Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168335.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_558, 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: 22977
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Found at i:1036 original size:25 final size:25
Alignment explanation
Indices: 1003--1054 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
993 ATTATTTATT
*
1003 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
1028 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
1053 TT
1 TT
1055 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:1061 original size:25 final size:25
Alignment explanation
Indices: 1008--1061 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
998 TTATTTTTTT
* ***
1008 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
1033 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
1058 AGTT
1 AGTT
1062 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:1161 original size:15 final size:15
Alignment explanation
Indices: 1141--1190 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
1131 CATAATGATT
1141 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
1156 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
1174 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
1189 AT
1 AT
1191 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:1173 original size:18 final size:18
Alignment explanation
Indices: 1150--1187 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1140 TATTTTAATA
1150 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
1168 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
1186 TT
1 TT
1188 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:1209 original size:17 final size:17
Alignment explanation
Indices: 1189--1222 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1179 AATATTGTTA
*
1189 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
1206 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
1223 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:1246 original size:19 final size:19
Alignment explanation
Indices: 1224--1273 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1214 TGATTTATTC
*
1224 ATTACTATATTTTTTAGTT
1 ATTACTATATTTTGTAGTT
*
1243 ATTACTATATTTTGTATTT
1 ATTACTATATTTTGTAGTT
1262 ATTACTATATTT
1 ATTACTATATTT
1274 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTACTATATTTTGTAGTT
Found at i:1291 original size:19 final size:19
Alignment explanation
Indices: 1257--1311 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1247 CTATATTTTG
*
1257 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTCAT
*
1277 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTCAT
* *
1296 TAATTATTTATTATTT
1 TATTTATTTCTTATTT
1312 TCGTGTCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATTTCTTATTTCAT
Found at i:1292 original size:38 final size:38
Alignment explanation
Indices: 1219--1293 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
1209 TTGTATGATT
*
1219 TATTCATTACTATATTTTTTAGTTATTACTATATTTTG
1 TATTCATTACTATATTTATTAGTTATTACTATATTTTG
* * *
1257 TATTTATTACTATATTTCATTATTTATTTCT-TATTTT
1 TATTCATTACTATATTT-ATTAGTTATTACTATATTTT
1294 ATTAATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 22 0.69
39 10 0.31
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (38 bp):
TATTCATTACTATATTTATTAGTTATTACTATATTTTG
Found at i:1350 original size:17 final size:18
Alignment explanation
Indices: 1324--1512 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
1314 GTGTCGGTTC
*
1324 TATATATATTTA-TAAAT
1 TATATTTATTTATTAAAT
1341 TATATTTATTTATT--AT
1 TATATTTATTTATTAAAT
* * *
1357 T-TATGTA-TTATCACAGT
1 TATATTTATTTATTA-AAT
**
1374 TATAGATATTTATTTAAAT
1 TATATTTATTTA-TTAAAT
*
1393 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* **
1410 TATATTAAAATATTAAAT
1 TATATTTATTTATTAAAT
1428 TATATTTATATT-TTATATAT
1 TATATTTAT-TTATTA-A-AT
** *
1448 TAAATATATTAAAATATGAAAT
1 T--ATAT-TT-ATTTATTAAAT
*
1470 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* ** *
1487 TATATTAAAATATGAAAT
1 TATATTTATTTATTAAAT
1505 TATATTTA
1 TATATTTA
1513 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:1406 original size:8 final size:8
Alignment explanation
Indices: 1393--1499 Score: 72
Period size: 8 Copynumber: 12.6 Consensus size: 8
1383 TTATTTAAAT
*
1393 TATATTTA
1 TATATTAA
1401 TATATTAAA
1 TATATT-AA
1410 TATATTAA
1 TATATTAA
*
1418 AATATTAAA
1 TATATT-AA
*
1427 TTATATTTA
1 -TATATTAA
*
1436 TAT-TTTA
1 TATATTAA
1443 TATATTAAA
1 TATATT-AA
1452 TATATTAA
1 TATATTAA
* *
1460 AATATGAAA
1 TATAT-TAA
*
1469 TTATATTTA
1 -TATATTAA
1478 TATATTAAA
1 TATATT-AA
1487 TATATTAA
1 TATATTAA
*
1495 AATAT
1 TATAT
1500 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:1423 original size:77 final size:76
Alignment explanation
Indices: 1354--1512 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 76
1344 ATTTATTTAT
* * * *
1354 TATTTATGTATTATCACAGTTATAGATATT-TAT-TTAAATTATATTTATATATTAAATATATTA
1 TATTTATATATTAT-ACA-TTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTA
1417 AAATATTAAATTA
64 AAATATTAAATTA
* * *
1430 TATTTATATTTTATATATTAAATATATTAAAATATGAAATTATATTTATATATTAAATATATTAA
1 TATTTATATATTATACATTAAAGATATT-AAATATGAAATTATATTTATATATTAAATATATTAA
*
1495 AATATGAAATTA
65 AATATTAAATTA
1507 TATTTA
1 TATTTA
1513 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:1426 original size:35 final size:35
Alignment explanation
Indices: 1389--1512 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
1379 ATATTTATTT
*
1389 AAATTATATTTATATATTAAATATATTAAAATATTAA
1 AAATTATATTTATATATTAAATATATTAAAATA-T-G
1426 ATTATATTTATATTTTATATATTAAATATATTAAAATATG
1 A--A-A-TTATA-TTTATATATTAAATATATTAAAATATG
1466 AAATTATATTTATATATTAAATATATTAAAATATG
1 AAATTATATTTATATATTAAATATATTAAAATATG
1501 AAATTATATTTA
1 AAATTATATTTA
1513 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:1531 original size:4 final size:4
Alignment explanation
Indices: 1524--1651 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
1514 ATAAATATCT
*
1524 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
* *
1569 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
*
1617 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
1652 AAAAACAAAG
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:1546 original size:13 final size:13
Alignment explanation
Indices: 1537--1614 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
1527 AATAATATAA
1537 TAATAAAATAAAC
1 TAATAAAATAAAC
1550 TAATAAAATAAAC
1 TAATAAAATAAAC
1563 -----AAATAAA-
1 TAATAAAATAAAC
1570 TAAT-AAATAAA-
1 TAATAAAATAAAC
1581 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
1595 TAATAAAATAAAC
1 TAATAAAATAAAC
*
1608 AAATAAA
1 TAATAAA
1615 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:1651 original size:45 final size:44
Alignment explanation
Indices: 1530--1647 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
1520 ATCTATAAAT
*
1530 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
1575 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
1620 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
1648 TAAAAAAAAC
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:3783 original size:30 final size:30
Alignment explanation
Indices: 3736--4074 Score: 671
Period size: 30 Copynumber: 11.3 Consensus size: 30
3726 AAATGGTGTT
3736 CCATTGTCGTC-AATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3765 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3795 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3825 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3855 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3885 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3915 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3945 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
3975 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
4005 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
4035 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
4065 CCATTGTCGT
1 CCATTGTCGT
4075 TAACTAGTCT
Statistics
Matches: 309, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
29 11 0.04
30 298 0.96
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:4115 original size:18 final size:18
Alignment explanation
Indices: 4088--4322 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
4078 CTAGTCTCCA
*
4088 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
4106 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
4124 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
4142 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
4160 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4178 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4196 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4214 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4232 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
4250 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4268 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4286 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4304 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
4322 T
1 T
4323 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:4663 original size:18 final size:18
Alignment explanation
Indices: 4640--4677 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4630 TTTTTTGCGC
4640 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
4658 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
4676 AT
1 AT
4678 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:6646 original size:79 final size:78
Alignment explanation
Indices: 6485--6654 Score: 313
Period size: 79 Copynumber: 2.2 Consensus size: 78
6475 AGTAAAAAGA
* *
6485 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
6550 TTATCTTAATAAT
66 TTATCTTAATAAT
6563 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAAATGTAATACGTAATAATGGT
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGT-AATGTAATACGTAATAATGGT
6628 CTTATCTTAATAAT
65 CTTATCTTAATAAT
6642 ATGTAATATTATA
1 ATGTAATATTATA
6655 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
78 41 0.46
79 48 0.54
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:6657 original size:15 final size:15
Alignment explanation
Indices: 6637--6669 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6627 TCTTATCTTA
6637 ATAATATGTAATATT
1 ATAATATGTAATATT
6652 ATAATATGTAATATT
1 ATAATATGTAATATT
6667 ATA
1 ATA
6670 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:6740 original size:92 final size:93
Alignment explanation
Indices: 6558--6834 Score: 522
Period size: 92 Copynumber: 3.0 Consensus size: 93
6548 TCTTATCTTA
6558 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAAATGTAATACGTAATA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGT-AATGTAATACGTAATA
6623 ATGGTCTTATCTTAATAATATGTAATATT
65 ATGGTCTTATCTTAATAATATGTAATATT
6652 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGT-ATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
6716 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
6744 ATAATATGTAATATTATA-TTCACTTTGATTGTGGAAAGCGTAATACGTAATGTAATACGTAATA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGG-AAGCGTAATACGTAATGTAATACGTAATA
6808 ATGGTCTTATCTTAATAATATGTAATA
65 ATGGTCTTATCTTAATAATATGTAATA
6835 ATGGTCTTAA
Statistics
Matches: 181, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
91 16 0.09
92 69 0.38
93 55 0.30
94 41 0.23
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:6749 original size:15 final size:15
Alignment explanation
Indices: 6729--6761 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6719 TCTTATCTTA
6729 ATAATATGTAATATT
1 ATAATATGTAATATT
6744 ATAATATGTAATATT
1 ATAATATGTAATATT
6759 ATA
1 ATA
6762 TTCACTTTGA
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:9240 original size:21 final size:20
Alignment explanation
Indices: 9215--9282 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
9205 TTCCATTATT
*
9215 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
9236 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
9254 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
9275 ATATAATT
1 ATATAATT
9283 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:9247 original size:6 final size:6
Alignment explanation
Indices: 9223--9280 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
9213 TTATATAATT
*
9223 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
9269 ATATAA ATATAA
1 ATATAA ATATAA
9281 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:9259 original size:27 final size:26
Alignment explanation
Indices: 9215--9280 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
9205 TTCCATTATT
*
9215 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
9242 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
9269 ATATAAATATAA
1 ATATAAATATAA
9281 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:11250 original size:23 final size:23
Alignment explanation
Indices: 11224--11269 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11214 TATATTGTAA
11224 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
11247 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
11270 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
Found at i:16778 original size:21 final size:21
Alignment explanation
Indices: 16754--16797 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
16744 GATTCTTTGC
16754 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
16775 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
16796 TT
1 TT
16798 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTGAGATTTTATCTGATCTA
Found at i:16805 original size:21 final size:21
Alignment explanation
Indices: 16754--16805 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16744 GATTCTTTGC
*
16754 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
16775 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
16796 TTAT-AAATTT
1 TT-TGAAATTT
16806 GTATATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTATCTGATCTA
Found at i:17001 original size:20 final size:20
Alignment explanation
Indices: 16976--17053 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
16966 AACAATCAAA
16976 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
**
16996 TAAAATGAAAATAAAA--AA
1 TAAAATGAAAATAAAATTTT
*
17014 AAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
17034 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
17054 CGCGGGCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.30
20 35 0.70
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAATGAAAATAAAATTTT
Found at i:17019 original size:38 final size:38
Alignment explanation
Indices: 16977--17049 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
16967 ACAATCAAAT
16977 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
17015 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
17050 TTTTCGCGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (38 bp):
AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
Found at i:17328 original size:24 final size:25
Alignment explanation
Indices: 17285--17348 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
17275 TGGAGCCTTA
**
17285 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
17310 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
17334 ATTTAATAAATAATA
1 ATTTAATAAATAATA
17349 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATAAATAATAAAAATTTAAT
Found at i:17343 original size:18 final size:18
Alignment explanation
Indices: 17284--17322 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
17274 ATGGAGCCTT
17284 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
17302 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
17320 AAT
1 AAT
17323 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATATTTAATAAA
Found at i:17349 original size:14 final size:14
Alignment explanation
Indices: 17330--17357 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17320 AATAAAAATT
17330 TAATATTTAATAAA
1 TAATATTTAATAAA
17344 TAATATTTAATAAA
1 TAATATTTAATAAA
17358 AAAATTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTTAATAAA
Found at i:17362 original size:18 final size:18
Alignment explanation
Indices: 17288--17362 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
17278 AGCCTTAATT
**
17288 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
17306 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
17325 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
17344 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
17362 T
1 T
17363 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 24 0.51
19 2 0.04
20 5 0.11
21 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAAAAAAA
Found at i:19532 original size:15 final size:15
Alignment explanation
Indices: 19512--19541 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19502 TTTTTTAGTG
19512 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
19527 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
19542 TTTTTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
AACGTGTCATTTTTT
Found at i:20141 original size:14 final size:14
Alignment explanation
Indices: 20124--20154 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20114 GATGGATATA
20124 TATCGTATAATTCT
1 TATCGTATAATTCT
20138 TATCGTATAATTCT
1 TATCGTATAATTCT
20152 TAT
1 TAT
20155 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:21466 original size:18 final size:18
Alignment explanation
Indices: 21440--21480 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
21430 TAATGTTCAT
*
21440 ATATTATCATATAATAGA
1 ATATAATCATATAATAGA
21458 ATATAATCATATAATAGA
1 ATATAATCATATAATAGA
21476 ATATA
1 ATATA
21481 CAACAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
ATATAATCATATAATAGA
Found at i:21660 original size:10 final size:10
Alignment explanation
Indices: 21645--21696 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
21635 TTCAAAAATC
21645 ATCATATAAT
1 ATCATATAAT
21655 ATCATATAAT
1 ATCATATAAT
*
21665 AATGA-ATAAT
1 -ATCATATAAT
21675 CAT-ATAATAAT
1 -ATCAT-ATAAT
21686 ATCATATAAT
1 ATCATATAAT
21696 A
1 A
21697 AGGAGTATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 1 0.03
10 25 0.69
11 10 0.28
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (10 bp):
ATCATATAAT
Found at i:21666 original size:13 final size:14
Alignment explanation
Indices: 21645--21697 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
21635 TTCAAAAATC
*
21645 ATCATATAAT-ATC
1 ATCATATAATAATA
21658 AT-ATAATAATGAATA
1 ATCAT-ATAAT-AATA
21673 ATCATATAATAAT-
1 ATCATATAATAATA
21686 ATCATATAATAA
1 ATCATATAATAA
21698 GGAGTATTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 2 0.06
13 19 0.54
14 3 0.09
15 9 0.26
16 2 0.06
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (14 bp):
ATCATATAATAATA
Found at i:22108 original size:180 final size:181
Alignment explanation
Indices: 21676--22418 Score: 1420
Period size: 180 Copynumber: 4.1 Consensus size: 181
21666 ATGAATAATC
*
21676 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
21741 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
21806 AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
21857 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
21922 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
21987 AATCAAAGACGC-AAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
22037 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
22102 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
22167 AATCAAAGACGC-AAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
22217 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
*
22282 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATCAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
*
22347 AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCAGAT
131 AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
* *
22398 -GAGAATAATATCATATAATAA
1 ATATAATAATATCATATAATAA
22419 TGAATAATCC
Statistics
Matches: 556, Mismatches: 5, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
180 378 0.68
181 178 0.32
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (181 bp):
ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
AATCAAAGACGCAAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
Done.