Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016036.1 Corchorus capsularis cultivar CVL-1 contig16057, 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: 41962
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2854 original size:101 final size:100
Alignment explanation
Indices: 2705--2936 Score: 358
Period size: 100 Copynumber: 2.3 Consensus size: 100
2695 TAAGCTAAAG
* *
2705 ATAAAGATTTAACCTTTGAATAAAAGACT-AATTTTTAAGTAATTGGTAAATAAAAATGTCATCT
1 ATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGGCATCT
* *
2769 TTGGGTTAAAGATTGAATTTTTAGAGTAATTAGTAA
66 TTGGGTGAAAGATTGAA-TTTTAGAGTAACTAGTAA
*
2805 ATAAAGATTTAACTTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGGCATCT
1 ATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGGCATCT
* *
2870 TTGGGTGAAAGGTTGAATTTTAGAGTAGCTAGTAA
66 TTGGGTGAAAGATTGAATTTTAGAGTAACTAGTAA
* * *
2905 ATAAGGATTTGACCTTTGAATAAAAGTTTGAA
1 ATAAAGATTTAACCTTTGAATAAAAGATTGAA
2937 GATTTAAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 71 0.59
101 49 0.41
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.37
Consensus pattern (100 bp):
ATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGGCATCT
TTGGGTGAAAGATTGAATTTTAGAGTAACTAGTAA
Found at i:2886 original size:50 final size:50
Alignment explanation
Indices: 2725--2890 Score: 201
Period size: 50 Copynumber: 3.3 Consensus size: 50
2715 AACCTTTGAA
*
2725 TAAAAGACT-AATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGG
1 TAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGG
* * * * * **
2774 TTAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGAT-TTAACTTTTGAA
1 TAAAAGATTGAATTTTTA-AGTAATTGGTAAATAAAAATGTCATC-TTTGGG
*
2825 TAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGGCATCTTTGGG
1 TAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGG
* *
2875 TGAAAGGTTGAATTTT
1 TAAAAGATTGAATTTT
2891 AGAGTAGCTA
Statistics
Matches: 95, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
49 7 0.07
50 47 0.49
51 41 0.43
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (50 bp):
TAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGG
Found at i:2936 original size:50 final size:50
Alignment explanation
Indices: 2708--2936 Score: 178
Period size: 50 Copynumber: 4.6 Consensus size: 50
2698 GCTAAAGATA
* * *
2708 AAGATTTAACCTTTGAATAAAAGACT-AATTTTTA-AGTAATTGGTAAAT
1 AAGATTTGACCTTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
* * * * ** *
2756 AAAAATGTCATCTTTGGGTTAAAGATTGAATTTTTAGAGTAATTAGTAAAT
1 -AAGATTTGACCTTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
* * *
2807 AAAGATTTAACTTTTGAATAAAAGATTGAATTTTTA-AGTAATTGGTAAAT
1 -AAGATTTGACCTTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
* * * * ** * * **
2857 AAAAATGGCATCTTTGGGTGAAAGGTTGAA-TTTTAGAGTAGCTAGTAAAT
1 AAGATTTG-ACCTTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
*
2907 AAGGATTTGACCTTTGAATAAAAGTTTGAA
1 AA-GATTTGACCTTTGAATAAAAGATTGAA
2937 GATTTAAAAA
Statistics
Matches: 136, Mismatches: 39, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
49 27 0.20
50 65 0.48
51 44 0.32
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.37
Consensus pattern (50 bp):
AAGATTTGACCTTTGAATAAAAGATTGAATTTTTAGAGTAATTAGTAAAT
Found at i:4009 original size:55 final size:55
Alignment explanation
Indices: 3693--3987 Score: 520
Period size: 55 Copynumber: 5.4 Consensus size: 55
3683 CAATCCAAAC
* * *
3693 AGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTCAAAGTAAC
1 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
3747 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
1 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
*
3802 AATAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
1 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
*
3857 AGTAATCAGTAAATAAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
1 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
* *
3912 AGTAATCAGTAAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
1 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
3967 AGTAATCAGTAAATCAGTAAT
1 AGTAATCAGTAAATCAGTAAT
3988 CAGGAAAAAA
Statistics
Matches: 230, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
54 26 0.11
55 204 0.89
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (55 bp):
AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
Found at i:4022 original size:16 final size:15
Alignment explanation
Indices: 4001--4032 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3991 GAAAAAAGAT
4001 AGTAATCAGTAAATTG
1 AGTAATCAGT-AATTG
4017 AGTAATCAGTAATTG
1 AGTAATCAGTAATTG
4032 A
1 A
4033 AGAGCCTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (15 bp):
AGTAATCAGTAATTG
Found at i:4331 original size:22 final size:21
Alignment explanation
Indices: 4306--4612 Score: 194
Period size: 21 Copynumber: 14.0 Consensus size: 21
4296 ATGGTAATTA
*
4306 GTAATCAGTAAAAAGCAAGAAG
1 GTAATCAGTAAAAAGTAA-AAG
* *
4328 GTAATCA--ACAAGAGTAAAATA
1 GTAATCAGTA-AAAAGTAAAA-G
* * *
4349 ATAAGCAGTAAAAAGTAAAATA
1 GTAATCAGTAAAAAGTAAAA-G
* *
4371 GTAATCAGT-AAGAGTAAAAAA
1 GTAATCAGTAAAAAGT-AAAAG
* *
4392 GTAATAAGTAAGAAGTAAAAG
1 GTAATCAGTAAAAAGTAAAAG
* *
4413 GAAATCAGT-AAGAGTAAAAAG
1 GTAATCAGTAAAAAGT-AAAAG
* *
4434 GTGATCAGTAAAGAGTAAAAAG
1 GTAATCAGTAAAAAGT-AAAAG
* *
4456 CTAATCAGCAAGAAA-TAAAAAG
1 GTAATCAGTAA-AAAGT-AAAAG
*
4478 GTAATCAGTAAAAAGCAAAAG
1 GTAATCAGTAAAAAGTAAAAG
*
4499 GCAATCAGTAAAAAGTAAAAG
1 GTAATCAGTAAAAAGTAAAAG
* * *
4520 AGTGATCAGTAAAAAAAGAGCAGAAAATA
1 -GTAATCAGT---AAAA-AG--TAAAA-G
4549 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAGTAAAA-AGTAAAA-G
4572 GTAATCAGT-AAAAGTAAGAAG
1 GTAATCAGTAAAAAGTAA-AAG
*
4593 GTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAAAGTAAAA
4613 TCCGTAAAGA
Statistics
Matches: 229, Mismatches: 36, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
20 7 0.03
21 92 0.40
22 88 0.38
23 17 0.07
25 11 0.05
26 2 0.01
28 12 0.05
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (21 bp):
GTAATCAGTAAAAAGTAAAAG
Found at i:4388 original size:21 final size:21
Alignment explanation
Indices: 4328--4715 Score: 186
Period size: 21 Copynumber: 17.9 Consensus size: 21
4318 AAGCAAGAAG
**
4328 GTAATCAACAAGAGTAAAATA
1 GTAATCAGTAAGAGTAAAATA
* * *
4349 ATAAGCAGTAAAAAGTAAAATA
1 GTAATCAGT-AAGAGTAAAATA
*
4371 GTAATCAGTAAGAGTAAAAAA
1 GTAATCAGTAAGAGTAAAATA
* *
4392 GTAATAAGTAAGAAGTAAAA-G
1 GTAATCAGTAAG-AGTAAAATA
*
4413 GAAATCAGTAAGAGTAAAA-A
1 GTAATCAGTAAGAGTAAAATA
*
4433 GGTGATCAGTAAAGAGTAAAA-A
1 -GTAATCAGT-AAGAGTAAAATA
* *
4455 GCTAATCAGCAAGAAATAAAA-A
1 G-TAATCAGTAAG-AGTAAAATA
* * *
4477 GGTAATCAGTAAAAAGCAAAA-G
1 -GTAATCAGT-AAGAGTAAAATA
* * *
4499 GCAATCAGTAAAAAGTAAAAGA
1 GTAATCAGT-AAGAGTAAAATA
* *
4521 GTGATCAGTAAAAAAAGAGCAGAAAATA
1 GTAATCAGT-----AAGAG--TAAAATA
*
4549 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAGT--AAGAGTAAAATA
* *
4572 GTAATCAGTAAAAGTAAGAA-G
1 GTAATCAGTAAGAGTAA-AATA
*
4593 GTAATCAGTAAAGAGTAAAATCC
1 GTAATCAGT-AAGAGTAAAAT-A
* *
4616 GTAA--AG-AATCAGTAAAAGA
1 GTAATCAGTAA-GAGTAAAATA
*
4635 -TAATCAGTAAGAGTAAAACA
1 GTAATCAGTAAGAGTAAAATA
* * * *
4655 GTAACCAATAAGAGCAAAGT-
1 GTAATCAGTAAGAGTAAAATA
* *
4675 GATAATTAGTAAGAGTCAAATA
1 G-TAATCAGTAAGAGTAAAATA
4697 GTAATCAGTAAAGAGTAAA
1 GTAATCAGT-AAGAGTAAA
4716 GGGTGATCAG
Statistics
Matches: 284, Mismatches: 56, Indels: 53
0.72 0.14 0.13
Matches are distributed among these distances:
18 3 0.01
19 2 0.01
20 25 0.09
21 122 0.43
22 86 0.30
23 21 0.07
25 7 0.02
26 5 0.02
28 13 0.05
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (21 bp):
GTAATCAGTAAGAGTAAAATA
Found at i:4408 original size:28 final size:29
Alignment explanation
Indices: 4350--4409 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
4340 AGTAAAATAA
**
4350 TAAGCAGTAAAAAGTAAAATAGTAATCAG
1 TAAGCAGTAAAAAGTAAAATAGTAAGAAG
*
4379 TAAG-AGTAAAAAAGTAATA-AGTAAGAAG
1 TAAGCAGT-AAAAAGTAAAATAGTAAGAAG
4407 TAA
1 TAA
4410 AAGGAAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.20
Consensus pattern (29 bp):
TAAGCAGTAAAAAGTAAAATAGTAAGAAG
Found at i:4498 original size:43 final size:42
Alignment explanation
Indices: 4306--4612 Score: 185
Period size: 43 Copynumber: 7.0 Consensus size: 42
4296 ATGGTAATTA
* * **
4306 GTAATCAGTAAAAAGCAAGAAGGTAATCAACAAGAGTAAAATA-
1 GTAATCAGTAAAAAG-AAAAAGCTAATCAGTAAGAGTAAAA-AG
* * *
4349 ATAAGCAGTAAAAAGTAAAATAG-TAATCAGTAAGAGTAAAAAA
1 GTAATCAGTAAAAAG-AAAA-AGCTAATCAGTAAGAGTAAAAAG
* * * **
4392 GTAATAAGTAAGAAGTAAAAGGAAATCAGTAAGAGTAAAAAG
1 GTAATCAGTAAAAAGAAAAAGCTAATCAGTAAGAGTAAAAAG
* * * *
4434 GTGATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAATAAAAAG
1 GTAATCAGTAAAAAG-AAAAAGCTAATCAGTAAG-AGTAAAAAG
* *
4478 GTAATCAGTAAAAAGCAAAAGGC-AATCAGTAAAAAGT-AAAAG
1 GTAATCAGTAAAAAG-AAAAAGCTAATCAGT-AAGAGTAAAAAG
* *
4520 AGTGATCAGTAAAAAAAGAGCAGAAAATAG-TAATCAGTAAAAGAGTAAAATG
1 -GTAATCAGT----AAA-A--AGAAAA-AGCTAATCAGT--AAGAGTAAAAAG
* *
4572 GTAATCAGT-AAAAGTAAGAAGGTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAAAG-AAAAAGCTAATCAGT-AAGAGTAAAA
4613 TCCGTAAAGA
Statistics
Matches: 209, Mismatches: 35, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.01
42 38 0.18
43 88 0.42
44 42 0.20
45 1 0.00
46 2 0.01
47 3 0.01
48 1 0.00
49 4 0.02
50 10 0.05
51 14 0.07
52 4 0.02
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (42 bp):
GTAATCAGTAAAAAGAAAAAGCTAATCAGTAAGAGTAAAAAG
Found at i:6133 original size:11 final size:11
Alignment explanation
Indices: 6114--6150 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
6104 GGTAATAAAT
*
6114 AAAAGAGAGTA
1 AAAAAAGAGTA
6125 AAAAAAGAGTA
1 AAAAAAGAGTA
*
6136 AGAAAAGAGTA
1 AAAAAAGAGTA
6147 AAAA
1 AAAA
6151 TGATAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (11 bp):
AAAAAAGAGTA
Found at i:7962 original size:31 final size:31
Alignment explanation
Indices: 7813--7949 Score: 193
Period size: 31 Copynumber: 4.4 Consensus size: 31
7803 ACGGTGTCCG
7813 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
7844 ATGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
7875 ACATGTCACGCCATGTGTACCAAAATGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
7906 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
7937 ACGTGGCATGCCA
1 ACGTGGCACGCCA
7950 GATGTTTCAA
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 93 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:7992 original size:93 final size:93
Alignment explanation
Indices: 7819--7992 Score: 215
Period size: 93 Copynumber: 1.9 Consensus size: 93
7809 TCCGACGTGG
* * * *
7819 CACGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGACACATGTCAC
1 CACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACAAAAAAATGACACATGGCAC
** *
7884 GCCATGTGTACCAAAATGTGACACATGT
66 GCCACATGCACCAAAATGTGACACATGT
* * * * *
7912 CACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCAGATGTTTCAAAAAAATGGCACGTGGCA
1 CACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATG-TACAAAAAAATGACACATGGCA
*
7977 TGCCACATGCA-CAAAA
65 CGCCACATGCACCAAAA
7993 GGATACATGC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 44 0.66
94 23 0.34
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.17
Consensus pattern (93 bp):
CACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACAAAAAAATGACACATGGCAC
GCCACATGCACCAAAATGTGACACATGT
Found at i:10818 original size:18 final size:20
Alignment explanation
Indices: 10795--10834 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10785 AGAGTTACAT
*
10795 TTATAAG-CAAA-AAATTAA
1 TTATAAGTCAAATAAAATAA
10813 TTATAAGTCAAATAAAATAA
1 TTATAAGTCAAATAAAATAA
10833 TT
1 TT
10835 GCACGTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
TTATAAGTCAAATAAAATAA
Found at i:29163 original size:27 final size:27
Alignment explanation
Indices: 29133--29187 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
29123 TTACTCCATC
*
29133 TGTTTCTTTTTAATTGTCCCTTTCCCT
1 TGTTCCTTTTTAATTGTCCCTTTCCCT
*
29160 TGTTCCTTTTTAATTGTCTCTTTCCCT
1 TGTTCCTTTTTAATTGTCCCTTTCCCT
29187 T
1 T
29188 ATTTTCCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.60
Consensus pattern (27 bp):
TGTTCCTTTTTAATTGTCCCTTTCCCT
Found at i:30088 original size:41 final size:41
Alignment explanation
Indices: 30029--30106 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
30019 GTCCCTCCTA
*
30029 ATAATTAAGGAAACAAATTAAATTCACGTTTAGCCCCCCTG
1 ATAATTAAGGAAACAAATTAAATCCACGTTTAGCCCCCCTG
* * *
30070 ATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
1 ATAATTAAGGAAACAAATTAAATCCACGTTTAGCCCC
30107 TAGTTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (41 bp):
ATAATTAAGGAAACAAATTAAATCCACGTTTAGCCCCCCTG
Found at i:34656 original size:108 final size:107
Alignment explanation
Indices: 34477--34794 Score: 366
Period size: 114 Copynumber: 2.9 Consensus size: 107
34467 TTGAGTTTCG
* * * * *
34477 ATAGCTTTCATCACTCAGAGCTCATGGAACTTGGGACATGACTATTGCTGGAAACGTGGCGTTGA
1 ATAGCTTTCGTCACTCAGAGCTCATAGAAATTAGGACATGACTATAGCTGGAAACGTGGCG-TGA
34542 TATTTCTTGTTAGTAAATCTTGATTATTAATTGTTGAGCGTGC
65 TATTTCTTGTTAGTAAATCTTGATTATTAATTGTTGAGCGTGC
* * * * *
34585 ATAGCTTTTGTCAGTCAGAGCTCATAGAAATCAGGACATGACTTATAGCTGGAAACATGGCGTCA
1 ATAGCTTTCGTCACTCAGAGCTCATAGAAATTAGGACATGAC-TATAGCTGGAAACGTGGCGTGA
* * * * *
34650 TGTTTCTTGTTAGTAAATCTTGGCTGTGGCTGTTTATTGTTGAGTGTGC
65 TATTTCTTGTTAGTAAATCTT-G--AT---TATTAATTGTTGAGCGTGC
* * * * *
34699 ATTGCTTTCGTCACCCAAAGCTCATATAAATTAGGACATGACCTATGGCTGGAAACGTGGCGGTG
1 ATAGCTTTCGTCACTCAGAGCTCATAGAAATTAGGACATGA-CTATAGCTGGAAACGTGGC-GTG
34764 ATATTTCTTGTTAGTAAATCTTGATTATTAA
64 ATATTTCTTGTTAGTAAATCTTGATTATTAA
34795 ATTTTGGCCG
Statistics
Matches: 172, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
108 57 0.33
109 22 0.13
111 1 0.01
112 1 0.01
114 67 0.39
115 24 0.14
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (107 bp):
ATAGCTTTCGTCACTCAGAGCTCATAGAAATTAGGACATGACTATAGCTGGAAACGTGGCGTGAT
ATTTCTTGTTAGTAAATCTTGATTATTAATTGTTGAGCGTGC
Found at i:34828 original size:20 final size:21
Alignment explanation
Indices: 34798--34836 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34788 TTATTAAATT
34798 TTGGCCGTGGCATCATTTTTC
1 TTGGCCGTGGCATCATTTTTC
*
34819 TTGG-CGTGGCGTCATTTT
1 TTGGCCGTGGCATCATTTT
34837 AAAAAACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.08, C:0.21, G:0.28, T:0.44
Consensus pattern (21 bp):
TTGGCCGTGGCATCATTTTTC
Done.