Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168362.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_582, 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: 22435
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Found at i:289 original size:24 final size:23
Alignment explanation
Indices: 253--303 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
243 TTTTTTGGTA
253 TTTTTTTTCTTTTATATTAC-TAT
1 TTTTTTTTCTTTTATATT-CGTAT
* *
276 TTTTTATTTGTTTTTTATTCGTAT
1 TTTTT-TTTCTTTTATATTCGTAT
300 TTTT
1 TTTT
304 AAAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTTTCTTTTATATTCGTAT
Found at i:484 original size:17 final size:19
Alignment explanation
Indices: 464--505 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
454 ATGCTTTCAG
464 TTTTAC-TTGTTTT-AATT
1 TTTTACGTTGTTTTAAATT
481 TTTT-CGTTGTTTTAAAATT
1 TTTTACGTTGTTTT-AAATT
500 TTTTAC
1 TTTTAC
506 ATTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 11 0.52
19 8 0.38
20 1 0.05
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTACGTTGTTTTAAATT
Found at i:1335 original size:15 final size:14
Alignment explanation
Indices: 1317--1362 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1307 AATTTTTGTC
1317 CTTTTTATTTTCTT
1 CTTTTTATTTTCTT
*
1331 ACTTTTTATATT-TT
1 -CTTTTTATTTTCTT
1345 CTTTTT-TTTTCTT
1 CTTTTTATTTTCTT
1358 -TTTTT
1 CTTTTT
1363 GTGCTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 2 0.07
15 10 0.36
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTTTATTTTCTT
Found at i:1353 original size:9 final size:10
Alignment explanation
Indices: 1341--1430 Score: 56
Period size: 10 Copynumber: 8.4 Consensus size: 10
1331 ACTTTTTATA
1341 TTTTCTTTTT
1 TTTTCTTTTT
1351 TTTTCTTTTT
1 TTTTCTTTTT
*
1361 TTGTGCTTTATT
1 TT-TTCTTT-TT
1373 TATTT-TTTTCT
1 T-TTTCTTTT-T
* **
1384 TTTGCTTTAA
1 TTTTCTTTTT
1394 TTTTCTTTCTT
1 TTTTCTTT-TT
*
1405 ATTTTATTTTT
1 -TTTTCTTTTT
*
1416 ATTTCTTTCTT
1 TTTTCTTT-TT
1427 TTTT
1 TTTT
1431 TATAGTTTCA
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
10 28 0.47
11 20 0.33
12 11 0.18
13 1 0.02
ACGTcount: A:0.08, C:0.10, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:1735 original size:21 final size:21
Alignment explanation
Indices: 1711--1750 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1701 TTTTTCTCAA
1711 ATTTT-ATTTTATATATTTTGT
1 ATTTTCATTTTATA-ATTTTGT
*
1732 ATTTTCATTTTTTAATTTT
1 ATTTTCATTTTATAATTTT
1751 TTCTTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (21 bp):
ATTTTCATTTTATAATTTTGT
Found at i:1889 original size:7 final size:6
Alignment explanation
Indices: 1843--1870 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1833 GTGCACATTC
1843 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1871 CATCTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:2098 original size:18 final size:18
Alignment explanation
Indices: 2077--2129 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2067 TTTGGTATTT
2077 TATTTAATTTTTCTTTTA
1 TATTTAATTTTTCTTTTA
*
2095 TA-TTAATATTTTCTCTTA
1 TATTTAAT-TTTTCTTTTA
*
2113 -ATTTATTTTTTCATTTT
1 TATTTAATTTTTC-TTTT
2130 TTTTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTAATTTTTCTTTTA
Found at i:2193 original size:16 final size:15
Alignment explanation
Indices: 2167--2196 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2157 AAAGTTTAAA
2167 ATTTTTTATTTTTTC
1 ATTTTTTATTTTTTC
2182 ATTTTCTTATTTTTT
1 ATTTT-TTATTTTTT
2197 GTCTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTATTTTTTC
Found at i:2656 original size:15 final size:14
Alignment explanation
Indices: 2615--2662 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
2605 AATTTTTGTC
*
2615 TTTTTATTTTCTTA
1 TTTTTATTTTTTTA
*
2629 CTTTTTATATTTTTA
1 -TTTTTATTTTTTTA
2644 TTTTTATTTTTTTTA
1 TTTTTA-TTTTTTTA
2659 TTTT
1 TTTT
2663 ATCATTGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:2729 original size:16 final size:16
Alignment explanation
Indices: 2704--2737 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2694 ATAATTTTTC
*
2704 TTCAACTTTTTCTCCT
1 TTCAAATTTTTCTCCT
*
2720 TTCAAATTTTTCTTCT
1 TTCAAATTTTTCTCCT
2736 TT
1 TT
2738 TTTTTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCAAATTTTTCTCCT
Found at i:4261 original size:21 final size:21
Alignment explanation
Indices: 4216--4261 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4206 TTTCTTTTCC
* **
4216 TTTTTTTTGACTTTTTTTGTT
1 TTTTTTTTGACTTTTTATGCA
*
4237 TTTTTTTTTACTTTTTATGCA
1 TTTTTTTTGACTTTTTATGCA
4258 TTTT
1 TTTT
4262 CTTAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTTTGACTTTTTATGCA
Found at i:4762 original size:12 final size:12
Alignment explanation
Indices: 4745--4770 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4735 ATTTCCTTAC
4745 TTTTTTTTGTTT
1 TTTTTTTTGTTT
4757 TTTTTTTTGTTT
1 TTTTTTTTGTTT
4769 TT
1 TT
4771 AGTACTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:5717 original size:14 final size:12
Alignment explanation
Indices: 5665--5720 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
5655 TTTCTTTTTG
5665 TTTTTATTTATAT
1 TTTTTATTT-TAT
*
5678 TTTTTA--TTAA
1 TTTTTATTTTAT
*
5688 CTTTTATTTTAT
1 TTTTTATTTTAT
5700 TTTTTATCTTTGAT
1 TTTTTAT-TTT-AT
5714 TTTTTAT
1 TTTTTAT
5721 ATCTTTTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 7 0.20
11 1 0.03
12 9 0.26
13 9 0.26
14 9 0.26
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:6455 original size:10 final size:10
Alignment explanation
Indices: 6442--6512 Score: 52
Period size: 10 Copynumber: 6.5 Consensus size: 10
6432 ACTTTTTATA
*
6442 TTTTTTGTTT
1 TTTTTTCTTT
6452 TTTTTTCTTT
1 TTTTTTCTTT
*
6462 TTTTGTGCTTT
1 TTTT-TTCTTT
* *
6473 ATTTATCTTTT
1 TTTTTTC-TTT
6484 TTCTTTTGCTTAAT
1 TT-TTTT-CTT--T
6498 TTTTTTCTTT
1 TTTTTTCTTT
6508 TTTTT
1 TTTTT
6513 ATAGTTTCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
10 20 0.42
11 12 0.25
12 8 0.17
13 5 0.10
14 3 0.06
ACGTcount: A:0.06, C:0.08, G:0.06, T:0.80
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:6455 original size:18 final size:18
Alignment explanation
Indices: 6434--6515 Score: 53
Period size: 18 Copynumber: 4.4 Consensus size: 18
6424 ATTTTCTTAC
*
6434 TTTTTATATTTTTTGTTT
1 TTTTTATATTTTTTCTTT
*
6452 TTTTT-TCTTTTTT-TGTGCT
1 TTTTTATATTTTTTCT-T--T
*
6471 TTATTTATCTTTTTTCTTT
1 TT-TTTATATTTTTTCTTT
**
6490 TGCTTA-ATTTTTTTCTTT
1 TTTTTATA-TTTTTTCTTT
6508 TTTTTATA
1 TTTTTATA
6516 GTTTCATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
16 1 0.02
17 8 0.16
18 22 0.44
19 6 0.12
20 3 0.06
21 9 0.18
22 1 0.02
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTATATTTTTTCTTT
Found at i:6483 original size:21 final size:18
Alignment explanation
Indices: 6442--6485 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
6432 ACTTTTTATA
*
6442 TTTTTTGTTTTTTTTTCT
1 TTTTTTGTTTTTTTATCT
6460 TTTTTTGTGCTTTATTTATCT
1 TTTTTTGT--TTT-TTTATCT
6481 TTTTT
1 TTTTT
6486 CTTTTGCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
20 3 0.14
21 11 0.50
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.82
Consensus pattern (18 bp):
TTTTTTGTTTTTTTATCT
Found at i:6529 original size:21 final size:19
Alignment explanation
Indices: 6505--6553 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
6495 AATTTTTTTC
6505 TTTTTTTTATAGTTTCATAAA
1 TTTTTTTTATAGTTT--TAAA
* *
6526 TTTTTATTA-AGTTTTGAA
1 TTTTTTTTATAGTTTTAAA
6544 TTTTTTTTAT
1 TTTTTTTTAT
6554 TTTTCTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTTTTTATAGTTTTAAA
Found at i:6927 original size:12 final size:11
Alignment explanation
Indices: 6907--6950 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
6897 GTGCACATTC
6907 TTTTATTTTTA
1 TTTTATTTTTA
6918 TTTGTATTTTT-
1 TTT-TATTTTTA
*
6929 TATTAATTTTTA
1 T-TTTATTTTTA
6941 TTTTATTTTT
1 TTTTATTTTT
6951 CATCTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:7076 original size:25 final size:24
Alignment explanation
Indices: 7032--7087 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
7022 AAACTAAAAG
7032 TTTTTTTCCATTTTGTTTTTGAAA
1 TTTTTTTCCATTTTGTTTTTGAAA
* *
7056 TTTTTATT-CATTTTGTCTTTTTATA
1 TTTTT-TTCCATTTTGT-TTTTGAAA
7081 TTTTTTT
1 TTTTTTT
7088 GATTCGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.73
Consensus pattern (24 bp):
TTTTTTTCCATTTTGTTTTTGAAA
Found at i:7186 original size:18 final size:18
Alignment explanation
Indices: 7165--7218 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
7155 TTTCGTATTT
7165 TATTTAATTTTTCTTTTA
1 TATTTAATTTTTCTTTTA
*
7183 TA-TTAATATTTTCTCTTA
1 TATTTAAT-TTTTCTTTTA
* *
7201 -ATTTATTTTTTCATTTA
1 TATTTAATTTTTCTTTTA
7218 T
1 T
7219 TTTTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTAATTTTTCTTTTA
Found at i:7284 original size:16 final size:15
Alignment explanation
Indices: 7258--7287 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
7248 AAAGTTCAAA
7258 ATTTTTTATTTTTTC
1 ATTTTTTATTTTTTC
7273 ATTTTCTTATTTTTT
1 ATTTT-TTATTTTTT
7288 TGTCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTATTTTTTC
Found at i:7737 original size:13 final size:13
Alignment explanation
Indices: 7719--7750 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
7709 TTTTCTTACT
7719 TTTTATATTTTTA
1 TTTTATATTTTTA
*
7732 TTTTATTTTTTTA
1 TTTTATATTTTTA
7745 TTTTAT
1 TTTTAT
7751 CATTGTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATATTTTTA
Found at i:7815 original size:16 final size:16
Alignment explanation
Indices: 7790--7823 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7780 ATAATTTTTC
*
7790 TTCAACTTTTTCTCCT
1 TTCAAATTTTTCTCCT
*
7806 TTCAAATTTTTCTTCT
1 TTCAAATTTTTCTCCT
7822 TT
1 TT
7824 TTTTTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCAAATTTTTCTCCT
Found at i:8454 original size:12 final size:12
Alignment explanation
Indices: 8437--8486 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
8427 AGTTAAGATC
8437 ATCTTGTAATTT
1 ATCTTGTAATTT
*
8449 ATCTTGAAATTT
1 ATCTTGTAATTT
* *
8461 GT-TT-TTATTT
1 ATCTTGTAATTT
*
8471 ATCGTGTAATTT
1 ATCTTGTAATTT
8483 ATCT
1 ATCT
8487 AATTAACAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
10 5 0.18
11 3 0.11
12 20 0.71
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (12 bp):
ATCTTGTAATTT
Found at i:8702 original size:17 final size:17
Alignment explanation
Indices: 8646--8705 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 17
8636 TTTTTTAGTA
*
8646 CTTTT-TTTTCTTTTTC
1 CTTTTATTTTATTTTTC
* * *
8662 CTTTTGCTTTAAATTTT-
1 CTTTT-ATTTTATTTTTC
*
8679 CTCTTATTTTATTTTTC
1 CTTTTATTTTATTTTTC
8696 CTTTTATTTT
1 CTTTTATTTT
8706 TTTGCTTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
16 13 0.39
17 13 0.39
18 7 0.21
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTATTTTTC
Found at i:9341 original size:24 final size:24
Alignment explanation
Indices: 9295--9341 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
9285 TTTCTTTTCC
* **
9295 TTTTTTAACTTTTTTTGTTTTTTT
1 TTTTTTAACTTTTTATGCATTTTT
*
9319 TTTTTTTACTTTTTATGCATTTT
1 TTTTTTAACTTTTTATGCATTTT
9342 CTTAATTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (24 bp):
TTTTTTAACTTTTTATGCATTTTT
Found at i:10311 original size:20 final size:21
Alignment explanation
Indices: 10288--10345 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
10278 TTAACTTTTA
*
10288 TTTTATTTTTATCTTTG-ATT
1 TTTTATTTTTTTCTTTGTATT
10308 TTTTATATCTTTTTC-TTGTATT
1 TTTTAT-T-TTTTTCTTTGTATT
*
10330 TGTTATTTTTTTCTTT
1 TTTTATTTTTTTCTTT
10346 AAACTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 12 0.38
21 7 0.22
22 13 0.41
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTATTTTTTTCTTTGTATT
Found at i:10536 original size:18 final size:17
Alignment explanation
Indices: 10515--10561 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
10505 TTGTTTTTTA
10515 TTTATATTTTTAAAAAAT
1 TTTATATTTTT-AAAAAT
*
10533 TTTATAAATTTT-AAAAT
1 TTTAT-ATTTTTAAAAAT
*
10550 TTTTTATTTTTA
1 TTTATATTTTTA
10562 TTTTTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 5 0.21
19 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATTTTTAAAAAT
Found at i:11642 original size:20 final size:20
Alignment explanation
Indices: 11617--11654 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11607 ATTCCATTTC
11617 ATTTTTGAAATTTTTCTTCA
1 ATTTTTGAAATTTTTCTTCA
* *
11637 ATTTTTGTATTTTTTCTT
1 ATTTTTGAAATTTTTCTT
11655 TTTTAGTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTTTGAAATTTTTCTTCA
Found at i:12018 original size:22 final size:21
Alignment explanation
Indices: 11978--12018 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
11968 TTTTTCTCAA
11978 ATTTTATTTTATATATTTTGT
1 ATTTTATTTTATATATTTTGT
* *
11999 ATTTTCATTTTTTATTTTTT
1 ATTTT-ATTTTATATATTTT
12019 TCTTGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTTATTTTATATATTTTGT
Found at i:12130 original size:12 final size:11
Alignment explanation
Indices: 12110--12153 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
12100 GTGCACATTC
12110 TTTTATTTTTA
1 TTTTATTTTTA
12121 TTTGTATTTTT-
1 TTT-TATTTTTA
*
12132 TATTAATTTTTA
1 T-TTTATTTTTA
12144 TTTTATTTTT
1 TTTTATTTTT
12154 CATCTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:12388 original size:18 final size:18
Alignment explanation
Indices: 12367--12420 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
12357 TTTCGTATTT
12367 TATTTAATTTTTCTTTTA
1 TATTTAATTTTTCTTTTA
*
12385 TA-TTAATATTTTCTCTTA
1 TATTTAAT-TTTTCTTTTA
* *
12403 -ATTTATTTTTTCATTTA
1 TATTTAATTTTTCTTTTA
12420 T
1 T
12421 TTTTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTAATTTTTCTTTTA
Found at i:12486 original size:16 final size:15
Alignment explanation
Indices: 12460--12489 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12450 AAAGTTCAAA
12460 ATTTTTTATTTTTTC
1 ATTTTTTATTTTTTC
12475 ATTTTCTTATTTTTT
1 ATTTT-TTATTTTTT
12490 TGTCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTATTTTTTC
Found at i:12939 original size:13 final size:13
Alignment explanation
Indices: 12921--12952 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12911 TTTTCTTACT
12921 TTTTATATTTTTA
1 TTTTATATTTTTA
*
12934 TTTTATTTTTTTA
1 TTTTATATTTTTA
12947 TTTTAT
1 TTTTAT
12953 CATTGTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATATTTTTA
Found at i:13017 original size:16 final size:16
Alignment explanation
Indices: 12992--13025 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12982 ATAATTTTTC
*
12992 TTCAACTTTTTCTCCT
1 TTCAAATTTTTCTCCT
*
13008 TTCAAATTTTTCTTCT
1 TTCAAATTTTTCTCCT
13024 TT
1 TT
13026 TTTTTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCAAATTTTTCTCCT
Found at i:13661 original size:12 final size:12
Alignment explanation
Indices: 13644--13693 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
13634 AGTTAAGATC
13644 ATCTTGTAATTT
1 ATCTTGTAATTT
*
13656 ATCTTGAAATTT
1 ATCTTGTAATTT
* *
13668 GT-TT-TTATTT
1 ATCTTGTAATTT
*
13678 ATCGTGTAATTT
1 ATCTTGTAATTT
13690 ATCT
1 ATCT
13694 AATTAACAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
10 5 0.18
11 3 0.11
12 20 0.71
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (12 bp):
ATCTTGTAATTT
Found at i:13914 original size:17 final size:17
Alignment explanation
Indices: 13857--13921 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
13847 TTTTTTAGTA
* *
13857 CTTTTTTTTTCTTTTTC
1 CTTTTATTTTATTTTTC
* * *
13874 CTTTTGCTTTAAATTTT-
1 CTTTT-ATTTTATTTTTC
*
13891 CTCTTATTTTATTTTTC
1 CTTTTATTTTATTTTTC
13908 CTTTTATTTT-TTTT
1 CTTTTATTTTATTTT
13922 GCTTTTTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
16 12 0.32
17 18 0.49
18 7 0.19
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (17 bp):
CTTTTATTTTATTTTTC
Found at i:15512 original size:14 final size:12
Alignment explanation
Indices: 15460--15515 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
15450 CTTCCTTTTG
15460 TTTTTATTTATAT
1 TTTTTATTT-TAT
*
15473 TTTTTA-TTCA-
1 TTTTTATTTTAT
*
15483 CTTTTATTTTAT
1 TTTTTATTTTAT
15495 TTTTTATCTTTGAT
1 TTTTTAT-TTT-AT
15509 TTTTTAT
1 TTTTTAT
15516 ATCTTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 8 0.23
13 9 0.26
14 9 0.26
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:15532 original size:22 final size:20
Alignment explanation
Indices: 15491--15546 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
15481 CACTTTTATT
*
15491 TTATTTTTTATCTT-TGATTTT
1 TTATTTTTT-TCTTGT-ATTTG
15512 TTATATCTTTTTCTTGTATTTG
1 TTAT-T-TTTTTCTTGTATTTG
15534 TTATTTTTTTCTT
1 TTATTTTTTTCTT
15547 TAAACTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
22 13 0.42
23 5 0.16
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (20 bp):
TTATTTTTTTCTTGTATTTG
Found at i:15614 original size:107 final size:107
Alignment explanation
Indices: 15503--15736 Score: 427
Period size: 107 Copynumber: 2.2 Consensus size: 107
15493 ATTTTTTATC
*
15503 TTTGATTTTTTATATCTTTTTCTTGTATTTGTTATTTTTTTCTTTAAACTAAAAGTTTTTTCTAT
1 TTTGATTTTCTATATCTTTTTCTTGTATTTGTTATTTTTTTCTTTAAACTAAAAGTTTTTTCTAT
*
15568 TTTATATTTCAAATTTTTATTCATTTTGTCTTTTTATATTTT
66 TTTATATTTCAAATTTTTATTCATTTTCTCTTTTTATATTTT
15610 TTTGATTTTCTATATCTTTTTCTTGTATTTGTTATTTTTTTCTTTAAACTAAAAGTTTTTTCTAT
1 TTTGATTTTCTATATCTTTTTCTTGTATTTGTTATTTTTTTCTTTAAACTAAAAGTTTTTTCTAT
15675 TTTATATTTCAAATTTTTATTCATTTTCTCTTTTTATATTTT
66 TTTATATTTCAAATTTTTATTCATTTTCTCTTTTTATATTTT
*
15717 TTTTATTTTCT-TA-CTTTTTC
1 TTTGATTTTCTATATCTTTTTC
15737 ATTTTTTTTC
Statistics
Matches: 124, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
105 7 0.06
106 2 0.02
107 115 0.93
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.68
Consensus pattern (107 bp):
TTTGATTTTCTATATCTTTTTCTTGTATTTGTTATTTTTTTCTTTAAACTAAAAGTTTTTTCTAT
TTTATATTTCAAATTTTTATTCATTTTCTCTTTTTATATTTT
Found at i:15814 original size:25 final size:28
Alignment explanation
Indices: 15763--15814 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
15753 TGGTATTTTA
*
15763 TTTTATTTTTTCTTTTATATTACTATTC
1 TTTTATTTGTTCTTTTATATTACTATTC
15791 TTTTATTTGTT-TTTTAT-TTA-TATT
1 TTTTATTTGTTCTTTTATATTACTATT
15815 TTTAAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 6 0.26
28 10 0.43
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTATTTGTTCTTTTATATTACTATTC
Found at i:16910 original size:20 final size:20
Alignment explanation
Indices: 16885--16922 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16875 ATTCCATTTC
16885 ATTTTTGAAATTTTTCTTCA
1 ATTTTTGAAATTTTTCTTCA
* *
16905 ATTTTTGTATTTTTTCTT
1 ATTTTTGAAATTTTTCTT
16923 TTTTAGTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTTTGAAATTTTTCTTCA
Found at i:17303 original size:22 final size:21
Alignment explanation
Indices: 17263--17303 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17253 TTTTTCTCAA
17263 ATTTTATTTTATATATTTTGT
1 ATTTTATTTTATATATTTTGT
* *
17284 ATTTTCATTTTTTATTTTTT
1 ATTTT-ATTTTATATATTTT
17304 TCTTGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTTATTTTATATATTTTGT
Found at i:17415 original size:12 final size:11
Alignment explanation
Indices: 17395--17438 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
17385 GTGCACATTC
17395 TTTTATTTTTA
1 TTTTATTTTTA
17406 TTTGTATTTTT-
1 TTT-TATTTTTA
*
17417 TATTAATTTTTA
1 T-TTTATTTTTA
17429 TTTTATTTTT
1 TTTTATTTTT
17439 CATCTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:17564 original size:25 final size:24
Alignment explanation
Indices: 17520--17575 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
17510 AAACTAAAAG
17520 TTTTTTTCCATTTTGTTTTTGAAA
1 TTTTTTTCCATTTTGTTTTTGAAA
* *
17544 TTTTTATT-CATTTTGTCTTTTTATA
1 TTTTT-TTCCATTTTGT-TTTTGAAA
17569 TTTTTTT
1 TTTTTTT
17576 GATTCGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.73
Consensus pattern (24 bp):
TTTTTTTCCATTTTGTTTTTGAAA
Found at i:17670 original size:17 final size:17
Alignment explanation
Indices: 17650--17709 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
17640 TTTTTTCGTA
17650 TTTTATTTAATTTTTTC
1 TTTTATTTAATTTTTTC
*
17667 TTTTATATTAATATTTTC
1 TTTTAT-TTAATTTTTTC
*
17685 TCTTAATTT-ATTTTTTC
1 T-TTTATTTAATTTTTTC
*
17702 ATTTATTT
1 TTTTATTT
17710 TTATTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.17
17 13 0.36
18 13 0.36
19 4 0.11
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTTAATTTTTTC
Found at i:17771 original size:16 final size:15
Alignment explanation
Indices: 17745--17774 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17735 AAAGTTCAAA
17745 ATTTTTTATTTTTTC
1 ATTTTTTATTTTTTC
17760 ATTTTCTTATTTTTT
1 ATTTT-TTATTTTTT
17775 GTCTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTATTTTTTC
Found at i:18220 original size:13 final size:13
Alignment explanation
Indices: 18202--18233 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18192 TTTTCTTACT
18202 TTTTATATTTTTA
1 TTTTATATTTTTA
*
18215 TTTTATTTTTTTA
1 TTTTATATTTTTA
18228 TTTTAT
1 TTTTAT
18234 CATTGTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATATTTTTA
Found at i:18298 original size:16 final size:16
Alignment explanation
Indices: 18273--18306 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18263 ATAATTTTTC
*
18273 TTCAACTTTTTCTCCT
1 TTCAAATTTTTCTCCT
*
18289 TTCAAATTTTTCTTCT
1 TTCAAATTTTTCTCCT
18305 TT
1 TT
18307 TTTTTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCAAATTTTTCTCCT
Found at i:18701 original size:20 final size:18
Alignment explanation
Indices: 18659--18703 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
18649 TTTATAAACT
*
18659 AATTTTTTTCTATTTTGT
1 AATTTTTTTCTATTTTGA
*
18677 CATTTTTTTCTTCATTTTGA
1 AATTTTTTTC-T-ATTTTGA
18697 AATTTTT
1 AATTTTT
18704 ATTACTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 9 0.41
19 1 0.05
20 12 0.55
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (18 bp):
AATTTTTTTCTATTTTGA
Found at i:18940 original size:12 final size:12
Alignment explanation
Indices: 18923--18972 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
18913 AGTTAAGATC
18923 ATCTTGTAATTT
1 ATCTTGTAATTT
*
18935 ATCTTGAAATTT
1 ATCTTGTAATTT
* *
18947 GT-TT-TTATTT
1 ATCTTGTAATTT
*
18957 ATCGTGTAATTT
1 ATCTTGTAATTT
18969 ATCT
1 ATCT
18973 AATTAACAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
10 5 0.18
11 3 0.11
12 20 0.71
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (12 bp):
ATCTTGTAATTT
Found at i:19201 original size:16 final size:16
Alignment explanation
Indices: 19168--19200 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19158 AAATTTTCTC
19168 TTATTTTATTTTCCTT
1 TTATTTTATTTTCCTT
*
19184 TTATTTT-TTTTGCTT
1 TTATTTTATTTTCCTT
19199 TT
1 TT
19201 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (16 bp):
TTATTTTATTTTCCTT
Found at i:20496 original size:12 final size:12
Alignment explanation
Indices: 20481--20505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20471 TTGGTTTTTC
20481 TCATTTTTGTTT
1 TCATTTTTGTTT
20493 TCATTTTTGTTT
1 TCATTTTTGTTT
20505 T
1 T
20506 TTGCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TCATTTTTGTTT
Found at i:20526 original size:28 final size:28
Alignment explanation
Indices: 20469--20528 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
20459 TCTATTATTC
*
20469 TTTTGGTTTTTCTCATTTTTGTTTTCAT
1 TTTTGGTTTTTCTCATTTTTGTATTCAT
*
20497 TTTTGTTTTTTGCT-ATTTTT-TATTCTAT
1 TTTTGGTTTTT-CTCATTTTTGTATTC-AT
20525 TTTT
1 TTTT
20529 ATAATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.14
28 22 0.79
29 2 0.07
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.75
Consensus pattern (28 bp):
TTTTGGTTTTTCTCATTTTTGTATTCAT
Found at i:20798 original size:14 final size:12
Alignment explanation
Indices: 20746--20801 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
20736 CTTCCTTTTG
20746 TTTTTATTTATAT
1 TTTTTATTT-TAT
*
20759 TTTTTA-TTCA-
1 TTTTTATTTTAT
*
20769 CTTTTATTTTAT
1 TTTTTATTTTAT
20781 TTTTTATCTTTGAT
1 TTTTTAT-TTT-AT
20795 TTTTTAT
1 TTTTTAT
20802 ATCTTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 8 0.23
13 9 0.26
14 9 0.26
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:20799 original size:21 final size:21
Alignment explanation
Indices: 20775--20834 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
20765 TTCACTTTTA
20775 TTTTATTTTTTATCTTTG-ATT
1 TTTTATTTTTT-TCTTTGTATT
20796 TTTTATATCTTTTTC-TTGTATT
1 TTTTAT-T-TTTTTCTTTGTATT
*
20818 TGTTATTTTTTTTCTTT
1 TTTTA-TTTTTTTCTTT
20835 AAACTAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 15 0.45
22 13 0.39
23 5 0.15
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.77
Consensus pattern (21 bp):
TTTTATTTTTTTCTTTGTATT
Found at i:20866 original size:24 final size:24
Alignment explanation
Indices: 20839--20887 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20829 TTCTTTAAAC
20839 TAAAAGTTTT-TTCTATTTTATATT
1 TAAAAGTTTTATTC-ATTTTATATT
* *
20863 TAAAATTTTTATTCATTTTGTATT
1 TAAAAGTTTTATTCATTTTATATT
20887 T
1 T
20888 TTATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (24 bp):
TAAAAGTTTTATTCATTTTATATT
Done.