Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010634.1 Corchorus capsularis cultivar CVL-1 contig10655, 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: 45045
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:811 original size:14 final size:15
Alignment explanation
Indices: 774--811 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
764 TATGTAAGAT
*
774 AAAAACAAAACTAGA
1 AAAAACAAAACTAAA
789 AAAAA-AAAAC-AAA
1 AAAAACAAAACTAAA
802 AAAAACAAAA
1 AAAAACAAAA
812 AGCTTAACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 9 0.43
15 5 0.24
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAACAAAACTAAA
Found at i:1425 original size:11 final size:11
Alignment explanation
Indices: 1409--1449 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
1399 TTTGACATTT
1409 AATTATAAAAA
1 AATTATAAAAA
1420 AATTATATAAAAA
1 AA-T-TATAAAAA
*
1433 AATTTTAAAAA
1 AATTATAAAAA
1444 AATTAT
1 AATTAT
1450 GTTTTGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 14 0.54
12 2 0.08
13 10 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:1430 original size:13 final size:13
Alignment explanation
Indices: 1412--1449 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1402 GACATTTAAT
1412 TATAAAAAAATTA
1 TATAAAAAAATTA
1425 TATAAAAAAATT-
1 TATAAAAAAATTA
1437 T-TAAAAAAATTA
1 TATAAAAAAATTA
1449 T
1 T
1450 GTTTTGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 2 0.08
13 12 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TATAAAAAAATTA
Found at i:1598 original size:2 final size:2
Alignment explanation
Indices: 1587--1638 Score: 56
Period size: 2 Copynumber: 26.5 Consensus size: 2
1577 ACGGATGGAG
*
1587 TA TA TA -A TA TA TA CTA TA CA CTA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
1629 TA TA T- TA TA T
1 TA TA TA TA TA T
1639 TATTTGAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
1 3 0.07
2 37 0.86
3 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7120 original size:26 final size:26
Alignment explanation
Indices: 7091--7147 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
7081 CACCGACCCA
* *
7091 ATGACCTGTGAACCGATGCACTAAAC
1 ATGACCTATGAACCGATACACTAAAC
* *
7117 ATGACCTATGAACCGGTACAGTAAAC
1 ATGACCTATGAACCGATACACTAAAC
7143 ATGAC
1 ATGAC
7148 GTAAAAGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (26 bp):
ATGACCTATGAACCGATACACTAAAC
Found at i:7500 original size:33 final size:33
Alignment explanation
Indices: 7458--7552 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 33
7448 CTTTTACACT
7458 GAGCCTCCCCACTAGGACGGC-TCAGCCACGACG
1 GAGCCTCCCCACTAGGACGGCTTC-GCCACGACG
* * *
7491 GAGCCTCCCCACTGGGGCGGCTTCGCCACGACA
1 GAGCCTCCCCACTAGGACGGCTTCGCCACGACG
* * *
7524 G-GCCACCCTCA-TGGGGCGGCTTCGCCACG
1 GAGCCTCCC-CACTAGGACGGCTTCGCCACG
7553 GCAGGGCGCC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 24 0.43
33 30 0.54
34 2 0.04
ACGTcount: A:0.16, C:0.42, G:0.31, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTTCGCCACGACG
Found at i:7583 original size:30 final size:32
Alignment explanation
Indices: 7503--7606 Score: 149
Period size: 32 Copynumber: 3.3 Consensus size: 32
7493 GCCTCCCCAC
* *
7503 TGGGGCGGCTTCGCCACGACAGGCCACCCTCA
1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
*
7535 TGGGGCGGCTTCGCCACGGCAGGGCGCCCT-A
1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
* *
7566 TGGCGCGG-TTTGCCACGGCAGGCCGCCCTCA
1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
7597 TGGGGCGGCT
1 TGGGGCGGCT
7607 AGACCAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
30 19 0.30
31 16 0.25
32 28 0.44
ACGTcount: A:0.11, C:0.37, G:0.38, T:0.14
Consensus pattern (32 bp):
TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
Found at i:11312 original size:15 final size:15
Alignment explanation
Indices: 11294--11359 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
11284 AAGAATATAT
11294 TTTTTAAAGGATTTA
1 TTTTTAAAGGATTTA
*
11309 TTTTTGAAGGA--TA
1 TTTTTAAAGGATTTA
* *
11322 --TTT-AAGAATGTA
1 TTTTTAAAGGATTTA
11334 TTTTTTAAAGGATTTA
1 -TTTTTAAAGGATTTA
11350 TTTTTGAAAG
1 TTTTT-AAAG
11360 ATATATTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
10 4 0.10
11 3 0.08
12 2 0.05
13 2 0.05
15 18 0.45
16 11 0.28
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TTTTTAAAGGATTTA
Found at i:11312 original size:16 final size:16
Alignment explanation
Indices: 11291--11359 Score: 53
Period size: 16 Copynumber: 4.8 Consensus size: 16
11281 TTTAAGAATA
11291 TATTTTTTAAAGGATT
1 TATTTTTTAAAGGATT
*
11307 TA-TTTTTGAAGGA--
1 TATTTTTTAAAGGATT
* *
11320 TA---TTT-AAGAATG
1 TATTTTTTAAAGGATT
11332 TATTTTTTAAAGGATT
1 TATTTTTTAAAGGATT
*
11348 TATTTTTGAAAG
1 TATTTTTTAAAG
11360 ATATATTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 4 0.10
11 3 0.07
12 2 0.05
13 2 0.05
15 13 0.31
16 18 0.43
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (16 bp):
TATTTTTTAAAGGATT
Found at i:11316 original size:41 final size:41
Alignment explanation
Indices: 11271--11363 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
11261 TTCTCCATTG
11271 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
*
11312 TTGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
*
11353 TTGAAAGATAT
1 TTGAAGGATAT
11364 ATTATGATGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (41 bp):
TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
Found at i:12919 original size:141 final size:139
Alignment explanation
Indices: 12712--12972 Score: 350
Period size: 141 Copynumber: 1.9 Consensus size: 139
12702 ATTTAAGAAA
* * * * *
12712 TATATTTTAAAAATTCTATTATATCTAAGTTTTTTTATTGAATTAGTAAAATGATTAAAATAAAA
1 TATATTTAAAAAATTCTATTATATATAAGTTTTTTTATTAAAATAGTAAAATGAGTAAAATAAAA
12777 TAGTTATAAGGATA-T-TA-TAATTAAATAAAAAGATAGAGGTTTTTAGTTGAGTAAAAGTGTAA
66 TAGTTATAAGGATATTATATTAATTAAATAAAAA-ATAGA-GTTTTTAGTTGAGTAAAAGTGTAA
12839 AACTATAAAAG
129 AACTATAAAAG
* *
12850 TATATTTAAAAAAATTCTAATATATATATAAGTTTTTTTTATTAAAATAGTAAAATG-GTGAATT
1 TATATTT-AAAAAATTCT-AT-TATATATAAG-TTTTTTTATTAAAATAGTAAAATGAGTAAAAT
* *
12914 TAAATAGTTATAAGGATATTATATTTAATTAATTAAAAAATAGAGTTTTTAGTTGAGTA
62 AAAATAGTTATAAGGATATTATA-TTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTA
12973 CAAAACTATA
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
138 7 0.07
139 9 0.08
140 2 0.02
141 30 0.28
142 23 0.22
143 17 0.16
144 5 0.05
145 13 0.12
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (139 bp):
TATATTTAAAAAATTCTATTATATATAAGTTTTTTTATTAAAATAGTAAAATGAGTAAAATAAAA
TAGTTATAAGGATATTATATTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAAGTGTAAAA
CTATAAAAG
Found at i:15318 original size:31 final size:31
Alignment explanation
Indices: 15283--15341 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15273 TATCTAACCT
* *
15283 TAGACTTGTATGATTCAATTTTCAATCTCCG
1 TAGACTTGTATGATTAAACTTTCAATCTCCG
15314 TAGACTTGTATGATTAAACTTTCAATCT
1 TAGACTTGTATGATTAAACTTTCAATCT
15342 TGATCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (31 bp):
TAGACTTGTATGATTAAACTTTCAATCTCCG
Found at i:21706 original size:21 final size:22
Alignment explanation
Indices: 21675--21738 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
21665 GATAAATATG
21675 TACTATT-TGATGAGCTTTCTT
1 TACTATTGTGATGAGCTTTCTT
* * *
21696 TCCT-TTGTGATTGA-CTAT-AT
1 TACTATTGTGA-TGAGCTTTCTT
21716 TACTATTGTGATGAGCTTTCTT
1 TACTATTGTGATGAGCTTTCTT
21738 T
1 T
21739 TTTCTGTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
20 9 0.28
21 18 0.56
22 5 0.16
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.52
Consensus pattern (22 bp):
TACTATTGTGATGAGCTTTCTT
Found at i:21733 original size:42 final size:41
Alignment explanation
Indices: 21670--21765 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 41
21660 CAAGAGATAA
21670 ATATGTACTATTTGATGAGCTTTCTTTCCTT-TGTGATTGACT
1 ATAT-TACTATTTGATGAGCTTTCTTT-CTTCTGTGATTGACT
* *
21712 ATATTACTATTGTGATGAGCTTTCTTTTTTCTGTGATTGGCT
1 ATATTACTATT-TGATGAGCTTTCTTTCTTCTGTGATTGACT
21754 ATATTACTATTT
1 ATATTACTATTT
21766 ACAAGTATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (41 bp):
ATATTACTATTTGATGAGCTTTCTTTCTTCTGTGATTGACT
Found at i:23856 original size:45 final size:43
Alignment explanation
Indices: 23798--23914 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 43
23788 AAGACCTCAA
* * *
23798 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAG
1 TATG-AATATTGATAACCT-CCATATGAAATATTGATAACC-ACAG
* *
23843 TATGAGATATTGATAACCTCCATATGATATATTGATAACCACAT
1 TATGA-ATATTGATAACCTCCATATGAAATATTGATAACCACAG
* *
23887 TATGAATATTTAAAAACCTCCATATGAA
1 TATGAATA-TTGATAACCTCCATATGAA
23915 TTGTTAGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 3 0.05
44 28 0.46
45 30 0.49
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (43 bp):
TATGAATATTGATAACCTCCATATGAAATATTGATAACCACAG
Found at i:23874 original size:22 final size:22
Alignment explanation
Indices: 23754--23914 Score: 96
Period size: 22 Copynumber: 7.3 Consensus size: 22
23744 ATGATCCCAT
* * *
23754 TATGAAATTTTGTTAACCTCCG
1 TATGAAATATTGATAACCTCCA
* * * *
23776 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATATTGATA-ACCTCCA
* *
23798 TATGAAATTTTGATAACTTCCCA
1 TATGAAATATTGATAACCT-CCA
* **
23821 -ATGAAATTTTGATAACCAACA
1 TATGAAATATTGATAACCTCCA
*
23842 GTATGAGATATTGATAACCTCCA
1 -TATGAAATATTGATAACCTCCA
* *
23865 TATGATATATTGATAACC-ACA
1 TATGAAATATTGATAACCTCCA
* *
23886 TTATG-AATATTTAAAAACCTCCA
1 -TATGAAATA-TTGATAACCTCCA
23909 TATGAA
1 TATGAA
23915 TTGTTAGCAA
Statistics
Matches: 108, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
21 8 0.07
22 77 0.71
23 23 0.21
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (22 bp):
TATGAAATATTGATAACCTCCA
Found at i:23905 original size:44 final size:45
Alignment explanation
Indices: 23829--23913 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
23819 CAATGAAATT
* *
23829 TTGATAACCAACAGTATGAGATATTGATAACCTCCATATGATATA
1 TTGATAACCAACAGTATGAGATATTAAAAACCTCCATATGATATA
*
23874 TTGATAACC-ACATTATGA-ATATTTAAAAACCTCCATATGA
1 TTGATAACCAACAGTATGAGATA-TTAAAAACCTCCATATGA
23914 ATTGTTAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 3 0.08
44 24 0.67
45 9 0.25
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (45 bp):
TTGATAACCAACAGTATGAGATATTAAAAACCTCCATATGATATA
Found at i:23952 original size:22 final size:22
Alignment explanation
Indices: 23927--23990 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
23917 GTTAGCAATT
* *
23927 ACACTCTGAAATTTTGATAATC
1 ACACTATGAAATTTTGATAACC
*
23949 ACACTATGAAATTGTGATAACC
1 ACACTATGAAATTTTGATAACC
* *
23971 TCGCTATGAAATTTTGATAA
1 ACACTATGAAATTTTGATAA
23991 ATCTTCCTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (22 bp):
ACACTATGAAATTTTGATAACC
Found at i:24005 original size:23 final size:23
Alignment explanation
Indices: 23974--24058 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
23964 GATAACCTCG
*
23974 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
23997 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
* *
24020 CTATAAAATTTTTAT-AATTTTC
1 CTATAAAATTTTGATAAATCTTC
* * *
24042 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
24059 CTACAAATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 15 0.30
23 35 0.70
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.44
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:24057 original size:45 final size:45
Alignment explanation
Indices: 23935--24058 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
23925 TTACACTCTG
* * *
23935 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
23979 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* * *
24025 AAATTTTTAT-AATTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
24059 CTACAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 11 0.16
45 34 0.51
46 22 0.33
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:24096 original size:22 final size:22
Alignment explanation
Indices: 24070--24138 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
24060 TACAAATTTA
24070 GATAATCTCCCTATGATTTTTT
1 GATAATCTCCCTATGATTTTTT
** *
24092 GATAATCTCATTATGAAAATTTTT
1 GATAATCTCCCTATG--ATTTTTT
*
24116 -A-AATCTCCCTATGATATTTT
1 GATAATCTCCCTATGATTTTTT
24136 GAT
1 GAT
24139 CTACATACTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 5 0.14
21 1 0.03
22 23 0.64
23 1 0.03
24 6 0.17
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.46
Consensus pattern (22 bp):
GATAATCTCCCTATGATTTTTT
Found at i:24151 original size:44 final size:41
Alignment explanation
Indices: 24073--24157 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 41
24063 AAATTTAGAT
*
24073 AATCTCCCTATGATTTTTTGATAATCTCATTATGAAAATTTTTA
1 AATCTCCCTATGATATTTTG--AATCTCATTATG-AAATTTTTA
24117 AATCTCCCTATGATATTTTG-ATCTACATACTATGAAATTTT
1 AATCTCCCTATGATATTTTGAATCT-CAT--TATGAAATTTT
24158 GATAACCCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
41 4 0.11
42 3 0.08
43 7 0.19
44 23 0.62
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (41 bp):
AATCTCCCTATGATATTTTGAATCTCATTATGAAATTTTTA
Found at i:24383 original size:22 final size:22
Alignment explanation
Indices: 24331--24476 Score: 123
Period size: 22 Copynumber: 6.6 Consensus size: 22
24321 AATCACATTT
*
24331 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
24353 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
24375 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
24397 TGAAATTCTAATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
24419 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
24441 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
24463 TGAAATTTTGATAA
1 TGAAATTTTGATAA
24477 TCTAATCTCT
Statistics
Matches: 96, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
21 1 0.01
22 93 0.97
23 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:24464 original size:66 final size:66
Alignment explanation
Indices: 24350--24478 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
24340 GATAACCTCT
* * * ** *
24350 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTAATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTAATAATCAC
24415 A
66 A
* * * *
24416 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTAATAATC
24479 TAATCTCTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTAATAATCAC
A
Found at i:24469 original size:88 final size:88
Alignment explanation
Indices: 24306--24472 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
24296 ATAAATACCA
* ** * * **
24306 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
24371 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
24394 CTATGAAATTCTAATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
*
24458 CACTATGAAATTTTG
65 CACTATAAAATTTTG
24473 ATAATCTAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 64 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:24494 original size:25 final size:23
Alignment explanation
Indices: 24394--24504 Score: 93
Period size: 22 Copynumber: 4.9 Consensus size: 23
24384 GTTGACCCCT
* *
24394 CTATGAAATTCTAATAATC-ACA
1 CTATGAAATTTTGATAATCAACA
* * ** *
24416 TTATGTAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCAACA
*
24438 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCAACA
*
24460 CTATGAAATTTTGATAATCTAATCT
1 CTATGAAATTTTGATAATC-AA-CA
*
24485 CTATGAAATTTCGATAATCA
1 CTATGAAATTTTGATAATCA
24505 GTCTGTGAGA
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 1 0.01
22 46 0.66
23 1 0.01
24 3 0.04
25 19 0.27
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCAACA
Found at i:24614 original size:22 final size:22
Alignment explanation
Indices: 24575--24687 Score: 86
Period size: 22 Copynumber: 5.1 Consensus size: 22
24565 TATAACCTTC
* * *
24575 ATAACCACACTATAAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
* *
24597 ATAACCTCCCCATGAAATATT-
1 ATAACCTCCCTATGAAATTTTG
**
24618 AGTAACCTCCAAATGAAATTTTG
1 A-TAACCTCCCTATGAAATTTTG
* * **
24641 TTAACCACAGTATGAAATTCTT-
1 ATAACCTCCCTATGAAATT-TTG
*
24663 ATAACCTCGCTATGAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
24685 ATA
1 ATA
24688 TCTCTTTGAT
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
21 3 0.04
22 65 0.93
23 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
ATAACCTCCCTATGAAATTTTG
Found at i:24753 original size:22 final size:22
Alignment explanation
Indices: 24723--24907 Score: 156
Period size: 22 Copynumber: 8.3 Consensus size: 22
24713 TTGTGATAAT
* **
24723 TAACAACCCTATGAAATTTCAA
1 TAACCACCCTATGAAATTTTGA
* *
24745 TAACCACCCTAAGAAATTTTAA
1 TAACCACCCTATGAAATTTTGA
* *
24767 TAACACGATCCTATGAAATTTTGG
1 TAAC-C-ACCCTATGAAATTTTGA
*
24791 TAACCACACTATGAAATTTTGA
1 TAACCACCCTATGAAATTTTGA
** * *
24813 TAACTTCCATATGAAATTTTGG
1 TAACCACCCTATGAAATTTTGA
* *
24835 TAACCACACTATGCAATTTTGA
1 TAACCACCCTATGAAATTTTGA
* * *
24857 TAACC-TCCTCATGAAATTATAA
1 TAACCACCCT-ATGAAATTTTGA
* * *
24879 TAACTATCTTATGAAATTTTGA
1 TAACCACCCTATGAAATTTTGA
24901 TAACCAC
1 TAACCAC
24908 ATAGAGACAA
Statistics
Matches: 127, Mismatches: 32, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
21 2 0.02
22 103 0.81
23 5 0.04
24 17 0.13
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCACCCTATGAAATTTTGA
Found at i:24841 original size:44 final size:43
Alignment explanation
Indices: 24730--24905 Score: 174
Period size: 44 Copynumber: 4.0 Consensus size: 43
24720 AATTAACAAC
*** * * *
24730 CCTATGAAATTTCAATAACCACCCTAAGAAATTTTAATAACACGAT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC-C--T
*
24776 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCT
*
24819 CCATATGAAATTTTGGTAACCACACTATGCAATTTTGATAACCT
1 CC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCT
* ** * *
24863 CCTCATGAAATTATAATAACTATC-TTATGAAATTTTGATAACC
1 CCT-ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
24906 ACATAGAGAC
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
43 4 0.04
44 72 0.64
45 1 0.01
46 35 0.31
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCT
Found at i:25026 original size:22 final size:22
Alignment explanation
Indices: 25001--25042 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24991 GTTAGCAATT
* *
25001 ACACTCTGAAATTTTGATAATC
1 ACACTATGAAATTGTGATAATC
25023 ACACTATGAAATTGTGATAA
1 ACACTATGAAATTGTGATAA
25043 CCTCGTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
ACACTATGAAATTGTGATAATC
Found at i:25081 original size:23 final size:23
Alignment explanation
Indices: 25053--25132 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
25043 CCTCGTTATG
25053 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
25076 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
25099 AAATTTTGAT-AATTTTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
25121 AAATCTTGATAA
1 AAATTTTGATAA
25133 CTACAAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.33
23 32 0.67
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:25131 original size:45 final size:45
Alignment explanation
Indices: 25009--25132 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
24999 TTACACTCTG
* ** *
25009 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
25053 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
25099 AAATTTTGAT-AATTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
25133 CTACAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 11 0.16
45 34 0.51
46 22 0.33
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:25166 original size:22 final size:22
Alignment explanation
Indices: 25011--25212 Score: 110
Period size: 22 Copynumber: 9.4 Consensus size: 22
25001 ACACTCTGAA
* * *
25011 ATTTTGATAATCACACTATGAA
1 ATTTTGATAATCTCCCTATGAT
* * ** *
25033 ATTGTGATAACCTCGTTATGAA
1 ATTTTGATAATCTCCCTATGAT
* * *
25055 ATTTTGATAAATCTTCCTATAAA
1 ATTTTGAT-AATCTCCCTATGAT
* * *
25078 ATTTTGATAAACCTCCCTATAAA
1 ATTTTGAT-AATCTCCCTATGAT
* * * *
25101 ATTTTGATAATTTTCTTATGAA
1 ATTTTGATAATCTCCCTATGAT
* *
25123 ATCTTGATAA-CT-AC-A--A-
1 ATTTTGATAATCTCCCTATGAT
25139 ATTTTGATAATCTCCCTATGAT
1 ATTTTGATAATCTCCCTATGAT
* * ** *
25161 TTTTTGATAACCTCATTATGAA
1 ATTTTGATAATCTCCCTATGAT
*
25183 ATTTTGTTAATCTCCCTATGAT
1 ATTTTGATAATCTCCCTATGAT
25205 ATTTTGAT
1 ATTTTGAT
25213 CTACATATAT
Statistics
Matches: 137, Mismatches: 36, Indels: 14
0.73 0.19 0.07
Matches are distributed among these distances:
16 9 0.07
17 3 0.02
18 1 0.01
19 2 0.01
21 2 0.01
22 82 0.60
23 38 0.28
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
ATTTTGATAATCTCCCTATGAT
Found at i:25525 original size:66 final size:66
Alignment explanation
Indices: 25428--25555 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
25418 GATAACCTCT
* * * ** *
25428 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
25493 A
66 A
* * *
25494 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAAT
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAAT
25556 TTTCCTATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:25547 original size:88 final size:88
Alignment explanation
Indices: 25384--25550 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
25374 AGAAATACCA
* * * **
25384 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
25449 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
25472 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
25535 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
25551 ATAATTTTCC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 61 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:25610 original size:22 final size:22
Alignment explanation
Indices: 25384--25655 Score: 143
Period size: 22 Copynumber: 12.5 Consensus size: 22
25374 AGAAATACCA
25384 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
25407 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
25428 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
25450 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
*
25472 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
25495 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
25516 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
**
25538 CTATGAAATTTTGATAAT-TTT
1 CTATGAAATTTTGATAATCACT
25559 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC--A-CT
*
25584 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
25606 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
* * *
25626 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
25647 -TATGAAATT
1 CTATGAAATT
25656 GAGACTTTTA
Statistics
Matches: 194, Mismatches: 40, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.01
20 16 0.08
21 33 0.17
22 124 0.64
23 2 0.01
24 4 0.02
25 14 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:25744 original size:22 final size:21
Alignment explanation
Indices: 25691--25745 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
25681 CACTATAAAC
**
25691 TTTTGATAACCTCCCCATGAAA
1 TTTTG-TAACCTCCAAATGAAA
*
25713 TATTAGTAACCTCCAAATGAAA
1 T-TTTGTAACCTCCAAATGAAA
25735 TTTTGTTAACC
1 TTTTG-TAACC
25746 ACACTATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 3 0.11
22 21 0.78
23 3 0.11
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (21 bp):
TTTTGTAACCTCCAAATGAAA
Found at i:25920 original size:44 final size:43
Alignment explanation
Indices: 25868--25967 Score: 155
Period size: 44 Copynumber: 2.3 Consensus size: 43
25858 AATAACCTGA
*
25868 TCCTATGAAATTTTGGTAACCACACAATGAAATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACAATGAAATTTTGATAACC
* *
25911 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TCC-TATGAAATTTTGGTAACCACACAATGAAATTTTGATAACC
25955 TCCTCATGAAATT
1 TCCT-ATGAAATT
25968 ATAATAACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
43 4 0.08
44 48 0.92
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACAATGAAATTTTGATAACC
Found at i:25954 original size:66 final size:66
Alignment explanation
Indices: 25870--26001 Score: 160
Period size: 66 Copynumber: 2.0 Consensus size: 66
25860 TAACCTGATC
* * * *
25870 CTATGAAATTTTGGTAACCACAC-AATGAAATTTTGATAACT-TCCATATGAAATTTTGGTAACC
1 CTATGAAATTTTGATAACCAC-CTAATGAAATTATAATAACTAT-CATATGAAATTTTGATAACC
25933 ACA
64 ACA
* * * *
25936 CTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACTATCTTATGAAATTTTGATAACCAC
1 CTATGAAATTTTGATAACCACCTAATGAAATTATAATAACTATCATATGAAATTTTGATAACCAC
26001 A
66 A
26002 TAGAGACAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.02
66 54 0.96
67 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACCTAATGAAATTATAATAACTATCATATGAAATTTTGATAACCAC
A
Found at i:25967 original size:22 final size:21
Alignment explanation
Indices: 25868--25998 Score: 118
Period size: 22 Copynumber: 6.0 Consensus size: 21
25858 AATAACCTGA
*
25868 TCCTATGAAATTTTGGTAACC
1 TCCTATGAAATTTTGATAACC
* * *
25889 ACACAATGAAATTTTGATAACT
1 TC-CTATGAAATTTTGATAACC
*
25911 TCCATATGAAATTTTGGTAACC
1 TCC-TATGAAATTTTGATAACC
* *
25933 ACACTATGGAATTTTGATAACC
1 TC-CTATGAAATTTTGATAACC
* * *
25955 TCCTCATGAAATTATAATAACTA
1 TCCT-ATGAAATTTTGATAAC-C
*
25978 TCTTATGAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACC
25999 ACATAGAGAC
Statistics
Matches: 85, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
21 4 0.05
22 77 0.91
23 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:26140 original size:19 final size:20
Alignment explanation
Indices: 26109--26146 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
26099 TATTGACATT
26109 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
26128 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
26147 AAATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:26439 original size:168 final size:165
Alignment explanation
Indices: 26161--26464 Score: 407
Period size: 167 Copynumber: 1.8 Consensus size: 165
26151 AATAGTAAAG
* *
26161 GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTATAATTCGGTTTAAATTAAAATT
1 GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTACAATTCGGTATAAATTAAAATT
* *
26226 TTTAATTAATAAAATTATACTAAATTTTGATAATGGAAATTTAGAAATATATTTGGAAAAAAGGG
66 TTTAATTAATAAAAGTATACTAAATTTTAATAATGGAAATTTAGAAATATATTT-GAAAAAAGGG
*
26291 TGCAATCGAAAAACATAAAGTTTACTATTATTCGTA
130 TACAATCGAAAAACATAAAGTTTACTATTATTCGTA
* * * *
26327 GAAATTTGCATGTTCGTCAA-TGAAAATCAATTTTACAAAACTTACAATTCGGTATAAATTGAAA
1 GAAATTTACATGTTCATCAACT-AAAATCAATTTGAC-AAACTTACAATTCGGTATAAATTAAAA
** **
26391 TTTTATAATTAATTTTCAAGTA-A-TAAATTTTAATAATGTCAATTTAGAAATATATTTGAAAAA
64 TTTT-TAATTAA--TAAAAGTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTGAAAAA
*
26454 GGGGTACAATC
126 AGGGTACAATC
26465 AAAGACAAAG
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
165 1 0.01
166 31 0.26
167 43 0.36
168 38 0.32
169 1 0.01
170 5 0.04
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (165 bp):
GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTACAATTCGGTATAAATTAAAATT
TTTAATTAATAAAAGTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTGAAAAAAGGGT
ACAATCGAAAAACATAAAGTTTACTATTATTCGTA
Found at i:26526 original size:38 final size:37
Alignment explanation
Indices: 26469--26550 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
26459 ACAATCAAAG
*
26469 ACAAAGACAAGAAGAAAAATCAAATACAACGATTGGAA
1 ACAAAAACAAGAAGAAAAATCAAATACAACG-TTGGAA
* **
26507 ACAAAAACAA-AAGACAAAATTAAATAGGACGTTGGAA
1 ACAAAAACAAGAAGA-AAAATCAAATACAACGTTGGAA
*
26544 ATAAAAA
1 ACAAAAA
26551 GGCAAATTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 16 0.42
38 22 0.58
ACGTcount: A:0.62, C:0.11, G:0.15, T:0.12
Consensus pattern (37 bp):
ACAAAAACAAGAAGAAAAATCAAATACAACGTTGGAA
Found at i:26697 original size:31 final size:31
Alignment explanation
Indices: 26662--26727 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
26652 TGACAATTTA
*
26662 GAAATATGTTTTAGAAAA-AAGGGTAAAATTG
1 GAAATATGTTTTA-AAAATAAGGGTAAAATCG
*
26693 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTAAAATCG
26724 GAAA
1 GAAA
26728 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTAAAATCG
Found at i:27605 original size:17 final size:19
Alignment explanation
Indices: 27583--27633 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
27573 ATAAGAAAAA
*
27583 TAGGTTTTTCT-TA-GGTC
1 TAGGTTTTTATGTATGGTC
*
27600 TAGGTTTTTATGTATTGTC
1 TAGGTTTTTATGTATGGTC
27619 TAGGTTTTTATGTAT
1 TAGGTTTTTATGTAT
27634 TGTATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.33
18 2 0.07
19 18 0.60
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.57
Consensus pattern (19 bp):
TAGGTTTTTATGTATGGTC
Found at i:27621 original size:19 final size:19
Alignment explanation
Indices: 27597--27636 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
27587 TTTTTCTTAG
27597 GTCTAGGTTTTTATGTATT
1 GTCTAGGTTTTTATGTATT
27616 GTCTAGGTTTTTATGTATT
1 GTCTAGGTTTTTATGTATT
27635 GT
1 GT
27637 ATTTTATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.57
Consensus pattern (19 bp):
GTCTAGGTTTTTATGTATT
Found at i:27941 original size:19 final size:21
Alignment explanation
Indices: 27912--27953 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
27902 ATAAACTATG
27912 AACTAAAATTG-AAATAATTA
1 AACTAAAATTGCAAATAATTA
*
27932 AACT-AAATTGCAAGTAATTA
1 AACTAAAATTGCAAATAATTA
27952 AA
1 AA
27954 ATAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AACTAAAATTGCAAATAATTA
Done.