Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013929.1 Corchorus olitorius cultivar O-4 contig13962, 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: 160219
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1997 original size:18 final size:19
Alignment explanation
Indices: 1974--2009 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1964 CACCACCCTT
*
1974 CTAAAAATTAG-AGAAAAA
1 CTAAAAACTAGAAGAAAAA
1992 CTAAAAACTAGAAGAAAA
1 CTAAAAACTAGAAGAAAA
2010 GAATTGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.67, C:0.08, G:0.11, T:0.14
Consensus pattern (19 bp):
CTAAAAACTAGAAGAAAAA
Found at i:3679 original size:2 final size:2
Alignment explanation
Indices: 3674--3705 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3664 TATGTTCTTA
3674 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
3706 CTTATTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6980 original size:130 final size:130
Alignment explanation
Indices: 6836--7477 Score: 683
Period size: 130 Copynumber: 5.0 Consensus size: 130
6826 GCGTATCGAC
* * * *
6836 TTATAAAGTTGTTACGAATGGATTATAATTTCGCAACAACTTAAGAATTTGTTGTTACGAATATT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTT-AGAATTTGTTGTTACGAAAATT
* * * * *
6901 ATAAATATTGGCAACAACTAAAAAA-TATTGTGTAAAATACCATAAAAATCACTTAGGCAAAGTT
65 GTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
6965 T
130 T
* * * * * *
6966 TTATAAAGTTGTTACAAATAGTTTATTATTTCGCAGCAATTTAAAAAGTTGTTGTTAC-------
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTT-AGAATTTGTTGTTACGAAAATT
* * *
7024 G-AAACATTGACAACAACTAAAAAAGTGTTGTGTAAAATGCCATCAAAATTACTTAGGCAACGTT
65 GTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
7088 T
130 T
* *
7089 TTATAAAGTTGTTACGAATACTTTATGATTTCGCAACAACTTCAGAATTTGTTGTTACGAATATT
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTT-AGAATTTGTTGTTACGAAAATT
* * *
7154 GTAAACATTGACAACAACTAAAAAAGTGTTGTGTAAAATATCATCAAAATCACTTATGCAACGTT
65 GTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
7219 T
130 T
* * * * * **
7220 TTATAAAGTTGTTATGAATAGTTTTTTATTTCGTAACAACTTTGTTTTTGTTGTTACGAAAATTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAGAATTTGTTGTTACGAAAATTG
* * * * * * **
7285 TAAGCATTAGCAGCAATTAAAAAAGTGTTGTGCAAAATACCATCAAAATCACTTAGTCAACGACT
66 TAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
* * * * * * * ** * *
7350 TCATAAAATTATTACGAATAGATTATGATTTCACAACGACTTTGTCTTTATTGTTACGAAAACTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAGAATTTGTTGTTACGAAAATTG
* ** * *
7415 TAAGCATTGGCAACAACTAAAAACTTCGTTAG-GTAAAATACCATCAAAATCTCTAAGGCAACG
66 TAAACATTGGCAACAACTAAAAAAGT-GTT-GTGTAAAATACCATCAAAATCACTTAGGCAACG
7478 ACTTTTAATT
Statistics
Matches: 431, Mismatches: 70, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
122 21 0.05
123 85 0.20
130 197 0.46
131 127 0.29
132 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (130 bp):
TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAGAATTTGTTGTTACGAAAATTG
TAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
Found at i:17040 original size:24 final size:24
Alignment explanation
Indices: 16994--17040 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
16984 ATAATAACTC
*
16994 TTTTAGTAATCTTAAAAGCTTTTT
1 TTTTAGTAATCTTAAAAGATTTTT
* * *
17018 TTTTATTAATTTTATAAGATTTT
1 TTTTAGTAATCTTAAAAGATTTT
17041 AGAAAGTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTAGTAATCTTAAAAGATTTTT
Found at i:21537 original size:37 final size:37
Alignment explanation
Indices: 21487--21557 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
21477 ATATAATTAT
* *
21487 TCATAAAATTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAATTATGTCTATATGAAAAGACATGTATTGA
*
21524 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAATTATGTCTATATGAAAAGACATGTAT
21558 GTTGATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.37
Consensus pattern (37 bp):
TCATAAAATTATGTCTATATGAAAAGACATGTATTGA
Found at i:25437 original size:21 final size:21
Alignment explanation
Indices: 25413--25452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25403 CGAGTTGGGA
25413 TGATAAAAGGAGAGAAGAGGT
1 TGATAAAAGGAGAGAAGAGGT
* * *
25434 TGATACAGGGAGATAAGAG
1 TGATAAAAGGAGAGAAGAG
25453 TTTCCCCAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.38, T:0.15
Consensus pattern (21 bp):
TGATAAAAGGAGAGAAGAGGT
Found at i:29141 original size:2 final size:2
Alignment explanation
Indices: 29134--29168 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29124 TTCTTTCTTT
29134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29169 TGTTGATCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30688 original size:3 final size:3
Alignment explanation
Indices: 30680--30705 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30670 TATTGATGCC
30680 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
30706 CTATCACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:47492 original size:37 final size:37
Alignment explanation
Indices: 47446--47520 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
47436 TTTAATCCTT
* * * *
47446 CTTTTGTAAAGAGTATAGCTAATATTTTGGCTGTGTG
1 CTTTAGTAAAGAGTATAACTAATATCTTGGCTGCGTG
*
47483 CTTTAGTAAAGAGTATAATTAATATCTTGGCTGCGTG
1 CTTTAGTAAAGAGTATAACTAATATCTTGGCTGCGTG
47520 C
1 C
47521 AGTAGCCAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.40
Consensus pattern (37 bp):
CTTTAGTAAAGAGTATAACTAATATCTTGGCTGCGTG
Found at i:51292 original size:21 final size:21
Alignment explanation
Indices: 51268--51309 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
51258 TTTAGTCTGA
51268 AAAGAGTATGATCAAAAGGAG
1 AAAGAGTATGATCAAAAGGAG
51289 AAAGAGTATGATCAAAAGGAG
1 AAAGAGTATGATCAAAAGGAG
51310 CTTAAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.29, T:0.14
Consensus pattern (21 bp):
AAAGAGTATGATCAAAAGGAG
Found at i:79188 original size:20 final size:20
Alignment explanation
Indices: 79163--79203 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
79153 TCTCCTATCT
79163 AATTAAA-GTTACTAAAAACA
1 AATTAAAGGTTA-TAAAAACA
*
79183 AATTAAAGGTTATCAAAACA
1 AATTAAAGGTTATAAAAACA
79203 A
1 A
79204 TAATGATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTAAAGGTTATAAAAACA
Found at i:81327 original size:109 final size:109
Alignment explanation
Indices: 81110--81311 Score: 350
Period size: 109 Copynumber: 1.9 Consensus size: 109
81100 CCATAATAAT
* *
81110 TAATTGATTAATCTAAATGAAATAAAAATACATGTTTACCCTTTAAAGGAATACTAACATTTTAA
1 TAATTAATTAATCTAAATGAAATAAAAATACATGTTTACCCTTTAAAGGAATACTAAAATTTTAA
*
81175 AATTAAAAAAGGTATTTTAAATATTTCAAATCAAGATTTTTGAA
66 AATTAAAAAAGGTATTTCAAATATTTCAAATCAAGATTTTTGAA
* *
81219 TAATTAATTAATCTAAATGAAATAAAGATACATGTTTACTCTTTAAAGGAATACTAAAATTTTAA
1 TAATTAATTAATCTAAATGAAATAAAAATACATGTTTACCCTTTAAAGGAATACTAAAATTTTAA
*
81284 AATTAAAAAGGGTATTTCAAATATTTCA
66 AATTAAAAAAGGTATTTCAAATATTTCA
81312 CGTCATGGTT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 87 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (109 bp):
TAATTAATTAATCTAAATGAAATAAAAATACATGTTTACCCTTTAAAGGAATACTAAAATTTTAA
AATTAAAAAAGGTATTTCAAATATTTCAAATCAAGATTTTTGAA
Found at i:83862 original size:63 final size:63
Alignment explanation
Indices: 83793--83920 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
83783 CACACTCTTG
*
83793 ACTTGACTCTTGAGTGGGGATAATGACTTCATTGTCCTCACTCCACAGCAGTTCACTTTTTCA
1 ACTTGACTCTTGAGTGGGGATAATGACTTCATTGTCCCCACTCCACAGCAGTTCACTTTTTCA
83856 ACTTGACTCTTGAGTGGGGATAATGACTTCATTGTCCCCACTCCACAGCAGTTCACTTTTTCA
1 ACTTGACTCTTGAGTGGGGATAATGACTTCATTGTCCCCACTCCACAGCAGTTCACTTTTTCA
83919 AC
1 AC
83921 AAAGTTAATG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.34
Consensus pattern (63 bp):
ACTTGACTCTTGAGTGGGGATAATGACTTCATTGTCCCCACTCCACAGCAGTTCACTTTTTCA
Found at i:88596 original size:4 final size:4
Alignment explanation
Indices: 88587--88618 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
88577 ATCTTGTCAT
88587 GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA
88619 CAATCACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:95013 original size:8 final size:8
Alignment explanation
Indices: 95000--95024 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
94990 CCAACGTCTC
95000 TTCCAATT
1 TTCCAATT
95008 TTCCAATT
1 TTCCAATT
95016 TTCCAATT
1 TTCCAATT
95024 T
1 T
95025 CCTTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TTCCAATT
Found at i:95850 original size:63 final size:63
Alignment explanation
Indices: 95726--95850 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
95716 GGCACAATCT
* * **
95726 CCAGACTTGCGTGAGAAACTAAACCAAAAGAGGGAGGCAGACAAGATAGATAAGCGGTTGAAG
1 CCAGACTTGCGGGAGAAACTAAACCAAAAGAGAGAGGCAGACAAGATAGATAAGCAATTGAAG
* *
95789 CCAGACTTGCGGGAGAAACTAAA-CAAAAGGAGAGAGGCGGATGAA-ATAGATAAGCAATTGAA
1 CCAGACTTGCGGGAGAAACTAAACCAAAA-GAGAGAGGCAGA-CAAGATAGATAAGCAATTGAA
95851 AAATGTTAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
62 5 0.09
63 47 0.87
64 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.30, T:0.13
Consensus pattern (63 bp):
CCAGACTTGCGGGAGAAACTAAACCAAAAGAGAGAGGCAGACAAGATAGATAAGCAATTGAAG
Found at i:96729 original size:41 final size:41
Alignment explanation
Indices: 96684--96762 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
96674 CTCGATGAAA
*
96684 TGGATTTGAGAGGAATGGCCGAAGGCTTGTTACTCCTCATG
1 TGGATTTGAGAGAAATGGCCGAAGGCTTGTTACTCCTCATG
* * *
96725 TGGATTTGAGAGAAATGGTCTAAGGCTTGTTATTCCTC
1 TGGATTTGAGAGAAATGGCCGAAGGCTTGTTACTCCTC
96763 GTTATCAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (41 bp):
TGGATTTGAGAGAAATGGCCGAAGGCTTGTTACTCCTCATG
Found at i:101832 original size:20 final size:20
Alignment explanation
Indices: 101770--101839 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
101760 TATATATAAG
101770 AAACAATAATATATAATGAA
1 AAACAATAATATATAATGAA
* * * **
101790 AAACTATAGATATCTTACCAA
1 AAACAATA-ATATATAATGAA
101811 AAACAATAATATATAATGAA
1 AAACAATAATATATAATGAA
*
101831 AAACCATAA
1 AAACAATAA
101840 ATGTCTATGC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.60, C:0.11, G:0.04, T:0.24
Consensus pattern (20 bp):
AAACAATAATATATAATGAA
Found at i:108382 original size:30 final size:32
Alignment explanation
Indices: 108346--108408 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
108336 CGGATGTAAA
*
108346 TTCATGT-GATTG-CAAGAGTAAATATGGTGT
1 TTCATGTAAATTGACAAGAGTAAATATGGTGT
*
108376 TTCATGTAAATTGACAAGGGTAAATATGGTGT
1 TTCATGTAAATTGACAAGAGTAAATATGGTGT
108408 T
1 T
108409 CCATTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 7 0.24
31 4 0.14
32 18 0.62
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (32 bp):
TTCATGTAAATTGACAAGAGTAAATATGGTGT
Found at i:108401 original size:32 final size:30
Alignment explanation
Indices: 108346--108417 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 30
108336 CGGATGTAAA
*
108346 TTCATGTGATTGCAAGAGTAAATATGGTGT
1 TTCATGTAATTGCAAGAGTAAATATGGTGT
*
108376 TTCATGTAAATTGACAAGGGTAAATATGGTGT
1 TTCATGT-AATTG-CAAGAGTAAATATGGTGT
*
108408 TCCAT-TAATT
1 TTCATGTAATT
108418 TTTTGTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.30
31 5 0.14
32 21 0.57
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (30 bp):
TTCATGTAATTGCAAGAGTAAATATGGTGT
Found at i:118814 original size:2 final size:2
Alignment explanation
Indices: 118801--118876 Score: 95
Period size: 2 Copynumber: 39.5 Consensus size: 2
118791 TCAGATTTCT
* *
118801 TA TA TA TG TA TA TA TA TA TA TA TA TA T- TA TA TT TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
118841 TA TA TA TA TA TA TA TA TA AA TA AA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118877 TATGTCGGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
1 3 0.05
2 60 0.95
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:120953 original size:16 final size:16
Alignment explanation
Indices: 120934--120973 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
120924 ACCCGCCCGA
*
120934 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
120950 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
120966 ACCCGAAC
1 ACCCGAAC
120974 TCGACCCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.40, G:0.15, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:121804 original size:13 final size:12
Alignment explanation
Indices: 121768--121814 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
121758 TCAATCTTTA
*
121768 TATATATTGATAA
1 TATATATT-ATAT
*
121781 TA-ATGTTATAT
1 TATATATTATAT
121792 TATATTATTATAT
1 TATA-TATTATAT
121805 TATATATTAT
1 TATATATTAT
121815 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:121971 original size:17 final size:18
Alignment explanation
Indices: 121949--121994 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
121939 CAAACTCGAG
121949 CCCGAACCCGACCC-AAA
1 CCCGAACCCGACCCGAAA
* *
121966 CCCGAACCCTACCCGAGA
1 CCCGAACCCGACCCGAAA
121984 -CCGAACCCGAC
1 CCCGAACCCGAC
121995 ATAACCAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.30, C:0.52, G:0.15, T:0.02
Consensus pattern (18 bp):
CCCGAACCCGACCCGAAA
Found at i:122024 original size:16 final size:16
Alignment explanation
Indices: 121983--122086 Score: 65
Period size: 16 Copynumber: 6.6 Consensus size: 16
121973 CCTACCCGAG
*
121983 ACCGAACCCG-ACATA
1 ACCGAACCCGAAAATA
*
121998 ACCAGAGCCCGAAAATA
1 ACC-GAACCCGAAAATA
* **
122015 TCCGAACCCG-ACTTA
1 ACCGAACCCGAAAATA
*
122030 ACTCGAGCCCGAAAAT-
1 AC-CGAACCCGAAAATA
*
122046 ACCGGAACCTGAAAA-A
1 ACC-GAACCCGAAAATA
*
122062 ACCGAACCCG-AAGTA
1 ACCGAACCCGAAAATA
*
122077 CCCGAACCCG
1 ACCGAACCCG
122087 TTCGAGCCCG
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
14 2 0.03
15 24 0.36
16 33 0.49
17 8 0.12
ACGTcount: A:0.38, C:0.36, G:0.17, T:0.09
Consensus pattern (16 bp):
ACCGAACCCGAAAATA
Found at i:122025 original size:32 final size:31
Alignment explanation
Indices: 121983--122054 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
121973 CCTACCCGAG
121983 ACCGAACCCGACATAAC-CAGAGCCCGAAAAT
1 ACCGAACCCGACATAACTC-GAGCCCGAAAAT
*
122014 ATCCGAACCCGACTTAACTCGAGCCCGAAAAT
1 A-CCGAACCCGACATAACTCGAGCCCGAAAAT
122046 ACCGGAACC
1 ACC-GAACC
122055 TGAAAAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 3 0.08
32 33 0.89
33 1 0.03
ACGTcount: A:0.38, C:0.36, G:0.17, T:0.10
Consensus pattern (31 bp):
ACCGAACCCGACATAACTCGAGCCCGAAAAT
Found at i:129557 original size:57 final size:57
Alignment explanation
Indices: 129495--129646 Score: 226
Period size: 57 Copynumber: 2.8 Consensus size: 57
129485 AATGGAACCA
*
129495 TCGACATGCTCTTTTTCTTCGTATCCAATCATCAAAGGCTTATTATCTCCTCCACCG
1 TCGACATGCTCTTTTTCTTCGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCG
*
129552 TCGACATGCTCTTTTTCTTTGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCG
1 TCGACATGCTCTTTTTCTTCGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCG
* *
129609 ACAACATGCTC----T-TT-GTATCCAATCAACAAAGGCTTATT
1 TCGACATGCTCTTTTTCTTCGTATCCAATCAACAAAGGCTTATT
129647 TTGAGAAGGG
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
51 24 0.26
52 2 0.02
53 1 0.01
57 64 0.70
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.36
Consensus pattern (57 bp):
TCGACATGCTCTTTTTCTTCGTATCCAATCAACAAAGGCTTATTATCTCCTCCACCG
Found at i:135716 original size:22 final size:24
Alignment explanation
Indices: 135690--135739 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
135680 GCTTGGAATC
*
135690 TCTGA-AA-AGGCTAGGGTTTTCT
1 TCTGAGAAGAGGCTAGGGTCTTCT
135712 TCTGAGGAAGAGGCTAGGGTCTTCT
1 TCTGA-GAAGAGGCTAGGGTCTTCT
135737 TCT
1 TCT
135740 CTTCAGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
24 2 0.08
25 17 0.71
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (24 bp):
TCTGAGAAGAGGCTAGGGTCTTCT
Found at i:146922 original size:18 final size:19
Alignment explanation
Indices: 146893--146928 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
146883 CACATACACA
146893 AAAAGAGGCCCAACACATG
1 AAAAGAGGCCCAACACATG
146912 AAAAG-GGCCCAACACAT
1 AAAAGAGGCCCAACACAT
146929 CTCTTTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.28, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAGAGGCCCAACACATG
Found at i:147636 original size:27 final size:27
Alignment explanation
Indices: 147595--147650 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
147585 ACGGCAGAGT
* *
147595 TGGTATGCCAGCAGCGGGAATCGTGGC
1 TGGTATGCCAACAGCGGGAATCATGGC
*
147622 TGGTATGCCAACAGCGGTAATCATGGC
1 TGGTATGCCAACAGCGGGAATCATGGC
147649 TG
1 TG
147651 TCCAGCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (27 bp):
TGGTATGCCAACAGCGGGAATCATGGC
Found at i:148481 original size:37 final size:37
Alignment explanation
Indices: 148429--148753 Score: 244
Period size: 37 Copynumber: 9.1 Consensus size: 37
148419 AAGCTCTCCT
* *
148429 ACCCTCTATACCGCAGAGCTCCCCTTACGGCGATAGC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* * *
148466 ACCCTCTTTATCGCAGGGCTCCTCTTACCGCGATAGC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* * * * ** * *
148503 ACCCTCTTTA-CGTAGAGCTCTCCATGCCATGGTAGT
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* ** *
148539 ACCCTCTTTACCGCAGAGCTCCTCTTATGGCCATAGC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* * * * * *
148576 ACACTCTTTGCGGCAGAGCTCTCCTTACAGCGGTAGC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
*
148613 ACCCTCTTCACCGCAGAGCT---C-T--C-C--T---
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* * *
148638 ACCCTCTTTACCACAGAGCTCCCCTTACGGCGATAAC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* *
148675 ACCTTCTTTACCGCAGAGCTCCCCTTACCGCGGTAGC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
* * ** **
148712 ACCCTTTTTACCGTAGAGCTCTTCTTACTACGATAGC
1 ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
148749 ACCCT
1 ACCCT
148754 TTTTTACAGC
Statistics
Matches: 218, Mismatches: 57, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
25 18 0.08
28 2 0.01
29 1 0.00
30 1 0.00
32 1 0.00
33 1 0.00
34 2 0.01
36 26 0.12
37 166 0.76
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.26
Consensus pattern (37 bp):
ACCCTCTTTACCGCAGAGCTCCCCTTACCGCGATAGC
Found at i:148510 original size:19 final size:18
Alignment explanation
Indices: 148429--148510 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 18
148419 AAGCTCTCCT
148429 ACCCTCTATACCGCAGAGC
1 ACCCTCT-TACCGCAGAGC
* * *
148448 TCCC-CTTACGGCGATAGC
1 ACCCTCTTACCGC-AGAGC
* *
148466 ACCCTCTTTATCGCAGGGC
1 ACCCTC-TTACCGCAGAGC
* *
148485 -TCCTCTTACCGCGATAGC
1 ACCCTCTTACCGC-AGAGC
148503 ACCCTCTT
1 ACCCTCTT
148511 TACGTAGAGC
Statistics
Matches: 45, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
17 11 0.24
18 16 0.36
19 13 0.29
20 5 0.11
ACGTcount: A:0.18, C:0.40, G:0.17, T:0.24
Consensus pattern (18 bp):
ACCCTCTTACCGCAGAGC
Found at i:148709 original size:99 final size:99
Alignment explanation
Indices: 148538--148733 Score: 268
Period size: 99 Copynumber: 2.0 Consensus size: 99
148528 GCCATGGTAG
* * * * * * *
148538 TACCCTCTTTACCGCAGAGCTCCTCTTATGGCCATAGCACACTCTTTGCGGCAGAGCTCTCCTTA
1 TACCCTCTTTACCACAGAGCTCCCCTTACGGCCATAACACACTCTTTACCGCAGAGCTCCCCTTA
148603 CAGCGGTAGCACCCTCTTCACCGCAGAGCTCTCC
66 CAGCGGTAGCACCCTCTTCACCGCAGAGCTCTCC
*
148637 TACCCTCTTTACCACAGAGCTCCCCTTACGGCGATAACAC-CTTCTTTACCGCAGAGCTCCCCTT
1 TACCCTCTTTACCACAGAGCTCCCCTTACGGCCATAACACAC-TCTTTACCGCAGAGCTCCCCTT
* * * *
148701 ACCGCGGTAGCACCCTTTTTACCGTAGAGCTCT
65 ACAGCGGTAGCACCCTCTTCACCGCAGAGCTCT
148734 TCTTACTACG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 1 0.01
99 83 0.99
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.26
Consensus pattern (99 bp):
TACCCTCTTTACCACAGAGCTCCCCTTACGGCCATAACACACTCTTTACCGCAGAGCTCCCCTTA
CAGCGGTAGCACCCTCTTCACCGCAGAGCTCTCC
Found at i:149223 original size:50 final size:50
Alignment explanation
Indices: 149163--149271 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
149153 ATTGAGATGC
* *
149163 GGCATAAGAAGCCTATGGCATAAGGCATGAGATGCAGTGTCAAACATTAT
1 GGCATAAGAAGCCTATGGCATAAGGCATGAGATGAAGCGTCAAACATTAT
* **
149213 GGCATCAGAAGTTTATGGCATAAGGCATGAGATGAAGCGTCAAACATTAT
1 GGCATAAGAAGCCTATGGCATAAGGCATGAGATGAAGCGTCAAACATTAT
*
149263 GGCACAAGA
1 GGCATAAGA
149272 CATGAGATGC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.21
Consensus pattern (50 bp):
GGCATAAGAAGCCTATGGCATAAGGCATGAGATGAAGCGTCAAACATTAT
Found at i:149276 original size:34 final size:34
Alignment explanation
Indices: 149225--149312 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
149215 CATCAGAAGT
* * *
149225 TTATGGCATAAGGCATGAGATGAAGCGTCAAACA-
1 TTATGGCACAAGACATGAGATGAAGC-ACAAACAC
** *
149259 TTATGGCACAAGACATGAGATGCGGCACAGACAC
1 TTATGGCACAAGACATGAGATGAAGCACAAACAC
149293 TTATGGCACAAGACATGAGA
1 TTATGGCACAAGACATGAGA
149313 CATGGCATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 5 0.11
34 42 0.89
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (34 bp):
TTATGGCACAAGACATGAGATGAAGCACAAACAC
Found at i:149447 original size:36 final size:37
Alignment explanation
Indices: 149407--149494 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
149397 CCCAAGAGCT
* * *
149407 ACGGCATAGGTCCCAACTG-GGGAGCCATAAGCCGCC
1 ACGGCATAAGTCCCAACAGCGAGAGCCATAAGCCGCC
* *
149443 ACGGCATAAGTCCCAAGAGCGAGAGCCATAAGCCGTC
1 ACGGCATAAGTCCCAACAGCGAGAGCCATAAGCCGCC
*
149480 ACGGCATAAGCCCCA
1 ACGGCATAAGTCCCA
149495 TCGTCGGAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
36 16 0.36
37 29 0.64
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (37 bp):
ACGGCATAAGTCCCAACAGCGAGAGCCATAAGCCGCC
Found at i:149539 original size:27 final size:27
Alignment explanation
Indices: 149500--149558 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
149490 CCCCATCGTC
*
149500 GGAGCTACGACATAAGTCCCAACCGCG
1 GGAGCTACAACATAAGTCCCAACCGCG
*
149527 GGAGCTACAACATAAGTCCTAACCGCG
1 GGAGCTACAACATAAGTCCCAACCGCG
*
149554 AGAGC
1 GGAGC
149559 CATAAGCCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.31, G:0.25, T:0.12
Consensus pattern (27 bp):
GGAGCTACAACATAAGTCCCAACCGCG
Found at i:149618 original size:21 final size:20
Alignment explanation
Indices: 149592--149631 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
149582 CCCACCGCGG
149592 GAGCTACGACATAAGTCCCCC
1 GAGCTACGACATAAG-CCCCC
* *
149613 GAGCTATGGCATAAGCCCC
1 GAGCTACGACATAAGCCCC
149632 AACCGCGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.35, G:0.23, T:0.15
Consensus pattern (20 bp):
GAGCTACGACATAAGCCCCC
Found at i:149645 original size:85 final size:87
Alignment explanation
Indices: 149443--149695 Score: 291
Period size: 85 Copynumber: 2.9 Consensus size: 87
149433 ATAAGCCGCC
** * * *
149443 ACGGCATAAGTCCCAAGAGCGAGAGCCATAAGCCGTCACGGCATAAG-CCCCATCGTC-GGAGCT
1 ACGGCATAAGTCCCAACCGCGAGAGCCATAAGCCGCCACAGCATAAGTCCCCACCG-CGGGAGCT
149506 ACGACATAAGTCCCAACCGCGGGAGCT
65 ACGACATAAGT-CC--CCGC-GGAGCT
** *
149533 ACAACATAAGTCCTAACCGCGAGAGCCATAAGCCGCCACAGCATAAGTCCCCACCGCGGGAGCTA
1 ACGGCATAAGTCCCAACCGCGAGAGCCATAAGCCGCCACAGCATAAGTCCCCACCGCGGGAGCTA
149598 CGACATAAGTCCCC-C-GAGCT
66 CGACATAAGTCCCCGCGGAGCT
* * * * * *
149618 ATGGCATAAGCCCCAACCGCGAAAGCCAGAAGCCGCCA-TGACATAAGTCCCTACCGCGGGAGCT
1 ACGGCATAAGTCCCAACCGCGAGAGCCATAAGCCGCCACAG-CATAAGTCCCCACCGCGGGAGCT
149682 ACGACATAAGTCCC
65 ACGACATAAGTCCC
149696 AAGAGCGGGA
Statistics
Matches: 143, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
84 1 0.01
85 72 0.50
87 1 0.01
88 2 0.01
90 43 0.30
91 24 0.17
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (87 bp):
ACGGCATAAGTCCCAACCGCGAGAGCCATAAGCCGCCACAGCATAAGTCCCCACCGCGGGAGCTA
CGACATAAGTCCCCGCGGAGCT
Found at i:149816 original size:27 final size:27
Alignment explanation
Indices: 149782--149835 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
149772 CATAATTGCA
149782 GCGGGAGCCATAGCCATACTACCAACT
1 GCGGGAGCCATAGCCATACTACCAACT
** * *
149809 GCGGGAGCTGTGGCCATAGTACCAACT
1 GCGGGAGCCATAGCCATACTACCAACT
149836 TCCAAAGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.17
Consensus pattern (27 bp):
GCGGGAGCCATAGCCATACTACCAACT
Found at i:149901 original size:46 final size:48
Alignment explanation
Indices: 149834--149926 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 48
149824 ATAGTACCAA
*
149834 CTTCCAAAGTCACCTGTGAGTTG-CG-AAAAAAAAAGGAGCAAAATTG
1 CTTCCAAAGTCACCTGTGAGTTGTCGCAAAAAAAAACGAGCAAAATTG
*
149880 CTTCCAAAGTCACCTGTGAGTTGTGGCAAAAAAAAACGAGCAAAATT
1 CTTCCAAAGTCACCTGTGAGTTGTCGCAAAAAAAAACGAGCAAAATT
149927 TCCAAATGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 23 0.53
47 1 0.02
48 19 0.44
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (48 bp):
CTTCCAAAGTCACCTGTGAGTTGTCGCAAAAAAAAACGAGCAAAATTG
Found at i:150104 original size:26 final size:24
Alignment explanation
Indices: 150052--150125 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
150042 CCTGTGGAAG
150052 GAAGCCAACCACTATTCTACCGCA
1 GAAGCCAACCACTATTCTACCGCA
*
150076 GAAGCCAACCACCATATTCTACCGTA
1 GAAGCCAACCA-C-TATTCTACCGCA
* *
150102 GAAGCCAATCACTATTCTAGCGCA
1 GAAGCCAACCACTATTCTACCGCA
150126 AAAGTCAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.48
25 2 0.05
26 21 0.48
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.19
Consensus pattern (24 bp):
GAAGCCAACCACTATTCTACCGCA
Found at i:152994 original size:18 final size:19
Alignment explanation
Indices: 152962--152997 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
152952 CACATACACA
*
152962 AAAAGAGGCCTAACACATT
1 AAAAGAGGCCAAACACATT
152981 AAAAG-GGCCAAACACAT
1 AAAAGAGGCCAAACACAT
152998 CTCTTTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAAGAGGCCAAACACATT
Found at i:153704 original size:27 final size:27
Alignment explanation
Indices: 153665--153719 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
153655 GCGGCAGAGT
153665 TGGTATGCCAACAGCGGGAATCATGGC
1 TGGTATGCCAACAGCGGGAATCATGGC
* *
153692 TGGTATGCGAACATCGGGAATCATGGC
1 TGGTATGCCAACAGCGGGAATCATGGC
153719 T
1 T
153720 ATCCAGCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (27 bp):
TGGTATGCCAACAGCGGGAATCATGGC
Found at i:154054 original size:16 final size:15
Alignment explanation
Indices: 154005--154094 Score: 65
Period size: 13 Copynumber: 6.5 Consensus size: 15
153995 TGTAAAATGT
154005 TAATTATA-TA-TAA
1 TAATTATATTATTAA
*
154018 TAATTAAATT-TTAA
1 TAATTATATTATTAA
154032 TTTAATTATATTATTAA
1 --TAATTATATTATTAA
154049 TAAATTAT-TT-TT-A
1 T-AATTATATTATTAA
154062 TAATT-T-TTATTAA
1 TAATTATATTATTAA
*
154075 TAA-TATA-TATTAC
1 TAATTATATTATTAA
154088 TAATTAT
1 TAATTAT
154095 TAATATGTCA
Statistics
Matches: 63, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
11 3 0.05
12 7 0.11
13 22 0.35
14 9 0.14
15 3 0.05
16 15 0.24
17 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATATTATTAA
Found at i:155213 original size:37 final size:37
Alignment explanation
Indices: 155129--155260 Score: 131
Period size: 37 Copynumber: 3.6 Consensus size: 37
155119 GGGCTTTTCT
* * * * *
155129 ACCCTCTTTACTGCAGAGCTCCCTTTACGGTGATAAC
1 ACCCTCTTTACCGCAGAACTCCCTTTACCGTGGTAGC
* *
155166 ACCCTTTTTACCGCAGAACTCCCTTTACCGCGGTAGC
1 ACCCTCTTTACCGCAGAACTCCCTTTACCGTGGTAGC
* * * **
155203 ACTCTCTTTA-CGCAAAACTCTCTTTGTCGTGGTAGC
1 ACCCTCTTTACCGCAGAACTCCCTTTACCGTGGTAGC
* *
155239 ACCCTCTTTATCGCAGAGCTCC
1 ACCCTCTTTACCGCAGAACTCC
155261 ATTTGACGGC
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
36 30 0.39
37 46 0.61
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (37 bp):
ACCCTCTTTACCGCAGAACTCCCTTTACCGTGGTAGC
Found at i:158460 original size:1 final size:1
Alignment explanation
Indices: 158454--158479 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
158444 GAGACATAAC
158454 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
158480 CAAACACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:159818 original size:47 final size:41
Alignment explanation
Indices: 159721--159802 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
159711 GGAGACAGCC
159721 GCTATATCTATATACTATATAAGTCTAAACTTCAAAACCAT
1 GCTATATCTATATACTATATAAGTCTAAACTTCAAAACCAT
*
159762 GCTATATCTATATACTATATAAGTCTAAATTTCAAAACCAT
1 GCTATATCTATATACTATATAAGTCTAAACTTCAAAACCAT
159803 TGACCTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.35
Consensus pattern (41 bp):
GCTATATCTATATACTATATAAGTCTAAACTTCAAAACCAT
Found at i:159973 original size:111 final size:111
Alignment explanation
Indices: 159779--160002 Score: 421
Period size: 111 Copynumber: 2.0 Consensus size: 111
159769 CTATATACTA
*
159779 TATAAGTCTAAATTTCAAAACCATTGACCTGTAATATCTAAAATAACCTTTTTAATTTTAAAAGT
1 TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTTTTTAATTTTAAAAGT
*
159844 TTAGTATCATTTAAAGGGTAAACATGTATTTATTAAATTAAACTTT
66 TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
*
159890 TATAAGTCTAAACTTCAAAACCATTGATCTGTAATATCTAAAATAACCTTTTTAATTTTAAAAGT
1 TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTTTTTAATTTTAAAAGT
159955 TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
66 TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
160001 TA
1 TA
160003 AGGTTCAATA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (111 bp):
TATAAGTCTAAACTTCAAAACCATTGACCTGTAATATCTAAAATAACCTTTTTAATTTTAAAAGT
TTAGTATCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTT
Done.