Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016045.1 Corchorus olitorius cultivar O-4 contig16078, 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: 43446
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:2364 original size:6 final size:6
Alignment explanation
Indices: 2348--2379 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2338 TGAACAAACA
*
2348 AAACTT GAACTT AAACTT AAACTT AAACTT AA
1 AAACTT AAACTT AAACTT AAACTT AAACTT AA
2380 TTAAGAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (6 bp):
AAACTT
Found at i:2462 original size:11 final size:11
Alignment explanation
Indices: 2448--2472 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2438 TTCCACCAAA
2448 AAAAATAAAAG
1 AAAAATAAAAG
2459 AAAAATAAAAG
1 AAAAATAAAAG
2470 AAA
1 AAA
2473 TGGAACCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:14203 original size:21 final size:20
Alignment explanation
Indices: 14164--14208 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
14154 AAATAACAAT
* *
14164 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
14184 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
14205 TAAA
1 TAAA
14209 TCTAACTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:16494 original size:30 final size:32
Alignment explanation
Indices: 16458--16519 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
16448 ATAAAATGAG
* *
16458 TAGCCCA-TATATAA-GTGGGTTGTGCCGTGC
1 TAGCCCATTATATAATATGGGTCGTGCCGTGC
*
16488 TAGCCCATTTTATAATATGGGTCGTGCCGTGC
1 TAGCCCATTATATAATATGGGTCGTGCCGTGC
16520 CAATCCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 6 0.22
32 14 0.52
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (32 bp):
TAGCCCATTATATAATATGGGTCGTGCCGTGC
Found at i:16817 original size:22 final size:22
Alignment explanation
Indices: 16789--16843 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
16779 TACATTAAAA
*
16789 ATGGGTCGTGCTCCGTCGGCAC
1 ATGGGTCGTGCTCCGCCGGCAC
**
16811 ATGGGTCGTGCTGTGCCGGCAC
1 ATGGGTCGTGCTCCGCCGGCAC
*
16833 GTGGGTCGTGC
1 ATGGGTCGTGC
16844 CGTGCCATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.07, C:0.27, G:0.42, T:0.24
Consensus pattern (22 bp):
ATGGGTCGTGCTCCGCCGGCAC
Found at i:17384 original size:89 final size:89
Alignment explanation
Indices: 17266--17570 Score: 520
Period size: 89 Copynumber: 3.4 Consensus size: 89
17256 CCTGTTGGCT
* *
17266 GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTAAACATTCTATAGCAACGGAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTAAACATTCTATAGCAACGTAAGCCGTAGGTA
*
17331 TATCTCCAATCATACTATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* *
17355 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCATAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTAAACATTCTATAGCAACGTAAGCCGTAGGTA
17420 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* *
17444 GTTTGTGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTAAACATTCTATAGCAACGTAAGCCGTAGGTA
17509 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* * *
17533 GTTTATGGCTATACCAACGCCACACGCCGTTTGTAAAC
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTAAAC
17571 TGTGGGGTCA
Statistics
Matches: 204, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 204 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (89 bp):
GTTTATGGCTATACCAACGCCACCCGCTGTTGGTAAACATTCTATAGCAACGTAAGCCGTAGGTA
TATCTCCAATCATACCATTTTTTG
Found at i:27087 original size:161 final size:161
Alignment explanation
Indices: 26898--27213 Score: 578
Period size: 161 Copynumber: 2.0 Consensus size: 161
26888 GAGAACCGTC
*
26898 GAACATCAGGAAGAGAATCGCCAGAACTCTCCTTCTAAATGGAGAGGAAAACAAATAAGAATGAG
1 GAACATCAAGAAGAGAATCGCCAGAACTCTCCTTCTAAATGGAGAGGAAAACAAATAAGAATGAG
*
26963 ATTGGAAGATTTAGTGGACTGAATCGAAGATTGGAAGCAGAGAAAGTGGAGTGGCGAAGTGAATC
66 ATTGGAAGATTTAGTGGACTGAATCGAAGATTGGAAGCAGAGAAAGTGGAGTGGCCAAGTGAATC
27028 GAAGCAAGTGGAAAAATCCCCAAATGGCGAG
131 GAAGCAAGTGGAAAAATCCCCAAATGGCGAG
* * *
27059 GAACATCAAGAAGAGAATCGCTAGAACTCTCCTTCTAAATGGCGAGGAAAAGAAATAAGAATGAG
1 GAACATCAAGAAGAGAATCGCCAGAACTCTCCTTCTAAATGGAGAGGAAAACAAATAAGAATGAG
*
27124 ATTGGAAGATTTAGTGGACTGAATCGAAGATTGGAAGTAGAGAAAGTGGAGTGGCCAAGTGAATC
66 ATTGGAAGATTTAGTGGACTGAATCGAAGATTGGAAGCAGAGAAAGTGGAGTGGCCAAGTGAATC
27189 GAAGCAAGTGGAAAAATCCCCAAAT
131 GAAGCAAGTGGAAAAATCCCCAAAT
27214 TTTGTATTTC
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
161 149 1.00
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.18
Consensus pattern (161 bp):
GAACATCAAGAAGAGAATCGCCAGAACTCTCCTTCTAAATGGAGAGGAAAACAAATAAGAATGAG
ATTGGAAGATTTAGTGGACTGAATCGAAGATTGGAAGCAGAGAAAGTGGAGTGGCCAAGTGAATC
GAAGCAAGTGGAAAAATCCCCAAATGGCGAG
Found at i:28463 original size:15 final size:15
Alignment explanation
Indices: 28439--28472 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28429 TCATCAAGAA
*
28439 CAAGTCCCTGCATAC
1 CAAGTACCTGCATAC
*
28454 CAAGTACCTGCATAT
1 CAAGTACCTGCATAC
28469 CAAG
1 CAAG
28473 CTTCTGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAGTACCTGCATAC
Found at i:31908 original size:19 final size:20
Alignment explanation
Indices: 31867--31929 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
31857 TATCAATTTA
*
31867 TTTT-AATAATCTTATAAA-C
1 TTTTAAATAA-CTTATAAAGT
*
31886 TTTTAACTAA-TTATAAAGT
1 TTTTAAATAACTTATAAAGT
*
31905 TTTTAAATAACCTTATTAAGT
1 TTTTAAATAA-CTTATAAAGT
31926 TTTT
1 TTTT
31930 TAGGAACCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 7 0.19
19 13 0.36
20 4 0.11
21 12 0.33
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTAAATAACTTATAAAGT
Found at i:32075 original size:20 final size:20
Alignment explanation
Indices: 32016--32075 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
32006 CTTAATCTTA
*
32016 TTAAGTATTTTAGTGACCTCG
1 TTAAGT-TTTTAGTGACTTCG
* *
32037 TTAAGTTTTATAGTAACTTCT
1 TTAAGTTTT-TAGTGACTTCG
32058 TTAAGTTTTTAGTGACTT
1 TTAAGTTTTTAGTGACTT
32076 TATTAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.32
21 23 0.68
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (20 bp):
TTAAGTTTTTAGTGACTTCG
Found at i:32081 original size:20 final size:20
Alignment explanation
Indices: 32013--32081 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
32003 AATCTTAATC
*
32013 TTATTAAGTATTTTAGTGACC
1 TTATTAAGT-TTTTAGTGACT
** *
32034 TCGTTAAGTTTTATAGTAACT
1 TTATTAAGTTTT-TAGTGACT
32055 TCT-TTAAGTTTTTAGTGACT
1 T-TATTAAGTTTTTAGTGACT
32075 TTATTAA
1 TTATTAA
32082 TATTGTTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 23 0.59
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (20 bp):
TTATTAAGTTTTTAGTGACT
Found at i:33868 original size:201 final size:200
Alignment explanation
Indices: 33523--34433 Score: 1284
Period size: 201 Copynumber: 4.6 Consensus size: 200
33513 CCCTAAACTC
* * * * *
33523 TAATATTCAAAAC-TATTCCCTAAGGGGAAACATGTCAACCCTTAAACCTCGCACATGCAGTCTG
1 TAATATT-AATACATATTTCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTG
* * *
33587 CTAAACTCCACT-AGCGGTGTATTGTATAATATTTT-TTTTTGGATTATTATACAATACATTGTC
65 CTAAACTCCACTGA-CGGTGTATTGTATAAT-TTTTCTTATAGGATTATTATACAATACACTGTC
* *
33650 AGTGTAAATTTTGGACTCTATAAGCGAGTTAAGAAGTTGACACATACCCCATTTCATAATTAATC
128 AGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAT-
33715 AAATATATT
192 AAATATATT
* * *
33724 TAATATTAATACATATTTCCTTAGGGGACACATGTCGACCCTTAAACCCCGCACATGCAGTCTGC
1 TAATATTAATACATATTTCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
* * * *
33789 TAAACTCCAGTGACGGTTTATTGTATAATTCTTCTTATATGATTATTATACAATACACTGTCAGT
66 TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
* * *
33854 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACCCCATTTTATAATTAAGAAAA
131 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAA-TAAA
33919 TATATT
195 TATATT
*
33925 TAATATTAATACATA-TTCTCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTG
1 TAATATTAATACATATTTC-CTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTG
* * *
33989 CTAAACTCCACTGACGGTGTATTGTATACTTTTTCTTATAGGATTATTATACAATTCACTGTTAG
65 CTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAG
* * * *
34054 TGTAAATTTTAGACTCCATAAGTGGGTTAAGAGGTTGACACATACCCCATTTCATAATTAATTAA
130 TGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAA
34119 -ATATT
195 TATATT
* *
34124 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCACACGTGCAGTCTGC
1 TAATATTAATACATATTTCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
* *
34189 TAAACTACACTGACGGTATATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTC---
66 TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
34251 -TAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAATAAA
131 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATT-AATAAA
34315 TATATT
195 TATATT
* * * * * *
34321 TAATATTAATGCATATTTCCCT-ATGGGACACATGTCGACCCTTAAACCTCGCACGTGCATTATG
1 TAATATTAATACATATTT-CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTG
* *** * *
34385 CTAAACTCTACTGAAATTGTATTGTATAATTTTTCTTGTAGAATTATTA
65 CTAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTA
34434 ATTTATTGAG
Statistics
Matches: 637, Mismatches: 64, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
195 54 0.08
196 5 0.01
197 98 0.15
198 3 0.00
199 121 0.19
200 14 0.02
201 341 0.54
202 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (200 bp):
TAATATTAATACATATTTCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGT
GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAAT
ATATT
Found at i:34552 original size:21 final size:21
Alignment explanation
Indices: 34506--34553 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
34496 TTGATATATG
*
34506 CTTTATAGTAGCATTATTAAA
1 CTTTTTAGTAGCATTATTAAA
*
34527 CTTTTTAGTAAGC-TTATTTAA
1 CTTTTTAGT-AGCATTATTAAA
*
34548 GTTTTT
1 CTTTTT
34554 TATGATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.52
Consensus pattern (21 bp):
CTTTTTAGTAGCATTATTAAA
Found at i:34784 original size:21 final size:23
Alignment explanation
Indices: 34760--34802 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
34750 TATGAAGCTT
34760 TATTTTAGTAA-TTA-TATTAAC
1 TATTTTAGTAACTTATTATTAAC
34781 TATTTTAGTAACTTATTATTAA
1 TATTTTAGTAACTTATTATTAA
34803 ACTTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
TATTTTAGTAACTTATTATTAAC
Found at i:36258 original size:37 final size:39
Alignment explanation
Indices: 36194--36267 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
36184 ATTGAATGAG
36194 ACATGCTTCCAAGTTTTTTGTTCTCCACAATT-TTTTCA
1 ACATGCTTCCAAGTTTTTTGTTCTCCACAATTCTTTTCA
36232 ACATGCTTCCAAGTTTTTT-TTCTCCACAATTCTTTT
1 ACATGCTTCCAAGTTTTTTGTTCTCCACAATTCTTTT
36268 TTCTTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 12 0.34
38 23 0.66
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (39 bp):
ACATGCTTCCAAGTTTTTTGTTCTCCACAATTCTTTTCA
Found at i:36890 original size:17 final size:17
Alignment explanation
Indices: 36870--36903 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
36860 GAAGAAGAAC
36870 ATAAGAATACTTCTATA
1 ATAAGAATACTTCTATA
36887 ATAAGAATACTTCTATA
1 ATAAGAATACTTCTATA
36904 GTAATATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (17 bp):
ATAAGAATACTTCTATA
Found at i:36972 original size:12 final size:12
Alignment explanation
Indices: 36955--36979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36945 CTTGTCCCAG
36955 TCATCTAACCTC
1 TCATCTAACCTC
36967 TCATCTAACCTC
1 TCATCTAACCTC
36979 T
1 T
36980 TTGATTGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATCTAACCTC
Found at i:37695 original size:26 final size:24
Alignment explanation
Indices: 37644--37691 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
37634 TTAATTGAAA
37644 TTGATATATGGTATAAAAAAAGAT
1 TTGATATATGGTATAAAAAAAGAT
37668 TTGATATATGGTAT-AAAAAAGAT
1 TTGATATATGGTATAAAAAAAGAT
37691 T
1 T
37692 ATTTTGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (24 bp):
TTGATATATGGTATAAAAAAAGAT
Found at i:37739 original size:21 final size:21
Alignment explanation
Indices: 37689--37743 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
37679 TATAAAAAAG
*
37689 ATTATTTTGTCAAAACCATAT
1 ATTATTTTTTCAAAACCATAT
*
37710 GTATATTTTTTCAAAACCATCA-
1 AT-TATTTTTTCAAAACCAT-AT
37732 ATTATTTTTTCA
1 ATTATTTTTTCA
37744 TGAATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 17 0.59
23 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTATTTTTTCAAAACCATAT
Found at i:38004 original size:2 final size:2
Alignment explanation
Indices: 37997--38040 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
37987 TTGTTATCAT
37997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
38040 T
1 T
38041 TCTATACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39295 original size:17 final size:17
Alignment explanation
Indices: 39263--39295 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39253 AAATTCAAAA
39263 TCTATTGTAACTCTATC
1 TCTATTGTAACTCTATC
39280 TCTATATGTAAC-CTAT
1 TCTAT-TGTAACTCTAT
39296 ATAACTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (17 bp):
TCTATTGTAACTCTATC
Found at i:42303 original size:31 final size:31
Alignment explanation
Indices: 42265--42329 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
42255 ATATAAAGCT
*
42265 TTTAATTTAATAAATACTATTAAAATATAAA
1 TTTAATTTAATAAAAACTATTAAAATATAAA
* *
42296 TTTAATTTGATAAAAACTATTTAAATATAAA
1 TTTAATTTAATAAAAACTATTAAAATATAAA
42327 TTT
1 TTT
42330 TGATAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (31 bp):
TTTAATTTAATAAAAACTATTAAAATATAAA
Found at i:42332 original size:27 final size:29
Alignment explanation
Indices: 42269--42336 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
42259 AAAGCTTTTA
* *
42269 ATTTAATAAATACTATTAAAATATAAATTT
1 ATTTGATAAAAACTATTAAAATATAAA-TT
*
42299 AATTTGATAAAAACTATTTAAATATAAA-T
1 -ATTTGATAAAAACTATTAAAATATAAATT
42328 -TTTGATAAA
1 ATTTGATAAA
42337 GGATGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.26
29 1 0.03
31 24 0.71
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTTGATAAAAACTATTAAAATATAAATT
Found at i:42479 original size:11 final size:11
Alignment explanation
Indices: 42461--42495 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
42451 TTGACAGCAC
42461 AACAAAAACAA
1 AACAAAAACAA
* *
42472 AGCAAAAATAA
1 AACAAAAACAA
42483 AACAAAAACAA
1 AACAAAAACAA
42494 AA
1 AA
42496 AATAGAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:42699 original size:10 final size:10
Alignment explanation
Indices: 42686--42719 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
42676 TTTAATTTGA
42686 ATTTACGGAT
1 ATTTACGGAT
*
42696 ATTTATGGAT
1 ATTTACGGAT
42706 ATTTACGGAT
1 ATTTACGGAT
42716 ATTT
1 ATTT
42720 GGATAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (10 bp):
ATTTACGGAT
Done.