Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010754.1 Corchorus olitorius cultivar O-4 contig10786, 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: 38234
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:7479 original size:132 final size:129
Alignment explanation
Indices: 7321--7580 Score: 396
Period size: 132 Copynumber: 2.0 Consensus size: 129
7311 TTATCTAAAT
*
7321 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAACTA
*
7386 TTTCATTTTTACCATTTTACTATTTTAATTAAAAAAACTTAGATATATTAGAAATTTTT-AAATA
66 TTTCATTTTTACCATTTTACAATTTTAATT-AAAAAACTT--ATATATTA-AAATTTTTAAAATA
7450 TAC
127 TAC
* * * *
7453 TTTTATAGTTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTTTTACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAACTA
* * *
7518 TTTTATTTTTATCATTTTACAATTTTAATTAAAAAACTTATATATTATAATTTTTAAAATATA
66 TTTCATTTTTACCATTTTACAATTTTAATTAAAAAACTTATATATTAAAATTTTTAAAATATA
7581 TTCTTTTACA
Statistics
Matches: 118, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
128 7 0.06
129 15 0.13
131 9 0.08
132 87 0.74
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (129 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAAAATCCTTATAACTA
TTTCATTTTTACCATTTTACAATTTTAATTAAAAAACTTATATATTAAAATTTTTAAAATATAC
Found at i:8548 original size:18 final size:19
Alignment explanation
Indices: 8525--8561 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
8515 ATTGATTTAG
8525 TATTTATTCTT-ATATAAT
1 TATTTATTCTTCATATAAT
*
8543 TATTTATTGTTCATATAAT
1 TATTTATTCTTCATATAAT
8562 GAAATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTTATTCTTCATATAAT
Found at i:9295 original size:16 final size:16
Alignment explanation
Indices: 9276--9309 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9266 ATCAATTCAC
*
9276 GATATAAGGTTTGTAT
1 GATATAAGGTTGGTAT
9292 GATATAAGGTTGGTAT
1 GATATAAGGTTGGTAT
9308 GA
1 GA
9310 ACACGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.38
Consensus pattern (16 bp):
GATATAAGGTTGGTAT
Found at i:11584 original size:24 final size:24
Alignment explanation
Indices: 11557--11607 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11547 AAAAAGAAAA
11557 AAATGAAATTTGGTAACTAAAGTT
1 AAATGAAATTTGGTAACTAAAGTT
** *
11581 AAATGGTATTTGGTAATTAAAGTT
1 AAATGAAATTTGGTAACTAAAGTT
11605 AAA
1 AAA
11608 AGCGTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (24 bp):
AAATGAAATTTGGTAACTAAAGTT
Found at i:11621 original size:33 final size:32
Alignment explanation
Indices: 11580--11642 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
11570 TAACTAAAGT
* *
11580 TAAATGGTATTTGGTAATTAAAGTTAAAAGCG
1 TAAATGGTATTTGGTAATCAAAGTAAAAAGCG
11612 TAAATTGGTATTTGGTAATCAAAGTAAAAAG
1 TAAA-TGGTATTTGGTAATCAAAGTAAAAAG
11643 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (32 bp):
TAAATGGTATTTGGTAATCAAAGTAAAAAGCG
Found at i:11670 original size:24 final size:23
Alignment explanation
Indices: 11643--11720 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 23
11633 AAGTAAAAAG
11643 AAAAAAAAATGAAATTTGGTAATT
1 AAAAAAAAATGAAATTTGGTAA-T
*
11667 AAAACAAAAA-GAGTAATATGGTAA-
1 AAAA-AAAAATGA--AATTTGGTAAT
*
11691 AAAGAAAAAAGTTAAATTTGGTAAGT
1 AAA-AAAAAA-TGAAATTTGGTAA-T
11717 AAAA
1 AAAA
11721 TGAAATTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
24 23 0.53
25 7 0.16
26 13 0.30
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.23
Consensus pattern (23 bp):
AAAAAAAAATGAAATTTGGTAAT
Found at i:11713 original size:92 final size:89
Alignment explanation
Indices: 11514--11701 Score: 207
Period size: 92 Copynumber: 2.1 Consensus size: 89
11504 GTTACAAGGT
* * ** * *
11514 AAAAAGAGTAAATTGGTATATAATAAACAAAGTAAAAAGAAAAAAATGAAATTTGGTAACTAAAG
1 AAAAAGCGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGTAACTAAAA
** * * *
11579 TTAAATGGTATTTGGTAATTAAAGT
66 CAAAAAGGTATATGGTAA-TAAAGA
* *
11604 TAAAAGCGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAAAAATGAAATTTGGTAATTAA
1 AAAAAGCGTAAATTGGTATTTGGTAATCAAAGTAAAAAG--AAAAAAATGAAATTTGGTAACTAA
11669 AACAAAAAGAGTAATATGGTAA-AAAGA
64 AACAAAAAG-GT-ATATGGTAATAAAGA
11696 AAAAAG
1 AAAAAG
11702 TTAAATTTGG
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
90 33 0.41
92 37 0.46
93 2 0.03
94 8 0.10
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (89 bp):
AAAAAGCGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGTAACTAAAA
CAAAAAGGTATATGGTAATAAAGA
Found at i:11740 original size:24 final size:24
Alignment explanation
Indices: 11713--11768 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
11703 TAAATTTGGT
11713 AAGTAAAATGAAATTTGCTAACTA
1 AAGTAAAATGAAATTTGCTAACTA
* ** * *
11737 AAGTTAAATGGTATTTGGTAATTA
1 AAGTAAAATGAAATTTGCTAACTA
11761 AAGTAAAA
1 AAGTAAAA
11769 AGAGTAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (24 bp):
AAGTAAAATGAAATTTGCTAACTA
Found at i:11745 original size:19 final size:19
Alignment explanation
Indices: 11698--11745 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11688 TAAAAAGAAA
* *
11698 AAAGTTAAATTTGGTAAGT
1 AAAGTTAAATTTGCTAACT
* *
11717 AAAATGAAATTTGCTAACT
1 AAAGTTAAATTTGCTAACT
11736 AAAGTTAAAT
1 AAAGTTAAAT
11746 GGTATTTGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (19 bp):
AAAGTTAAATTTGCTAACT
Found at i:11778 original size:161 final size:164
Alignment explanation
Indices: 11556--11969 Score: 617
Period size: 161 Copynumber: 2.5 Consensus size: 164
11546 TAAAAAGAAA
* *
11556 AAAATGAAATTTGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTTAAAAGCGTAAATTGGT
1 AAAATGAAATTTGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
*
11621 ATTTGGTAATCAAAGTAAAAAGAAAAAAAAATGAAATTTGGTAATTAAAACAAAAAGAGTAATAT
66 ATTTGGTAATCAAAGTAAAAAGAAAAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATAT
**
11686 GGTAAAAAGA-A-AAAAGTTAAATTTG-GT-AA-GT
131 GGTAAAAAGAGATAAAAG-TAAA-AAGAGTAAATGT
*
11717 AAAATGAAATTTGCTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 AAAATGAAATTTGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * *
11782 ATTTGGAAATCAAAGTAAAAAG-AGAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTGATAT
66 ATTTGGTAATCAAAGTAAAAAGAAAAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATAT
*
11846 GGTAAAAAGAGATTAAAGTAAAAAGAGTAAAATTGT
131 GGTAAAAAGAGATAAAAGTAAAAAGAGT-AAA-TGT
* *
11882 AAAATGAAATTTGGTAACTAAAGTTAAATGGTATTCGGTAATTAAAATAAAAAGAGTAAATTGGT
1 AAAATGAAATTTGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
*
11947 ATTTGGTAAAT-ATAGTAAAAAGA
66 ATTTGGT-AATCAAAGTAAAAAGA
11970 GTAGAATTGG
Statistics
Matches: 229, Mismatches: 15, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
160 50 0.22
161 90 0.39
162 4 0.02
163 2 0.01
165 80 0.35
166 3 0.01
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.28
Consensus pattern (164 bp):
AAAATGAAATTTGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
ATTTGGTAATCAAAGTAAAAAGAAAAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATAT
GGTAAAAAGAGATAAAAGTAAAAAGAGTAAATGT
Found at i:11983 original size:34 final size:33
Alignment explanation
Indices: 11741--12000 Score: 167
Period size: 33 Copynumber: 7.9 Consensus size: 33
11731 TAACTAAAGT
11741 TAAA-TGGTATTTGGTAATTAAAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* *
11773 TAAATTGGTATTTGGAAATCAAAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* * ** * **
11806 AAAAAATGAAATTTGGCAATTAAAACAAAAAGAG
1 -TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* ****
11840 T-GATATGGTAAAAAG-AGATTAAAGTAAAAAGAG
1 TAAAT-TGGTATTTGGTA-ATTAAAGTAAAAAGAG
** * ** *
11873 TAAAATT-GTAAAAT-GAAATT-TGGTAACTAAAG-T
1 T-AAATTGGT-ATTTGGTAATTAAAGTAA--AAAGAG
* *
11906 TAAA-TGGTATTCGGTAATTAAAATAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* *
11938 TAAATTGGTATTTGGTAAATATAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
*
11971 TAGAATTGGTATTTGATAATTAAAGTAAAA
1 TA-AATTGGTATTTGGTAATTAAAGTAAAA
12001 TTGGTAAAAA
Statistics
Matches: 171, Mismatches: 41, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
31 6 0.04
32 24 0.14
33 81 0.47
34 58 0.34
35 2 0.01
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.28
Consensus pattern (33 bp):
TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
Found at i:15155 original size:26 final size:25
Alignment explanation
Indices: 15126--15175 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
15116 TTTTTTCGAA
15126 AAAATG-TTTTCAAGAAAAGGTTTTCC
1 AAAATGATTTTC-A-AAAAGGTTTTCC
15152 AAAATGACTTTTCAAAAAGGTTTT
1 AAAATGA-TTTTCAAAAAGGTTTT
15176 GAGTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 16 0.73
27 1 0.05
28 5 0.23
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (25 bp):
AAAATGATTTTCAAAAAGGTTTTCC
Found at i:15836 original size:4 final size:4
Alignment explanation
Indices: 15827--15860 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
15817 CATTCAACTC
*
15827 AAAG AAAG AAAG AAAC AAA- AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
15861 CAAAAAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:15851 original size:15 final size:16
Alignment explanation
Indices: 15826--15856 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
15816 ACATTCAACT
15826 CAAAGAAAGAAAGAAA
1 CAAAGAAAGAAAGAAA
15842 CAAA-AAAGAAAGAAA
1 CAAAGAAAGAAAGAAA
15857 GAAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
CAAAGAAAGAAAGAAA
Found at i:15851 original size:19 final size:19
Alignment explanation
Indices: 15827--15867 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
15817 CATTCAACTC
15827 AAAGAAAGAAAGAAACAAA
1 AAAGAAAGAAAGAAACAAA
15846 AAAGAAAGAAAGAAACAAA
1 AAAGAAAGAAAGAAACAAA
15865 AAA
1 AAA
15868 CTTGGCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAGAAACAAA
Found at i:16431 original size:17 final size:17
Alignment explanation
Indices: 16397--16433 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16387 CTCAAAAAGG
**
16397 TTTTAGAAAAAATTGTT
1 TTTTAGAAAAAAAAGTT
16414 TTTTAGAAAAAAAAGTT
1 TTTTAGAAAAAAAAGTT
16431 TTT
1 TTT
16434 CAAACGCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TTTTAGAAAAAAAAGTT
Found at i:16467 original size:10 final size:10
Alignment explanation
Indices: 16452--16476 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16442 AGTGCATGGC
16452 AAAAAAAACA
1 AAAAAAAACA
16462 AAAAAAAACA
1 AAAAAAAACA
16472 AAAAA
1 AAAAA
16477 GGGAGCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:16737 original size:29 final size:31
Alignment explanation
Indices: 16705--16771 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
16695 ATGCAATTTG
16705 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAATCAAGCAATTAA
* *
16734 GGATATAACGTTACGAAAATCGAGTAATTAA
1 GGATATAACGTTACGAAAATCAAGCAATTAA
16765 GGATATA
1 GGATATA
16772 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAATCAAGCAATTAA
Found at i:16938 original size:31 final size:31
Alignment explanation
Indices: 16901--17012 Score: 136
Period size: 31 Copynumber: 3.6 Consensus size: 31
16891 CCCTAACTGA
16901 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* * **
16932 TCATATCCTTAATTGTTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
***
16963 TTATATCCTTAATTGCTTG-CGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAAATC-GAAAACG
*
16994 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
17013 CTTATCATCT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:17177 original size:16 final size:16
Alignment explanation
Indices: 17140--17170 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17130 GCATTGCTTG
17140 GTAGAAAAATGTATTA
1 GTAGAAAAATGTATTA
17156 GTAGAAAAATGTATT
1 GTAGAAAAATGTATT
17171 CTTAGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (16 bp):
GTAGAAAAATGTATTA
Found at i:18086 original size:31 final size:31
Alignment explanation
Indices: 18048--18128 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
18038 CGTTACAAAA
**
18048 CAAGCAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* *
18079 CAAGCAATTAAGGATATGAGGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
18110 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
18129 TCAGTTAGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:18311 original size:29 final size:31
Alignment explanation
Indices: 18247--18313 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
18237 TTTAACGGAC
* * *
18247 TATATCCTTAATTGTTCGCTTTTCGTAACGT
1 TATATCCTTAATCGCTAGCTTTTCGTAACGT
18278 TATATCCTTAATCGCTAG-TTTT-GTAACGT
1 TATATCCTTAATCGCTAGCTTTTCGTAACGT
18307 TATATCC
1 TATATCC
18314 CAAATTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
30 4 0.12
31 15 0.45
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.46
Consensus pattern (31 bp):
TATATCCTTAATCGCTAGCTTTTCGTAACGT
Found at i:20092 original size:2 final size:2
Alignment explanation
Indices: 20085--20117 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20075 TTTTATTTTC
20085 AT AT AT AT 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 AT AT AT AT A
20118 AAGAAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23475 original size:33 final size:32
Alignment explanation
Indices: 23438--23580 Score: 122
Period size: 33 Copynumber: 4.7 Consensus size: 32
23428 GGTAATAATA
23438 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGA-TAAATTGGT
* * * **
23471 ATTTGGTAATCAAAGTAAAAAGAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGATAAATTGGT
* *
23503 ATTTGGTAACTAAAGT-------TAAA-TGCT
1 ATTTGGTAATTAAAGTAAAAAGATAAATTGGT
* *
23527 ATTTGGCAATTAAAGTTAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGA-TAAATTGGT
*
23560 ATTTGGTAATCAAAGTAAAAA
1 ATTTGGTAATTAAAGTAAAAA
23581 CTGTTAAAGT
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
24 16 0.19
25 3 0.04
32 23 0.27
33 43 0.51
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (32 bp):
ATTTGGTAATTAAAGTAAAAAGATAAATTGGT
Found at i:23523 original size:24 final size:24
Alignment explanation
Indices: 23496--23546 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
23486 TAAAAAGAAA
*
23496 AAATGAAATTTGGTAACTAAAGTT
1 AAATGAAATTTGGCAACTAAAGTT
** *
23520 AAATGCTATTTGGCAATTAAAGTT
1 AAATGAAATTTGGCAACTAAAGTT
23544 AAA
1 AAA
23547 AGAGTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (24 bp):
AAATGAAATTTGGCAACTAAAGTT
Found at i:25812 original size:25 final size:25
Alignment explanation
Indices: 25737--25814 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 25
25727 AAAAATTAAA
25737 GTAAAAAG-AAAAAA-TGAAATTTG
1 GTAAAAAGAAAAAAAGTGAAATTTG
* * *
25760 GTCATTAAAACAAAAAGAGT--AATATG
1 GT-A--AAAAGAAAAAAAGTGAAATTTG
25786 GTAAAAAGAAAAAAAGTGAAATTTG
1 GTAAAAAGAAAAAAAGTGAAATTTG
25811 GTAA
1 GTAA
25815 CTAAAGTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
23 14 0.33
24 1 0.02
25 10 0.24
26 11 0.26
27 5 0.12
28 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.22
Consensus pattern (25 bp):
GTAAAAAGAAAAAAAGTGAAATTTG
Found at i:25863 original size:33 final size:33
Alignment explanation
Indices: 25822--26081 Score: 120
Period size: 33 Copynumber: 7.9 Consensus size: 33
25812 TAACTAAAGT
25822 TAAA-TGGTATTTGGTAATTAAAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* *
25854 TAAATTGGTATTTAGTAATCAAAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* * ** * **
25887 AAAAAATGAAATTTGGCAATTAAAACAAAAAGAG
1 -TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* **** * *
25921 T-AATATGTTAAAAAG-AGATTAAAGTAAAAACAA
1 TAAAT-TGGTATTTGGTA-ATTAAAGTAAAAAGAG
* ** * ** *
25954 TAAAATGGTCAAAT-GAAATT-TGGTAACTAAAG-T
1 TAAATTGGT-ATTTGGTAATTAAAGTAA--AAAGAG
* ** * * *
25987 TAAA-CGGTATACGGTAATAAAAATAAAAACAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* *
26019 TAAATTGGTATTTGGTAAATATAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
*
26052 TAAAATTGGTATTTGATAATTAAAGTAAAA
1 T-AAATTGGTATTTGGTAATTAAAGTAAAA
26082 TTGGTATAAA
Statistics
Matches: 163, Mismatches: 51, Indels: 26
0.68 0.21 0.11
Matches are distributed among these distances:
31 5 0.03
32 22 0.13
33 78 0.48
34 58 0.36
ACGTcount: A:0.52, C:0.03, G:0.17, T:0.28
Consensus pattern (33 bp):
TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
Found at i:26063 original size:34 final size:33
Alignment explanation
Indices: 26010--26081 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
26000 GTAATAAAAA
* *
26010 TAAAAACAGTAAATTGGTATTTGGTAAATATAG
1 TAAAAACAGTAAATTGGTATTTGATAAATAAAG
* *
26043 TAAAAAGAGTAAAATTGGTATTTGATAATTAAAG
1 TAAAAACAGT-AAATTGGTATTTGATAAATAAAG
26077 TAAAA
1 TAAAA
26082 TTGGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 9 0.26
34 25 0.74
ACGTcount: A:0.50, C:0.01, G:0.17, T:0.32
Consensus pattern (33 bp):
TAAAAACAGTAAATTGGTATTTGATAAATAAAG
Found at i:28851 original size:564 final size:564
Alignment explanation
Indices: 27777--28898 Score: 1890
Period size: 564 Copynumber: 2.0 Consensus size: 564
27767 TCAAGAGGCA
*
27777 AGAATTGAAGATTGGAGCTTAAATTGCGAAGGATTGAAGACAAGCCATGAAGAAGCCCGAAAGCT
1 AGAATTGAAAATTGGAGCTTAAATTGCGAAGGATTGAAGACAAGCCATGAAGAAGCCCGAAAGCT
* *
27842 AAGGAATTTTGGATATTTTATATTGGATAATACTCAGCCCATACAAGCCCATAATTGGAATTAAA
66 AAGGAATTTTGGATATTTTATATGGGATAATACTCAGCCCATACAAGCCCACAATTGGAATTAAA
** * * *
27907 ATCCCAATTTGTGCTGCCTATATCCAAGAAAATCTCCAATTCATGCATATTCTCGCTTCTAGTCC
131 ATCCCAATTTGTGCCACCTATATCCAAGAAAATCTCCAATTCACGCATATTCCCGCTTCAAGTCC
* *
27972 TAACAGGATTAGGATTCAGCGCAGTCTCGGTAGAAAAATCATAACTTTTTGCTGCAATGTCTGTT
196 TAACAGGATTAGGATTCAGCGCAGTCTCGGTAGAAAAATCATAACTTTCTGCTGCAATGTCCGTT
* * *
28037 TTAGGCCTGCGAGTAGGCGTTGGAAAGATAATTCCGATATCTACAACTATCCTTTGAAGTTCAAG
261 TTAGACCCGCGAGTAGGCGTTGGAAAGATAATTCCGAGATCTACAACTATCCTTTGAAGTTCAAG
*
28102 ATATAGTTATGCCATCTTCAAGCCCAAAAACACCGTCGAAGTCCCTGCACGAATCCAGAATTTTT
326 ATACAGTTATGCCATCTTCAAGCCCAAAAACACCGTCGAAGTCCCTGCACGAATCCAGAATTTTT
* *
28167 CAGGATCCTATTTTGACTAGGATTTTGGTTCTAGGAAGACTTTTAGGCTAACGCGGAGACCAAGT
391 CAGGATCCTATTTTGACTAGGATTTTGGTTCTAGGAAGACTTTTAAGCTAACGCGGAGAACAAGT
*
28232 CAGCCCTAAAAACGTCCTAGACTCCTATCCTACTTAGAATTGGAGTTTGTAGGGTTATTTCCACT
456 CAGCCCTAAAAACGTCCTAGACTCCTATCCTACTTAGAATTGGAGTTTCTAGGGTTATTTCCACT
*
28297 ATAGATAGCCACCCTATGTAACACAAATCACACACACAATACCT
521 ATAAATAGCCACCCTATGTAACACAAATCACACACACAATACCT
*
28341 AGAATTGAAAATTGGAGCTTAAATTGCGAAGGATTGAAGACAAGCCATGAAGAAGCCTG-AAGCT
1 AGAATTGAAAATTGGAGCTTAAATTGCGAAGGATTGAAGACAAGCCATGAAGAAGCCCGAAAGCT
* * *
28405 AAGGAATTTTGGATATTTTATATGGGATAGTACTCAGTCCATATAAGCCCACAATTGGAATTAAA
66 AAGGAATTTTGGATATTTTATATGGGATAATACTCAGCCCATACAAGCCCACAATTGGAATTAAA
* *
28470 ATCCCAATTTGTGCCACCTATATCCAAGGAAATAC-CCAATTCCCGCATATTCCCGCTTCAAGTC
131 ATCCCAATTTGTGCCACCTATATCCAAGAAAAT-CTCCAATTCACGCATATTCCCGCTTCAAGTC
*
28534 CTAACAGGATTAGGATTCAGCGCAGTCTCGGTAGAAAAATCATCACTTTCTGCT-CAGATGTCCG
195 CTAACAGGATTAGGATTCAGCGCAGTCTCGGTAGAAAAATCATAACTTTCTGCTGCA-ATGTCCG
* * *
28598 TTTTAGACCCGTGAGTAGGCGTTGGAAAGCTAATTCCGAGATCTACAACTTTTCCTTTGAAGTTC
259 TTTTAGACCCGCGAGTAGGCGTTGGAAAGATAATTCCGAGATCTACAAC-TATCCTTTGAAGTTC
* * **
28663 AAGATGCAGTTCTGCCATCTTCAAGCCCAAAAATGCCGTCGAAGTCCCTGCACGAATCCAGAATT
323 AAGATACAGTTATGCCATCTTCAAGCCCAAAAACACCGTCGAAGTCCCTGCACGAATCCAGAATT
28728 TTTCAGGATCCTATTTTGACTAGGATTTTGGTTCTAGGAAGACTTTTAAGCTAACGCGGAGAACA
388 TTTCAGGATCCTATTTTGACTAGGATTTTGGTTCTAGGAAGACTTTTAAGCTAACGCGGAGAACA
* *
28793 AGTCAGCCCTAAAAACGTCCTAGACTCCTATCCTACTTAGGATTGGGGTTTCTAGGGTTATTTCC
453 AGTCAGCCCTAAAAACGTCCTAGACTCCTATCCTACTTAGAATTGGAGTTTCTAGGGTTATTTCC
28858 ACTATAAATAGCCACCCTATGTAACACAAATCACACACACA
518 ACTATAAATAGCCACCCTATGTAACACAAATCACACACACA
28899 CAATATCTAG
Statistics
Matches: 521, Mismatches: 34, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
562 2 0.00
563 222 0.43
564 297 0.57
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (564 bp):
AGAATTGAAAATTGGAGCTTAAATTGCGAAGGATTGAAGACAAGCCATGAAGAAGCCCGAAAGCT
AAGGAATTTTGGATATTTTATATGGGATAATACTCAGCCCATACAAGCCCACAATTGGAATTAAA
ATCCCAATTTGTGCCACCTATATCCAAGAAAATCTCCAATTCACGCATATTCCCGCTTCAAGTCC
TAACAGGATTAGGATTCAGCGCAGTCTCGGTAGAAAAATCATAACTTTCTGCTGCAATGTCCGTT
TTAGACCCGCGAGTAGGCGTTGGAAAGATAATTCCGAGATCTACAACTATCCTTTGAAGTTCAAG
ATACAGTTATGCCATCTTCAAGCCCAAAAACACCGTCGAAGTCCCTGCACGAATCCAGAATTTTT
CAGGATCCTATTTTGACTAGGATTTTGGTTCTAGGAAGACTTTTAAGCTAACGCGGAGAACAAGT
CAGCCCTAAAAACGTCCTAGACTCCTATCCTACTTAGAATTGGAGTTTCTAGGGTTATTTCCACT
ATAAATAGCCACCCTATGTAACACAAATCACACACACAATACCT
Found at i:33417 original size:17 final size:17
Alignment explanation
Indices: 33397--33430 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33387 GGTAGGTAAA
*
33397 AAAAAAATTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
*
33414 AAAAGAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
33431 GCAAGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAAAAGTGTTTTCAT
Found at i:36557 original size:28 final size:28
Alignment explanation
Indices: 36501--36557 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
36491 ACTCACCTTA
*** *
36501 GAAATCGAAGCACAAAATCTGGAATTTC
1 GAAATCGAAGCACAAAATCCCCAAATTC
*
36529 GAAATGGAAGCACAAAATCCCCAAATTC
1 GAAATCGAAGCACAAAATCCCCAAATTC
36557 G
1 G
36558 CGATTTTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (28 bp):
GAAATCGAAGCACAAAATCCCCAAATTC
Found at i:36979 original size:31 final size:29
Alignment explanation
Indices: 36925--36997 Score: 121
Period size: 31 Copynumber: 2.5 Consensus size: 29
36915 CTTTACTTCC
36925 CATTTTGGTCA-TTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTTCATGTCCAGGGG
36953 CATTTTGGTCATTTTCTTCCATGTCCAGGGG
1 CATTTTGGTCATTTT-TT-CATGTCCAGGGG
36984 CATTTTGGTCATTT
1 CATTTTGGTCATTT
36998 CAAGTGTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 11 0.26
29 3 0.07
30 2 0.05
31 26 0.62
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (29 bp):
CATTTTGGTCATTTTTTCATGTCCAGGGG
Done.