Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014840.1 Corchorus olitorius cultivar O-4 contig14873, 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: 116525
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2742 original size:2 final size:2
Alignment explanation
Indices: 2735--2763 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2725 GTTCATTTAG
2735 TA 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 T
2764 GAGGGAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17774 original size:29 final size:29
Alignment explanation
Indices: 17741--17896 Score: 231
Period size: 29 Copynumber: 5.4 Consensus size: 29
17731 GAATTGACTC
17741 AAATGCCCCTGAATATGCAAAAATGACCA
1 AAATGCCCCTGAATATGCAAAAATGACCA
* * * *
17770 GAATGCCCCTGGATGTGCAAAAATAACCA
1 AAATGCCCCTGAATATGCAAAAATGACCA
17799 AAATGCCCCTGAATATGCAAAAATGACCA
1 AAATGCCCCTGAATATGCAAAAATGACCA
* * * *
17828 AAATGTCCTTGGATGTGCAAAAATGACCA
1 AAATGCCCCTGAATATGCAAAAATGACCA
17857 AAATGCCCCTGAATATGCAAAAATGACCA
1 AAATGCCCCTGAATATGCAAAAATGACCA
*
17886 AAATACCCCTG
1 AAATGCCCCTG
17897 GACGTGCGAA
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 110 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.19
Consensus pattern (29 bp):
AAATGCCCCTGAATATGCAAAAATGACCA
Found at i:17811 original size:58 final size:58
Alignment explanation
Indices: 17741--17903 Score: 272
Period size: 58 Copynumber: 2.8 Consensus size: 58
17731 GAATTGACTC
*
17741 AAATGCCCCTGAATATGCAAAAATGACCAGAATGCCCCTGGATGTGCAAAAATAACCA
1 AAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGGATGTGCAAAAATAACCA
* * *
17799 AAATGCCCCTGAATATGCAAAAATGACCAAAATGTCCTTGGATGTGCAAAAATGACCA
1 AAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGGATGTGCAAAAATAACCA
* *
17857 AAATGCCCCTGAATATGCAAAAATGACCAAAATACCCCTGGACGTGC
1 AAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGGATGTGC
17904 GAATGACCAA
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 97 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (58 bp):
AAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGGATGTGCAAAAATAACCA
Found at i:32629 original size:16 final size:16
Alignment explanation
Indices: 32602--32639 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
32592 ATTTGACTAA
32602 TAATTAGAATCAATTG
1 TAATTAGAATCAATTG
* *
32618 TGATTAGGATCAATTG
1 TAATTAGAATCAATTG
32634 TAATTA
1 TAATTA
32640 TTAATTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (16 bp):
TAATTAGAATCAATTG
Found at i:37306 original size:16 final size:16
Alignment explanation
Indices: 37279--37316 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
37269 ATTGTTTGAC
37279 TAATTAGAATCAATTG
1 TAATTAGAATCAATTG
* *
37295 TGATTAGGATCAATTG
1 TAATTAGAATCAATTG
37311 TAATTA
1 TAATTA
37317 TTAATTACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (16 bp):
TAATTAGAATCAATTG
Found at i:57047 original size:22 final size:21
Alignment explanation
Indices: 56995--57048 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
56985 GCTTCTTGGA
56995 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
57016 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
57035 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
57049 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:59607 original size:19 final size:21
Alignment explanation
Indices: 59565--59608 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
59555 ATTGTATCTA
* *
59565 TATAACTATCTATATATAATC
1 TATAACTATCTATATAAAAAC
59586 TATAACTAT-T-TATAAAAAC
1 TATAACTATCTATATAAAAAC
59605 TATA
1 TATA
59609 TATATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 1 0.05
21 9 0.43
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAACTATCTATATAAAAAC
Found at i:59610 original size:21 final size:22
Alignment explanation
Indices: 59562--59610 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
59552 GAAATTGTAT
*
59562 CTATATAACTATCTATATATAA
1 CTATATAACTATCTATATAAAA
* *
59584 -TCTATAACTATTTATA-AAAA
1 CTATATAACTATCTATATAAAA
59604 CTATATA
1 CTATATA
59611 TATTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (22 bp):
CTATATAACTATCTATATAAAA
Found at i:60529 original size:20 final size:20
Alignment explanation
Indices: 60504--60542 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
60494 CATATAAAAT
*
60504 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
60524 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
60543 TTTTTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:60691 original size:15 final size:15
Alignment explanation
Indices: 60671--60700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60661 GTGACCAAGC
60671 CGCGGCTCGGTCGCG
1 CGCGGCTCGGTCGCG
*
60686 CGCGGCTTGGTCGCG
1 CGCGGCTCGGTCGCG
60701 AGCCGTGGTC
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:0.00, C:0.37, G:0.47, T:0.17
Consensus pattern (15 bp):
CGCGGCTCGGTCGCG
Found at i:60732 original size:54 final size:54
Alignment explanation
Indices: 60632--60746 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
60622 GCGACTGAGC
* * *
60632 CGCGACTTGGCCGCGAGCCGTGGTCGCACGTGACCAAGCCGCGGCTCGGTCGCG
1 CGCGGCTTGGCCGCGAGCCGTGGTCGCACGTGACCAAACCACGGCTCGGTCGCG
* ** ** * *
60686 CGCGGCTTGGTCGCGAGCCGTGGTCGTTCGTGAGTAAACCATGGCTCGGTCGTG
1 CGCGGCTTGGCCGCGAGCCGTGGTCGCACGTGACCAAACCACGGCTCGGTCGCG
*
60740 AGCGGCT
1 CGCGGCT
60747 CGCGACTGTG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.11, C:0.31, G:0.39, T:0.18
Consensus pattern (54 bp):
CGCGGCTTGGCCGCGAGCCGTGGTCGCACGTGACCAAACCACGGCTCGGTCGCG
Found at i:60927 original size:17 final size:17
Alignment explanation
Indices: 60905--60947 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
60895 AATAATTGAG
60905 ATTTGAA-AATTGAGAAA
1 ATTTGAAGAATTGA-AAA
60922 ATTTGAGAGAATTGAAAA
1 ATTTGA-AGAATTGAAAA
*
60940 TTTTGAAG
1 ATTTGAAG
60948 TTTGAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.33
Consensus pattern (17 bp):
ATTTGAAGAATTGAAAA
Found at i:64062 original size:94 final size:93
Alignment explanation
Indices: 63902--64089 Score: 342
Period size: 94 Copynumber: 2.0 Consensus size: 93
63892 AAGGTTATCA
63902 TAAATCCCAACAATTGTAAAAAACACATTTGTAATGATATTTTAATCTAAGTCTTTTGTAATATA
1 TAAATCCCAACAATTGTAAAAAACACATTTGTAATGATATTTTAATCTAAGTCTTTTGTAATATA
*
63967 TAATTATAATATTTTTAATCCAAAATTT
66 TAATTATAATATTTTTAAACCAAAATTT
63995 TAAATCCCAACAATTGTAAAAAA-ACTTATTTGTAATGATATTTTAATCTAAGTCTTTTGTAATA
1 TAAATCCCAACAATTGTAAAAAACAC--ATTTGTAATGATATTTTAATCTAAGTCTTTTGTAATA
64059 TATAATTATAATATTTTTAAACCAAAATTT
64 TATAATTATAATATTTTTAAACCAAAATTT
64089 T
1 T
64090 TATAGTCGAG
Statistics
Matches: 92, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
92 2 0.02
93 23 0.25
94 67 0.73
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (93 bp):
TAAATCCCAACAATTGTAAAAAACACATTTGTAATGATATTTTAATCTAAGTCTTTTGTAATATA
TAATTATAATATTTTTAAACCAAAATTT
Found at i:70324 original size:36 final size:36
Alignment explanation
Indices: 70277--70346 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
70267 TTCAATAAGC
* * *
70277 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATAATCATATTTCTTA
*
70313 TTACATTTTTTGTAATTTTGATAATCATATTTCT
1 TTACATCTTTTGTAATTTTGATAATCATATTTCT
70347 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATAATCATATTTCTTA
Found at i:71376 original size:25 final size:24
Alignment explanation
Indices: 71342--71388 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
71332 ACATTTGCAC
71342 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
71367 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
71389 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:71434 original size:39 final size:40
Alignment explanation
Indices: 71379--71459 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
71369 ATACCTAAGA
* *
71379 ATTTAATTAATGTAAGTATTTTAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
71418 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
71458 AT
1 AT
71460 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
Found at i:71447 original size:21 final size:21
Alignment explanation
Indices: 71384--71453 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
71374 TAAGAATTTA
*
71384 ATTAATGTAAGTATTTTAGTT
1 ATTAATATAAGTATTTTAGTT
** *
71405 A-T--TAT-AGTATTACATTT
1 ATTAATATAAGTATTTTAGTT
71422 AATTAATATAAGTATTTTAGTT
1 -ATTAATATAAGTATTTTAGTT
71444 ATTATATATA
1 ATTA-ATATA
71454 TTACATAGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 11
0.67 0.13 0.20
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 1 0.03
20 1 0.03
21 8 0.22
22 14 0.39
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (21 bp):
ATTAATATAAGTATTTTAGTT
Found at i:71452 original size:22 final size:22
Alignment explanation
Indices: 71391--71453 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 22
71381 TTAATTAATG
71391 TAAGTATTTTAGTTATTATAGTA
1 TAAGTATTTTAGTTATTATA-TA
* *
71414 TTA-CA-TTTA---ATTA-ATA
1 TAAGTATTTTAGTTATTATATA
71430 TAAGTATTTTAGTTATTATATA
1 TAAGTATTTTAGTTATTATATA
71452 TA
1 TA
71454 TTACATAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 13
0.64 0.09 0.28
Matches are distributed among these distances:
16 4 0.13
17 2 0.07
18 8 0.27
21 8 0.27
22 6 0.20
23 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (22 bp):
TAAGTATTTTAGTTATTATATA
Found at i:71753 original size:39 final size:40
Alignment explanation
Indices: 71698--71778 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
71688 ATACCTAAGA
* * *
71698 ATTTAATTCATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
*
71737 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
71777 AT
1 AT
71779 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
Found at i:72076 original size:2 final size:2
Alignment explanation
Indices: 72069--72100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
72059 CCGGTTCAAG
72069 AT AT AT 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 AT AT AT
72101 GCACGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75338 original size:17 final size:18
Alignment explanation
Indices: 75301--75356 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
75291 CCGCGCGCAG
75301 AAGAAAGGGAAGATAGAA
1 AAGAAAGGGAAGATAGAA
* *
75319 AAGAAATGGAA-ATCGAA
1 AAGAAAGGGAAGATAGAA
75336 AAGGAAAAGGAGAAGA-AGAA
1 AA-G-AAAGG-GAAGATAGAA
75356 A
1 A
75357 TTCATTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.23
18 11 0.37
19 4 0.13
20 7 0.23
21 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.30, T:0.05
Consensus pattern (18 bp):
AAGAAAGGGAAGATAGAA
Found at i:76211 original size:19 final size:20
Alignment explanation
Indices: 76184--76221 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
76174 GTTAAAAACA
*
76184 AAATAAAAACTATCCATTAT
1 AAATAAAAACTACCCATTAT
76204 AAAT-AAAACTACCCATTA
1 AAATAAAAACTACCCATTA
76222 AAGGATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAAAACTACCCATTAT
Found at i:77095 original size:25 final size:25
Alignment explanation
Indices: 77054--77194 Score: 210
Period size: 25 Copynumber: 5.6 Consensus size: 25
77044 TAGCCTATGT
*
77054 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
* *
77079 GCTTGCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
* * *
77104 GCTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGCTC
*
77129 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGCTC
77154 GTTTTCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
*
77179 GTTTTCCAAACACAAG
1 GTTTTCCAAACGCAAG
77195 AACATGAGCG
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 108 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGCTC
Found at i:79158 original size:20 final size:22
Alignment explanation
Indices: 79127--79172 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
79117 ATTGATAAAA
*
79127 GTATAGCATA-TTTCATAATCT
1 GTATAGCATATTTTAATAATCT
79148 GTATAGC-TATTTTAATAATCT
1 GTATAGCATATTTTAATAATCT
79169 -TATA
1 GTATA
79173 TAAGAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (22 bp):
GTATAGCATATTTTAATAATCT
Found at i:86784 original size:2 final size:2
Alignment explanation
Indices: 86777--86810 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
86767 TAATATGTAG
86777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86811 CACGCTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88617 original size:12 final size:12
Alignment explanation
Indices: 88587--88634 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
88577 AGGTATCTAT
88587 GGATATATCGAAC
1 GGATATATCG-AC
* *
88600 GGATATGTCGAT
1 GGATATATCGAC
88612 GGATATATCGAC
1 GGATATATCGAC
88624 GGATATATCGA
1 GGATATATCGA
88635 GGTATCGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 22 0.71
13 9 0.29
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (12 bp):
GGATATATCGAC
Found at i:88619 original size:25 final size:24
Alignment explanation
Indices: 88580--88634 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
88570 TTAATACAGG
*
88580 TATCTATGGATATATCGAACGGATA
1 TATCGATGGATATATCG-ACGGATA
*
88605 TGTCGATGGATATATCGACGGATA
1 TATCGATGGATATATCGACGGATA
88629 TATCGA
1 TATCGA
88635 GGTATCGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.31
Consensus pattern (24 bp):
TATCGATGGATATATCGACGGATA
Found at i:89643 original size:10 final size:10
Alignment explanation
Indices: 89628--89673 Score: 83
Period size: 10 Copynumber: 4.6 Consensus size: 10
89618 AAATTAATAT
89628 GGATATTTAC
1 GGATATTTAC
89638 GGATATTTAC
1 GGATATTTAC
*
89648 GGATACTTAC
1 GGATATTTAC
89658 GGATATTTAC
1 GGATATTTAC
89668 GGATAT
1 GGATAT
89674 ATCGAGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (10 bp):
GGATATTTAC
Found at i:103442 original size:12 final size:11
Alignment explanation
Indices: 103424--103455 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
103414 AAGGGTGGAG
103424 AGAGAGAGAGA
1 AGAGAGAGAGA
103435 AGGAGAGAGAGA
1 A-GAGAGAGAGA
103447 AGAGAGAGA
1 AGAGAGAGA
103456 AAGCTAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (11 bp):
AGAGAGAGAGA
Found at i:106038 original size:1 final size:1
Alignment explanation
Indices: 106032--106058 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
106022 CGACCACTAC
106032 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
106059 CAGTAGCACG
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.