Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168418.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_632, 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: 21042
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1297 original size:17 final size:17
Alignment explanation
Indices: 1275--1308 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1265 TTAGATTTAC
1275 TTATAATAGATAATAGA
1 TTATAATAGATAATAGA
1292 TTATAATAGATAATAGA
1 TTATAATAGATAATAGA
1309 ATAAGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TTATAATAGATAATAGA
Found at i:1362 original size:11 final size:11
Alignment explanation
Indices: 1343--1389 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
1333 GTAATAAGGA
*
1343 TATATAATAAG
1 TATAAAATAAG
1354 TATAAAATAAG
1 TATAAAATAAG
1365 T-T-AAATAAG
1 TATAAAATAAG
1374 TATAAAATAAG
1 TATAAAATAAG
1385 TATAA
1 TATAA
1390 GTATAATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 8 0.24
10 2 0.06
11 23 0.70
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (11 bp):
TATAAAATAAG
Found at i:1400 original size:9 final size:9
Alignment explanation
Indices: 1345--1421 Score: 54
Period size: 9 Copynumber: 8.2 Consensus size: 9
1335 AATAAGGATA
1345 TATAATAAG
1 TATAATAAG
1354 TATAAAATAAG
1 TAT--AATAAG
1365 T-TAAATAAG
1 TAT-AATAAG
1374 TATAA-AA-
1 TATAATAAG
1381 TA-AGTATAAG
1 TATA--ATAAG
1391 TATAATAAG
1 TATAATAAG
*
1400 TATAATAATAA
1 TATAAT-A-AG
1411 TATAATAAG
1 TATAATAAG
1420 TA
1 TA
1422 ATGGACAACC
Statistics
Matches: 56, Mismatches: 2, Indels: 20
0.72 0.03 0.26
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 3 0.05
9 29 0.52
10 6 0.11
11 15 0.27
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (9 bp):
TATAATAAG
Found at i:1407 original size:35 final size:36
Alignment explanation
Indices: 1349--1421 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 36
1339 AGGATATATA
1349 ATAAGTATAAAATAAGTTAAATAAGT-ATAAAATAAGT
1 ATAAGTAT-AAATAAGTTAAATAA-TAATAAAATAAGT
*
1386 ATAAGTAT-AATAAG-TATAATAATAATATAATAAGT
1 ATAAGTATAAATAAGTTA-AATAATAATAAAATAAGT
1421 A
1 A
1422 ATGGACAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 3 0.09
35 22 0.67
37 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (36 bp):
ATAAGTATAAATAAGTTAAATAATAATAAAATAAGT
Found at i:1410 original size:15 final size:15
Alignment explanation
Indices: 1276--1412 Score: 58
Period size: 15 Copynumber: 8.9 Consensus size: 15
1266 TAGATTTACT
1276 TATAATAGATAAT-AG
1 TATAATA-ATAATAAG
*
1291 -ATTATAATAGATAA-
1 TATAATAATA-ATAAG
*
1305 TAGAATAAGTAATAAAG
1 TATAATAA-TAAT-AAG
1322 TAATCGAATAAGTAATAAG
1 T-AT--AATAA-TAATAAG
*
1341 GAT-AT-ATAATAAG
1 TATAATAATAATAAG
1354 TATAA-AATAAGTTAA-
1 TATAATAATAA--TAAG
*
1369 -ATAAGTATAAAATAAG
1 TATAA-TA-ATAATAAG
1385 TATAAGT-ATAATAAG
1 TATAA-TAATAATAAG
1400 TATAATAATAATA
1 TATAATAATAATA
1413 TAATAAGTAA
Statistics
Matches: 95, Mismatches: 8, Indels: 38
0.67 0.06 0.27
Matches are distributed among these distances:
13 12 0.13
14 18 0.19
15 31 0.33
16 8 0.08
17 10 0.11
18 3 0.03
19 3 0.03
20 10 0.11
ACGTcount: A:0.57, C:0.01, G:0.12, T:0.31
Consensus pattern (15 bp):
TATAATAATAATAAG
Found at i:1414 original size:20 final size:20
Alignment explanation
Indices: 1293--1421 Score: 77
Period size: 20 Copynumber: 6.1 Consensus size: 20
1283 GATAATAGAT
*
1293 TATAATAGATAATAGAATAAG
1 TATAATA-ATAATATAATAAG
* **
1314 TAATAA-AGTAATCGAATAAG
1 T-ATAATAATAATATAATAAG
**
1334 TAATAAGGAT-ATATAATAAG
1 T-ATAATAATAATATAATAAG
1354 TATAA-AATAAGT-TAAATAAG
1 TATAATAATAA-TAT-AATAAG
1374 TATAAAATAAGTATAAGTATAATAAG
1 TAT--AAT-A--ATAA-TATAATAAG
1400 TATAATAATAATATAATAAG
1 TATAATAATAATATAATAAG
1420 TA
1 TA
1422 ATGGACAACC
Statistics
Matches: 89, Mismatches: 7, Indels: 25
0.74 0.06 0.21
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 47 0.53
21 7 0.08
22 6 0.07
23 1 0.01
24 4 0.04
26 15 0.17
27 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.12, T:0.30
Consensus pattern (20 bp):
TATAATAATAATATAATAAG
Found at i:1414 original size:26 final size:25
Alignment explanation
Indices: 1355--1415 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
1345 TATAATAAGT
*
1355 ATAAAATAAGTTAAATAAGTATAAA
1 ATAATATAAGTTAAATAAGTATAAA
1380 ATAAGTATAAG-TATAATAAGTATAATA
1 ATAA-TATAAGTTA-AATAAGTATAA-A
1407 ATAATATAA
1 ATAATATAA
1416 TAAGTAATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 6 0.19
26 21 0.66
27 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (25 bp):
ATAATATAAGTTAAATAAGTATAAA
Found at i:1613 original size:7 final size:7
Alignment explanation
Indices: 1594--1661 Score: 72
Period size: 7 Copynumber: 9.9 Consensus size: 7
1584 AAAAAAAAAG
1594 AAATATT
1 AAATATT
1601 -AA-ATT
1 AAATATT
1606 AAATATT
1 AAATATT
1613 AAAATATT
1 -AAATATT
1621 AAA-ATT
1 AAATATT
1627 AAATATT
1 AAATATT
*
1634 AAAAAAATT
1 --AAATATT
1643 AAATATT
1 AAATATT
1650 AAA-ATT
1 AAATATT
1656 AAATAT
1 AAATAT
1662 ATATTGTGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
5 3 0.06
6 16 0.31
7 20 0.38
8 7 0.13
9 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATATT
Found at i:1630 original size:13 final size:13
Alignment explanation
Indices: 1603--1661 Score: 73
Period size: 13 Copynumber: 4.2 Consensus size: 13
1593 GAAATATTAA
1603 ATTAAATATTAAAAT
1 ATTAAA-ATT-AAAT
1618 ATTAAAATTAAAT
1 ATTAAAATTAAAT
1631 ATTAAAAAAATTAAAT
1 ATT---AAAATTAAAT
1647 ATTAAAATTAAAT
1 ATTAAAATTAAAT
1660 AT
1 AT
1662 ATATTGTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
13 19 0.46
14 3 0.07
15 6 0.15
16 13 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAAATTAAAT
Found at i:1640 original size:16 final size:16
Alignment explanation
Indices: 1621--1653 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1611 TTAAAATATT
1621 AAAATTAAATATTAAA
1 AAAATTAAATATTAAA
1637 AAAATTAAATATTAAA
1 AAAATTAAATATTAAA
1653 A
1 A
1654 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTAAATATTAAA
Found at i:1652 original size:29 final size:32
Alignment explanation
Indices: 1594--1661 Score: 106
Period size: 29 Copynumber: 2.2 Consensus size: 32
1584 AAAAAAAAAG
1594 AAATATTAAATTAAATATTAAAATATTAAAATT
1 AAATATTAAA-TAAATATTAAAATATTAAAATT
1627 AAATATTAAA-AAA-ATT-AAATATTAAAATT
1 AAATATTAAATAAATATTAAAATATTAAAATT
1656 AAATAT
1 AAATAT
1662 ATATTGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 19 0.54
30 3 0.09
31 3 0.09
33 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATATTAAATAAATATTAAAATATTAAAATT
Found at i:5112 original size:22 final size:22
Alignment explanation
Indices: 5081--5131 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5071 GTTGTTTTTA
*
5081 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
5103 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
5125 -AATTCTA
1 GAATTCTA
5132 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
GAATTCTAATTATATAAGAAAT
Found at i:6199 original size:25 final size:25
Alignment explanation
Indices: 6166--6217 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
6156 ATTATTTATT
*
6166 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
6191 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
6216 TT
1 TT
6218 AGGAGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTTTAGTTTACAGTCTTCGAATGA
Found at i:6224 original size:25 final size:25
Alignment explanation
Indices: 6171--6224 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
6161 TTATTTTTTT
* ***
6171 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
6196 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
6221 AGTT
1 AGTT
6225 GGATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (25 bp):
AGTTTACAGTCTTCGAATGATTAGG
Found at i:6324 original size:15 final size:15
Alignment explanation
Indices: 6304--6353 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
6294 CATAATGATT
6304 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
6319 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
6337 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
6352 AT
1 AT
6354 ATTGTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.53
18 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
ATTTTAATATTGTTA
Found at i:6336 original size:18 final size:18
Alignment explanation
Indices: 6313--6350 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6303 TATTTTAATA
6313 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
6331 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
6349 TT
1 TT
6351 AATATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGTTAATTTTAATATTG
Found at i:6372 original size:17 final size:17
Alignment explanation
Indices: 6352--6385 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6342 AATATTGTTA
*
6352 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
6369 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
6386 CATTACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
ATATTGTATGATTTATT
Found at i:6427 original size:19 final size:18
Alignment explanation
Indices: 6380--6455 Score: 91
Period size: 19 Copynumber: 4.1 Consensus size: 18
6370 TATTGTATGA
*
6380 TTTATTCATTACTATATT
1 TTTATTTATTACTATATT
*
6398 TTTAGTTATTACTATATT
1 TTTATTTATTACTATATT
6416 TTGTATTTATTACTATATT
1 TT-TATTTATTACTATATT
*
6435 TCATTATTTATTTCT-TATT
1 T--TTATTTATTACTATATT
6454 TT
1 TT
6456 ATTAATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
17 1 0.02
18 18 0.35
19 21 0.41
20 10 0.20
21 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATTTATTACTATATT
Found at i:6459 original size:19 final size:19
Alignment explanation
Indices: 6419--6474 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
6409 CTATATTTTG
* *
6419 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTTAT
6439 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTTAT
* *
6458 TAATTATTTATTATTTT
1 TATTTATTTCTTATTTT
6475 CGTGTCGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTATTTCTTATTTTAT
Found at i:6512 original size:17 final size:18
Alignment explanation
Indices: 6486--6674 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
6476 GTGTCGGTTC
*
6486 TATATATATTTA-TAAAT
1 TATATTTATTTATTAAAT
6503 TATATTTATTTATT--AT
1 TATATTTATTTATTAAAT
* * *
6519 T-TATGTA-TTATCACAGT
1 TATATTTATTTATTA-AAT
**
6536 TATAGATATTTATTTAAAT
1 TATATTTATTTA-TTAAAT
*
6555 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* **
6572 TATATTAAAATATTAAAT
1 TATATTTATTTATTAAAT
6590 TATATTTATATT-TTATATAT
1 TATATTTAT-TTATTA-A-AT
** *
6610 TAAATATATTAAAATATGAAAT
1 T--ATAT-TT-ATTTATTAAAT
*
6632 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* ** *
6649 TATATTAAAATATGAAAT
1 TATATTTATTTATTAAAT
6667 TATATTTA
1 TATATTTA
6675 AATAAATATC
Statistics
Matches: 130, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
14 4 0.03
15 5 0.04
16 3 0.02
17 42 0.32
18 35 0.27
19 18 0.14
20 9 0.07
22 7 0.05
23 4 0.03
24 3 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATTTATTTATTAAAT
Found at i:6568 original size:8 final size:8
Alignment explanation
Indices: 6555--6661 Score: 72
Period size: 8 Copynumber: 12.6 Consensus size: 8
6545 TTATTTAAAT
*
6555 TATATTTA
1 TATATTAA
6563 TATATTAAA
1 TATATT-AA
6572 TATATTAA
1 TATATTAA
*
6580 AATATTAAA
1 TATATT-AA
*
6589 TTATATTTA
1 -TATATTAA
*
6598 TAT-TTTA
1 TATATTAA
6605 TATATTAAA
1 TATATT-AA
6614 TATATTAA
1 TATATTAA
* *
6622 AATATGAAA
1 TATAT-TAA
*
6631 TTATATTTA
1 -TATATTAA
6640 TATATTAAA
1 TATATT-AA
6649 TATATTAA
1 TATATTAA
*
6657 AATAT
1 TATAT
6662 GAAATTATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.09
8 36 0.46
9 27 0.34
10 9 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (8 bp):
TATATTAA
Found at i:6585 original size:77 final size:76
Alignment explanation
Indices: 6516--6674 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 76
6506 ATTTATTTAT
* * * *
6516 TATTTATGTATTATCACAGTTATAGATATT-TAT-TTAAATTATATTTATATATTAAATATATTA
1 TATTTATATATTAT-ACA-TTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTA
6579 AAATATTAAATTA
64 AAATATTAAATTA
* * *
6592 TATTTATATTTTATATATTAAATATATTAAAATATGAAATTATATTTATATATTAAATATATTAA
1 TATTTATATATTATACATTAAAGATATT-AAATATGAAATTATATTTATATATTAAATATATTAA
*
6657 AATATGAAATTA
65 AATATTAAATTA
6669 TATTTA
1 TATTTA
6675 AATAAATATC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 9 0.12
75 2 0.03
76 14 0.19
77 47 0.65
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (76 bp):
TATTTATATATTATACATTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTAAA
ATATTAAATTA
Found at i:6588 original size:35 final size:35
Alignment explanation
Indices: 6551--6674 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
6541 ATATTTATTT
*
6551 AAATTATATTTATATATTAAATATATTAAAATATTAA
1 AAATTATATTTATATATTAAATATATTAAAATA-T-G
6588 ATTATATTTATATTTTATATATTAAATATATTAAAATATG
1 A--A-A-TTATA-TTTATATATTAAATATATTAAAATATG
6628 AAATTATATTTATATATTAAATATATTAAAATATG
1 AAATTATATTTATATATTAAATATATTAAAATATG
6663 AAATTATATTTA
1 AAATTATATTTA
6675 AATAAATATC
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
35 39 0.48
36 5 0.06
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 6 0.07
42 25 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (35 bp):
AAATTATATTTATATATTAAATATATTAAAATATG
Found at i:6693 original size:4 final size:4
Alignment explanation
Indices: 6686--6813 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
6676 ATAAATATCT
*
6686 ATAA AT-A ATATA AT-A ATAAA ATAA ACT-A ATAAA ATAA ACAA ATAA
1 ATAA ATAA ATA-A ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA
* *
6731 AT-A ATAA ATAA ATAA TTAAA ATAA ACT-A ATAAA ATAA ACAA ATAA AT-A
1 ATAA ATAA ATAA ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA ATAA
*
6779 AGAA ATAA AT-A ATAA ATAA AT-A ATACA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA A
6814 AAAACAAAGC
Statistics
Matches: 99, Mismatches: 8, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
3 22 0.22
4 57 0.58
5 20 0.20
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:6708 original size:13 final size:13
Alignment explanation
Indices: 6699--6776 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
6689 AATAATATAA
6699 TAATAAAATAAAC
1 TAATAAAATAAAC
6712 TAATAAAATAAAC
1 TAATAAAATAAAC
6725 -----AAATAAA-
1 TAATAAAATAAAC
6732 TAAT-AAATAAA-
1 TAATAAAATAAAC
6743 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
6757 TAATAAAATAAAC
1 TAATAAAATAAAC
*
6770 AAATAAA
1 TAATAAA
6777 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
8 7 0.12
11 10 0.18
12 1 0.02
13 36 0.63
14 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAATAAAC
Found at i:6813 original size:45 final size:44
Alignment explanation
Indices: 6692--6809 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
6682 ATCTATAAAT
*
6692 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
6737 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
6782 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
6810 TAAAAAAACA
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
42 10 0.14
43 7 0.10
44 6 0.09
45 47 0.67
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (44 bp):
AATAAATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
Found at i:8931 original size:30 final size:30
Alignment explanation
Indices: 8897--9056 Score: 320
Period size: 30 Copynumber: 5.3 Consensus size: 30
8887 AAATGGTGTT
8897 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8927 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8957 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8987 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
9017 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
9047 CCATTGTCGT
1 CCATTGTCGT
9057 TAACTAGTCT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 130 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:9097 original size:18 final size:18
Alignment explanation
Indices: 9070--9304 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
9060 CTAGTCTCCA
*
9070 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
9088 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
9106 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
9124 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
9142 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9160 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9178 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9196 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9214 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
9232 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9250 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9268 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9286 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9304 T
1 T
9305 CTCGATTCTG
Statistics
Matches: 213, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.02
18 205 0.96
19 4 0.02
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (18 bp):
TTTTTCATTCACTATAGG
Found at i:9645 original size:18 final size:18
Alignment explanation
Indices: 9622--9659 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9612 TTTTTTGCGC
9622 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
9640 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
9658 AT
1 AT
9660 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:11596 original size:78 final size:78
Alignment explanation
Indices: 11467--11635 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
11457 AGTAAAAAGA
* *
11467 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
11532 TTATCTTAATAAT
66 TTATCTTAATAAT
11545 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
11610 TTATCTTAATAAT
66 TTATCTTAATAAT
11623 ATGTAATATTATA
1 ATGTAATATTATA
11636 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:11638 original size:15 final size:15
Alignment explanation
Indices: 11618--11650 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11608 TCTTATCTTA
11618 ATAATATGTAATATT
1 ATAATATGTAATATT
11633 ATAATATGTAATATT
1 ATAATATGTAATATT
11648 ATA
1 ATA
11651 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:11731 original size:15 final size:15
Alignment explanation
Indices: 11711--11743 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11701 TCTTATCTTA
11711 ATAATATGTAATATT
1 ATAATATGTAATATT
11726 ATAATATGTAATATT
1 ATAATATGTAATATT
11741 ATA
1 ATA
11744 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:11832 original size:93 final size:93
Alignment explanation
Indices: 11540--11816 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
11530 TCTTATCTTA
11540 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
11605 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
11633 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
11698 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
11726 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
11791 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
11817 ATGGTCTTAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:14219 original size:21 final size:20
Alignment explanation
Indices: 14194--14261 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
14184 TTCCATTATT
*
14194 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
14215 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
14233 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
14254 ATATAATT
1 ATATAATT
14262 TCAAGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 3 0.07
21 22 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATTATATAAATATAA
Found at i:14226 original size:6 final size:6
Alignment explanation
Indices: 14202--14259 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
14192 TTATATAATT
*
14202 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
14248 ATATAA ATATAA
1 ATATAA ATATAA
14260 TTTCAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 34 0.72
7 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:14238 original size:27 final size:26
Alignment explanation
Indices: 14194--14259 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
14184 TTCCATTATT
*
14194 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
14221 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
14248 ATATAAATATAA
1 ATATAAATATAA
14260 TTTCAAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 30 0.83
28 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATATAAAATAAATAATATAA
Found at i:16230 original size:23 final size:23
Alignment explanation
Indices: 16204--16249 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16194 TATATTGTAA
16204 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
16227 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
16250 GGGGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
CCAATCATTTATCTTATTACTTG
Done.