Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015614.1 Corchorus capsularis cultivar CVL-1 contig15635, 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: 109485
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2903 original size:13 final size:13
Alignment explanation
Indices: 2885--2909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2875 ACATGCATTA
2885 AAAACGGACATGT
1 AAAACGGACATGT
2898 AAAACGGACATG
1 AAAACGGACATG
2910 AATATGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.24, T:0.12
Consensus pattern (13 bp):
AAAACGGACATGT
Found at i:3107 original size:27 final size:27
Alignment explanation
Indices: 3077--3151 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
3067 AGTAGACTTA
* * *
3077 AAATGACTAGAATGCCGCTGAACATAC
1 AAATGACCAAAATGCCCCTGAACATAC
* *
3104 AAATGACCAAAATGCCCCTGAACTTGC
1 AAATGACCAAAATGCCCCTGAACATAC
3131 AAATGACCAAAATGCCCCTGA
1 AAATGACCAAAATGCCCCTGA
3152 CACCGAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATAC
Found at i:7668 original size:11 final size:10
Alignment explanation
Indices: 7650--7683 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
7640 GAAGTTCGTG
7650 TTTTGAAGAT
1 TTTTGAAGAT
7660 TTCTTGAAGAT
1 TT-TTGAAGAT
7671 ATTTTGAAGAT
1 -TTTTGAAGAT
7682 TT
1 TT
7684 GAAGAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:23679 original size:30 final size:30
Alignment explanation
Indices: 23643--23722 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
23633 CAAAGGATCA
*
23643 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCAACC
*
23673 AATGGCATCTTTGGTGTGATTCCTCCAACC
1 AATGGCATCTTTGGTGCGATTCCTCCAACC
* ***
23703 ATTGATGTCTTTGGTGCGAT
1 AATGGCATCTTTGGTGCGAT
23723 CCCATCTCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCAACC
Found at i:26123 original size:30 final size:30
Alignment explanation
Indices: 26087--26149 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
26077 TCTTCAAGGG
*
26087 GGAGGGAATGATGCGCCCAAGG-CTTTTCAT
1 GGAGGGAATGATGCG-CCAAGGTCTTATCAT
*
26117 GGAGGGAATTATGCGCCAAGGTCTTATCAT
1 GGAGGGAATGATGCGCCAAGGTCTTATCAT
26147 GGA
1 GGA
26150 CTAGAAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGTCTTATCAT
Found at i:26709 original size:9 final size:8
Alignment explanation
Indices: 26649--26707 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 8
26639 ATACTTATGT
26649 GTGA-TTA
1 GTGATTTA
26656 GTGATATATA
1 GTGAT-T-TA
26666 GTGATTTA
1 GTGATTTA
26674 GTGACTTATA
1 GTGA-TT-TA
26684 GTCTGA-TTA
1 G--TGATTTA
26693 GTGATTTA
1 GTGATTTA
26701 GTGATTT
1 GTGATTT
26708 TATTTAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
7 7 0.16
8 16 0.36
9 7 0.16
10 11 0.25
12 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (8 bp):
GTGATTTA
Found at i:31778 original size:16 final size:16
Alignment explanation
Indices: 31757--31791 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31747 ACAATTCAGA
31757 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
31773 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
31789 AAG
1 AAG
31792 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:32114 original size:19 final size:18
Alignment explanation
Indices: 32090--32125 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32080 AGTCAAATTA
*
32090 TCATCAATTCGAGATCAAG
1 TCATCAAATCGA-ATCAAG
32109 TCATCAAATCGAATCAA
1 TCATCAAATCGAATCAA
32126 ATCAAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (18 bp):
TCATCAAATCGAATCAAG
Found at i:42605 original size:36 final size:36
Alignment explanation
Indices: 42533--42605 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
42523 TTAAATAAAA
* * *
42533 TAAAAAGCAGAAACAGAAAATAAAAATATATTTTTT
1 TAAAAAGCAAAAACAGAAAAGAAAAATATATCTTTT
* *
42569 TAAAAAGGAAAAACGGAAAAGAAAAAT-TAATCTTTT
1 TAAAAAGCAAAAACAGAAAAGAAAAATAT-ATCTTTT
42605 T
1 T
42606 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (36 bp):
TAAAAAGCAAAAACAGAAAAGAAAAATATATCTTTT
Found at i:45667 original size:23 final size:23
Alignment explanation
Indices: 45641--45720 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
45631 TAAAGGGACC
45641 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** * * *
45664 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT---TGAACT
45691 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
45714 GTCTTCC
1 GTCTTCC
45721 AATTCCATTC
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 19 0.46
24 3 0.07
25 4 0.10
26 3 0.07
27 12 0.29
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:45693 original size:50 final size:50
Alignment explanation
Indices: 45618--45725 Score: 189
Period size: 50 Copynumber: 2.2 Consensus size: 50
45608 GTCTTACAAC
* *
45618 TCCAACTCAAACTTAAAGGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
1 TCCAATTCAAACTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
*
45668 TCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
1 TCCAATTCAAACTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
45718 TCCAATTC
1 TCCAATTC
45726 CATTCTTTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (50 bp):
TCCAATTCAAACTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
Found at i:56545 original size:51 final size:51
Alignment explanation
Indices: 56487--56758 Score: 332
Period size: 51 Copynumber: 5.4 Consensus size: 51
56477 GAGTTGATGG
* *
56487 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTGTGATTAGTTTGTAAA
1 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAAA
* * * * *
56538 TAAAAATGAGATCTTTGAACTAAATGATGGAACTTTTGACTAATTTATAAA
1 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAAA
* * *
56589 TAAAAATGAGAA-CTTTGGACTAAAAGATTGAACTTTTAATTAATTTGCAAA
1 TAAAAATGA-AATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAAA
* * * * *
56640 TAAAAATGAGATCTTTGAACTAAATGATTGAACTTGTGATTAGTTTGTACA
1 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAAA
* * * * *
56691 TAAAAATGAGATCCTTGAACTATAAGATTGAATTTTTGACTAATTTG-AAA
1 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAAA
*
56741 TAAAAATGAAACCTTTGA
1 TAAAAATGAAATCTTTGA
56759 TCCATGAAGA
Statistics
Matches: 185, Mismatches: 34, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
50 18 0.10
51 166 0.90
52 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (51 bp):
TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAAA
Found at i:56788 original size:153 final size:152
Alignment explanation
Indices: 56487--56802 Score: 408
Period size: 153 Copynumber: 2.1 Consensus size: 152
56477 GAGTTGATGG
*
56487 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTGTGATTAGTTTGTAAATAAAAATGAGATCT
1 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTGTGATTAGTTTGTAAATAAAAATGAGATCC
* *
56552 TTGAACTAAATGATGGAACTTTTGACTAATTTATAAATAAAAATGAGAACTTTGGACTAAAAGAT
66 TTGAACTAAATGATGGAACTTTTGACTAATTTAGAAATAAAAATGAGAACTTTGGACCAAAAGAT
**
56617 TGAACTTTTAATTAATTTGCAAA
131 TGAACGCTTAATTAATTTG-AAA
* * *
56640 TAAAAATGAGATCTTTGAACTAAATGATTGAACTTGTGATTAGTTTGTACATAAAAATGAGATCC
1 TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTGTGATTAGTTTGTAAATAAAAATGAGATCC
* * *
56705 TTGAACTATAA-GATTGAATTTTTGACTAATTT-GAAATAAAAATGA-AACCTTT-GATCCATGA
66 TTGAACTA-AATGATGGAACTTTTGACTAATTTAGAAATAAAAATGAGAA-CTTTGGA-CCA-AA
* **
56766 AGATT-AAGGCTTCGTTAGATTTGAAA
127 AGATTGAACGCTTAATTA-ATTTGAAA
*
56792 TAAAAGTGAAA
1 TAAAAATGAAA
56803 CCTGTAATCC
Statistics
Matches: 142, Mismatches: 16, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
151 4 0.03
152 37 0.26
153 99 0.70
154 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (152 bp):
TAAAAATGAAATCTTTGAACTAAAAGATTGAACTTGTGATTAGTTTGTAAATAAAAATGAGATCC
TTGAACTAAATGATGGAACTTTTGACTAATTTAGAAATAAAAATGAGAACTTTGGACCAAAAGAT
TGAACGCTTAATTAATTTGAAA
Found at i:57436 original size:47 final size:47
Alignment explanation
Indices: 57382--57475 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
57372 AAAGATCAAC
* *
57382 ATTGTCTTTTTCCTAAATTG-CCCTTCCTAGTCGGAAGGTGTTGTTTA
1 ATTGTCTTTTTCC-AAATTGCCCCTCCCTAGCCGGAAGGTGTTGTTTA
57429 ATTGTCTTTTTCCAAATTGCCCCTCCCTAGCCGGAAGGTGTTGTTTA
1 ATTGTCTTTTTCCAAATTGCCCCTCCCTAGCCGGAAGGTGTTGTTTA
57476 GTTTTCCCAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 6 0.14
47 38 0.86
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.41
Consensus pattern (47 bp):
ATTGTCTTTTTCCAAATTGCCCCTCCCTAGCCGGAAGGTGTTGTTTA
Found at i:57678 original size:40 final size:41
Alignment explanation
Indices: 57445--57658 Score: 290
Period size: 41 Copynumber: 5.2 Consensus size: 41
57435 TTTTTCCAAA
* * * *
57445 TTGCCCCTCCCTAGCCGGAAGGTGTTGTTTAGTTTTCCCAGT
1 TTGCCCTTCCCCA-CCGGAAGGTGTTGTTTACTTTTCCTAGT
*
57487 TTGCCCTTCCCCACCAGAAGGTGTTGTTTACTTTTCCTAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTAGT
** *
57528 CCGCCCTTCCCCACCGGAAGTTGTTGTTTACTTTTCCTAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTAGT
* *
57569 TTGCCCTTCCCCACTGGAAGGTGTTGTTTAC-ATTCCT-GTT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTAG-T
*
57609 TTGCCCTTCCCCACCGGAAGGTGTTGTTTAC-CTTCCTAGT
1 TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTAGT
57649 TTGCCCTTCC
1 TTGCCCTTCC
57659 TGGTCGAAAG
Statistics
Matches: 154, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 52 0.34
41 90 0.58
42 11 0.07
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.37
Consensus pattern (41 bp):
TTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTAGT
Found at i:57702 original size:49 final size:49
Alignment explanation
Indices: 57641--57783 Score: 166
Period size: 49 Copynumber: 3.0 Consensus size: 49
57631 GTTGTTTACC
*
57641 TTCCTAGTTTGCCCTTCCTGGTCGAAAGGTGTTGTTTAATTTC-GTCTTA
1 TTCCTAGTTTGCCCTTCCTGGTCGAAAGGTGTTGTTT-AGTTCGGTCTTA
* * * * * *
57690 TTCCAAGTTTGCCCTTCCCGGTCGGAAGGTGCTATTTAGTTCGGTTTTA
1 TTCCTAGTTTGCCCTTCCTGGTCGAAAGGTGTTGTTTAGTTCGGTCTTA
***
57739 TTCCTAGTTTGCCCTTCCTCACCGAAAGGTGTTGTTT-GTT-GGTCT
1 TTCCTAGTTTGCCCTTCCTGGTCGAAAGGTGTTGTTTAGTTCGGTCT
57784 GCTTAGGCGT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
47 4 0.05
48 7 0.09
49 66 0.86
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (49 bp):
TTCCTAGTTTGCCCTTCCTGGTCGAAAGGTGTTGTTTAGTTCGGTCTTA
Found at i:65255 original size:30 final size:31
Alignment explanation
Indices: 65206--65279 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
65196 GAAGAAAATG
* * *
65206 CAATTTAGGATACACCGTTA-CGACTTCTGT
1 CAATTCAGGATATAACGTTATCGACTTCTGT
* ** *
65236 TAATTCAGGATATAACGTTATCGTGTTGTGT
1 CAATTCAGGATATAACGTTATCGACTTCTGT
65267 CAATTCAGGATAT
1 CAATTCAGGATAT
65280 TTTTTAACAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
CAATTCAGGATATAACGTTATCGACTTCTGT
Found at i:69610 original size:41 final size:41
Alignment explanation
Indices: 69544--69667 Score: 160
Period size: 41 Copynumber: 3.0 Consensus size: 41
69534 GGGTTCAACA
* *
69544 TTGTTTACTCTTCCTAGTCTTCCCTTCCCCACCGGAAGGTG
1 TTGTTTACTTTTCCTAGTCTACCCTTCCCCACCGGAAGGTG
* * * *
69585 TTGTTTACTTTTCCTAATCTGCCCTTCCCCATCGAAAGGTG
1 TTGTTTACTTTTCCTAGTCTACCCTTCCCCACCGGAAGGTG
* * *
69626 TTTTTTAC-TTTCCCAGTTTACCCTTCCCCACCGGAAGGTG
1 TTGTTTACTTTTCCTAGTCTACCCTTCCCCACCGGAAGGTG
69666 TT
1 TT
69668 ATTTCTATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 28 0.39
41 43 0.61
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.39
Consensus pattern (41 bp):
TTGTTTACTTTTCCTAGTCTACCCTTCCCCACCGGAAGGTG
Found at i:69918 original size:110 final size:110
Alignment explanation
Indices: 69725--69944 Score: 386
Period size: 110 Copynumber: 2.0 Consensus size: 110
69715 TTTTTGTCAT
69725 GTTTTCACGTGTAATAAAAGGTTTCAACTCACTTAAAACAAAGAAAAGACTAAGAATATAGGATT
1 GTTTTCACGTGTAATAAAAGGTTTCAACTCACTTAAAACAAAGAAAAGACTAAGAATATAGGATT
* * *
69790 AAGGACTAAAGGCAACCTTTTTATTTTAGACCCACATTGAATCTA
66 AAGGACTAAAAGCAACCTTTTGATTTTAGACCCACATTAAATCTA
*
69835 GTTTTCATGTGTAATAAAAGGTTTCAACTCACTTAAAACAAAGAAAAGACTAAGAATATAGGATT
1 GTTTTCACGTGTAATAAAAGGTTTCAACTCACTTAAAACAAAGAAAAGACTAAGAATATAGGATT
* *
69900 GAGGACTAAAAGTAACCTTTTGATTTTAGACCCACATTAAATCTA
66 AAGGACTAAAAGCAACCTTTTGATTTTAGACCCACATTAAATCTA
69945 ATTAGACTTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 104 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (110 bp):
GTTTTCACGTGTAATAAAAGGTTTCAACTCACTTAAAACAAAGAAAAGACTAAGAATATAGGATT
AAGGACTAAAAGCAACCTTTTGATTTTAGACCCACATTAAATCTA
Found at i:71221 original size:15 final size:15
Alignment explanation
Indices: 71180--71225 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
71170 TTTTTTGCCC
71180 TCTTGTTCTTCTTTAAT
1 TCTTGTTCTTCTTT--T
*
71197 T-TT-TTTTTCTTTT
1 TCTTGTTCTTCTTTT
71210 TCTTGTTCTTCTTTT
1 TCTTGTTCTTCTTTT
71225 T
1 T
71226 TTTTCTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 2 0.08
15 18 0.72
16 2 0.08
17 1 0.04
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.76
Consensus pattern (15 bp):
TCTTGTTCTTCTTTT
Found at i:75413 original size:20 final size:21
Alignment explanation
Indices: 75375--75413 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
75365 AACAAAATAG
*
75375 AGTAAAAACTCATATAAAAGT
1 AGTAAAAACTCATAGAAAAGT
*
75396 AGTAAAAAGT-ATAGAAAA
1 AGTAAAAACTCATAGAAAA
75414 ATAGCTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (21 bp):
AGTAAAAACTCATAGAAAAGT
Found at i:75724 original size:136 final size:135
Alignment explanation
Indices: 75451--75796 Score: 622
Period size: 136 Copynumber: 2.5 Consensus size: 135
75441 GCTCGATCAG
75451 TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAAGGTGTGGAAGAGATAAAGATTCAATC
1 TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAAGGTGTGGAAGAGAT-AAGATTCAATC
75516 TAAC-GTCATATTTGAATCCCACTTTTAATCCAACCGTTGGATAAGATAAAGATAGATTCTCTAC
65 TAACGGTCATATTTGAATCCCACTTTTAATCCAACCGTTGGATAAGATAAAGATAGATTCTCTAC
75580 AAGTGA
130 AAGTGA
*
75586 TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAATGTGTGGAAGAGATATAGATTCAATC
1 TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAAGGTGTGGAAGAGATA-AGATTCAATC
*
75651 TAACGGTCATATTTGAATCCCACTTTTTATCCAACCGTTGGATAAGATAAAGATAGATTCTCTAC
65 TAACGGTCATATTTGAATCCCACTTTTAATCCAACCGTTGGATAAGATAAAGATAGATTCTCTAC
75716 AAGTGA
130 AAGTGA
75722 TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATC
1 TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAAGGTGTGGAAGAGATAA-GATTCAATC
* *
75787 CAATGGTCAT
65 TAACGGTCAT
75797 GATCGAGCTC
Statistics
Matches: 203, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
134 1 0.00
135 67 0.33
136 135 0.67
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (135 bp):
TTGGATATTGTGTTGGATTTTCTGACTTTTGTTGGATAAGGTGTGGAAGAGATAAGATTCAATCT
AACGGTCATATTTGAATCCCACTTTTAATCCAACCGTTGGATAAGATAAAGATAGATTCTCTACA
AGTGA
Found at i:82645 original size:6 final size:6
Alignment explanation
Indices: 82634--82660 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
82624 ATTAATCTGC
82634 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
82661 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:84662 original size:21 final size:21
Alignment explanation
Indices: 84612--84669 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
84602 AGTGTGTGTA
*
84612 ATTTATTTCTTAAT-ATTATTT
1 ATTTATTT-TTAATAATAATTT
*
84633 A-TAATTTTTTAATAATAATTT
1 ATTTA-TTTTTAATAATAATTT
*
84654 ATTTATTTTCAATAAT
1 ATTTATTTTTAATAAT
84670 TAAAACCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 7 0.23
21 21 0.70
22 2 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTATTTTTAATAATAATTT
Found at i:93590 original size:23 final size:24
Alignment explanation
Indices: 93562--93620 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
93552 CCGGTTATGC
93562 CCGGGCATGGCCGA-GTC-CTGTGG
1 CCGGGCATGGCCGATGTCGC-GTGG
93585 CCGGGCATGGCC-ATGTCGCGTGG
1 CCGGGCATGGCCGATGTCGCGTGG
93608 CCGGTG-ATGGCCG
1 CCGG-GCATGGCCG
93621 GGCATCTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 1 0.03
23 29 0.91
24 2 0.06
ACGTcount: A:0.08, C:0.31, G:0.44, T:0.17
Consensus pattern (24 bp):
CCGGGCATGGCCGATGTCGCGTGG
Found at i:93642 original size:33 final size:33
Alignment explanation
Indices: 93605--93711 Score: 171
Period size: 33 Copynumber: 3.2 Consensus size: 33
93595 CCATGTCGCG
93605 TGGCCGGTGATGGC-CGGGCATCTCCAAGTCACA
1 TGGCCGGTG-TGGCGCGGGCATCTCCAAGTCACA
*
93638 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCACA
1 TGGCCGGTGTGGCGCGGGCATCTCCAAGTCACA
* *
93671 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCACG
1 TGGCCGGTGTGGCGCGGGCATCTCCAAGTCACA
93704 TGGCCGGT
1 TGGCCGGT
93712 CACAAGTGCT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
32 3 0.04
33 68 0.96
ACGTcount: A:0.14, C:0.30, G:0.36, T:0.21
Consensus pattern (33 bp):
TGGCCGGTGTGGCGCGGGCATCTCCAAGTCACA
Found at i:93658 original size:66 final size:66
Alignment explanation
Indices: 93586--93711 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
93576 GTCCTGTGGC
* * * *
93586 CGGGCATGGCCATGTCGCGTGGCCGGTGATGGC-CGGGCATCTCCAAGTCACATGGCCGGTGTTG
1 CGGGCATCGCCAAGTCACATGGCCGGTG-TGGCGCGGGCATCTCCAAGTCACATGGCCGGTGTTG
93650 CG
65 CG
* * *
93652 CGGGCATCTCCAAGTCACATGGCCGGTGTTGCGCGGGCATCTCCAAGTCACGTGGCCGGT
1 CGGGCATCGCCAAGTCACATGGCCGGTGTGGCGCGGGCATCTCCAAGTCACATGGCCGGT
93712 CACAAGTGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
65 3 0.06
66 49 0.94
ACGTcount: A:0.13, C:0.30, G:0.37, T:0.20
Consensus pattern (66 bp):
CGGGCATCGCCAAGTCACATGGCCGGTGTGGCGCGGGCATCTCCAAGTCACATGGCCGGTGTTGC
G
Found at i:94687 original size:17 final size:17
Alignment explanation
Indices: 94642--94689 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
94632 AAGTAACAAA
94642 GAAAAATAAAAAGTAAAC
1 GAAAAATAAAAAG-AAAC
* *
94660 TAAAAA-CAAAAGAAAC
1 GAAAAATAAAAAGAAAC
*
94676 GAAAAATTAAAAGA
1 GAAAAATAAAAAGA
94690 TAAAAAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 9 0.36
17 11 0.44
18 5 0.20
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.10
Consensus pattern (17 bp):
GAAAAATAAAAAGAAAC
Found at i:96367 original size:21 final size:21
Alignment explanation
Indices: 96343--96391 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
96333 GCGTTGGGCG
*
96343 CCCATGTGGCATGCTTGGCAC
1 CCCATGTGGCATGCTTCGCAC
** *
96364 CCCATGTGGTTTGCTTCGCGC
1 CCCATGTGGCATGCTTCGCAC
96385 CCCATGT
1 CCCATGT
96392 ACTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.29
Consensus pattern (21 bp):
CCCATGTGGCATGCTTCGCAC
Found at i:107562 original size:11 final size:10
Alignment explanation
Indices: 107544--107577 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
107534 AATTGTCTTC
107544 AAATCTTCAA
1 AAATCTTCAA
107554 AATATCTTCAA
1 AA-ATCTTCAA
107565 GAAATCTTCAA
1 -AAATCTTCAA
107576 AA
1 AA
107578 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:109380 original size:32 final size:32
Alignment explanation
Indices: 109339--109399 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
109329 GTAAAAATAG
*
109339 TAATTAGTAAA-TCAGTAATTAAGAGAAAAGAT
1 TAATCAGTAAAGTCA-TAATTAAGAGAAAAGAT
* *
109371 TAATCAGTAAAGTGATAGTTAAGAGAAAA
1 TAATCAGTAAAGTCATAATTAAGAGAAAA
109400 AATAAAGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.92
33 2 0.08
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.26
Consensus pattern (32 bp):
TAATCAGTAAAGTCATAATTAAGAGAAAAGAT
Done.