Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013339.1 Kokia drynarioides strain JFW-HI SEQ_128361, 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: 46210
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:9851 original size:59 final size:57
Alignment explanation
Indices: 9787--10101 Score: 358
Period size: 59 Copynumber: 5.4 Consensus size: 57
9777 TAAACATTTA
* * *
9787 AGGGTAAAAAGGGTAA-TTTTGATAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCCG
1 AGGGTAAAAATGG-AATTTTTGA-AGTTTCGAGGTCAAAAATGGA-TTTTTGGA-AGTTCG
*
9846 GGGGT-AAAATGGTAATTTTTGAAAGTTTC-AGTGTCAAAAATGGAATTTTTGGAAGTTCG
1 AGGGTAAAAATGG-AATTTTTG-AAGTTTCGAG-GTCAAAAATGG-ATTTTTGGAAGTTCG
*
9905 AGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTT-GAAGTTTCGAGGTCAAAAAT-GGATTTTTGGAAGTTCG
9964 AGGGTAAAAATGGAATTTTTGGAAGTTTTACGA--TCAAAAATGGGATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTT-GAAG-TTT-CGAGGTCAAAAAT-GGATTTTTGGAAGTTCG
* *
10023 AGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-TAAAATAGGATTTTTGGAAGTTC-
1 AGGGTAAAAATGGAATTTTT-GAAGTTTCGAGGTCAAAAAT-GGATTTTTGGAAGTTCG
10080 AGGGGTAAAAATGGAATTTTTG
1 A-GGGTAAAAATGGAATTTTTG
10102 GACAGTTTAG
Statistics
Matches: 231, Mismatches: 11, Indels: 30
0.85 0.04 0.11
Matches are distributed among these distances:
57 4 0.02
58 55 0.24
59 152 0.66
60 17 0.07
61 3 0.01
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (57 bp):
AGGGTAAAAATGGAATTTTTGAAGTTTCGAGGTCAAAAATGGATTTTTGGAAGTTCG
Found at i:9895 original size:30 final size:29
Alignment explanation
Indices: 9823--10108 Score: 300
Period size: 29 Copynumber: 9.7 Consensus size: 29
9813 TTCGAGGTCG
* * *
9823 AAAATGGAGTTTTTGGACA-TCCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
* *
9851 AAAATGGTAATTTTTGAAAGTTTC-AGTGTCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-A
*
9882 AAAATGGAATTTTTGGAAGTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
9911 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
9941 AAAATAGG-ATTTTTGGAAGTTCGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTCGAGGGTA
** * *
9970 AAAATGGAATTTTTGGAAGTTTTACGATCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
*
10000 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
10029 AAAATGGAATTTTTGGAAGTTTCG-GGGTT
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
10058 AAAATAGG-ATTTTTGGAAGTTC-AGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTCGA-GGGTA
10087 AAAATGGAATTTTTGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
10109 TAGGGACCCT
Statistics
Matches: 219, Mismatches: 21, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
28 15 0.07
29 120 0.55
30 75 0.34
31 9 0.04
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:9913 original size:118 final size:118
Alignment explanation
Indices: 9787--10101 Score: 419
Period size: 118 Copynumber: 2.7 Consensus size: 118
9777 TAAACATTTA
* * *
9787 AGGGTAAAAAGGGTAA-TTTT-GATAGTTTCGAGGTCGAAAAT-GGAGTTTTTGGACA-TCCGGG
1 AGGGTAAAAATGG-AATTTTTGGA-AGTTTCGAGGTCAAAAATAGGA-TTTTTGGA-AGTTCGGG
*
9848 GGT-AAAATGGTAATTTTTGAAAGTTTCA-GTGTCAAAAATGGAATTTTTGGAAGTTCG
62 GGTAAAAATGG-AATTTTTGAAAGTTTCACG-ATCAAAAATGGAATTTTTGGAAGTTCG
* *
9905 AGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGAGGGTA
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTA
* * *
9970 AAAATGGAATTTTTGGAAGTTTTACGATCAAAAATGGGATTTTTGGAAGTTCG
66 AAAATGGAATTTTTGAAAGTTTCACGATCAAAAATGGAATTTTTGGAAGTTCG
* * *
10023 AGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-TAAAATAGGATTTTTGGAAGTTCAGGGGTA
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTA
10087 AAAATGGAATTTTTG
66 AAAATGGAATTTTTG
10102 GACAGTTTAG
Statistics
Matches: 177, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
117 45 0.25
118 119 0.67
119 13 0.07
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (118 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTA
AAAATGGAATTTTTGAAAGTTTCACGATCAAAAATGGAATTTTTGGAAGTTCG
Found at i:11129 original size:16 final size:16
Alignment explanation
Indices: 11108--11161 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
11098 ACGTTATTTA
11108 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
11124 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
* *
11136 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
11152 TTATTATTAA
1 TTATTATTAA
11162 TAGTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:11143 original size:19 final size:19
Alignment explanation
Indices: 11087--11143 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
11077 TTTCCTTTTT
11087 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAA--TTATTTA
*
11108 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
11127 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
11144 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 21 0.64
21 12 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:13529 original size:59 final size:57
Alignment explanation
Indices: 13465--13779 Score: 358
Period size: 59 Copynumber: 5.4 Consensus size: 57
13455 TAAACATTTA
* * *
13465 AGGGTAAAAAGGGTAA-TTTTGATAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCCG
1 AGGGTAAAAATGG-AATTTTTGA-AGTTTCGAGGTCAAAAATGGA-TTTTTGGA-AGTTCG
*
13524 GGGGT-AAAATGGTAATTTTTGAAAGTTTC-AGTGTCAAAAATGGAATTTTTGGAAGTTCG
1 AGGGTAAAAATGG-AATTTTTG-AAGTTTCGAG-GTCAAAAATGG-ATTTTTGGAAGTTCG
*
13583 AGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTT-GAAGTTTCGAGGTCAAAAAT-GGATTTTTGGAAGTTCG
13642 AGGGTAAAAATGGAATTTTTGGAAGTTTTACGA--TCAAAAATGGGATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTT-GAAG-TTT-CGAGGTCAAAAAT-GGATTTTTGGAAGTTCG
* *
13701 AGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-TAAAATAGGATTTTTGGAAGTTC-
1 AGGGTAAAAATGGAATTTTT-GAAGTTTCGAGGTCAAAAAT-GGATTTTTGGAAGTTCG
13758 AGGGGTAAAAATGGAATTTTTG
1 A-GGGTAAAAATGGAATTTTTG
13780 GACAGTTTAG
Statistics
Matches: 231, Mismatches: 11, Indels: 30
0.85 0.04 0.11
Matches are distributed among these distances:
57 4 0.02
58 55 0.24
59 152 0.66
60 17 0.07
61 3 0.01
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (57 bp):
AGGGTAAAAATGGAATTTTTGAAGTTTCGAGGTCAAAAATGGATTTTTGGAAGTTCG
Found at i:13573 original size:30 final size:29
Alignment explanation
Indices: 13501--13786 Score: 300
Period size: 29 Copynumber: 9.7 Consensus size: 29
13491 TTCGAGGTCG
* * *
13501 AAAATGGAGTTTTTGGACA-TCCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
* *
13529 AAAATGGTAATTTTTGAAAGTTTC-AGTGTCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-A
*
13560 AAAATGGAATTTTTGGAAGTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
13589 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
13619 AAAATAGG-ATTTTTGGAAGTTCGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTCGAGGGTA
** * *
13648 AAAATGGAATTTTTGGAAGTTTTACGATCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
*
13678 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
13707 AAAATGGAATTTTTGGAAGTTTCG-GGGTT
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
13736 AAAATAGG-ATTTTTGGAAGTTC-AGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTCGA-GGGTA
13765 AAAATGGAATTTTTGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
13787 TAGGGACCCT
Statistics
Matches: 219, Mismatches: 21, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
28 15 0.07
29 120 0.55
30 75 0.34
31 9 0.04
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:13591 original size:118 final size:118
Alignment explanation
Indices: 13465--13779 Score: 419
Period size: 118 Copynumber: 2.7 Consensus size: 118
13455 TAAACATTTA
* * *
13465 AGGGTAAAAAGGGTAA-TTTT-GATAGTTTCGAGGTCGAAAAT-GGAGTTTTTGGACA-TCCGGG
1 AGGGTAAAAATGG-AATTTTTGGA-AGTTTCGAGGTCAAAAATAGGA-TTTTTGGA-AGTTCGGG
*
13526 GGT-AAAATGGTAATTTTTGAAAGTTTCA-GTGTCAAAAATGGAATTTTTGGAAGTTCG
62 GGTAAAAATGG-AATTTTTGAAAGTTTCACG-ATCAAAAATGGAATTTTTGGAAGTTCG
* *
13583 AGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGAGGGTA
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTA
* * *
13648 AAAATGGAATTTTTGGAAGTTTTACGATCAAAAATGGGATTTTTGGAAGTTCG
66 AAAATGGAATTTTTGAAAGTTTCACGATCAAAAATGGAATTTTTGGAAGTTCG
* * *
13701 AGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-TAAAATAGGATTTTTGGAAGTTCAGGGGTA
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTA
13765 AAAATGGAATTTTTG
66 AAAATGGAATTTTTG
13780 GACAGTTTAG
Statistics
Matches: 177, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
117 45 0.25
118 119 0.67
119 13 0.07
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (118 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTA
AAAATGGAATTTTTGAAAGTTTCACGATCAAAAATGGAATTTTTGGAAGTTCG
Found at i:14807 original size:16 final size:16
Alignment explanation
Indices: 14786--14839 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
14776 ACGTTATTTA
14786 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
14802 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
* *
14814 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
14830 TTATTATTAA
1 TTATTATTAA
14840 TAGTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:14821 original size:19 final size:19
Alignment explanation
Indices: 14765--14821 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
14755 TTTCCTTTTT
14765 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAA--TTATTTA
*
14786 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
14805 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
14822 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 21 0.64
21 12 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:15465 original size:15 final size:15
Alignment explanation
Indices: 15445--15489 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
15435 ACTTTGGGCC
*
15445 ATTGGGCCGTTTGTA
1 ATTGGGCCATTTGTA
15460 ATTGGGCCATTTGTA
1 ATTGGGCCATTTGTA
15475 ATTGGGCCATTTGTA
1 ATTGGGCCATTTGTA
15490 CTTTGTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (15 bp):
ATTGGGCCATTTGTA
Found at i:15542 original size:17 final size:16
Alignment explanation
Indices: 15520--15581 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
15510 TTGGACTTTC
15520 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
15537 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
15554 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
15570 TAAATTCAATTT
1 TAAATTTAATTT
15582 CCAATAGGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 16 0.43
17 15 0.41
18 6 0.16
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:15587 original size:16 final size:17
Alignment explanation
Indices: 15535--15587 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
15525 TTAATTTTAT
*
15535 AATAAATTTAAATTTCA
1 AATAAACTTAAATTTCA
15552 AATAAACTTAAATTT-A
1 AATAAACTTAAATTTCA
* *
15568 AATAAA-TTCAATTTCC
1 AATAAACTTAAATTTCA
15584 AATA
1 AATA
15588 GGTCCAGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 7 0.22
16 11 0.34
17 14 0.44
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAACTTAAATTTCA
Found at i:21058 original size:76 final size:76
Alignment explanation
Indices: 20957--21110 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
20947 ATCTATGATG
20957 TAGTAATAAACTAATTAAAATTTTGAAAAACATAAATGTATTTATCAATTAATAGTATAGTTATG
1 TAGTAATAAACTAATTAAAATTTTGAAAAACATAAATGTATTTATCAATTAATAGTATAGTTATG
21022 ATAAGTAAAGA
66 ATAAGTAAAGA
21033 TAGTAATAAACTAATTAAAATTTTGAAAAACATAAATGTATTTATCAATTAATAGTATAGTTATG
1 TAGTAATAAACTAATTAAAATTTTGAAAAACATAAATGTATTTATCAATTAATAGTATAGTTATG
21098 ATAAGTAAAGA
66 ATAAGTAAAGA
21109 TA
1 TA
21111 TTGTTTTCAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (76 bp):
TAGTAATAAACTAATTAAAATTTTGAAAAACATAAATGTATTTATCAATTAATAGTATAGTTATG
ATAAGTAAAGA
Found at i:22591 original size:47 final size:47
Alignment explanation
Indices: 22522--22625 Score: 181
Period size: 47 Copynumber: 2.2 Consensus size: 47
22512 TAGGCTAGTG
*
22522 GCCATGCTTTTACTTGAAACTACTACAATCTATATTTAAAAGTAATA
1 GCCATGCTTTTACTTGAAACTACTACAATCTAGATTTAAAAGTAATA
*
22569 GCCATGCTTTTACTTGAAACTACTACCATCTAGATTTAAAAGTAATA
1 GCCATGCTTTTACTTGAAACTACTACAATCTAGATTTAAAAGTAATA
*
22616 CCCATGCTTT
1 GCCATGCTTT
22626 CATCAGGGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (47 bp):
GCCATGCTTTTACTTGAAACTACTACAATCTAGATTTAAAAGTAATA
Found at i:23421 original size:28 final size:28
Alignment explanation
Indices: 23377--23451 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
23367 ATATTTATAT
*
23377 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTAAATAATTTTA
* **
23405 TATATT-TTTTATTTATTAAATTTTTTTA
1 TATATTATTTTA-ATATTAAATAATTTTA
* *
23433 TATAATTATCTTAACATTA
1 TAT-ATTATTTTAATATTA
23452 TTTTAATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.14
28 21 0.57
29 7 0.19
30 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (28 bp):
TATATTATTTTAATATTAAATAATTTTA
Found at i:26319 original size:10 final size:11
Alignment explanation
Indices: 26299--26337 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
26289 TTAAAAAAAA
*
26299 TTATGATATTT
1 TTATAATATTT
26310 TTAT-ATATTT
1 TTATAATATTT
*
26320 TTTTAATATTT
1 TTATAATATTT
26331 TTATAAT
1 TTATAAT
26338 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TTATAATATTT
Found at i:27995 original size:31 final size:30
Alignment explanation
Indices: 27937--27996 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
27927 TTTTTTTTCC
* * * *
27937 AAAAAAATTTAGGGTTTATTGAGATTTTTT
1 AAAAAAAATTAGGGTTAATTAAAATTTTTT
27967 AAAAAAAATTAGGGTCTAATTAAAATTTTT
1 AAAAAAAATTAGGGT-TAATTAAAATTTTT
27997 ATAGATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (30 bp):
AAAAAAAATTAGGGTTAATTAAAATTTTTT
Found at i:31355 original size:21 final size:21
Alignment explanation
Indices: 31330--31370 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31320 AATAAGTTTA
*
31330 TTTTAA-AATAATTTTATATTC
1 TTTTAATAA-AATCTTATATTC
31351 TTTTAATAAAATCTTATATT
1 TTTTAATAAAATCTTATATT
31371 TCAATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAATAAAATCTTATATTC
Found at i:32749 original size:19 final size:19
Alignment explanation
Indices: 32727--32771 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
32717 TTATATTAGG
32727 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
32746 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
32765 ATTTAAT
1 ATTTAAT
32772 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:33616 original size:22 final size:21
Alignment explanation
Indices: 33591--33633 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
33581 TATTTCTTTC
33591 AATTCTGTTTTCTTTTATTTTT
1 AATTCTG-TTTCTTTTATTTTT
*
33613 AATTTTGTTTCTTTTATTTTT
1 AATTCTGTTTCTTTTATTTTT
33634 CCTCAGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (21 bp):
AATTCTGTTTCTTTTATTTTT
Found at i:39487 original size:35 final size:35
Alignment explanation
Indices: 39448--39517 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
39438 AATAACCAAA
* * * *
39448 ACATAAATTTACTAACGGTTTAGTGATATTAAGTG
1 ACATAAACTTACTAACAGTTCAGTGACATTAAGTG
*
39483 ACATAAACTTACTAACAGTTCATTGACATTAAGTG
1 ACATAAACTTACTAACAGTTCAGTGACATTAAGTG
39518 TAGTTTACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (35 bp):
ACATAAACTTACTAACAGTTCAGTGACATTAAGTG
Found at i:41692 original size:24 final size:23
Alignment explanation
Indices: 41644--41693 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
41634 AAATAAATTG
41644 ATTTTTTTGTTAAAAATTTCATCC
1 ATTTTTTTGTTAAAAA-TTCATCC
41668 ATTTTTTCTGTTAAAAA-TCAGTCC
1 ATTTTTT-TGTTAAAAATTCA-TCC
41692 AT
1 AT
41694 ATATGCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.12
24 12 0.50
25 9 0.38
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (23 bp):
ATTTTTTTGTTAAAAATTCATCC
Found at i:42090 original size:2 final size:2
Alignment explanation
Indices: 42079--42110 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
42069 ACTACCCTTG
42079 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42111 TGAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.