37 0.33
30 18 0.16
31 11 0.10
32 2 0.02
33 12 0.11
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (28 bp):
TAAAATATATTTAAAATTAAAATAAAAA
Found at i:1491076 original size:86 final size:86
Alignment explanation
Indices: 1490928--1491086 Score: 209
Period size: 86 Copynumber: 1.8 Consensus size: 86
1490918 AAATATTTTG
*
1490928 AAGTTAAAATAAAAATAAAATATATTTAAAATTTAAAGTAATAATATAAAATATTTAGTAAATAA
1 AAGTAAAAATAAAAATAAAATATATTTAAAATTTAAAGTAATAATATAAAATATTTAGTAAATAA
1490993 -AGATAAAATGTATACTTTGAA
66 TA-ATAAAATGTATACTTTGAA
* * **
1491014 AAGTAAAAATAATAATAAAATATATTCTTAAAATTT-TAGTAA-AA-ATAAAATATTTTTTTAAA
1 AAGTAAAAATAAAAATAAAATATA-T-TTAAAATTTAAAGTAATAATATAAAATA-TTTAGTAAA
1491076 TAATAATAAAA
63 TAATAATAAAA
1491087 ATAAAATACT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
85 8 0.12
86 40 0.62
87 7 0.11
88 9 0.14
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.35
Consensus pattern (86 bp):
AAGTAAAAATAAAAATAAAATATATTTAAAATTTAAAGTAATAATATAAAATATTTAGTAAATAA
TAATAAAATGTATACTTTGAA
Found at i:1492138 original size:29 final size:29
Alignment explanation
Indices: 1492104--1492176 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
1492094 TTGGTTTAGT
1492104 AGGAATATAAGATTACCGTGTTTGGTTAA
1 AGGAATATAAGATTACCGTGTTTGGTTAA
1492133 AGGAATATAAGATTACCGTGTTTGGTTAA
1 AGGAATATAAGATTACCGTGTTTGGTTAA
*
1492162 AGGAATAAAAGATTA
1 AGGAATATAAGATTA
1492177 TTAGAATGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (29 bp):
AGGAATATAAGATTACCGTGTTTGGTTAA
Found at i:1492264 original size:22 final size:22
Alignment explanation
Indices: 1492236--1492284 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1492226 CTACAAATTG
*
1492236 TAAAATATTTCTATATTTTCTT
1 TAAAATATTTATATATTTTCTT
1492258 TAAAATATTTATATATTTTCTT
1 TAAAATATTTATATATTTTCTT
1492280 TAAAA
1 TAAAA
1492285 AATTAAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TAAAATATTTATATATTTTCTT
Found at i:1493070 original size:5 final size:5
Alignment explanation
Indices: 1493054--1493087 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
1493044 TATTCATCCA
1493054 TATAT ATATAT TATAT TATAT TATAT ATATAT TA
1 TATAT -TATAT TATAT TATAT TATAT -TATAT TA
1493088 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 17 0.63
6 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:1494695 original size:42 final size:42
Alignment explanation
Indices: 1494648--1494734 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
1494638 CACCGGCTTA
1494648 TGCTTTGTTCTGTATGAACACAATTGAAAACCATCAAATTTT
1 TGCTTTGTTCTGTATGAACACAATTGAAAACCATCAAATTTT
*
1494690 TGCTTTGTTCTGTATTAACACAATTGAAAACCATCAAATTTT
1 TGCTTTGTTCTGTATGAACACAATTGAAAACCATCAAATTTT
1494732 TGC
1 TGC
1494735 ACTTCAATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (42 bp):
TGCTTTGTTCTGTATGAACACAATTGAAAACCATCAAATTTT
Found at i:1495018 original size:22 final size:20
Alignment explanation
Indices: 1494978--1495052 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 20
1494968 CTATAAAAAA
1494978 TTTAAAATTATTA-TATATTT
1 TTTAAAATT-TTATTATATTT
*
1494998 TAATTAAAATTTTATTTTATTT
1 T--TTAAAATTTTATTATATTT
*
1495020 TTTAAAAATTTTA-TAAATTCAT
1 TTT-AAAATTTTATTATATT--T
1495042 TTTAAAATTTT
1 TTTAAAATTTT
1495053 CATCCTCCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 7 0.15
21 20 0.43
22 19 0.41
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAAATTTTATTATATTT
Found at i:1495728 original size:16 final size:16
Alignment explanation
Indices: 1495703--1495735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1495693 ACAACCTGAT
1495703 AAATTTTAAAA-AAAA
1 AAATTTTAAAATAAAA
1495718 AAATATTTAAAATAAAA
1 AAAT-TTTAAAATAAAA
1495735 A
1 A
1495736 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTTTAAAATAAAA
Found at i:1495757 original size:22 final size:21
Alignment explanation
Indices: 1495702--1495761 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
1495692 CACAACCTGA
1495702 TAAATTTTAAAAAAAAAAATATT
1 TAAA-TTT-AAAAAAAAAATATT
*
1495725 TAAA-ATAAAAATAAAAATTATT
1 TAAATTTAAAAA-AAAAA-TATT
*
1495747 TATATTTAAAAAAAA
1 TAAATTTAAAAAAAA
1495762 GAAAACACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 10 0.32
23 10 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATTTAAAAAAAAAATATT
Found at i:1501072 original size:24 final size:26
Alignment explanation
Indices: 1501023--1501085 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
1501013 TTTAAATGAA
1501023 AATAAAATATTTAAAATTAAGTTAAT
1 AATAAAATATTTAAAATTAAGTTAAT
*
1501049 AATAAAATATTT-CAA-TAAGTTAAT
1 AATAAAATATTTAAAATTAAGTTAAT
* *
1501073 TA-AAAATACTTAA
1 AATAAAATATTTAA
1501086 TATATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 8 0.25
24 10 0.31
25 2 0.06
26 12 0.38
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (26 bp):
AATAAAATATTTAAAATTAAGTTAAT
Found at i:1505363 original size:22 final size:22
Alignment explanation
Indices: 1505335--1505387 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1505325 ACACACATTC
1505335 CATCTTACGTGTGGGGAATGCA
1 CATCTTACGTGTGGGGAATGCA
1505357 CATCTTACGTGTGGGGAATGCA
1 CATCTTACGTGTGGGGAATGCA
*
1505379 C-TATTACGT
1 CATCTTACGT
1505388 TGTAGGATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (22 bp):
CATCTTACGTGTGGGGAATGCA
Found at i:1508322 original size:21 final size:21
Alignment explanation
Indices: 1508296--1508340 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1508286 GATTTCTGGG
* *
1508296 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1508317 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1508338 CAA
1 CAA
1508341 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1508808 original size:20 final size:22
Alignment explanation
Indices: 1508768--1508824 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1508758 TGAATGTGTG
*
1508768 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
1508790 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
1508810 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
1508825 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:1509392 original size:31 final size:31
Alignment explanation
Indices: 1509354--1509540 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
1509344 AGGGTCGAGG
1509354 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1509385 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
**
1509416 GTTTACCTATGTTCTTTAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1509447 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1509478 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1509509 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1509540 G
1 G
1509541 GTCCTTCGGG
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1526802 original size:42 final size:43
Alignment explanation
Indices: 1526747--1526868 Score: 158
Period size: 42 Copynumber: 2.9 Consensus size: 43
1526737 TATAATGTTG
* *
1526747 TTTTGTCTACAAACGCCACTAATTCTCTTGTCTTTAGTTA-CGT
1 TTTTG-CTACAAACGCCGCTAATTCTCTTGTCTTTAGTTAGCAT
*
1526790 TTTTGCTACAAACGCCGCTAATTCTCTTGTATTTAG-TAGCAT
1 TTTTGCTACAAACGCCGCTAATTCTCTTGTCTTTAGTTAGCAT
* * * *
1526832 TTTTACCAGAAACGCCGCTAGTTCTCTTGTCTTTAGT
1 TTTTGCTACAAACGCCGCTAATTCTCTTGTCTTTAGT
1526869 GGCGTTTGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.90
43 5 0.07
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (43 bp):
TTTTGCTACAAACGCCGCTAATTCTCTTGTCTTTAGTTAGCAT
Found at i:1532036 original size:32 final size:32
Alignment explanation
Indices: 1532000--1532062 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1531990 ACTACTGTAA
*
1532000 ATCTAGAATTACTCCAATAGTTTTATCTATAG
1 ATCTAGAATTACTCCAAGAGTTTTATCTATAG
1532032 ATCTAGAATTACTCCAAGAGTTTTATCTATA
1 ATCTAGAATTACTCCAAGAGTTTTATCTATA
1532063 ATATTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (32 bp):
ATCTAGAATTACTCCAAGAGTTTTATCTATAG
Found at i:1536407 original size:20 final size:20
Alignment explanation
Indices: 1536361--1536398 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536351 ATATAAATTA
*
1536361 AAAATTATTTGATATGATAT
1 AAAATTATTGGATATGATAT
1536381 ATAAATTA-TGGATATGAT
1 A-AAATTATTGGATATGAT
1536399 TTTAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
AAAATTATTGGATATGATAT
Found at i:1537075 original size:14 final size:14
Alignment explanation
Indices: 1537053--1537091 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1537043 TTGTAAAATG
*
1537053 AATTATATTTCTTGAA
1 AATTAT-TTTC-TAAA
1537069 AATTATTTTCTAAA
1 AATTATTTTCTAAA
1537083 AATTATTTT
1 AATTATTTT
1537092 ACGGTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 4 0.18
16 6 0.27
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (14 bp):
AATTATTTTCTAAA
Found at i:1537360 original size:10 final size:10
Alignment explanation
Indices: 1537345--1537383 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1537335 ATTAAAATAC
1537345 TTATTATTAA
1 TTATTATTAA
1537355 TTATTATTAA
1 TTATTATTAA
1537365 TTATT-TATAA
1 TTATTAT-TAA
1537375 -TATTATTAA
1 TTATTATTAA
1537384 AATATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATTATTAA
Found at i:1537530 original size:23 final size:24
Alignment explanation
Indices: 1537454--1537532 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 24
1537444 AATATTCAAC
1537454 AATATAATATTA-AT-TATATTAAT
1 AATATAATATTATATAT-TATTAAT
1537477 AAT-T--TATTATATATTATTAAAT
1 AATATAATATTATATATTATT-AAT
1537499 AAAAGTATAATATTATATATTA-TAAT
1 --AA-TATAATATTATATATTATTAAT
1537525 AATATAAT
1 AATATAAT
1537533 TATAACAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
20 5 0.11
21 6 0.13
22 5 0.11
23 9 0.19
24 4 0.09
25 1 0.02
26 4 0.09
27 1 0.02
28 12 0.26
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
AATATAATATTATATATTATTAAT
Found at i:1537563 original size:19 final size:18
Alignment explanation
Indices: 1537507--1537565 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
1537497 ATAAAAGTAT
1537507 AATATTA-TATATTATAA
1 AATATTATTATATTATAA
* **
1537524 TAATATAATTATAACAATAA
1 -AATATTATTAT-ATTATAA
1537544 AATATTATTATATTATTAA
1 AATATTATTATATTA-TAA
1537563 AAT
1 AAT
1537566 TATCAATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.25
19 19 0.59
20 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTATTATATTATAA
Found at i:1539521 original size:22 final size:23
Alignment explanation
Indices: 1539493--1539537 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1539483 AAAACATTAC
*
1539493 TTAAGTGTTATAATTGTT-ATAA
1 TTAAGTGATATAATTGTTGATAA
1539515 TTAAGTGATATAATTGTTGATAA
1 TTAAGTGATATAATTGTTGATAA
1539538 CAATGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (23 bp):
TTAAGTGATATAATTGTTGATAA
Found at i:1554572 original size:54 final size:54
Alignment explanation
Indices: 1554488--1554739 Score: 317
Period size: 54 Copynumber: 4.7 Consensus size: 54
1554478 TATGTGTACA
* * *
1554488 ATCGACACTAAGTATGTAACCCACGGAATTCATAATATGTTTATGAACGACCGT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCGT
* * *
1554542 ATCGACACTAAGTGTGCTACCCACATAATTCATAATATGTTTATGAACGATCGT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCGT
* * *
1554596 ATCGACACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGTCCAT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCGT
* * * * *
1554650 ATCGACACTAAGTGTGCAACCCAAAAAATTCATATTATGTTTATGAATGACTGT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCGT
* * * * *
1554704 ATCGGCTCTACGTGTGCACCCCAAAGAACTT-ATAAT
1 ATCGACACTAAGTGTGCAACCCACAGAA-TTCATAAT
1554740 GATTTGAAAA
Statistics
Matches: 171, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 169 0.99
55 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (54 bp):
ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCGT
Found at i:1557138 original size:30 final size:30
Alignment explanation
Indices: 1557102--1557174 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1557092 CCCAAAGGAC
1557102 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1557132 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1557162 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1557175 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1562162 original size:30 final size:30
Alignment explanation
Indices: 1562126--1562225 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
1562116 CCCGAAGGAC
*
1562126 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
1562156 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
* *** * *
1562186 CTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCATAAAGATCCTCGGT-AA
1562217 CTATCCATA
1 CTATCCATA
1562226 TGTTCCCTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
30 51 0.84
31 10 0.16
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGATCCTCGGTAA
Found at i:1567838 original size:26 final size:26
Alignment explanation
Indices: 1567802--1567855 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1567792 CAACTTGTGC
*
1567802 AAGTTGTTTACTTAATGTTTTACATA
1 AAGTTGTTTACTTAATGATTTACATA
1567828 AAGTTGTTTACTTAATGATTTACATA
1 AAGTTGTTTACTTAATGATTTACATA
1567854 AA
1 AA
1567856 CATTGAGATA
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:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (26 bp):
AAGTTGTTTACTTAATGATTTACATA
Found at i:1568395 original size:19 final size:20
Alignment explanation
Indices: 1568367--1568408 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1568357 CCCCTGCTCT
*
1568367 ATTTTTATTTTAAATT-AAA
1 ATTTTCATTTTAAATTCAAA
*
1568386 ATTTTCATTTTAATTTCAAA
1 ATTTTCATTTTAAATTCAAA
1568406 ATT
1 ATT
1568409 ATTTTACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTCATTTTAAATTCAAA
Found at i:1568534 original size:20 final size:21
Alignment explanation
Indices: 1568501--1568566 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
1568491 ATCATAAATT
1568501 ATTTTA-AA-TTTATTTGT-A
1 ATTTTATAATTTTATTTGTAA
*
1568519 ATTTTATAATTTTATTTTTAA
1 ATTTTATAATTTTATTTGTAA
* * *
1568540 ATTATATAATTTGA-TTATAA
1 ATTTTATAATTTTATTTGTAA
1568560 ATTTTAT
1 ATTTTAT
1568567 GCATTTGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 6 0.15
19 2 0.05
20 19 0.47
21 13 0.32
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
ATTTTATAATTTTATTTGTAA
Found at i:1568547 original size:21 final size:21
Alignment explanation
Indices: 1568495--1568551 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1568485 ATTTTAATCA
* *
1568495 TAAATTATTTTAAATTTATTTG
1 TAAATTA-TATAATTTTATTTG
* *
1568517 T-AATTTTATAATTTTATTTT
1 TAAATTATATAATTTTATTTG
1568537 TAAATTATATAATTT
1 TAAATTATATAATTT
1568552 GATTATAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 12 0.41
21 16 0.55
22 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TAAATTATATAATTTTATTTG
Found at i:1571748 original size:13 final size:13
Alignment explanation
Indices: 1571730--1571766 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1571720 ATAAGTTGTT
1571730 TTACGATTTATAA
1 TTACGATTTATAA
1571743 TTACGATTTATAA
1 TTACGATTTATAA
1571756 TTACGATTTAT
1 TTACGATTTAT
1571767 GTGCTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (13 bp):
TTACGATTTATAA
Done.