Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012671.1 Corchorus capsularis cultivar CVL-1 contig12692, 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: 16146
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:2623 original size:16 final size:15
Alignment explanation
Indices: 2602--2631 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2592 CAAAAGGTTT
2602 TCAAAAATCTAAAAAA
1 TCAAAAATC-AAAAAA
2618 TCAAAAATCAAAAA
1 TCAAAAATCAAAAA
2632 TGAAAAAAAG
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:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
TCAAAAATCAAAAAA
Found at i:5624 original size:15 final size:14
Alignment explanation
Indices: 5604--5633 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5594 AACTTGAAAT
5604 ATGGTTTTCAACAAG
1 ATGGTTTTCAA-AAG
5619 ATGGTTTTCAAAAG
1 ATGGTTTTCAAAAG
5633 A
1 A
5634 GTCACGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (14 bp):
ATGGTTTTCAAAAG
Found at i:5659 original size:91 final size:88
Alignment explanation
Indices: 5523--5687 Score: 260
Period size: 91 Copynumber: 1.8 Consensus size: 88
5513 TGGAGGAGTC
*
5523 CAACAAAATGGTTTTCAAAAGTCATGATTTCCAAAAGATTTTGATAAAATGGTTTTCCGAAAATG
1 CAACAAAATGGTTTTCAAAAGTCACGATTTCCAAAAGATTTTGATAAAATGGTTTTCC-AAAATG
5588 ATTTCAAACTTGAAATATGGTTTT
65 ATTTCAAACTTGAAATATGGTTTT
* *
5612 CAACAAGATGGTTTTCAAAAGAGTCACGATTAT-CAAAAGATTTTGATAAAATGGTTTTTCAAAA
1 CAACAAAATGGTTTTC-AAA-AGTCACGATT-TCCAAAAGATTTTGATAAAATGGTTTTCCAAAA
5676 TGATTTCAAACT
63 TGATTTCAAACT
5688 CGTTTTCCCG
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
89 15 0.21
90 19 0.27
91 35 0.50
92 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (88 bp):
CAACAAAATGGTTTTCAAAAGTCACGATTTCCAAAAGATTTTGATAAAATGGTTTTCCAAAATGA
TTTCAAACTTGAAATATGGTTTT
Found at i:6041 original size:19 final size:18
Alignment explanation
Indices: 6019--6064 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
6009 AAAGGATGAA
**
6019 AAAGTGAAAATTGAAAGTG
1 AAAGTGAAAATT-AAAAAG
*
6038 AAAGGGAAAATTAAAAAG
1 AAAGTGAAAATTAAAAAG
6056 AAAGTGAAA
1 AAAGTGAAA
6065 GGAAAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (18 bp):
AAAGTGAAAATTAAAAAG
Found at i:6390 original size:6 final size:6
Alignment explanation
Indices: 6375--6422 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
6365 CAAAAAAATG
*
6375 AAAGAA AAA-AA AAA-AA GAAGAA AGAAG-A AAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
6421 AA
1 AA
6423 GAGAGAAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 12 0.32
6 22 0.59
7 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:6429 original size:21 final size:20
Alignment explanation
Indices: 6375--6420 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
6365 CAAAAAAATG
*
6375 AAAGAA-AAAAAAAAAAGAA
1 AAAGAAGAAAAGAAAAAGAA
6394 GAAAGAAGAAAAGAAAAAGAA
1 -AAAGAAGAAAAGAAAAAGAA
6415 AAAGAA
1 AAAGAA
6421 AAGAGAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAAAGAAAAAGAA
Found at i:6435 original size:33 final size:34
Alignment explanation
Indices: 6375--6440 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
6365 CAAAAAAATG
6375 AAAGAAAAAAAAAAAAGAAGAAAGAAGAAAAGAA
1 AAAGAAAAAAAAAAAAGAAGAAAGAAGAAAAGAA
* * *
6409 AAAGAAAAAGAAAAGAG-AGAAGGAAGAAAAGA
1 AAAGAAAAAAAAAAAAGAAGAAAGAAGAAAAGA
6441 GGCTCTGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (34 bp):
AAAGAAAAAAAAAAAAGAAGAAAGAAGAAAAGAA
Found at i:6438 original size:27 final size:29
Alignment explanation
Indices: 6375--6440 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 29
6365 CAAAAAAATG
6375 AAAGAAAA-AAAAAAAAGAAGAAAGAAGA
1 AAAGAAAAGAAAAAAAAGAAGAAAGAAGA
*
6403 AAAGAAAAAGAAAAAGAAAAGAGAGAAGGAAGA
1 AAAG-AAAAG-AAAA-AAAAGA-AGAAAGAAGA
6436 AAAGA
1 AAAGA
6441 GGCTCTGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.12
29 4 0.12
31 4 0.12
32 7 0.22
33 13 0.41
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (29 bp):
AAAGAAAAGAAAAAAAAGAAGAAAGAAGA
Found at i:7266 original size:8 final size:8
Alignment explanation
Indices: 7253--7286 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
7243 AGGGTGGTCT
7253 TTCTTCAA
1 TTCTTCAA
7261 TTCTTCAA
1 TTCTTCAA
*
7269 TTATTCAA
1 TTCTTCAA
*
7277 TACTTCAA
1 TTCTTCAA
7285 TT
1 TT
7287 TACTTCAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (8 bp):
TTCTTCAA
Found at i:7312 original size:58 final size:58
Alignment explanation
Indices: 7243--7621 Score: 542
Period size: 58 Copynumber: 6.5 Consensus size: 58
7233 TATTTTTCAA
* *
7243 AGGGTGGTCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAACATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
*
7301 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATCTACTTCAAAAGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTC-AAAGATCC
*
7360 GGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAAAGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTC--AAAGATCC
* *
7420 GGGGTGATCTTTCTTCAATTCCTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
* * * * *
7478 AGGGTGATCTTTCTTCAATTCCTCAATCATTCAATCCTTCAATTTATTTCAATGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
* ** ** * *
7536 AGGGTGGTCTTTCTTCAATTCTTCAATCGTTCAATGTTTCAATTTACTTCGATGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
* *
7594 AAGGTGGTCTTTCTTCAAATTCTTCAAT
1 AGGGTGATCTTTCTTC-AATTCTTCAAT
7622 GCTTCAATTT
Statistics
Matches: 299, Mismatches: 19, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
58 175 0.59
59 66 0.22
60 58 0.19
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (58 bp):
AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
Found at i:7383 original size:8 final size:8
Alignment explanation
Indices: 7370--7403 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
7360 GGGGTGATCT
7370 TTCTTCAA
1 TTCTTCAA
7378 TTCTTCAA
1 TTCTTCAA
*
7386 TTATTCAA
1 TTCTTCAA
*
7394 TACTTCAA
1 TTCTTCAA
7402 TT
1 TT
7404 TACTTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (8 bp):
TTCTTCAA
Found at i:7618 original size:9 final size:8
Alignment explanation
Indices: 7604--7740 Score: 59
Period size: 8 Copynumber: 18.0 Consensus size: 8
7594 AAGGTGGTCT
7604 TTCTTCAAA
1 TTCTTC-AA
7613 TTCTTCAA
1 TTCTTCAA
*
7621 TGCTTCAA
1 TTCTTCAA
7629 -T-TTCAA
1 TTCTTCAA
7635 TTCTTCAAA
1 TTCTTC-AA
7644 TTCAAATTCAA
1 TTC---TTCAA
7655 TTCTTCAA
1 TTCTTCAA
7663 TTC--CAA
1 TTCTTCAA
7669 --CTTCAA
1 TTCTTCAA
7675 TGT-TTCAA
1 T-TCTTCAA
*
7683 -T-TTCAT
1 TTCTTCAA
7689 TTCTTCAA
1 TTCTTCAA
*
7697 --ATTCAA
1 TTCTTCAA
*
7703 TCCTTCAA
1 TTCTTCAA
7711 TGT-TTCAA
1 T-TCTTCAA
7719 TT-TT-AA
1 TTCTTCAA
*
7725 TTCCTCAA
1 TTCTTCAA
*
7733 TGCTTCAA
1 TTCTTCAA
7741 ATTCAATTTC
Statistics
Matches: 100, Mismatches: 10, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
4 1 0.01
6 25 0.25
7 6 0.06
8 49 0.49
9 11 0.11
11 5 0.05
12 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:7628 original size:8 final size:7
Alignment explanation
Indices: 7614--7802 Score: 51
Period size: 8 Copynumber: 26.7 Consensus size: 7
7604 TTCTTCAAAT
7614 TCTTCAA
1 TCTTCAA
7621 TGCTTCAA
1 T-CTTCAA
7629 T-TTCAA
1 TCTTCAA
7635 TTCTTCAA
1 -TCTTCAA
*
7643 -ATTCAA
1 TCTTCAA
*
7649 -ATTCAA
1 TCTTCAA
7655 TTCTTCAA
1 -TCTTCAA
*
7663 T-TCCAA
1 TCTTCAA
7669 -CTTCAA
1 TCTTCAA
*
7675 TGTTTCAA
1 T-CTTCAA
*
7683 T-TTCATT
1 TCTTCA-A
7690 TCTTCAA
1 TCTTCAA
*
7697 -ATTCAA
1 TCTTCAA
7703 TCCTTCAA
1 T-CTTCAA
*
7711 TGTTTCAA
1 T-CTTCAA
*
7719 T-TTTAA
1 TCTTCAA
*
7725 TTCCTCAA
1 -TCTTCAA
7733 TGCTTCAA
1 T-CTTCAA
*
7741 -ATTCAA
1 TCTTCAA
7747 T-TTCAA
1 TCTTCAA
7753 TCTATCAA
1 TCT-TCAA
*
7761 TGTTTCAA
1 T-CTTCAA
7769 T-TTCAA
1 TCTTCAA
*
7775 TATTTCAA
1 T-CTTCAA
*
7783 TGTTTCAA
1 T-CTTCAA
7791 T-TTCAA
1 TCTTCAA
7797 TTCTTC
1 -TCTTC
7803 CAGTTCTTCC
Statistics
Matches: 141, Mismatches: 18, Indels: 45
0.69 0.09 0.22
Matches are distributed among these distances:
6 59 0.42
7 8 0.06
8 73 0.52
9 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (7 bp):
TCTTCAA
Found at i:7635 original size:14 final size:13
Alignment explanation
Indices: 7616--7917 Score: 71
Period size: 14 Copynumber: 21.0 Consensus size: 13
7606 CTTCAAATTC
7616 TTCAATGCTTCAAT
1 TTCAAT-CTTCAAT
*
7630 TTCAATTCTTCAAA
1 TTCAA-TCTTCAAT
*
7644 TTCAA-ATTCAATT
1 TTCAATCTTCAA-T
* *
7657 CTTCAAT-TCCAAC
1 -TTCAATCTTCAAT
*
7670 TTCAATGTTTCAAT
1 TTCAAT-CTTCAAT
* *
7684 TTCATTTCTTCAAA
1 TTCA-ATCTTCAAT
7698 TTCAATCCTTCAATGT
1 TTCAAT-CTTCAA--T
*
7714 TTCAAT-TTTAAT
1 TTCAATCTTCAAT
*
7726 TCCTCAATGCTTCAAA
1 T--TCAAT-CTTCAAT
7742 TTCAAT-TTCAAT
1 TTCAATCTTCAAT
*
7754 CTATCAATGTTTCAAT
1 -T-TCAAT-CTTCAAT
*
7770 TTCAATATTTCAATGT
1 TTCAAT-CTTCAA--T
7786 TTCAAT-TTCAATT
1 TTCAATCTTCAA-T
*
7799 CTTCCAGTTCTTCCAA-
1 -TT-CA-ATCTT-CAAT
*
7815 TTCGATCCTTCAAAGT
1 TTCAAT-CTTC-AA-T
7831 TTCAAT-TTCAACAT
1 TTCAATCTTC-A-AT
*
7845 TTCATTGCTTCAAGT
1 TTCAAT-CTTCAA-T
7860 TTCAATTCTTCAAAT
1 TTCAA-TCTTC-AAT
* *
7875 TTGACTCTTCAACAT
1 TTCAATCTTC-A-AT
7890 TTCAAT-TTCAATT
1 TTCAATCTTCAA-T
7903 ATTCAATGCTTCAAT
1 -TTCAAT-CTTCAAT
7918 GATCCAGGGT
Statistics
Matches: 220, Mismatches: 28, Indels: 79
0.67 0.09 0.24
Matches are distributed among these distances:
12 19 0.09
13 7 0.03
14 119 0.54
15 29 0.13
16 41 0.19
17 2 0.01
18 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (13 bp):
TTCAATCTTCAAT
Found at i:7653 original size:20 final size:19
Alignment explanation
Indices: 7624--7684 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
7614 TCTTCAATGC
*
7624 TTCAATTTCAATTCTTCAAA
1 TTCAAATTCAATTCTTC-AA
7644 TTCAAATTCAATTCTTCAA
1 TTCAAATTCAATTCTTCAA
*
7663 TTCCAACTTCAATGT-TTCAA
1 TT-CAAATTCAAT-TCTTCAA
7683 TT
1 TT
7685 TCATTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.11
20 32 0.86
21 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (19 bp):
TTCAAATTCAATTCTTCAA
Found at i:7748 original size:22 final size:23
Alignment explanation
Indices: 7691--7748 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
7681 AATTTCATTT
7691 CTTCAAATTCAA-TCCTTCAATG
1 CTTCAAATTCAATTCCTTCAATG
* * *
7713 TTTCAATTTTAATTCC-TCAATG
1 CTTCAAATTCAATTCCTTCAATG
7735 CTTCAAATTCAATT
1 CTTCAAATTCAATT
7749 TCAATCTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (23 bp):
CTTCAAATTCAATTCCTTCAATG
Found at i:7752 original size:50 final size:50
Alignment explanation
Indices: 7692--7798 Score: 137
Period size: 50 Copynumber: 2.1 Consensus size: 50
7682 ATTTCATTTC
* *
7692 TTCAAATTCAATCCT-TCAATGTTTCAATTTTAAT-TCCTCAATGCTTCAAA
1 TTCAATTTCAAT-CTATCAATGTTTCAATTTCAATAT-CTCAATGCTTCAAA
* * *
7742 TTCAATTTCAATCTATCAATGTTTCAATTTCAATATTTCAATGTTTCAAT
1 TTCAATTTCAATCTATCAATGTTTCAATTTCAATATCTCAATGCTTCAAA
7792 TTCAATT
1 TTCAATT
7799 CTTCCAGTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
49 2 0.04
50 47 0.94
51 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.46
Consensus pattern (50 bp):
TTCAATTTCAATCTATCAATGTTTCAATTTCAATATCTCAATGCTTCAAA
Found at i:7767 original size:22 final size:22
Alignment explanation
Indices: 7742--7797 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
7732 ATGCTTCAAA
*
7742 TTCAATTTCAATCTATCAATGT
1 TTCAATTTCAATATATCAATGT
*
7764 TTCAATTTCAATATTTCAATGT
1 TTCAATTTCAATATATCAATGT
7786 TTCAATTTCAAT
1 TTCAATTTCAAT
7798 TCTTCCAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (22 bp):
TTCAATTTCAATATATCAATGT
Found at i:7946 original size:8 final size:8
Alignment explanation
Indices: 7933--7979 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
7923 AGGGTGATCT
7933 TTCTTCAA
1 TTCTTCAA
7941 TTCTTCAA
1 TTCTTCAA
*
7949 TTATTCAA
1 TTCTTCAA
*
7957 TGCTTCAA
1 TTCTTCAA
*
7965 TTCCTCAA
1 TTCTTCAA
*
7973 TTATTCA
1 TTCTTCA
7980 TGTGAGACCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.02, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:14469 original size:75 final size:75
Alignment explanation
Indices: 14379--14536 Score: 298
Period size: 75 Copynumber: 2.1 Consensus size: 75
14369 GTGTTTTCTA
*
14379 AATATTTTGAAAATAAATATTTATCGGTCCCCCAATGTTATTTAGGATTAGTTGAAGGGTAGATT
1 AATATTTAGAAAATAAATATTTATCGGTCCCCCAATGTTATTTAGGATTAGTTGAAGGGTAGATT
14444 GAGCATGCAT
66 GAGCATGCAT
14454 AATATTTAGAAAATAAATATTTATCGGTCCCCCAATGTTATTTAGGATTAGTTGAAGGGTAGATT
1 AATATTTAGAAAATAAATATTTATCGGTCCCCCAATGTTATTTAGGATTAGTTGAAGGGTAGATT
14519 GAGCATGCAT
66 GAGCATGCAT
14529 AACTATTT
1 AA-TATTT
14537 TGTGAAATTG
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 76 0.94
76 5 0.06
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (75 bp):
AATATTTAGAAAATAAATATTTATCGGTCCCCCAATGTTATTTAGGATTAGTTGAAGGGTAGATT
GAGCATGCAT
Found at i:14881 original size:15 final size:15
Alignment explanation
Indices: 14858--14887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14848 ATCGGTTGAA
*
14858 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
14873 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
14888 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:15459 original size:22 final size:22
Alignment explanation
Indices: 15434--15476 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15424 AAATGACAAT
*
15434 GCTTCAATTTCAATTTTTCAAC
1 GCTTCAATTTCAATTCTTCAAC
*
15456 GCTTCAATTTCAGTTCTTCAA
1 GCTTCAATTTCAATTCTTCAA
15477 ATTCCAAATG
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:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (22 bp):
GCTTCAATTTCAATTCTTCAAC
Found at i:15467 original size:58 final size:59
Alignment explanation
Indices: 15398--15514 Score: 191
Period size: 58 Copynumber: 2.0 Consensus size: 59
15388 ATTCTTTATT
*
15398 GCTTAAATTTCAGTTCTTCAAATTCCAAATGACAATGCTTCAAT-TTCAATTTTTCAAC
1 GCTTAAATTTCAGTTCTTCAAATTCCAAATGACAATGCTTCAATCTTCAATGTTTCAAC
* *
15456 GCTTCAATTTCAGTTCTTCAAATTCCAAATGCCAATGCTTCAATCCTTCAATGTTTCAA
1 GCTTAAATTTCAGTTCTTCAAATTCCAAATGACAATGCTTCAAT-CTTCAATGTTTCAA
15515 TTTCAATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 42 0.78
60 12 0.22
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (59 bp):
GCTTAAATTTCAGTTCTTCAAATTCCAAATGACAATGCTTCAATCTTCAATGTTTCAAC
Found at i:15519 original size:22 final size:22
Alignment explanation
Indices: 15502--15552 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
15492 GCTTCAATCC
* *
15502 TTCAATGTTTCAATTTCAATTT
1 TTCAATGTGTCAATTTCAATAT
*
15524 TTCAATGTGTGAATTTCAATAT
1 TTCAATGTGTCAATTTCAATAT
15546 TTCAATG
1 TTCAATG
15553 CTTTAAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (22 bp):
TTCAATGTGTCAATTTCAATAT
Found at i:15521 original size:14 final size:15
Alignment explanation
Indices: 15488--15529 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
15478 TTCCAAATGC
*
15488 CAATGCTTCAATCCTT
1 CAATGTTTCAAT-CTT
15504 CAATGTTTCAAT-TT
1 CAATGTTTCAATCTT
*
15518 CAATTTTTCAAT
1 CAATGTTTCAAT
15530 GTGTGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
16 11 0.46
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (15 bp):
CAATGTTTCAATCTT
Found at i:15616 original size:96 final size:95
Alignment explanation
Indices: 15439--15619 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 95
15429 ACAATGCTTC
* * * *
15439 AATTTCAATTTTTCAACGCTTCAATTTCAGTTCTTCAAATTCCAAATGCCAATGCTTCAATCCTT
1 AATTTCAATATTTCAACGCTTCAAATCCAATTCTTCAAATTCCAAATGCCAATGCTTCAAT-CTT
* *
15504 CAATGTTTCAATTTCAATTTTTCAATGTGTG
65 CAATATGTCAATTTCAATTTTTCAATGTGTG
* * * *
15535 AATTTCAATATTTCAATGCTTTAAATCCAATTCTTCAAATTCCAAATGTCAATGTTTCAAT-TTC
1 AATTTCAATATTTCAACGCTTCAAATCCAATTCTTCAAATTCCAAATGCCAATGCTTCAATCTTC
15599 AATATGTCAATGCTTCAATTT
66 AATATGTCAAT--TTCAATTT
15620 CTATTCTTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 12 0.16
96 61 0.84
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (95 bp):
AATTTCAATATTTCAACGCTTCAAATCCAATTCTTCAAATTCCAAATGCCAATGCTTCAATCTTC
AATATGTCAATTTCAATTTTTCAATGTGTG
Found at i:15617 original size:22 final size:22
Alignment explanation
Indices: 15562--15646 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
15552 GCTTTAAATC
* *
15562 CAATTCTTCAAATTCCAA-ATGT
1 CAATGCTTC-AATTTCAATATGT
*
15584 CAATGTTTCAATTTCAATATGT
1 CAATGCTTCAATTTCAATATGT
* *
15606 CAATGCTTCAATTTCTAT-TCTT
1 CAATGCTTCAATTTCAATAT-GT
*
15628 CCATTGCTTCAATTTCAAT
1 -CAATGCTTCAATTTCAAT
15647 TCTTCGAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 8 0.15
22 28 0.54
23 16 0.31
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (22 bp):
CAATGCTTCAATTTCAATATGT
Found at i:15677 original size:14 final size:14
Alignment explanation
Indices: 15635--15680 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
15625 CTTCCATTGC
*
15635 TTCAATTTCAATTC
1 TTCAATTTCAATTT
15649 TTCGAA-TTCAA-TT
1 TTC-AATTTCAATTT
15662 TTCAATTTCAATTT
1 TTCAATTTCAATTT
15676 TTCAA
1 TTCAA
15681 AGCCTCCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 9 0.32
14 15 0.54
15 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.50
Consensus pattern (14 bp):
TTCAATTTCAATTT
Done.