Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011729.1 Corchorus capsularis cultivar CVL-1 contig11750, 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: 72843
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3435 original size:177 final size:178
Alignment explanation
Indices: 3110--3534 Score: 462
Period size: 177 Copynumber: 2.4 Consensus size: 178
3100 TCACCGAAAT
* * * * **
3110 AACTAATTTTTCAGAAGCATTTTGATATTTGAAACATCAAATTTAGCTTTCGAGTTATTCATGAA
1 AACTAATTTTTCGGAAGCTTTTTTATATTTGAAACATTAAA-TTAGCTTTCGAGTCCTTCATGAA
* * * * * *
3175 AGTCGTATAGATTATGGAAAAAACTTTTAATAGACACTTGAATTACCTCAATCGGACATCTGGAG
65 AGTCGTATAGATTATAGAAAAAACTTTTAAGAGACACTTGAATAACCTCAATCAGACATATGAAG
* * * * *
3240 CAAAAATTATGTAATATTAAGTAGGCT-ATCTATTCCCGCTAACCAA-AGC
130 CAAAAATTAAGTAATATTAAGT-GGATCACCCATTCCCACTAACCAATA-C
* *
3289 AACTAATTTTTTGGAAGCTTTTTTTATATTTGAAATATTAAATTAGCTTTCGAGTCCTTCATGAA
1 AACTAATTTTTCGGAAGC-TTTTTTATATTTGAAACATTAAATTAGCTTTCGAGTCCTTCATGAA
* * * * * *
3354 AGTTGT-T-GATTATATAACAACCTTTTAAGAGACACTTGAATAACTTTAATCAGACATATGAAG
65 AGTCGTATAGATTATAGAAAAAACTTTTAAGAGACACTTGAATAACCTCAATCAGACATATGAAG
* * * *
3417 CAAAACTTAAGTAATATTAAGTGGATCGCCCGTTCCCATTAACCAATAC
130 CAAAAATTAAGTAATATTAAGTGGATCACCCATTCCCACTAACCAATAC
* * * * *
3466 AACTAATTTTTCGGAAGCATTTGTTACACTTGAAACATTAAGTTTAGTTTTCGAGTCCTTCATGA
1 AACTAATTTTTCGGAAGC-TTTTTTATATTTGAAACATTAA-ATTAGCTTTCGAGTCCTTCATGA
3531 AAGT
64 AAGT
3535 GGTAGATCGT
Statistics
Matches: 205, Mismatches: 37, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
176 3 0.01
177 114 0.56
178 27 0.13
179 42 0.20
180 19 0.09
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (178 bp):
AACTAATTTTTCGGAAGCTTTTTTATATTTGAAACATTAAATTAGCTTTCGAGTCCTTCATGAAA
GTCGTATAGATTATAGAAAAAACTTTTAAGAGACACTTGAATAACCTCAATCAGACATATGAAGC
AAAAATTAAGTAATATTAAGTGGATCACCCATTCCCACTAACCAATAC
Found at i:3965 original size:179 final size:179
Alignment explanation
Indices: 3665--4028 Score: 710
Period size: 179 Copynumber: 2.0 Consensus size: 179
3655 ATTATATTAA
3665 AATTTAAAATGTTAGAAAGTCAAAATTACCCTCAAAAGTTTGTGAAAATAACTAAAAAACCAAAA
1 AATTTAAAATGTTAGAAAGTCAAAATTACCCTCAAAAGTTTGTGAAAATAACTAAAAAACCAAAA
*
3730 GTAAAATGACTAAAAAACCAAACTGAATAGTATCAAAATGAATGTAGTCATTTGGTTAGGAAAAA
66 CTAAAATGACTAAAAAACCAAACTGAATAGTATCAAAATGAATGTAGTCATTTGGTTAGGAAAAA
*
3795 TTTTGAGGGTAATTTAGTATTTTCACTTCTTCTTATTAGTGTTTTTTAT
131 TTTTGAGGGTAATTTAGTATTTCCACTTCTTCTTATTAGTGTTTTTTAT
3844 AATTTAAAATGTTAGAAAGTCAAAATTACCCTCAAAAGTTTGTGAAAATAACTAAAAAACCAAAA
1 AATTTAAAATGTTAGAAAGTCAAAATTACCCTCAAAAGTTTGTGAAAATAACTAAAAAACCAAAA
3909 CTAAAATGACTAAAAAACCAAACTGAATAGTATCAAAATGAATGTAGTCATTTGGTTAGGAAAAA
66 CTAAAATGACTAAAAAACCAAACTGAATAGTATCAAAATGAATGTAGTCATTTGGTTAGGAAAAA
3974 TTTTGAGGGTAATTTAGTATTTCCACTTCTTCTTATTAGTGTTTTTTAT
131 TTTTGAGGGTAATTTAGTATTTCCACTTCTTCTTATTAGTGTTTTTTAT
4023 AATTTA
1 AATTTA
4029 TAATTATGAT
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 183 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (179 bp):
AATTTAAAATGTTAGAAAGTCAAAATTACCCTCAAAAGTTTGTGAAAATAACTAAAAAACCAAAA
CTAAAATGACTAAAAAACCAAACTGAATAGTATCAAAATGAATGTAGTCATTTGGTTAGGAAAAA
TTTTGAGGGTAATTTAGTATTTCCACTTCTTCTTATTAGTGTTTTTTAT
Found at i:4197 original size:29 final size:28
Alignment explanation
Indices: 4119--4197 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
4109 CCCTTTTTAC
*
4119 CCTCTGAACTTGTACAATTTTGACATTTTG
1 CCTCTGAACTTG--CAATTTGGACATTTTG
* * *
4149 CCCCCTAAACTT-TAATTTTGGACATTTTG
1 -CCTCTGAACTTGCAA-TTTGGACATTTTG
4178 CCTCTTGAACTTGCAATTTG
1 CCTC-TGAACTTGCAATTTG
4198 AAGCCATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
28 5 0.13
29 22 0.58
30 2 0.05
31 9 0.24
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (28 bp):
CCTCTGAACTTGCAATTTGGACATTTTG
Found at i:5650 original size:22 final size:22
Alignment explanation
Indices: 5625--5772 Score: 117
Period size: 22 Copynumber: 6.8 Consensus size: 22
5615 TGAATATTTT
5625 TATGAAATTTTGATAATCATCC
1 TATGAAATTTTGATAATCATCC
*
5647 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAATCATCC
* * *
5668 TATGGAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAATCATCC
* * *
5689 ATAGGAAACTTTGATAA-CATAAC
1 -TATGAAATTTTGATAATCAT-CC
* **
5712 TATGAAATTTTAATAAAGATTCC
1 TATGAAATTTTGATAATCA-TCC
* *
5735 TATGAAATTTTG-TAACCTTCC
1 TATGAAATTTTGATAATCATCC
*
5756 TATG-ATTTTTGATAATC
1 TATGAAATTTTGATAATC
5773 TCCCTATAAT
Statistics
Matches: 98, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
20 6 0.06
21 30 0.31
22 47 0.48
23 14 0.14
24 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAATCATCC
Found at i:5785 original size:20 final size:20
Alignment explanation
Indices: 5733--5785 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
5723 AATAAAGATT
*
5733 CCTATGAAATTTTGTAACCTT
1 CCTATG-AATTTTGTAACCTC
* *
5754 CCTATGATTTTTGATAATCTC
1 CCTATGAATTTTG-TAACCTC
5775 CCTAT-AATTTT
1 CCTATGAATTTT
5786 TTGATACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (20 bp):
CCTATGAATTTTGTAACCTC
Found at i:7697 original size:2 final size:2
Alignment explanation
Indices: 7690--7720 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7680 GTAGTTGGAA
7690 AT AT 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 AT AT A
7721 AAATAGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8632 original size:123 final size:123
Alignment explanation
Indices: 8410--8653 Score: 346
Period size: 123 Copynumber: 2.0 Consensus size: 123
8400 TTTGGACGAA
** * * * * *
8410 AATTCAGATGCTAAAAATGATGTGGAGCATTCTTATTGGCTACTTTGGATCCTAATAAATGATGA
1 AATTCAGATGCTAAAAATGACATAGAGCATTCCTATTGGCCACGTTGGATCCTAATAAATGAGGA
8475 TAATCTAAATTTTCATTATTTTAATGATAAAATAATTAAAATATTATTTAATAATGGC
66 TAATCTAAATTTTCATTATTTTAATGATAAAATAATTAAAATATTATTTAATAATGGC
* *
8533 AATTCAGATGCTAAAGATGACATAGAGCATTCCTATTGGCCACGTTGGATCCTAATTAATGAGGA
1 AATTCAGATGCTAAAAATGACATAGAGCATTCCTATTGGCCACGTTGGATCCTAATAAATGAGGA
* * ** *
8598 TAATCTAACTTTTTATTATTTTAAT-AGTGGAATAATTAAAATATTTTTTAATAATG
66 TAATCTAAATTTTCATTATTTTAATGA-TAAAATAATTAAAATATTATTTAATAATG
8654 ACAGTTTAGA
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
122 1 0.01
123 105 0.99
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (123 bp):
AATTCAGATGCTAAAAATGACATAGAGCATTCCTATTGGCCACGTTGGATCCTAATAAATGAGGA
TAATCTAAATTTTCATTATTTTAATGATAAAATAATTAAAATATTATTTAATAATGGC
Found at i:10357 original size:31 final size:30
Alignment explanation
Indices: 10293--10356 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
10283 TCATTATGAC
*
10293 AAAAGAAATTTAGCTTATGATCCTCTTTGA
1 AAAAGAAATTTAGCTTATGATCCACTTTGA
10323 AAAATGAAATTT-GCTTATGATCCACTTTGA
1 AAAA-GAAATTTAGCTTATGATCCACTTTGA
10353 AAAA
1 AAAA
10357 AATTGATACC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (30 bp):
AAAAGAAATTTAGCTTATGATCCACTTTGA
Found at i:11569 original size:25 final size:24
Alignment explanation
Indices: 11532--11578 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
11522 CATTTTTACT
*
11532 TAATAACATGCATTTAAAAAAAAAC
1 TAATAACACGCA-TTAAAAAAAAAC
11557 TAATAACACGCATTAAAAAAAA
1 TAATAACACGCATTAAAAAAAA
11579 CAGTCAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (24 bp):
TAATAACACGCATTAAAAAAAAAC
Found at i:12436 original size:21 final size:21
Alignment explanation
Indices: 12424--12468 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
12414 TACATGTTAG
12424 ATTTGTTACTGTACAGATAAA
1 ATTTGTTACTGTACAGATAAA
12445 ATTTGTTACTGTACAGATGAAA
1 ATTTGTTACTGTACAGAT-AAA
12467 AT
1 AT
12469 AGTTGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (21 bp):
ATTTGTTACTGTACAGATAAA
Found at i:14093 original size:28 final size:28
Alignment explanation
Indices: 14060--14113 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
14050 AAAAACATGC
* *
14060 GTTTATATATTAATATTTTTTGAAGTAA
1 GTTTATATATTAATATTATTAGAAGTAA
14088 GTTTATATATTAATATTATTAGAAGT
1 GTTTATATATTAATATTATTAGAAGT
14114 CCAGAGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (28 bp):
GTTTATATATTAATATTATTAGAAGTAA
Found at i:14255 original size:23 final size:21
Alignment explanation
Indices: 14227--14269 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14217 TTCCTAATTA
14227 ATATTATGAAATAATATATATAT
1 ATATTAT-AAAT-ATATATATAT
*
14250 ATATTATTAATATATATATA
1 ATATTATAAATATATATATA
14270 AAACTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATATTATAAATATATATATAT
Found at i:15253 original size:22 final size:22
Alignment explanation
Indices: 15228--15270 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15218 ACTATATATA
*
15228 TCTAATTATTAGCTAATTAATT
1 TCTAATTAATAGCTAATTAATT
*
15250 TCTAATTAATAGTTAATTAAT
1 TCTAATTAATAGCTAATTAAT
15271 AATGAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (22 bp):
TCTAATTAATAGCTAATTAATT
Found at i:15759 original size:121 final size:121
Alignment explanation
Indices: 15545--15787 Score: 477
Period size: 121 Copynumber: 2.0 Consensus size: 121
15535 ACTTTCATTC
*
15545 ATTTTAAGTGTTAAATGATATTTTATTTTAAGTAAATAATTAACAATGAATCCATTACATATACA
1 ATTTTAAGTGTTAAATGATATTTTATTTTAAGTAAATAATTAACAATCAATCCATTACATATACA
15610 ATTTGATAAGAACCATCATTCTTATCTTTGGACTTTTATATAACCATCATATAGAA
66 ATTTGATAAGAACCATCATTCTTATCTTTGGACTTTTATATAACCATCATATAGAA
15666 ATTTTAAGTGTTAAATGATATTTTATTTTAAGTAAATAATTAACAATCAATCCATTACATATACA
1 ATTTTAAGTGTTAAATGATATTTTATTTTAAGTAAATAATTAACAATCAATCCATTACATATACA
15731 ATTTGATAAGAACCATCATTCTTATCTTTGGACTTTTATATAACCATCATATAGAA
66 ATTTGATAAGAACCATCATTCTTATCTTTGGACTTTTATATAACCATCATATAGAA
15787 A
1 A
15788 AGACCAACAA
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (121 bp):
ATTTTAAGTGTTAAATGATATTTTATTTTAAGTAAATAATTAACAATCAATCCATTACATATACA
ATTTGATAAGAACCATCATTCTTATCTTTGGACTTTTATATAACCATCATATAGAA
Found at i:20435 original size:21 final size:22
Alignment explanation
Indices: 20411--20456 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
20401 AAAAAAAGGG
**
20411 TTTGCTATTTACCG-CCCCCCT
1 TTTGCTAAATACCGTCCCCCCT
20432 TTTGCTAAATACCGTCCCCCCT
1 TTTGCTAAATACCGTCCCCCCT
20454 TTT
1 TTT
20457 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.13, C:0.39, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTGCTAAATACCGTCCCCCCT
Found at i:20650 original size:7 final size:7
Alignment explanation
Indices: 20613--20640 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
20603 AGTTAATTAA
20613 AATTTTT
1 AATTTTT
20620 AATTTTT
1 AATTTTT
20627 AATTTTT
1 AATTTTT
20634 AATTTTT
1 AATTTTT
20641 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:20729 original size:15 final size:14
Alignment explanation
Indices: 20709--20770 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 14
20699 TACTTAGTTG
20709 ATTAGTTTATGTTTA
1 ATTAGTTTAT-TTTA
*
20724 ATTAG--TA-TCTA
1 ATTAGTTTATTTTA
20735 ATTAGTTTATTATTA
1 ATTAGTTTATT-TTA
20750 ATTAG--TA-TTTA
1 ATTAGTTTATTTTA
20761 ATTAGTTTAT
1 ATTAGTTTAT
20771 GATTAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
11 16 0.42
12 1 0.03
13 8 0.21
14 1 0.03
15 12 0.32
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTAGTTTATTTTA
Found at i:20738 original size:26 final size:26
Alignment explanation
Indices: 20709--20776 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
20699 TACTTAGTTG
20709 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
20735 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
20761 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
20777 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:20824 original size:24 final size:25
Alignment explanation
Indices: 20785--20844 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
20775 AAAATGAAGG
*
20785 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
20808 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
20833 GAAATTAAGTTT
1 AAAATGAAGTTT
20845 AGGGTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:25605 original size:8 final size:7
Alignment explanation
Indices: 25588--25624 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
25578 TCATCAAACC
*
25588 AAAAATA
1 AAAAAGA
25595 AAAAAGA
1 AAAAAGA
25602 AAAAAGA
1 AAAAAGA
25609 AAAAAGA
1 AAAAAGA
25616 AAAGAAGA
1 AAA-AAGA
25624 A
1 A
25625 TTATCCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:31645 original size:27 final size:28
Alignment explanation
Indices: 31609--31672 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
31599 AAAGCCACCT
* *
31609 CTTCCTTCTCCTT-CAGAAAAGCAAAAC
1 CTTCCATCTCCTTCCAGAAAAACAAAAC
* *
31636 CTTTCATCT-CTTCCAGAAAAACGAAAC
1 CTTCCATCTCCTTCCAGAAAAACAAAAC
31663 CTTCCATCTC
1 CTTCCATCTC
31673 TAATGGCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.28
Consensus pattern (28 bp):
CTTCCATCTCCTTCCAGAAAAACAAAAC
Found at i:35831 original size:3 final size:3
Alignment explanation
Indices: 35823--35850 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35813 TTGAGCATTG
35823 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
35851 GTAAGAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35963 original size:12 final size:12
Alignment explanation
Indices: 35946--35987 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
35936 AATAATTTTA
35946 AGGGCACCTTGT
1 AGGGCACCTTGT
*
35958 AGGGCA--TT-A
1 AGGGCACCTTGT
35967 AGGGCACCTTGT
1 AGGGCACCTTGT
35979 AGGGCACCT
1 AGGGCACCT
35988 ACTTTCCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.24
10 2 0.08
11 2 0.08
12 15 0.60
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.21
Consensus pattern (12 bp):
AGGGCACCTTGT
Found at i:35969 original size:21 final size:21
Alignment explanation
Indices: 35943--35984 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35933 GAAAATAATT
35943 TTAAGGGCACCTTGTAGGGCA
1 TTAAGGGCACCTTGTAGGGCA
35964 TTAAGGGCACCTTGTAGGGCA
1 TTAAGGGCACCTTGTAGGGCA
35985 CCTACTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
TTAAGGGCACCTTGTAGGGCA
Found at i:37008 original size:16 final size:16
Alignment explanation
Indices: 36977--37019 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
36967 AATTACAAAC
*
36977 TTTTATAATGTGATTGA
1 TTTTAAAAT-TGATTGA
36994 TTTTAAAATTGATTGA
1 TTTTAAAATTGATTGA
*
37010 TTATAAAATT
1 TTTTAAAATT
37020 TGGGATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (16 bp):
TTTTAAAATTGATTGA
Found at i:42978 original size:6 final size:7
Alignment explanation
Indices: 42961--42993 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
42951 GATTTTATTA
42961 AAAAAAC
1 AAAAAAC
42968 AAAAAAC
1 AAAAAAC
42975 AAAAAAC
1 AAAAAAC
*
42982 AAAAAAT
1 AAAAAAC
42989 AAAAA
1 AAAAA
42994 TTCTGGCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAAAAC
Found at i:43182 original size:46 final size:47
Alignment explanation
Indices: 43114--43205 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 47
43104 GCCTGTGTCT
*
43114 TCTTGTTTATTACAAATGCCATT-AAGAAATACTCTAATCAAAGGTG
1 TCTTGTTTATTACAAATGCCATTAAAAAAATACTCTAATCAAAGGTG
* *
43160 TCTTGTTTATTACAAATTCCATTAAAAAAAATACTTTAATCAAAGG
1 TCTTGTTTATTACAAATGCCATT-AAAAAAATACTCTAATCAAAGG
43206 ACGAAAGGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 22 0.54
48 19 0.46
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (47 bp):
TCTTGTTTATTACAAATGCCATTAAAAAAATACTCTAATCAAAGGTG
Found at i:45154 original size:105 final size:105
Alignment explanation
Indices: 45045--45253 Score: 292
Period size: 105 Copynumber: 2.0 Consensus size: 105
45035 TGAAGGAGTG
* * * * * **
45045 CAGCCAGATTTGGTAACTTTTAATTCTATAATTGATGCTCTTTGCACGGAAAGGAGAATTGAAGA
1 CAGCCAGATGTGGTAACTTTCAACTCTATAATTGATACTCTTTGCAAGGAAAGGAGAACCGAAGA
* *
45110 AGCCGTTGAGGTATTGAATATGATGGCTGAAAGAGGTGTA
66 AGCCATTGAGGTATTGAATATAATGGCTGAAAGAGGTGTA
* *
45150 CAGCCAGATGTGGTAACTTTCAGCTCTTTAATTGATACTCTTTGCAAGGAAAGGAGAACCGAAGA
1 CAGCCAGATGTGGTAACTTTCAACTCTATAATTGATACTCTTTGCAAGGAAAGGAGAACCGAAGA
* * *
45215 AGCCATTGAGGTATTGGATCTAATGGCTGAAAGATGTGT
66 AGCCATTGAGGTATTGAATATAATGGCTGAAAGAGGTGT
45254 GAAACCTGAC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 90 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (105 bp):
CAGCCAGATGTGGTAACTTTCAACTCTATAATTGATACTCTTTGCAAGGAAAGGAGAACCGAAGA
AGCCATTGAGGTATTGAATATAATGGCTGAAAGAGGTGTA
Found at i:52531 original size:21 final size:20
Alignment explanation
Indices: 52507--52564 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
52497 TTTAATTTTT
52507 TTAATATTAATTAGTTTATGA
1 TTAATATTAATTAGTTTAT-A
*
52528 TTAATTTTAATTAG-TTA-A
1 TTAATATTAATTAGTTTATA
* *
52546 TTAAAATTACTTAGTTTAT
1 TTAATATTAATTAGTTTAT
52565 TAGTTTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 12 0.39
19 3 0.10
20 3 0.10
21 13 0.42
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (20 bp):
TTAATATTAATTAGTTTATA
Found at i:52583 original size:15 final size:15
Alignment explanation
Indices: 52559--52607 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
52549 AAATTACTTA
52559 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
52573 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
52585 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
52599 GATTAATTA
1 GTTTAATTA
52608 ATTCATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
11 9 0.31
13 4 0.14
14 4 0.14
15 12 0.41
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:54503 original size:18 final size:18
Alignment explanation
Indices: 54475--54516 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
54465 AGCAATCTGA
*
54475 TTTGTTGGGAACTGGTGAC
1 TTTG-TGGGAACTGATGAC
54494 TTTGTGGGAACTGATGAC
1 TTTGTGGGAACTGATGAC
54512 TTTGT
1 TTTGT
54517 CGGTGGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (18 bp):
TTTGTGGGAACTGATGAC
Found at i:56411 original size:32 final size:32
Alignment explanation
Indices: 56365--56439 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
56355 AATCACATAG
**
56365 ATTAGTAAATCTTATATTGTAATC-TATATAATT
1 ATTA-TAAATCTTATAAAGTAA-CGTATATAATT
56398 ATTATAAATCTTATAAAGTAACGTATATAATT
1 ATTATAAATCTTATAAAGTAACGTATATAATT
56430 ATTATAAATC
1 ATTATAAATC
56440 AAATGTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.87
33 4 0.10
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (32 bp):
ATTATAAATCTTATAAAGTAACGTATATAATT
Found at i:57653 original size:27 final size:27
Alignment explanation
Indices: 57615--57669 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
57605 CCCCTCATAA
*
57615 GAGGGAGATCCATATATGGGTGGGACT
1 GAGGGAGATCCATATATGGATGGGACT
57642 GAGGGAGATCCATATATGGATGGGACT
1 GAGGGAGATCCATATATGGATGGGACT
57669 G
1 G
57670 GGACTCGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.40, T:0.22
Consensus pattern (27 bp):
GAGGGAGATCCATATATGGATGGGACT
Found at i:57971 original size:15 final size:15
Alignment explanation
Indices: 57951--57993 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
57941 TTAATCGTAA
57951 ATAAACAAATTAAGT
1 ATAAACAAATTAAGT
57966 ATAAACAAATTAAGT
1 ATAAACAAATTAAGT
*
57981 ATAAACTAATTAA
1 ATAAACAAATTAA
57994 AACTAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (15 bp):
ATAAACAAATTAAGT
Found at i:58082 original size:22 final size:23
Alignment explanation
Indices: 58048--58093 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
58038 TAGTTAATCG
*
58048 TAAATTAACTAATTAAA-ACTAA
1 TAAACTAACTAATTAAATACTAA
*
58070 TAAACTAAGTAATTAAATACTAA
1 TAAACTAACTAATTAAATACTAA
58093 T
1 T
58094 TAATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAACTAACTAATTAAATACTAA
Found at i:58129 original size:15 final size:15
Alignment explanation
Indices: 58069--58140 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
58059 ATTAAAACTA
* *
58069 ATAAACTAAGTAATT
1 ATAAACTAATTAATC
58084 A-AATACTAATTAATC
1 ATAA-ACTAATTAATC
* *
58099 AAAAAAC-AA-AAATC
1 -ATAAACTAATTAATC
*
58113 ATGAACTAATTAATC
1 ATAAACTAATTAATC
58128 ATAAACTAATTAA
1 ATAAACTAATTAA
58141 ATACTAATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 8 0.18
15 28 0.62
16 3 0.07
17 2 0.04
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAAACTAATTAATC
Found at i:58156 original size:26 final size:28
Alignment explanation
Indices: 58116--58193 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 28
58106 AAAAATCATG
*
58116 AACTAATTAATCATAAACTAATTAAA-T
1 AACTAATTAAACATAAACTAATTAAACT
* *
58143 -ACTAATTAAACATAAATTGA-TAAACT
1 AACTAATTAAACATAAACTAATTAAACT
**
58169 AACTAATTTTA-ATAAACTAATTAAA
1 AACTAATTAAACATAAACTAATTAAA
58194 ATTAATCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 4 0.10
26 25 0.61
27 12 0.29
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.33
Consensus pattern (28 bp):
AACTAATTAAACATAAACTAATTAAACT
Found at i:58198 original size:18 final size:18
Alignment explanation
Indices: 58128--58199 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 18
58118 CTAATTAATC
*
58128 ATAAACTAATTAAATACTA
1 ATAAACTAATTAAA-ATTA
*
58147 ATTAAAC--A-T-AAATTG
1 A-TAAACTAATTAAAATTA
* **
58162 ATAAACTAACTAATTTTA
1 ATAAACTAATTAAAATTA
58180 ATAAACTAATTAAAATTA
1 ATAAACTAATTAAAATTA
58198 AT
1 AT
58200 CATAAACATT
Statistics
Matches: 40, Mismatches: 8, Indels: 11
0.68 0.14 0.19
Matches are distributed among these distances:
14 5 0.12
15 3 0.08
16 3 0.08
17 2 0.05
18 21 0.52
19 1 0.03
20 5 0.12
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.35
Consensus pattern (18 bp):
ATAAACTAATTAAAATTA
Found at i:58452 original size:23 final size:24
Alignment explanation
Indices: 58425--58483 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
58415 AAAATGAAGG
* *
58425 AAAATG-AGTTTGGAGATTTGTTA
1 AAAATGAAGTTTGAAGAGTTGTTA
*
58448 GAAATGAAGTTTGAAGAGTTGTTA
1 AAAATGAAGTTTGAAGAGTTGTTA
58472 AAAATGAAGTTT
1 AAAATGAAGTTT
58484 AGGGTTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (24 bp):
AAAATGAAGTTTGAAGAGTTGTTA
Found at i:58588 original size:21 final size:22
Alignment explanation
Indices: 58553--58597 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
58543 GTAAAAGTGT
58553 AAAAGGGGGGACGGTATTTAGC
1 AAAAGGGGGGACGGTATTTAGC
*
58575 AAAAGGGGGG-CGGTGTTTAGC
1 AAAAGGGGGGACGGTATTTAGC
58596 AA
1 AA
58598 TACAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.31, C:0.09, G:0.42, T:0.18
Consensus pattern (22 bp):
AAAAGGGGGGACGGTATTTAGC
Found at i:59351 original size:40 final size:40
Alignment explanation
Indices: 59296--59373 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
59286 CAATGTTATA
* *
59296 AAATCCATGTTATGCGAAGGAGCTTCCTTCATCATGAAAG
1 AAATCAATGTCATGCGAAGGAGCTTCCTTCATCATGAAAG
* *
59336 AAATCAATGTCATGCGAAGGAGCTTGCTTCATTATGAA
1 AAATCAATGTCATGCGAAGGAGCTTCCTTCATCATGAA
59374 GCTGATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (40 bp):
AAATCAATGTCATGCGAAGGAGCTTCCTTCATCATGAAAG
Found at i:64454 original size:210 final size:209
Alignment explanation
Indices: 64147--64583 Score: 581
Period size: 210 Copynumber: 2.1 Consensus size: 209
64137 GATGACCGAA
* * *
64147 AAAGGTTTGAAACCAAATGTCGTCACCTATAATTCTTTATCCGAGGGTTTTGCCAGTCAAGCCAA
1 AAAGGTGTGAAACCTAATATCGTCACCTATAATTCTTTATCCGAGGGTTTTGCCAGTCAAGCCAA
* * * *
64212 TGGAAAGAAGTGACAAACTTGTCTGACAGAATGGTCAATGAAGGAGTGCAGCCAGATCTCATAAC
66 TGGAAAGAAGTGACAAACATGTCTAACAGAATGATCAATGAAGGAGTGCAGCCAGATCCCATAAC
* * *
64277 TTTCAACTCTATAATCGGTGCTCTTTGCAAGGAAAGGAGAACTGAAGAAGCCATTGAGGTTATGG
131 TTGCAACTCTATAATCGATGCTCTTTGCAACGAAAGGAGAACTGAAGAAGCCATTGAGGTTATGG
64342 ATTTAATGGCTCAG
196 ATTTAATGGCTCAG
* * * * *
64356 AAAGGTGTGAAACCTAATATCTTCACGTATAATTCTTTAATCC-ATGGGTTTTGTC-GTTCAGGT
1 AAAGGTGTGAAACCTAATATCGTCACCTATAATTCTTT-ATCCGA-GGGTTTTGCCAG-TCAAGC
* * * ** *
64419 CAATGGAAGGAAGTGACAAGCATGTTTAACAGAATGATGGATGAAGGAGTGCAGCCAGATCCCGT
63 CAATGGAAAGAAGTGACAAACATGTCTAACAGAATGATCAATGAAGGAGTGCAGCCAGATCCCAT
* * * *
64484 AACTTGGAACTGTATGATTGATGCTCTTTGCAACGAAAGGAGAACTGAAGAAGCCATTGAGGTTA
128 AACTTGCAACTCTATAATCGATGCTCTTTGCAACGAAAGGAGAACTGAAGAAGCCATTGAGGTTA
*
64549 TGGATTTAATGGCTGAG
193 TGGATTTAATGGCTCAG
* *
64566 AAGGGTGCGAAACCTAAT
1 AAAGGTGTGAAACCTAAT
64584 GTCATTACTT
Statistics
Matches: 197, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
209 35 0.18
210 162 0.82
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (209 bp):
AAAGGTGTGAAACCTAATATCGTCACCTATAATTCTTTATCCGAGGGTTTTGCCAGTCAAGCCAA
TGGAAAGAAGTGACAAACATGTCTAACAGAATGATCAATGAAGGAGTGCAGCCAGATCCCATAAC
TTGCAACTCTATAATCGATGCTCTTTGCAACGAAAGGAGAACTGAAGAAGCCATTGAGGTTATGG
ATTTAATGGCTCAG
Found at i:65833 original size:6 final size:6
Alignment explanation
Indices: 65822--65861 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
65812 TAATCCTTCA
* *
65822 TCAAGT TCAAGT TCAACT TCAAGT TCAACT TCAAGT TCAA
1 TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAAGT TCAA
65862 CCCATACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (6 bp):
TCAAGT
Found at i:65842 original size:12 final size:12
Alignment explanation
Indices: 65822--65862 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
65812 TAATCCTTCA
*
65822 TCAAGTTCAAGT
1 TCAACTTCAAGT
65834 TCAACTTCAAGT
1 TCAACTTCAAGT
65846 TCAACTTCAAGT
1 TCAACTTCAAGT
65858 TCAAC
1 TCAAC
65863 CCATACCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (12 bp):
TCAACTTCAAGT
Done.