Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015662.1 Corchorus capsularis cultivar CVL-1 contig15683, 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: 107150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:648 original size:7 final size:7
Alignment explanation
Indices: 636--670 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
626 TGAAGTCACT
636 TAAAAAA
1 TAAAAAA
643 TAAAAAA
1 TAAAAAA
650 TAAATAAA
1 TAAA-AAA
658 -AAAAAA
1 TAAAAAA
664 TAAAAAA
1 TAAAAAA
671 AATTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.12
7 20 0.77
8 3 0.12
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:663 original size:21 final size:21
Alignment explanation
Indices: 637--685 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
627 GAAGTCACTT
637 AAAAAATAAAAAATAAATA-AA
1 AAAAAATAAAAAA-AAATATAA
*
658 AAAAAATAAAAAAAATTATAA
1 AAAAAATAAAAAAAAATATAA
679 AAAAAAT
1 AAAAAAT
686 CAACCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (21 bp):
AAAAAATAAAAAAAAATATAA
Found at i:664 original size:10 final size:10
Alignment explanation
Indices: 637--685 Score: 71
Period size: 11 Copynumber: 4.7 Consensus size: 10
627 GAAGTCACTT
637 AAAAAATAAA
1 AAAAAATAAA
647 AAATAAATAAA
1 AAA-AAATAAA
658 AAAAAATAAA
1 AAAAAATAAA
*
668 AAAAATTATAA
1 AAAAAATA-AA
679 AAAAAAT
1 AAAAAAT
686 CAACCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:1914 original size:28 final size:28
Alignment explanation
Indices: 1827--1916 Score: 69
Period size: 33 Copynumber: 3.0 Consensus size: 28
1817 CTTTCTCAGA
*
1827 TCTTCAATTCTC-GACCTCAGACAGGTCT
1 TCTTCAATT-TCAGACCTCAAACAGGTCT
*
1855 T-TCTCAATTTCA-ACATCGACCATACACTGGTCT
1 TCT-TCAATTTCAGACCTC-A--A-ACA--GGTCT
1888 TCTTCAATTTCAGACCTCAAACAGGTCT
1 TCTTCAATTTCAGACCTCAAACAGGTCT
1916 T
1 T
1917 TTTTAACATT
Statistics
Matches: 49, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
27 7 0.14
28 14 0.29
30 3 0.06
31 4 0.08
33 16 0.33
34 5 0.10
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (28 bp):
TCTTCAATTTCAGACCTCAAACAGGTCT
Found at i:5710 original size:99 final size:98
Alignment explanation
Indices: 5548--5830 Score: 433
Period size: 99 Copynumber: 2.9 Consensus size: 98
5538 GGTTTTCGCT
*
5548 TGCTATTTCCCAATATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
5613 GCCCTTTCCCGGACGGAAGGCACTTGTTTTTATC
66 GCCC-TTCCCGGACGGAAGGCACTTGTTTTTATC
* *
5647 TTCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAT
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
*
5712 GCCCTTCCCGAACGGAAGGCACTTGTTTTTATC
66 GCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
* *** * * *
5745 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACCAATTTTTATTTG-TTTCTTCCTAAAA
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTAT-TTCCCAAAA
5809 CGCCCCTTCCCGGACGGAAGGC
65 CG-CCCTTCCCGGACGGAAGGC
5831 GTCGCTTTTT
Statistics
Matches: 168, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
97 2 0.01
98 82 0.49
99 84 0.50
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (98 bp):
TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
GCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
Found at i:5816 original size:148 final size:148
Alignment explanation
Indices: 5548--5830 Score: 435
Period size: 148 Copynumber: 1.9 Consensus size: 148
5538 GGTTTTCGCT
* *
5548 TGCTATTTCCCAATATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
1 TGCTATTTCCCAAAATGCCCTTCCCGAACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
*** *
5613 GCCCTTTCCCGGACGGAAGGCACTTGTTTTTATCTTCTATTTCCCAAAATGCCCTTCCCGGACGG
66 GCCCTTTCCCGGACGGAAGGCACCAATTTTTATCTTCTATTTCCCAAAACGCCCTTCCCGGACGG
5678 AAGGCACTTGTTTTTATC
131 AAGGCACTTGTTTTTATC
*
5696 TGCTATTTCCCAAAATGCCCTTCCCGAACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAT
1 TGCTATTTCCCAAAATGCCCTTCCCGAACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
* * * *
5761 GCCC-TTCCCGGACGGAAGGTACCAATTTTTAT-TTGTTTCTTCCTAAAACGCCCCTTCCCGGAC
66 GCCCTTTCCCGGACGGAAGGCACCAATTTTTATCTTCTAT-TTCCCAAAACG-CCCTTCCCGGAC
5824 GGAAGGC
129 GGAAGGC
5831 GTCGCTTTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
146 4 0.03
147 33 0.27
148 85 0.70
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (148 bp):
TGCTATTTCCCAAAATGCCCTTCCCGAACGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAAC
GCCCTTTCCCGGACGGAAGGCACCAATTTTTATCTTCTATTTCCCAAAACGCCCTTCCCGGACGG
AAGGCACTTGTTTTTATC
Found at i:5840 original size:50 final size:49
Alignment explanation
Indices: 5548--5830 Score: 424
Period size: 49 Copynumber: 5.7 Consensus size: 49
5538 GGTTTTCGCT
*
5548 TGCTATTTCCCAATATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
*
5597 TGCTATTTCCCAAAACGCCCTTTCCCGGACGGAAGGCACTTGTTTTTATC
1 TGCTATTTCCCAAAATGCCC-TTCCCGGACGGAAGGCACTTGTTTTTATC
*
5647 TTCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
*
5696 TGCTATTTCCCAAAATGCCCTTCCCGAACGGAAGGCACTTGTTTTTATC
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
* *** *
5745 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACCAATTTTTATT
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
* * *
5794 TG-TTTCTTCCTAAAACGCCCCTTCCCGGACGGAAGGC
1 TGCTAT-TTCCCAAAATG-CCCTTCCCGGACGGAAGGC
5831 GTCGCTTTTT
Statistics
Matches: 215, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
48 2 0.01
49 148 0.69
50 65 0.30
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (49 bp):
TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTGTTTTTATC
Found at i:10134 original size:22 final size:21
Alignment explanation
Indices: 10094--10138 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
10084 AGTTTGCTAA
*
10094 ATAGGTTAGGTAAGTTTGGTGC
1 ATAGCTTAGGTAAGTTTGG-GC
10116 ATAGCTTAGGTAAAG-TTGGGC
1 ATAGCTTAGGT-AAGTTTGGGC
10137 AT
1 AT
10139 TACCTAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (21 bp):
ATAGCTTAGGTAAGTTTGGGC
Found at i:11684 original size:24 final size:24
Alignment explanation
Indices: 11644--11695 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11634 ATGATGTATT
* * *
11644 AAATTTAATATTCATAATA-ATTA
1 AAATTTAATAATAATAATATACTA
11667 AAATTATAATAATAATAATATACTA
1 AAATT-TAATAATAATAATATACTA
11692 AAAT
1 AAAT
11696 CATTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 12 0.50
25 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATTTAATAATAATAATATACTA
Found at i:19479 original size:6 final size:6
Alignment explanation
Indices: 19464--19496 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
19454 AGATTGGCCT
*
19464 AAGTGG AAGTGA AAGTGA AAGTGA AAGTGA AAG
1 AAGTGA AAGTGA AAGTGA AAGTGA AAGTGA AAG
19497 CAGAAAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.15
Consensus pattern (6 bp):
AAGTGA
Found at i:36423 original size:1 final size:1
Alignment explanation
Indices: 36417--36443 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
36407 CTTACTTTAG
36417 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
36444 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46200 original size:3 final size:3
Alignment explanation
Indices: 46194--46222 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46184 TTTTTCCTTA
46194 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
46223 ATTTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56589 original size:2 final size:2
Alignment explanation
Indices: 56582--56607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56572 TCGATGTAAA
56582 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
56608 GTAAGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61666 original size:17 final size:18
Alignment explanation
Indices: 61639--61673 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
61629 TAGGATATAA
61639 AAATCATTTGTTGATTTC
1 AAATCATTTGTTGATTTC
61657 AAAT-ATTTGTTGATTTC
1 AAATCATTTGTTGATTTC
61674 CAATTGGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
AAATCATTTGTTGATTTC
Found at i:62524 original size:11 final size:11
Alignment explanation
Indices: 62508--62546 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
62498 CACGATGGGT
62508 CACGTGCAATG
1 CACGTGCAATG
*
62519 CACGTGCAACG
1 CACGTGCAATG
* *
62530 TATGTGCAATG
1 CACGTGCAATG
62541 CACGTG
1 CACGTG
62547 GAAGTGAGTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (11 bp):
CACGTGCAATG
Found at i:63450 original size:2 final size:2
Alignment explanation
Indices: 63409--63433 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63399 TAACCTCACA
63409 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 A
63434 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65446 original size:91 final size:91
Alignment explanation
Indices: 65237--65530 Score: 355
Period size: 91 Copynumber: 3.3 Consensus size: 91
65227 TTTTGGCTCA
* * * * * * * *
65237 AACGAGACCAATTTCTGCCTTGGGTTGGAAATT-AA-TGC-GAGAGGATTTTACATAGACCTTTA
1 AACGAGTCCAGTTTCTGCCTTGGGTTCGAACTTCAAGGGCAGAAACGATTTTGCATAGACCTTTA
**
65299 ACATTGAAAGTTGCGGCA-AAAATAG
66 ATGTTGAAAGTTGCGGCATAAAATAG
* * * * *
65324 AACGAGTCCAGTTTCTGCCTTTGGTTTGAACTTCAAGGTCGGAAACGA-TTTGCCATAGACATTT
1 AACGAGTCCAGTTTCTGCCTTGGGTTCGAACTTCAAGGGCAGAAACGATTTTG-CATAGACCTTT
*
65388 AATGTTGAATGTTGCGGCATAAAATAG
65 AATGTTGAAAGTTGCGGCATAAAATAG
* *
65415 AACGAGTCCAGTTTCTGCCTTGGGTTCGAACTTCAAGGGCAGAAACGATTTTGCATGGACCTTTT
1 AACGAGTCCAGTTTCTGCCTTGGGTTCGAACTTCAAGGGCAGAAACGATTTTGCATAGACCTTTA
* * *
65480 ATGGTAAAAGTTGCGGCATAAAATGG
66 ATGTTGAAAGTTGCGGCATAAAATAG
65506 AACGAGTCCAGTTTCTGCCTTGGGT
1 AACGAGTCCAGTTTCTGCCTTGGGT
65531 GATTTTGCAT
Statistics
Matches: 176, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
87 28 0.16
88 2 0.01
89 4 0.02
90 31 0.18
91 107 0.61
92 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (91 bp):
AACGAGTCCAGTTTCTGCCTTGGGTTCGAACTTCAAGGGCAGAAACGATTTTGCATAGACCTTTA
ATGTTGAAAGTTGCGGCATAAAATAG
Found at i:65579 original size:70 final size:70
Alignment explanation
Indices: 65461--65600 Score: 208
Period size: 70 Copynumber: 2.0 Consensus size: 70
65451 GGGCAGAAAC
* * * *
65461 GATTTTGCATGGACCTTTTATGGTAAAAGTTGCGGCATAAAATGGAACGAGTCCAGTTTCTGCCT
1 GATTTTGCATAGACCTTTTATGGTAAAAGTTGCGGCATAAAATAGAACGAGTCCACTTTCTGACT
65526 TGGGT
66 TGGGT
* ** *
65531 GATTTTGCATAGACCTTTTATGTTAAAAGTTTTGGCATAAAATAGAACGAGTCCACTTTTTGACT
1 GATTTTGCATAGACCTTTTATGGTAAAAGTTGCGGCATAAAATAGAACGAGTCCACTTTCTGACT
65596 TGGGT
66 TGGGT
65601 TCGAACTTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (70 bp):
GATTTTGCATAGACCTTTTATGGTAAAAGTTGCGGCATAAAATAGAACGAGTCCACTTTCTGACT
TGGGT
Found at i:68140 original size:14 final size:14
Alignment explanation
Indices: 68115--68164 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
68105 TATTGAGATG
68115 CTCACT-TCACTCA
1 CTCACTCTCACTCA
68128 CTCACTCTCACTCA
1 CTCACTCTCACTCA
* *
68142 CTCACTCTCTCTCT
1 CTCACTCTCACTCA
*
68156 CTCTCTCTC
1 CTCACTCTC
68165 TCTCTTGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 6 0.18
14 27 0.82
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (14 bp):
CTCACTCTCACTCA
Found at i:68144 original size:18 final size:19
Alignment explanation
Indices: 68115--68154 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
68105 TATTGAGATG
68115 CTCACTTCACTCACTCACT
1 CTCACTTCACTCACTCACT
*
68134 CTCAC-TCACTCACTCTCT
1 CTCACTTCACTCACTCACT
68152 CTC
1 CTC
68155 TCTCTCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (19 bp):
CTCACTTCACTCACTCACT
Found at i:68958 original size:31 final size:31
Alignment explanation
Indices: 68920--68978 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
68910 TTTGAGAAAC
*
68920 TTTTGAAATGCCTATCATACCCTTATTTAAT
1 TTTTGAAATACCTATCATACCCTTATTTAAT
* *
68951 TTTTGAAATACCTATTATATCCTTATTT
1 TTTTGAAATACCTATCATACCCTTATTT
68979 TTCTAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTGAAATACCTATCATACCCTTATTTAAT
Found at i:69220 original size:44 final size:45
Alignment explanation
Indices: 69154--69241 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
69144 CCACAAGCAA
69154 AATCTCCATCTCCTTCGCCGAGTCCG-ACCTACCTCCATTATTTG
1 AATCTCCATCTCCTTCGCCGAGTCCGAACCTACCTCCATTATTTG
* * * * *
69198 AATCTCCATTTGCTTGGGCGAGTCCGAACCTACCTCTATTATTT
1 AATCTCCATCTCCTTCGCCGAGTCCGAACCTACCTCCATTATTT
69242 AGATTTCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 22 0.58
45 16 0.42
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.34
Consensus pattern (45 bp):
AATCTCCATCTCCTTCGCCGAGTCCGAACCTACCTCCATTATTTG
Found at i:70018 original size:2 final size:2
Alignment explanation
Indices: 70011--70035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70001 TCAAATTTGA
70011 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 A
70036 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71646 original size:2 final size:2
Alignment explanation
Indices: 71639--71672 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
71629 CGGATAAGCG
*
71639 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71673 TATTTAGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:72137 original size:232 final size:237
Alignment explanation
Indices: 71716--72160 Score: 661
Period size: 245 Copynumber: 1.9 Consensus size: 237
71706 TCAGCATAAA
* * *
71716 AAATAGCTTACAAATTGCATGATTGTAGGTGTACAATGGCTGGCTGATTTGCATTTTAATTTTCA
1 AAATAGCTTACAAATTGCATGATTGTAGATATACAATGGCTGGCTGACTTGCATTTTAATTTTCA
*
71781 TAATAATTTTGATTTACGTTTCTAATATTAATATATAGATAATTATAAATTTGCATTTTAGTTTT
66 TAATAATTTTGATTTACGTTTCTAATATT-ATATATAG---A--ATAAATTTGCATTTTAATTTT
* *
71846 CTTGATTATTTTGATTTGAAAATATTATACAATATAACACAATACTTTTTAATTGAAATTTTATA
125 CTTGATAATTTTGATTTGAAAATATTATACAATATAACACAATACTTTTTAACTGAAATTTTATA
71911 ATCATTAGAAATCTAACATCTACCACTAATAGTAACACTAACTATTTC
190 ATCATTAGAAATCTAACATCTACCACTAATAGTAACACTAACTATTTC
* *
71959 AAATAGCTTACAAATTGCTTGATTGTAGATATATGCATTGGCTGGCTGACTTGCATTTTAATTTT
1 AAATAGCTTACAAATTGCATGATTGTAGATATA--CAATGGCTGGCTGACTTGCATTTTAATTTT
*
72024 CATAATAATTTTGATTTACGTTTCTAATA-T-TA-ATAG-ATAACTTTGCATTTTAATTTTCTTG
64 CATAATAATTTTGATTTACGTTTCTAATATTATATATAGAATAAATTTGCATTTTAATTTTCTTG
*
72085 ATAATTTTGATTTG-ACA-A-TATACAATATAACACAATACTTTTTAACTGAAATTTTATAATCA
129 ATAATTTTGATTTGAAAATATTATACAATATAACACAATACTTTTTAACTGAAATTTTATAATCA
**
72147 TTAGACTTCTAACA
194 TTAGAAATCTAACA
72161 CTAATATAAC
Statistics
Matches: 188, Mismatches: 12, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
232 55 0.29
233 1 0.01
234 2 0.01
235 36 0.19
241 4 0.02
242 2 0.01
243 30 0.16
244 1 0.01
245 57 0.30
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (237 bp):
AAATAGCTTACAAATTGCATGATTGTAGATATACAATGGCTGGCTGACTTGCATTTTAATTTTCA
TAATAATTTTGATTTACGTTTCTAATATTATATATAGAATAAATTTGCATTTTAATTTTCTTGAT
AATTTTGATTTGAAAATATTATACAATATAACACAATACTTTTTAACTGAAATTTTATAATCATT
AGAAATCTAACATCTACCACTAATAGTAACACTAACTATTTC
Found at i:72960 original size:18 final size:18
Alignment explanation
Indices: 72937--72976 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
72927 TTTGTAGGAT
72937 TTCCCCATTAGGAAATCC
1 TTCCCCATTAGGAAATCC
72955 TTCCCCATTAGGAAATCC
1 TTCCCCATTAGGAAATCC
72973 TTCC
1 TTCC
72977 ATTTCTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.35, G:0.10, T:0.30
Consensus pattern (18 bp):
TTCCCCATTAGGAAATCC
Found at i:73240 original size:23 final size:23
Alignment explanation
Indices: 73200--73244 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
73190 GTTCGATAAA
*
73200 TGTTCATTTATTAGCTCGTTTAT
1 TGTTCATTTAATAGCTCGTTTAT
73223 TGTTCATTTAAATA-CTCGTTTA
1 TGTTCATTT-AATAGCTCGTTTA
73245 AAATTCGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (23 bp):
TGTTCATTTAATAGCTCGTTTAT
Found at i:78920 original size:16 final size:16
Alignment explanation
Indices: 78899--78941 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
78889 ATCTTTTTGC
78899 TCCTAAACTTGTAGGG
1 TCCTAAACTTGTAGGG
78915 TCCTAAACTTGTAGGG
1 TCCTAAACTTGTAGGG
78931 TCCTAAACTTG
1 TCCTAAACTTG
78942 CAATTTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (16 bp):
TCCTAAACTTGTAGGG
Found at i:91798 original size:42 final size:41
Alignment explanation
Indices: 91751--91830 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
91741 TGTTTGTCCA
* *
91751 ATGAATCTTAAAATCAATGAACACCGGGTAATCTTTAAATCT
1 ATGAATCTCAAAATCAATGAACA-CGGGTAATCCTTAAATCT
* *
91793 ATGAATCTCAAAATCAATGAATACTGGTAATCCTTAAA
1 ATGAATCTCAAAATCAATGAACACGGGTAATCCTTAAA
91831 AAACTAGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 13 0.38
42 21 0.62
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.30
Consensus pattern (41 bp):
ATGAATCTCAAAATCAATGAACACGGGTAATCCTTAAATCT
Found at i:92687 original size:6 final size:6
Alignment explanation
Indices: 92676--92702 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
92666 TCTTTAATTT
92676 ATTAGA ATTAGA ATTAGA ATTAGA ATT
1 ATTAGA ATTAGA ATTAGA ATTAGA ATT
92703 TTATTCATCC
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:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATTAGA
Found at i:97078 original size:3 final size:3
Alignment explanation
Indices: 97070--97116 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
97060 TCATTGCTCA
* *
97070 TCT TCT TCT TCT TCT TCT TCT TCCA TCT TCC TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT
97116 T
1 T
97117 TTCCTTGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:97104 original size:22 final size:22
Alignment explanation
Indices: 97073--97114 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
97063 TTGCTCATCT
*
97073 TCTTCTTCTTCTTCTTCTTCCA
1 TCTTCCTCTTCTTCTTCTTCCA
97095 TCTTCCTCTTCTTCTTCTTC
1 TCTTCCTCTTCTTCTTCTTC
97115 TTTTCCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (22 bp):
TCTTCCTCTTCTTCTTCTTCCA
Found at i:97104 original size:25 final size:25
Alignment explanation
Indices: 97068--97116 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
97058 ACTCATTGCT
*
97068 CATCTTCTTCTTCTTCTTCTTCTTC
1 CATCTTCCTCTTCTTCTTCTTCTTC
97093 CATCTTCCTCTTCTTCTTCTTCTT
1 CATCTTCCTCTTCTTCTTCTTCTT
97117 TTCCTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.59
Consensus pattern (25 bp):
CATCTTCCTCTTCTTCTTCTTCTTC
Found at i:99222 original size:29 final size:29
Alignment explanation
Indices: 99190--99249 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
99180 CTAATGAGAT
**
99190 ATAATTCAAATGTTAGGGACTAAAATGAA
1 ATAATTCAAACATTAGGGACTAAAATGAA
99219 ATAATTCAAACATTAGGGACTAAAATGAA
1 ATAATTCAAACATTAGGGACTAAAATGAA
99248 AT
1 AT
99250 TATAATAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (29 bp):
ATAATTCAAACATTAGGGACTAAAATGAA
Found at i:103085 original size:44 final size:44
Alignment explanation
Indices: 103029--103117 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
103019 AAAACTTGCG
103029 ATCATTAGCAATGTAACTATTTTCTAAAGCAGGTTCCAACTTCA
1 ATCATTAGCAATGTAACTATTTTCTAAAGCAGGTTCCAACTTCA
103073 ATCATTAGCAATGTAACTATTTTCTAAAGCAGGTTCCAACTTCA
1 ATCATTAGCAATGTAACTATTTTCTAAAGCAGGTTCCAACTTCA
103117 A
1 A
103118 ATATAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (44 bp):
ATCATTAGCAATGTAACTATTTTCTAAAGCAGGTTCCAACTTCA
Done.