Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017991.1 Corchorus olitorius cultivar O-4 contig18024, 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: 132373
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1193 original size:22 final size:22
Alignment explanation
Indices: 1163--1264 Score: 93
Period size: 22 Copynumber: 4.6 Consensus size: 22
1153 TCCAACGTAG
*
1163 AAATATTGATAA-CTACATTGCGA
1 AAAT-TTGATAACCT-CATTGTGA
1186 AAATTTGATAACCTCATTGTG-
1 AAATTTGATAACCTCATTGTGA
* * *
1207 AAATTTCGATAATCTCCTTATGA
1 AAATTT-GATAACCTCATTGTGA
*
1230 AAATTTGATAACCAT-AATGTGA
1 AAATTTGATAACC-TCATTGTGA
*
1252 AATTTTGATAACC
1 AAATTTGATAACC
1265 ACACTGAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
21 6 0.09
22 47 0.71
23 13 0.20
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (22 bp):
AAATTTGATAACCTCATTGTGA
Found at i:1389 original size:22 final size:22
Alignment explanation
Indices: 1184--1396 Score: 112
Period size: 22 Copynumber: 9.6 Consensus size: 22
1174 ACTACATTGC
* * * *
1184 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTAT
* * *
1206 GAAATTTCGATAATCTC-CTTAT
1 GAAATTTTGATAACCACAC-TAT
* * * *
1228 GAAAATTTGATAACCATAATGT
1 GAAATTTTGATAACCACACTAT
1250 GAAATTTTGATAACCACAC--T
1 GAAATTTTGATAACCACACTAT
* * *
1270 GAAGTTTTGATAACCATACAAT
1 GAAATTTTGATAACCACACTAT
* * *
1292 GAAGTTTTGATAACCTCATTGTATAT
1 GAAATTTTGATAACCACA----CTAT
* *
1318 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCACACTAT
* * * *
1340 -AAA-ATTGGTAATCGCACTAT
1 GAAATTTTGATAACCACACTAT
*
1360 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCACACTAT
*
1383 GAAATTTCGATAAC
1 GAAATTTTGATAAC
1397 TTCCCTATAA
Statistics
Matches: 145, Mismatches: 35, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
20 31 0.21
21 3 0.02
22 81 0.56
23 13 0.09
26 17 0.12
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:1483 original size:22 final size:22
Alignment explanation
Indices: 1430--1771 Score: 98
Period size: 22 Copynumber: 15.5 Consensus size: 22
1420 ATATTTTCTA
*
1430 TATGTAATTTTGATAACCTCTCC
1 TATGAAATTTTGATAACCTC-CC
*
1453 -AT-AATATTTTCATAACCTCCC
1 TATGAA-ATTTTGATAACCTCCC
*
1474 TATGAAATTTTGTTAACCAT-CC
1 TATGAAATTTTGATAACC-TCCC
*
1496 TAGGAAATTTTGATAA------
1 TATGAAATTTTGATAACCTCCC
* **
1512 GAACAAATTTTGATAACCTCCCTCCC
1 TATGAAATTTTGATAA----CCTCCC
* * *
1538 TATGAAATTTTGTTAACGT-TC
1 TATGAAATTTTGATAACCTCCC
* * * *
1559 TAAT-TAATTTTGATAATCACAC
1 T-ATGAAATTTTGATAACCTCCC
* ** * * *
1581 TATAAAATTTCAATAATCTTCG
1 TATGAAATTTTGATAACCTCCC
** *
1603 TATGAAATTTTGATAATTTCCA
1 TATGAAATTTTGATAACCTCCC
* * ***
1625 TAAGAGATTTTGATAACCTTTTTTT
1 TATGAAATTTTGATAACC---TCCC
* **
1650 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCCC
* *
1672 TATGAAATTTTGATAA-TTACAC
1 TATGAAATTTTGATAACCT-CCC
* * *
1694 TACGAAGTTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* *
1716 TATGAAATTTTGGTAA-CTACAC
1 TATGAAATTTTGATAACCT-CCC
* * *
1738 TATGAAATTGTAATAACCTTCC
1 TATGAAATTTTGATAACCTCCC
*
1760 TATGTAATTTTG
1 TATGAAATTTTG
1772 GTTTGATTGT
Statistics
Matches: 227, Mismatches: 68, Indels: 49
0.66 0.20 0.14
Matches are distributed among these distances:
16 13 0.06
21 20 0.09
22 160 0.70
23 6 0.03
25 16 0.07
26 12 0.05
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:1754 original size:44 final size:43
Alignment explanation
Indices: 1663--1773 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 43
1653 GAAATTTTGG
* * * * * *
1663 TAACCTCTGTATGAAATTTTGATAATTACACTACGAAGTTTTGA
1 TAACCTC-CTATGAAATTTTGGTAACTACACTACGAAATTGTAA
*
1707 TAACCTCCATATGAAATTTTGGTAACTACACTATGAAATTGTAA
1 TAACCTCC-TATGAAATTTTGGTAACTACACTACGAAATTGTAA
*
1751 TAACCTTCCTATGTAATTTTGGT
1 TAACC-TCCTATGAAATTTTGGT
1774 TTGATTGTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
44 54 0.95
45 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (43 bp):
TAACCTCCTATGAAATTTTGGTAACTACACTACGAAATTGTAA
Found at i:2558 original size:7 final size:6
Alignment explanation
Indices: 2541--2586 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
2531 AATTACGTAC
2541 TTTTGT TTTTGTT TTTTGT TTTTGTT TTTTGT TTTTGT TTTT-T TTT
1 TTTTGT TTTTG-T TTTTGT TTTTG-T TTTTGT TTTTGT TTTTGT TTT
2587 ATGAAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 4 0.11
6 22 0.58
7 12 0.32
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:2559 original size:13 final size:13
Alignment explanation
Indices: 2541--2583 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
2531 AATTACGTAC
2541 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
2554 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
2567 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
2580 TTTT
1 TTTT
2584 TTTATGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTTTGTTTTTGTT
Found at i:2565 original size:19 final size:19
Alignment explanation
Indices: 2541--2586 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2531 AATTACGTAC
2541 TTTTG-TTTTTGTTTTTTGT
1 TTTTGTTTTTTG-TTTTTGT
2560 TTTTGTTTTTTGTTTTTGT
1 TTTTGTTTTTTGTTTTTGT
2579 TTTT-TTTT
1 TTTTGTTTT
2587 ATGAAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 6 0.23
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (19 bp):
TTTTGTTTTTTGTTTTTGT
Found at i:3546 original size:26 final size:26
Alignment explanation
Indices: 3502--3559 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
3492 TTCGTAATAG
3502 TAAGAT-ATATAGTAGTAAGATAAAA
1 TAAGATAATATAGTAGTAAGATAAAA
*
3527 TAAGATAATA-AGATAGTAAGATAAGA
1 TAAGATAATATAG-TAGTAAGATAAAA
3553 TAAGATA
1 TAAGATA
3560 TAATATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (26 bp):
TAAGATAATATAGTAGTAAGATAAAA
Found at i:4234 original size:3 final size:3
Alignment explanation
Indices: 4228--4277 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
4218 TAGTAGTAAG
4228 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
4274 ATT A
1 ATT A
4278 GAATTTAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:7435 original size:268 final size:268
Alignment explanation
Indices: 6958--7500 Score: 978
Period size: 268 Copynumber: 2.0 Consensus size: 268
6948 CAAAATTAGC
* * *
6958 ATGATCATGGCGCCACTCAAGCCTTTGAACAAAACGTCTCCATTCAGAAAAGATGCTAAATACAG
1 ATGATCACGGCACCACTCAAGCCTTTGAACAAAACGCCTCCATTCAGAAAAGATGCTAAATACAG
**
7023 ACTCTAAACAATGGCAAATACGAATGTTAGGATGGGAAATCACAATGCTCGCACCATATGTGGTA
66 ACTCTAAACAATGGCAAATACGAATGCCAGGATGGGAAATCACAATGCTCGCACCATATGTGGTA
7088 ATCAAGTCGATGATCCTACCGAACATGAAGAGTGGCTTCCAATTCCAAAGACTGAGAACCTTTTG
131 ATCAAGTCGATGATCCTACCGAACATGAAGAGTGGCTTCCAATTCCAAAGACTGAGAACCTTTTG
*
7153 TTACATACTCCAAATGTCCAAGTCTTGAACCATTTCATGGGTCAATCTGTTATTCCCTCATGGCC
196 TTACATACTCCAAATGTCCAAGTCTTGAACCATTTCATGGGTCAATCCGTTATTCCCTCATGGCC
7218 AACCCCTG
261 AACCCCTG
*
7226 ATGATCACGGCACCACTCAAGCCTTTGAACAAAACGCCTCCATTCAGAAAAGATGCTAAATACAT
1 ATGATCACGGCACCACTCAAGCCTTTGAACAAAACGCCTCCATTCAGAAAAGATGCTAAATACAG
7291 ACTCTAAACAATGGCAAATACGAATGCCAGGATGGGAAATCACAATGCTCGCACCATATGTGGTA
66 ACTCTAAACAATGGCAAATACGAATGCCAGGATGGGAAATCACAATGCTCGCACCATATGTGGTA
* *
7356 ATCAAGTTGATGATCCTACCGAACTTGAAGAGTGGCTTCCAATTCCAAAGACTGAGAACCTTTTG
131 ATCAAGTCGATGATCCTACCGAACATGAAGAGTGGCTTCCAATTCCAAAGACTGAGAACCTTTTG
* *
7421 TTACATACTCCAAATGTCCAAGTCTTGAACTATTTCATGGGTCAATCCGTTATTTCCTCATGGCC
196 TTACATACTCCAAATGTCCAAGTCTTGAACCATTTCATGGGTCAATCCGTTATTCCCTCATGGCC
7486 AACCCCTG
261 AACCCCTG
*
7494 GTGATCA
1 ATGATCA
7501 GTTTTTGGTT
Statistics
Matches: 263, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
268 263 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (268 bp):
ATGATCACGGCACCACTCAAGCCTTTGAACAAAACGCCTCCATTCAGAAAAGATGCTAAATACAG
ACTCTAAACAATGGCAAATACGAATGCCAGGATGGGAAATCACAATGCTCGCACCATATGTGGTA
ATCAAGTCGATGATCCTACCGAACATGAAGAGTGGCTTCCAATTCCAAAGACTGAGAACCTTTTG
TTACATACTCCAAATGTCCAAGTCTTGAACCATTTCATGGGTCAATCCGTTATTCCCTCATGGCC
AACCCCTG
Found at i:8652 original size:14 final size:17
Alignment explanation
Indices: 8613--8646 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
8603 CCTTAGATAA
8613 AACTAG-AGAAAAATAG
1 AACTAGAAGAAAAATAG
8629 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
8646 A
1 A
8647 TGAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.12
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:9216 original size:29 final size:30
Alignment explanation
Indices: 9173--9237 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
9163 ATTCTTGCTC
* *
9173 CTTGAAATATTTCTTCAAT-GATCTTCATAT
1 CTTGAAATATATCTTCAATAAATCTTCA-AT
9203 CTTGAAAT-TATCTTCAATAAATCTTCAAT
1 CTTGAAATATATCTTCAATAAATCTTCAAT
*
9232 CATGAA
1 CTTGAA
9238 TTTCGAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (30 bp):
CTTGAAATATATCTTCAATAAATCTTCAAT
Found at i:15972 original size:29 final size:28
Alignment explanation
Indices: 15927--16009 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
15917 TTTTCTGATT
* *
15927 TTTGTTTAAGTGCGGGTTGTGCACTTGTG
1 TTTGTTTAAGTGTGGGTT-TGCACTTGGG
* *
15956 TTTGTTCAAGTGTGGGTTATACACTTGGG
1 TTTGTTTAAGTGTGGGTT-TGCACTTGGG
* *
15985 ATTGTTTTGAGTGTGGGTTTGCACT
1 TTTG-TTTAAGTGTGGGTTTGCACT
16010 CGTTTCAAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 32 0.73
30 12 0.27
ACGTcount: A:0.13, C:0.10, G:0.33, T:0.45
Consensus pattern (28 bp):
TTTGTTTAAGTGTGGGTTTGCACTTGGG
Found at i:17385 original size:16 final size:16
Alignment explanation
Indices: 17341--17387 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
17331 CGATGAACCC
17341 GTAACCCAGATGACCT
1 GTAACCCAGATGACCT
*
17357 G-ACACCC-GAATGACTT
1 GTA-ACCCAG-ATGACCT
17373 GTAACCCAGATGACC
1 GTAACCCAGATGACC
17388 CGAAGCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (16 bp):
GTAACCCAGATGACCT
Found at i:17399 original size:32 final size:32
Alignment explanation
Indices: 17341--17420 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
17331 CGATGAACCC
* *
17341 GTAACCCAGATGACCTGACACCCGAATGACTT
1 GTAACCCAGATGACCCGACACCCGAATGACTA
*
17373 GTAACCCAGATGACCCGA-AGCTCGAATGACTA
1 GTAACCCAGATGACCCGACA-CCCGAATGACTA
*
17405 GAAACCC-GAGTGACCC
1 GTAACCCAGA-TGACCC
17421 AAATGACCTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.07
32 39 0.93
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.15
Consensus pattern (32 bp):
GTAACCCAGATGACCCGACACCCGAATGACTA
Found at i:18415 original size:16 final size:15
Alignment explanation
Indices: 18394--18438 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
18384 AATGACTTGA
18394 GACCCGAAACCCGTAT
1 GACCCGAAACCCG-AT
18410 GACCCG-AACCCAGAT
1 GACCCGAAACCC-GAT
*
18425 AACCCGAAACCCGA
1 GACCCGAAACCCGA
18439 ATTGCCCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.36, C:0.40, G:0.18, T:0.07
Consensus pattern (15 bp):
GACCCGAAACCCGAT
Found at i:22141 original size:23 final size:24
Alignment explanation
Indices: 22102--22146 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
22092 AAAATTTTGT
*
22102 GTTTTGTGTCAAGAAAA-AAAAGA
1 GTTTTGCGTCAAGAAAATAAAAGA
22125 GTTTTGCGTCATA-AAAATAAAA
1 GTTTTGCGTCA-AGAAAATAAAA
22147 TTTTCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (24 bp):
GTTTTGCGTCAAGAAAATAAAAGA
Found at i:24597 original size:33 final size:33
Alignment explanation
Indices: 24560--24637 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
24550 GCGCTGCACA
24560 CTCCGCGCGCCTTGCCCAGCCATCCGCGCTATC
1 CTCCGCGCGCCTTGCCCAGCCATCCGCGCTATC
24593 CTCCGCGCGCCTTGCCCAGCCATCCGCGCTATC
1 CTCCGCGCGCCTTGCCCAGCCATCCGCGCTATC
24626 CTCCGCGCGCCT
1 CTCCGCGCGCCT
24638 CACCTGGTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.08, C:0.53, G:0.22, T:0.18
Consensus pattern (33 bp):
CTCCGCGCGCCTTGCCCAGCCATCCGCGCTATC
Found at i:24783 original size:21 final size:21
Alignment explanation
Indices: 24718--24791 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
24708 CCACTACCAA
* * *
24718 GCCACAACCGGCCATTCACCGA
1 GCCACCACCGGCCATGC-CCGT
** * * *
24740 GCCACCACCGGTTAAGTCTGT
1 GCCACCACCGGCCATGCCCGT
24761 GCCACCACCGGCCATGCCCGT
1 GCCACCACCGGCCATGCCCGT
*
24782 GCCATCACCG
1 GCCACCACCG
24792 TTGATGATTT
Statistics
Matches: 38, Mismatches: 14, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
21 27 0.71
22 11 0.29
ACGTcount: A:0.20, C:0.45, G:0.22, T:0.14
Consensus pattern (21 bp):
GCCACCACCGGCCATGCCCGT
Found at i:30521 original size:2 final size:2
Alignment explanation
Indices: 30514--30552 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
30504 ATAAACTAAC
*
30514 AT AT AT AT AT AT AT AT AC 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 AT AT AT AT A
30553 ATGTGTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:32787 original size:149 final size:149
Alignment explanation
Indices: 32517--32814 Score: 587
Period size: 149 Copynumber: 2.0 Consensus size: 149
32507 TTTTGTTTCT
32517 TGATCTCCTGTGTTTGTTTTCGATTGTTTAGTCTTGTACTTTCGTTTCGCGTCGGTGTCTAGTGC
1 TGATCTCCTGTGTTTGTTTTCGATTGTTTAGTCTTGTACTTTCGTTTCGCGTCGGTGTCTAGTGC
*
32582 CGGATCTTTCTTAGGTCTAGGGTTTAGTTTTCCTTTAAGTTTCTTAGTTAAACCATAGGATCTTT
66 CGGATCTTTCTTAGGTCTAGGGTTTAGTTTTCCTTTAAGTTTCTTAGTAAAACCATAGGATCTTT
32647 GAGCCTTTCTTTTCTTGTC
131 GAGCCTTTCTTTTCTTGTC
32666 TGATCTCCTGTGTTTGTTTTCGATTGTTTAGTCTTGTACTTTCGTTTCGCGTCGGTGTCTAGTGC
1 TGATCTCCTGTGTTTGTTTTCGATTGTTTAGTCTTGTACTTTCGTTTCGCGTCGGTGTCTAGTGC
32731 CGGATCTTTCTTAGGTCTAGGGTTTAGTTTTCCTTTAAGTTTCTTAGTAAAACCATAGGATCTTT
66 CGGATCTTTCTTAGGTCTAGGGTTTAGTTTTCCTTTAAGTTTCTTAGTAAAACCATAGGATCTTT
32796 GAGCCTTTCTTTTCTTGTC
131 GAGCCTTTCTTTTCTTGTC
32815 GAGTTTGTCT
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (149 bp):
TGATCTCCTGTGTTTGTTTTCGATTGTTTAGTCTTGTACTTTCGTTTCGCGTCGGTGTCTAGTGC
CGGATCTTTCTTAGGTCTAGGGTTTAGTTTTCCTTTAAGTTTCTTAGTAAAACCATAGGATCTTT
GAGCCTTTCTTTTCTTGTC
Found at i:45027 original size:13 final size:13
Alignment explanation
Indices: 45009--45033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44999 AATTTGAGCG
45009 CATGTGGATTTCT
1 CATGTGGATTTCT
45022 CATGTGGATTTC
1 CATGTGGATTTC
45034 GATTCGGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (13 bp):
CATGTGGATTTCT
Found at i:54096 original size:41 final size:42
Alignment explanation
Indices: 53979--54097 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 42
53969 TTTAGGCTGT
* * *
53979 TATTTATTCT-TTTATTCAATTTTGTCCCTGATCTA-AGGTAA
1 TATTTATT-TATTGATTCAATTTTGTCCCAGATTTAGAGGTAA
* * * *
54020 AATTTGTTAATTGATTCAATTTTGT-CCATACTTTAGA-GTAA
1 TATTTATTTATTGATTCAATTTTGTCCCAGA-TTTAGAGGTAA
*
54061 TATTTATTTATTGATTCAATTTTGTCCCGGATTTAGA
1 TATTTATTTATTGATTCAATTTTGTCCCAGATTTAGA
54098 ATTTTATTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
40 3 0.05
41 55 0.89
42 4 0.06
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (42 bp):
TATTTATTTATTGATTCAATTTTGTCCCAGATTTAGAGGTAA
Found at i:56489 original size:16 final size:17
Alignment explanation
Indices: 56457--56490 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
56447 TTTTTATTTT
*
56457 TATTTATTGATATATAA
1 TATTTATTGAAATATAA
56474 TATTTATT-AAATATAA
1 TATTTATTGAAATATAA
56490 T
1 T
56491 TTATACATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTATTGAAATATAA
Found at i:61664 original size:114 final size:110
Alignment explanation
Indices: 61477--61683 Score: 308
Period size: 114 Copynumber: 1.8 Consensus size: 110
61467 AAATTATACA
* *
61477 TCAACTTTAATATTAGTAAATAAAATGCAGACATGCGTAATTACGTCATTTGGGAAAGTTTTCTT
1 TCAACTTTAATATTAGTAAAT-AAACGCAGAAATGCGTAATTACGTCATTTGGGAAAGTTTTCTT
61542 GTCTTCCCCTTCCCCCTCTTTAATTTAATTTGTCCCTTATAGACAC
65 GTCTTCCCCTTCCCCCTCTTTAATTTAATTTGTCCCTTATAGACAC
* *
61588 TCAACTTTAATATTAGTAAAT-AACGCCAGAAATGCGTAATTAGGTCATTAATTTGGGGAAGTTT
1 TCAACTTTAATATTAGTAAATAAACG-CAGAAATGCGTAATTACGTC----ATTTGGGAAAGTTT
*
61652 TCTTTTCTTCCCCTTCCCCCTCTTTAATTTAA
61 TCTTGTCTTCCCCTTCCCCCTCTTTAATTTAA
61684 CTAGTTTTTG
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
109 3 0.03
110 18 0.21
111 21 0.24
114 44 0.51
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (110 bp):
TCAACTTTAATATTAGTAAATAAACGCAGAAATGCGTAATTACGTCATTTGGGAAAGTTTTCTTG
TCTTCCCCTTCCCCCTCTTTAATTTAATTTGTCCCTTATAGACAC
Found at i:74181 original size:7 final size:7
Alignment explanation
Indices: 74169--74208 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
74159 AAAGTAAAAA
74169 AAAAAGG
1 AAAAAGG
*
74176 AAAAAGA
1 AAAAAGG
74183 ACAAAATGG
1 A-AAAA-GG
74192 AAAAAGG
1 AAAAAGG
74199 AAAAAGG
1 AAAAAGG
74206 AAA
1 AAA
74209 TAAAAAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 19 0.66
8 8 0.28
9 2 0.07
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (7 bp):
AAAAAGG
Found at i:74545 original size:24 final size:24
Alignment explanation
Indices: 74516--74563 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
74506 ACACACGTGC
74516 TTCACACCTCCCATTTATAATTGA
1 TTCACACCTCCCATTTATAATTGA
** *
74540 TTCACACCTTGCATTTATATTTGA
1 TTCACACCTCCCATTTATAATTGA
74564 GATTCTGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (24 bp):
TTCACACCTCCCATTTATAATTGA
Found at i:78953 original size:58 final size:58
Alignment explanation
Indices: 78878--78993 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
78868 GGACTATGCT
* * *
78878 ATACACAACTGGGATAGAATAACTATTTAATTACTCCTAAGATTTGTAACTTAAATGA
1 ATACACAACTGGAATAGAATAACGATTCAATTACTCCTAAGATTTGTAACTTAAATGA
*
78936 ATACACAACTGGAATAGAATAACGGTTCAATTACTCCTAAGATTTGTAACTTAAATGA
1 ATACACAACTGGAATAGAATAACGATTCAATTACTCCTAAGATTTGTAACTTAAATGA
78994 GGATAAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (58 bp):
ATACACAACTGGAATAGAATAACGATTCAATTACTCCTAAGATTTGTAACTTAAATGA
Found at i:82310 original size:23 final size:24
Alignment explanation
Indices: 82280--82324 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
82270 GCATGCTAAC
82280 AAAAAAAATGC-AACAAAAAAGAA
1 AAAAAAAATGCAAACAAAAAAGAA
82303 AAAAAAAATGCAAACAAAAAAG
1 AAAAAAAATGCAAACAAAAAAG
82325 CAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (24 bp):
AAAAAAAATGCAAACAAAAAAGAA
Found at i:82619 original size:19 final size:18
Alignment explanation
Indices: 82591--82626 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
82581 AGAATTAAAT
82591 TAAAAGAAAACATAAAAAC
1 TAAAAGAAAA-ATAAAAAC
*
82610 TAAAATAAAAATAAAAA
1 TAAAAGAAAAATAAAAA
82627 TAAGTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
TAAAAGAAAAATAAAAAC
Found at i:87281 original size:32 final size:32
Alignment explanation
Indices: 87240--87304 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
87230 GGCTTGGAAA
*
87240 GAATGGATGATTGGGTGAACGGTTTTAAAATT
1 GAATGGATGATTGGGTGAACAGTTTTAAAATT
87272 GAATGGATGATTGGGTGAACAGTTTTAAAATT
1 GAATGGATGATTGGGTGAACAGTTTTAAAATT
87304 G
1 G
87305 GGGGATCGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (32 bp):
GAATGGATGATTGGGTGAACAGTTTTAAAATT
Found at i:101862 original size:2 final size:2
Alignment explanation
Indices: 101855--101881 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
101845 TTTAATTAAA
101855 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 A
101882 ATAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101887 original size:3 final size:3
Alignment explanation
Indices: 101879--101912 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
101869 ATATATATAT
101879 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
101913 GGTTAGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:110433 original size:19 final size:20
Alignment explanation
Indices: 110411--110448 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
110401 TTTTTTTGAG
110411 TAATTAATT-TTAATTTTTT
1 TAATTAATTCTTAATTTTTT
*
110430 TAATTTATTCTTAATTTTT
1 TAATTAATTCTTAATTTTT
110449 ATACTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TAATTAATTCTTAATTTTTT
Found at i:113902 original size:19 final size:18
Alignment explanation
Indices: 113878--113913 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
113868 TGAAGACTTA
113878 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
113897 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
113914 ATTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:114823 original size:19 final size:18
Alignment explanation
Indices: 114799--114834 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
114789 TGAAGACTTA
114799 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
114818 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
114835 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:114841 original size:30 final size:30
Alignment explanation
Indices: 114787--114846 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
114777 GAAGTTCGTG
* *
114787 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
114817 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
114847 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:115505 original size:919 final size:921
Alignment explanation
Indices: 113725--115567 Score: 3149
Period size: 919 Copynumber: 2.0 Consensus size: 921
113715 CTATTTTGTT
* * *
113725 AATATTTGTGTTTTGAGTCTTTATAAGATGTGAAATTGATAATTTGATAATTTTCACTACTTTTG
1 AATATTTGTGATTGGAGTCTTTATAAGATGTGAAATTGATAATTTGATAATTTCCACTACTTTTG
*
113790 GAGCTATTTTGATGTCTTTTTACACAGATATGAGCAAAGTAATTTTAAGTATAGATTTGGAGATT
66 GAGCTATTTTGATGACTTTTTACACAGATATGAGCAAAGTAATTTTAAGTATAGATTTGGAGATT
*
113855 CGAAGTTCATGTTTGAAGACTTATTGAAGACAATTTGAAGATTTGAAGACCATTGAAGAATTATT
131 CGAAGTTCATGTTTGAAGACTTATTGAAGACAATTTGAAGATTTGAAGACCATTGAAGAATTAAT
*
113920 TTCAAGAAGCAAGAATTGAAGAATGGAGCTTTAATTGCGAATGATTGAAGACAAGCCATGAAGAA
196 TTCAAGAAGCAAGAATTGAAGAATGGAGCTTTAATTGCGAAGGATTGAAGACAAGCCATGAAGAA
* * * *
113985 GCCTGGAAGCTAAGGAATTTTGGATATATAATATGGGAAAGTACTCAGCCCATATAATTATTAAT
261 GCCCGGAAGCTAAGGAATTTTGGATATATAATATGAGAAAATACTCAGCCCATATAATCATTAAT
*
114050 TGGAATTAAAATCCCAATTAATGACTCCTAAATTCAAGGAAATATCCAAAATCCCGTAGATTCCC
326 AGGAATTAAAATCCCAATTAATGACTCCTAAATTCAAGGAAATATCCAAAATCCCGTAGATTCCC
114115 GATTCTAAACCTAACAGGATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATAACTTTCTGCT
391 GATTCTAAACCTAACAGGATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATAACTTTCTGCT
* *
114180 CAGACCTCCGTTTGAAGCCCATGAGTACTCGTTGGAAAGCTAACTCCGACGTTTACAACTTTGCT
456 CAGACCTCCGTTTGAAGCCCATGAGTACTCGTTGGAAAGCTAACTCCGACGTCTACAACTTTCCT
* * * *
114245 TTGAAGTCCAAGACCCAGTTCTGCCGTTTTCAAGTCCAAAAATGACGTTGAAGTCCCTGCACGAA
521 TTGAAGTCCAAGACCCAGTTCTGCCATCTTCAAGCCCAAAAATGACGTCGAAGTCCCTGCACGAA
*
114310 TTCAGCAAAATTTCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGATTTTTAATCTAACT
586 TTCAGCAAAATTTCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGATCTTTAATCTAACT
* * * *
114375 TAGACTCTAAGTTAGACTCAAATCCGACTTAGACCCCTTTCCAAGTTAGGATTGGATTTTCTAGG
651 TACACTCTAAGTTAGACTCAAAACCGACTTAGACCCCTTTCCAAGTTAGGATTAGATTTCCTAGG
* *
114440 ATTATTTCCATTATAAATAGCCACCTTAGGTCTAGGTTTTTGATGTATGTAGATCTAGAGATTTT
716 ATTATTTCCACTATAAATAGCCACCTTAGGTCTAGGTTTCTGATGTATGTAGATCTAGAGATTTT
*
114505 ATTTTGAAGAATTGTTGAAGATTTGGAGGAGTTTTGCTCTAGGAGCCGCCGACCCCTCTACTTCC
781 ATTTTGAAGAATTGTTGAAGATTTGGAGGAGTTTTGCCCTAGGAGCCGCCGACCCCTCTACTTCC
*
114570 CATCCTTAGATAAGTTTTTCTTCTTTTCTTTGGATGCTCACTCAATTCATGAGTGAGTAATCCTT
846 CATCCATAGATAAGTTTTTCTTCTTTTCTTTGGATGCTCACTCAATTCATGAGTGAGTAATCCTT
114635 TTCTTTTCTCC
911 TTCTTTTCTCC
*
114646 AATATTTGTGATTGGAGTCTTTATGAGATGTGAAATTGATAATTTGATAATTTCCACTACTTTTG
1 AATATTTGTGATTGGAGTCTTTATAAGATGTGAAATTGATAATTTGATAATTTCCACTACTTTTG
* *
114711 GAGCTATTTTGATGACTTTTTACACAGATATGAGTAAAGTAATTTTGAGTATAGATTTGGAGATT
66 GAGCTATTTTGATGACTTTTTACACAGATATGAGCAAAGTAATTTTAAGTATAGATTTGGAGATT
* *
114776 TGAAGTTCGTGTTTGAAGACTTATTGAAGACAATTTGAAGATTTGAAGACCATTGAAGAA-TAAT
131 CGAAGTTCATGTTTGAAGACTTATTGAAGACAATTTGAAGATTTGAAGACCATTGAAGAATTAAT
*
114840 TTCAAG-AGCAAGAATTGAAGAATGGAGCTTTAATTGCGAAGGATTGAAGACAAGGCATGAAGAA
196 TTCAAGAAGCAAGAATTGAAGAATGGAGCTTTAATTGCGAAGGATTGAAGACAAGCCATGAAGAA
*
114904 GCCCGGAAGCTAAGGAATTTTGGATATTTAATATGAGAAAATACTCAGCCCATATAAATCATTAA
261 GCCCGGAAGCTAAGGAATTTTGGATATATAATATGAGAAAATACTCAGCCCATAT-AATCATTAA
*
114969 TAGGAATTAAAATCCCAATTAATGACTCCTATATTCAAGGAAATATCCAAAATCCCGTAGATTCC
325 TAGGAATTAAAATCCCAATTAATGACTCCTAAATTCAAGGAAATATCCAAAATCCCGTAGATTCC
* * *
115034 TGATTCTAATCCTAACAGGATTAGGATTTA-GCGCAGTTTTGGTAGAAAAATCATAACTTTCTGC
390 CGATTCTAAACCTAACAGGATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATAACTTTCTGC
* * ***
115098 TCAGACCTCCGTTTTAGGCTTGTGAGTACTCGTTGGAAAGCTAACTCCGA-GATCTACAACTTTC
455 TCAGACCTCCGTTTGAAGCCCATGAGTACTCGTTGGAAAGCTAACTCCGACG-TCTACAACTTTC
*
115162 CTTTGAAGTCCAAGACCCATTTCTGCCATCTTCAAGCCCAAAAATGACGTCGAAGTCCCTGCACG
519 CTTTGAAGTCCAAGACCCAGTTCTGCCATCTTCAAGCCCAAAAATGACGTCGAAGTCCCTGCACG
* *
115227 AATTCAGCAAAATTTCAGTATCCTATTTTGACTTGGATTCTACTCTATGAAGATCTTTAATCTAA
584 AATTCAGCAAAATTTCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGATCTTTAATCTAA
* *
115292 CTTACATTCTAAGTTAGACTCAAAACCGACTTAGACCTCTTTCCAAGTTAGGATTAGATTTCCTA
649 CTTACACTCTAAGTTAGACTCAAAACCGACTTAGACCCCTTTCCAAGTTAGGATTAGATTTCCTA
115357 GAGA-TATTTCCACTATAAATAGCCACCTTAGGTCTAGGTTTCTGATGTATGTAGATCTAGAGAT
714 G-GATTATTTCCACTATAAATAGCCACCTTAGGTCTAGGTTTCTGATGTATGTAGATCTAGAGAT
* * * *
115421 TTTATTTTGATGAATTGTTGAAGATTTGGAGGAG-TTTGCCCTAGGAGCCGTCGCCCCCCTCTTC
778 TTTATTTTGAAGAATTGTTGAAGATTTGGAGGAGTTTTGCCCTAGGAGCCGCCG-ACCCCTCTAC
115485 TTCCCATCCATAGATAAGTTTTTCTTCTTTTCTTTGGATGCTCACTCAATTCATGAGTGAGTAAT
842 TTCCCATCCATAGATAAGTTTTTCTTCTTTTCTTTGGATGCTCACTCAATTCATGAGTGAGTAAT
115550 CCTTTTCTTTTCTCC
907 CCTTTTCTTTTCTCC
115565 AAT
1 AAT
115568 GTAGAATTTA
Statistics
Matches: 867, Mismatches: 51, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
918 18 0.02
919 559 0.64
920 109 0.13
921 181 0.21
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (921 bp):
AATATTTGTGATTGGAGTCTTTATAAGATGTGAAATTGATAATTTGATAATTTCCACTACTTTTG
GAGCTATTTTGATGACTTTTTACACAGATATGAGCAAAGTAATTTTAAGTATAGATTTGGAGATT
CGAAGTTCATGTTTGAAGACTTATTGAAGACAATTTGAAGATTTGAAGACCATTGAAGAATTAAT
TTCAAGAAGCAAGAATTGAAGAATGGAGCTTTAATTGCGAAGGATTGAAGACAAGCCATGAAGAA
GCCCGGAAGCTAAGGAATTTTGGATATATAATATGAGAAAATACTCAGCCCATATAATCATTAAT
AGGAATTAAAATCCCAATTAATGACTCCTAAATTCAAGGAAATATCCAAAATCCCGTAGATTCCC
GATTCTAAACCTAACAGGATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATAACTTTCTGCT
CAGACCTCCGTTTGAAGCCCATGAGTACTCGTTGGAAAGCTAACTCCGACGTCTACAACTTTCCT
TTGAAGTCCAAGACCCAGTTCTGCCATCTTCAAGCCCAAAAATGACGTCGAAGTCCCTGCACGAA
TTCAGCAAAATTTCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGATCTTTAATCTAACT
TACACTCTAAGTTAGACTCAAAACCGACTTAGACCCCTTTCCAAGTTAGGATTAGATTTCCTAGG
ATTATTTCCACTATAAATAGCCACCTTAGGTCTAGGTTTCTGATGTATGTAGATCTAGAGATTTT
ATTTTGAAGAATTGTTGAAGATTTGGAGGAGTTTTGCCCTAGGAGCCGCCGACCCCTCTACTTCC
CATCCATAGATAAGTTTTTCTTCTTTTCTTTGGATGCTCACTCAATTCATGAGTGAGTAATCCTT
TTCTTTTCTCC
Found at i:117780 original size:26 final size:26
Alignment explanation
Indices: 117744--117955 Score: 112
Period size: 27 Copynumber: 7.9 Consensus size: 26
117734 TTAAGAGTGG
**
117744 ACTTAAAATGACCAACGTGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
117770 ACTTAAAATGACCAAAATGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* * *
117796 A-TGTGCAAATGGCTAAAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* * *
117823 A-TGTGCAAATGACTAGAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* * *
117850 A-TGTGCAAATGACTAGAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* *
117877 A-TGTGCAAATGACTAAAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* * *
117904 A-TGTGCAAATGACTAGAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* *
117931 A-TGTGCAAATGACTAAAATGCCCCT
1 ACT-T-AAAATGACCAAAATGCCCCT
117956 AGTTGATCCT
Statistics
Matches: 174, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
25 1 0.01
26 26 0.15
27 147 0.84
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (26 bp):
ACTTAAAATGACCAAAATGCCCCTGA
Found at i:117813 original size:27 final size:27
Alignment explanation
Indices: 117775--117955 Score: 317
Period size: 27 Copynumber: 6.7 Consensus size: 27
117765 CCTGAACTTA
*
117775 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
117802 AAATGGCTAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
117829 AAATGACTAGAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
117856 AAATGACTAGAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
117883 AAATGACTAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
117910 AAATGACTAGAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
117937 AAATGACTAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
117956 AGTTGATCCT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 147 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAATGTGC
Found at i:121308 original size:13 final size:15
Alignment explanation
Indices: 121280--121313 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
121270 ATTAATCTAA
121280 CTTTTTTCTCTCTCT
1 CTTTTTTCTCTCTCT
121295 CTTTTTT-TCT-TCT
1 CTTTTTTCTCTCTCT
121308 CTTTTT
1 CTTTTT
121314 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 3 0.16
15 7 0.37
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTTCTCTCTCT
Found at i:121309 original size:19 final size:18
Alignment explanation
Indices: 121281--121319 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
121271 TTAATCTAAC
121281 TTTTTTCTCTCTCTCTTT
1 TTTTTTCTCTCTCTCTTT
* *
121299 TTTTCTTCTCTTTTTCTTT
1 TTTT-TTCTCTCTCTCTTT
121318 TT
1 TT
121320 ATTATTCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTCTCTCTCTTT
Found at i:124193 original size:27 final size:27
Alignment explanation
Indices: 124163--124219 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
124153 AAATCACTAC
124163 TATAAACAATGGAATATGCAGGTCTAA
1 TATAAACAATGGAATATGCAGGTCTAA
* *
124190 TATAAACTATGGAATATGCTGGTCTAA
1 TATAAACAATGGAATATGCAGGTCTAA
124217 TAT
1 TAT
124220 GGAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (27 bp):
TATAAACAATGGAATATGCAGGTCTAA
Found at i:124724 original size:35 final size:34
Alignment explanation
Indices: 124680--125021 Score: 420
Period size: 35 Copynumber: 9.8 Consensus size: 34
124670 CGAGTTCATA
* *
124680 TTGAAGATGCTACATCGAGTCATCCGAGATCATTT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATCATTT
124715 TTGAAGATGCTACACCGAGTCATCTGAATTCATTT
1 TTGAAGATGCTACACCGAGTCATCTGAA-TCATTT
*
124750 TTGTAGATGCTACACCGAGTCATCTGAATTCATTT
1 TTGAAGATGCTACACCGAGTCATCTGAA-TCATTT
*
124785 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAA-TCATTT
* * *
124820 TTGAAGATGCTACGCCGAGTCATCCGGGATCATTT
1 TTGAAGATGCTACACCGAGTCAT-CTGAATCATTT
* *
124855 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATCATTT
*
124890 TTGAAGATGCTACACCGAGTCATCTGAAT-ATAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATCAT--TT
* * **
124925 TTGAATATGCTACACTGAGTCATCTGATTAT-AACT
1 TTGAAGATGCTACACCGAGTCATCTGA--ATCATTT
*
124960 TTGAAGATGCTACACCGAGTCATCTGAAT-ATAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATCAT--TT
124995 TTGAAGATGCTACACCGAGTCATCTGA
1 TTGAAGATGCTACACCGAGTCATCTGA
125022 GAAGATGGTA
Statistics
Matches: 276, Mismatches: 22, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
33 5 0.02
34 4 0.01
35 261 0.95
36 3 0.01
37 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (34 bp):
TTGAAGATGCTACACCGAGTCATCTGAATCATTT
Found at i:125127 original size:50 final size:50
Alignment explanation
Indices: 125037--125321 Score: 489
Period size: 50 Copynumber: 5.7 Consensus size: 50
125027 TGGTAATGTA
* * * *
125037 TCGTATGGAAACGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGAC
1 TCGTATGGAAACG-AGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
*
125088 TCGTATGGAAACGAGTTTCGCTTGTGGAAAAGCCTATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
125138 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
* *
125188 TCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
125238 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
*
125288 TCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
125322 GAAACATCCG
Statistics
Matches: 223, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
50 210 0.94
51 13 0.06
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
Found at i:125976 original size:50 final size:50
Alignment explanation
Indices: 125922--126070 Score: 226
Period size: 50 Copynumber: 3.0 Consensus size: 50
125912 CTTAAATGCC
* * *
125922 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* *
125972 CTTTGAAAAGCGAATTTTAATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * *
126022 GTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTT
126071 GTTATAAAAC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Done.