Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015951.1 Corchorus olitorius cultivar O-4 contig15984, 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: 42916
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:171 original size:13 final size:12
Alignment explanation
Indices: 148--194 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
138 AAGTTTATTG
148 ATAATATATAAT
1 ATAATATATAAT
160 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
173 ATAACAT-TATT
1 ATAATATATAAT
184 ATCAATATATA
1 AT-AATATATA
195 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:483 original size:31 final size:31
Alignment explanation
Indices: 448--519 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
438 TAAATTATTG
*
448 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
**
479 CAAATTATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAAAAAAATGAAAGTCTTAAATTAAA
510 CAAATTAAAA
1 CAAATTAAAA
520 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 4 0.12
31 29 0.85
32 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:2729 original size:113 final size:111
Alignment explanation
Indices: 2579--3101 Score: 669
Period size: 113 Copynumber: 4.6 Consensus size: 111
2569 GTTTCTGGCT
* ** * ***
2579 AAAACGCCGCTAAATGGGGGCGTTTG-TGGTTAAAAACGCCGCTATATTTAATCTTTTTCCCGGA
1 AAAACGCCGCTAAATGGGGGCGTCTGAT-GTTGGAAACGCCGCCATATTTAAT-TTTTTTTGGGA
** *
2643 AATGCAAATTGGGTAAAAATGAGACTAAAATATTA-CGGCGCTTCTA-CTC
64 AATATAAATTGGGTAAAAATGAGGC-AAAATA-TAGCGGCGCTTCTATC-C
* *
2692 AAAACGTCGCTAAATGGGGGCGTCTGATGCTGGAAACGCCGCCATATTT-A-TTTTTTTGGGAAA
1 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAATTTTTTTTGGGAAA
* * * *
2755 TATAAATTGAGTAAAAATGAGGCAGAAATATAGCGGCGCTTCCAACG
66 TATAAATTGGGTAAAAATGAGGCA-AAATATAGCGGCGCTTCTATCC
2802 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAATTATTTTTTTGGGA
1 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAA-T-TTTTTTTGGGA
*
2867 AATATAAATTGGGTAAAAATGAGGCAAAATATAGCGGCGCTTCCATCC
64 AATATAAATTGGGTAAAAATGAGGCAAAATATAGCGGCGCTTCTATCC
2915 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTCCATATTTAATTTTTT
1 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCG--------CCATATTTAATTTTTT
* *
2980 TTGGGAAATATAAATTGGGTAAAACTGAGGTAAAAATATAGCGGCGCTTCTATCC
58 TTGGGAAATATAAATTGGGTAAAAATGAGG-CAAAATATAGCGGCGCTTCTATCC
*
3035 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACTCGCGCCATATTTAATTTTTTTTGGGAA
1 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGC-CGCCATATTTAATTTTTTTTGGGAA
3100 AT
65 AT
3102 GTCTCAAATA
Statistics
Matches: 368, Mismatches: 24, Indels: 36
0.86 0.06 0.08
Matches are distributed among these distances:
109 3 0.01
110 91 0.25
111 2 0.01
112 1 0.00
113 127 0.35
114 37 0.10
119 34 0.09
120 61 0.17
121 12 0.03
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (111 bp):
AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAATTTTTTTTGGGAAA
TATAAATTGGGTAAAAATGAGGCAAAATATAGCGGCGCTTCTATCC
Found at i:2991 original size:119 final size:123
Alignment explanation
Indices: 2843--3084 Score: 420
Period size: 120 Copynumber: 2.0 Consensus size: 123
2833 GGAAACGCCG
*
2843 CCATATTTAATTATTTTTTTGGGAAATATAAATTGGGTAAAAATGAGG-CAAAATATAGCGGCGC
1 CCATATTTAATTATTTTTTTGGGAAATATAAATTGGGTAAAAATGAGGTAAAAATATAGCGGCGC
2907 TTCCATCCAAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGC-CGCCATATTT
66 TTCCATCCAAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCGCGCCATATTT
*
2964 CCATATTTAA-T-TTTTTTTGGGAAATATAAATTGGGTAAAACTGAGGTAAAAATATAGCGGCGC
1 CCATATTTAATTATTTTTTTGGGAAATATAAATTGGGTAAAAATGAGGTAAAAATATAGCGGCGC
* *
3027 TTCTATCCAAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACTCGCGCCATATTT
66 TTCCATCCAAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCGCGCCATATTT
3085 AATTTTTTTT
Statistics
Matches: 115, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
119 34 0.30
120 61 0.53
121 20 0.17
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (123 bp):
CCATATTTAATTATTTTTTTGGGAAATATAAATTGGGTAAAAATGAGGTAAAAATATAGCGGCGC
TTCCATCCAAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCGCGCCATATTT
Found at i:3068 original size:233 final size:222
Alignment explanation
Indices: 2579--3101 Score: 676
Period size: 223 Copynumber: 2.3 Consensus size: 222
2569 GTTTCTGGCT
* ** * ***
2579 AAAACGCCGCTAAATGGGGGCGTTTG-TGGTTAAAAACGCCGCTATATTTAATCTTTTTCCCGGA
1 AAAACGCCGCTAAATGGGGGCGTCTGAT-GTTGGAAACGCCGCCATATTTAAT-TTTTTTTGGGA
* * *
2643 AATGCAAATTGGGTAAAAATGAGACTAAAATATTACGGCGCTTCTACTCAAAACGTCGCTAAATG
64 AATACAAATTGGGTAAAAATGAGACTAAAATATTACGGCGCTTCCACTCAAAACGCCGCTAAATG
2708 GGGGCGTCTGATGCTGGAAACGCCGCCATATTTATTTTTTTGGGAAATATAAATTGAGTAAAAAT
129 GGGGCGTCTGATGCTGGAAACGCCGCCATATTTATTTTTTTGGGAAATATAAATTGAGTAAAAAT
* *
2773 GAGGCAGAAATATAGCGGCGCTTCCAACG
194 GAGGCAAAAATATAGCGGCGCTTCCAACC
2802 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAATTATTTTTTTGGGA
1 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAA-T-TTTTTTTGGGA
* *
2867 AATATAAATTGGGTAAAAATGAGGC-AAAATA-TAGCGGCGCTTCCA-TCCAAAACGCCGCTAAA
64 AATACAAATTGGGTAAAAATGAGACTAAAATATTA-CGGCGCTTCCACT-CAAAACGCCGCTAAA
*
2929 TGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTCCATATTTAATTTTTTTTGGGAAATATAAA
127 TGGGGGCGTCTGATGCTGGAAACGCCG--------CCATATTT-A-TTTTTTTGGGAAATATAAA
* * * * *
2994 TTGGGTAAAACTGAGGTAAAAATATAGCGGCGCTTCTATCC
182 TTGAGTAAAAATGAGGCAAAAATATAGCGGCGCTTCCAACC
*
3035 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACTCGCGCCATATTTAATTTTTTTTGGGAA
1 AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGC-CGCCATATTTAATTTTTTTTGGGAA
3100 AT
65 AT
3102 GTCTCAAATA
Statistics
Matches: 263, Mismatches: 22, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
222 3 0.01
223 101 0.38
224 32 0.12
231 8 0.03
232 15 0.06
233 92 0.35
234 12 0.05
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (222 bp):
AAAACGCCGCTAAATGGGGGCGTCTGATGTTGGAAACGCCGCCATATTTAATTTTTTTTGGGAAA
TACAAATTGGGTAAAAATGAGACTAAAATATTACGGCGCTTCCACTCAAAACGCCGCTAAATGGG
GGCGTCTGATGCTGGAAACGCCGCCATATTTATTTTTTTGGGAAATATAAATTGAGTAAAAATGA
GGCAAAAATATAGCGGCGCTTCCAACC
Found at i:5157 original size:52 final size:52
Alignment explanation
Indices: 5079--5212 Score: 259
Period size: 52 Copynumber: 2.6 Consensus size: 52
5069 CTCCTTGTAA
5079 GCAAATTCCCCTATATACCTGGTACTTTCCCCTATACGCCCATTTTTACCTC
1 GCAAATTCCCCTATATACCTGGTACTTTCCCCTATACGCCCATTTTTACCTC
*
5131 GCAAATTCCCTTATATACCTGGTACTTTCCCCTATACGCCCATTTTTACCTC
1 GCAAATTCCCCTATATACCTGGTACTTTCCCCTATACGCCCATTTTTACCTC
5183 GCAAATTCCCCTATATACCTGGTACTTTCC
1 GCAAATTCCCCTATATACCTGGTACTTTCC
5213 TTTTCCTTTC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 80 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (52 bp):
GCAAATTCCCCTATATACCTGGTACTTTCCCCTATACGCCCATTTTTACCTC
Found at i:5322 original size:14 final size:14
Alignment explanation
Indices: 5303--5330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5293 AAATTAAGAC
5303 TTATTTTATTGGGT
1 TTATTTTATTGGGT
5317 TTATTTTATTGGGT
1 TTATTTTATTGGGT
5331 GGAATTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.64
Consensus pattern (14 bp):
TTATTTTATTGGGT
Found at i:5456 original size:16 final size:17
Alignment explanation
Indices: 5435--5466 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5425 TGTCATATTC
5435 TGTAA-TAAACTTAATA
1 TGTAATTAAACTTAATA
5451 TGTAATTAAACTTAAT
1 TGTAATTAAACTTAAT
5467 CTCCTATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TGTAATTAAACTTAATA
Found at i:5859 original size:32 final size:32
Alignment explanation
Indices: 5823--5912 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
5813 AATAAAGAAG
* *
5823 CCACTAAATAGCGGCGTTTTTTTACGGAAACC
1 CCACTAAATAGCGGCGCTTTTGTACGGAAACC
* *
5855 CCACTAAATAGTGGCGCTTTTGTACGGAAACG
1 CCACTAAATAGCGGCGCTTTTGTACGGAAACC
** *
5887 CCACTATTTAGTGGCGCTTTTGTACG
1 CCACTAAATAGCGGCGCTTTTGTACG
5913 TAAATAGCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (32 bp):
CCACTAAATAGCGGCGCTTTTGTACGGAAACC
Found at i:17928 original size:22 final size:21
Alignment explanation
Indices: 17903--17945 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17893 GGTGTGTGTG
* *
17903 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATAGATTGGTTT-GTAGA
17925 TGTGATAGATTGGTTTGTAGA
1 TGTGATAGATTGGTTTGTAGA
17946 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (21 bp):
TGTGATAGATTGGTTTGTAGA
Found at i:17976 original size:25 final size:25
Alignment explanation
Indices: 17942--17990 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
17932 GATTGGTTTG
17942 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
17967 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
17991 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:18581 original size:21 final size:21
Alignment explanation
Indices: 18543--18582 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18533 ACTGGAAAAA
*
18543 CGTTGGTAAAAGTGTAAAATC
1 CGTTGGTAAAAGTATAAAATC
* *
18564 CGTTGGTATAGGTATAAAA
1 CGTTGGTAAAAGTATAAAA
18583 ATTCCTATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (21 bp):
CGTTGGTAAAAGTATAAAATC
Found at i:19210 original size:2 final size:2
Alignment explanation
Indices: 19203--19241 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19193 ACTCCGTTTA
19203 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
19242 CTCGGGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:22437 original size:25 final size:24
Alignment explanation
Indices: 22372--22438 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
22362 AAGAAAAGGA
* *
22372 AAAAGAAATTGAAAAAGGAAAAAC
1 AAAAGTAATTGAAAAACGAAAAAC
* *
22396 AAAA-TAACTTTGTAAAATCGAAAAAG
1 AAAAGTAA--TTG-AAAAACGAAAAAC
22422 AAAAGTAATTGAAAAAC
1 AAAAGTAATTGAAAAAC
22439 CTAAAAACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
23 2 0.06
24 9 0.26
25 6 0.18
26 14 0.41
27 3 0.09
ACGTcount: A:0.64, C:0.06, G:0.13, T:0.16
Consensus pattern (24 bp):
AAAAGTAATTGAAAAACGAAAAAC
Found at i:29445 original size:36 final size:38
Alignment explanation
Indices: 29370--29445 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
29360 AATGGTTTAA
* * * *
29370 TTAGTTTAATTTTCTATAAAGTTAGGTAAATTAGTAAT
1 TTAGTTTAATTCTCAATAAAGTTAGGTAAATGAGAAAT
29408 TTAGTTTAATTCTCAATAAA-TT-GGTAAA-GAGGAAAT
1 TTAGTTTAATTCTCAATAAAGTTAGGTAAATGA-GAAAT
29444 TT
1 TT
29446 TTTGAATTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
35 1 0.03
36 12 0.36
37 2 0.06
38 18 0.55
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.43
Consensus pattern (38 bp):
TTAGTTTAATTCTCAATAAAGTTAGGTAAATGAGAAAT
Found at i:33209 original size:22 final size:21
Alignment explanation
Indices: 33162--33212 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
33152 ATTTAAAAAA
33162 CTTTTTTGATGAGAACTTTCC
1 CTTTTTTGATGAGAACTTTCC
33183 CTTTTTTGATGAGAACTTTCC
1 CTTTTTTGATGAGAACTTTCC
33204 CTTTTTTGA
1 CTTTTTTGA
33213 AAACGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.51
Consensus pattern (21 bp):
CTTTTTTGATGAGAACTTTCC
Found at i:33421 original size:18 final size:18
Alignment explanation
Indices: 33386--33423 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
33376 CTTTTTAAAT
*
33386 TTTTTTATTATATTTTCC
1 TTTTTTATTATATCTTCC
33404 TTTTTTATTCAT-TCTTCC
1 TTTTTTATT-ATATCTTCC
33422 TT
1 TT
33424 ACTTGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATTATATCTTCC
Found at i:33554 original size:29 final size:26
Alignment explanation
Indices: 33522--33589 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
33512 CATTTTACTC
*
33522 TTTACTGATTACCCTTTTACTACTCCTTT
1 TTTACTGATTACCATTTT--TAC-CCTTT
*
33551 TTTATTGATTACCATTTTTACCCTTT
1 TTTACTGATTACCATTTTTACCCTTT
*
33577 TTAACTTGATTAC
1 TTTAC-TGATTAC
33590 TTTTTTAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 8 0.24
27 10 0.29
29 16 0.47
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTACTGATTACCATTTTTACCCTTT
Found at i:33606 original size:18 final size:17
Alignment explanation
Indices: 33574--33608 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
33564 ATTTTTACCC
*
33574 TTTTTAACTTGATTACT
1 TTTTTAACTTAATTACT
33591 TTTTTAACTTAAATTACT
1 TTTTTAACTT-AATTACT
33609 AGTTACCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTTAACTTAATTACT
Found at i:33736 original size:26 final size:26
Alignment explanation
Indices: 33661--33721 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
33651 ATTTTACCCT
** *
33661 TTTTTACT-TTAAAAACTGAATACCA
1 TTTTTACTCTTAATTACTAAATACCA
33686 TTTTTACTCTTAATTACTAAATACC-
1 TTTTTACTCTTAATTACTAAATACCA
33711 TTTTTACTCTT
1 TTTTTACTCTT
33722 TTTAACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTACTCTTAATTACTAAATACCA
Found at i:33776 original size:35 final size:35
Alignment explanation
Indices: 33686--33859 Score: 248
Period size: 35 Copynumber: 5.1 Consensus size: 35
33676 CTGAATACCA
*
33686 TTTTT-ACTCTTAATTACTAAATACC-TTTTTACTC
1 TTTTTAACT-TTAATTACCAAATACCATTTTTACTC
*
33720 TTTTTAAC-TTAATTACCAAATACCATTTGTACTC
1 TTTTTAACTTTAATTACCAAATACCATTTTTACTC
* * **
33754 TTCTCAACTTTAATTATTAAATACCATTTTTACTC
1 TTTTTAACTTTAATTACCAAATACCATTTTTACTC
33789 TTTTTAACTTTAATTACCAAATACCATTTTTACTC
1 TTTTTAACTTTAATTACCAAATACCATTTTTACTC
*
33824 TTTTTAACTTTAATTACCATATACCA-TTTTACTC
1 TTTTTAACTTTAATTACCAAATACCATTTTTACTC
33858 TT
1 TT
33860 CTCAATTTTT
Statistics
Matches: 125, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
33 15 0.12
34 29 0.23
35 81 0.65
ACGTcount: A:0.30, C:0.20, G:0.01, T:0.49
Consensus pattern (35 bp):
TTTTTAACTTTAATTACCAAATACCATTTTTACTC
Found at i:33897 original size:25 final size:25
Alignment explanation
Indices: 33845--33897 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
33835 AATTACCATA
**
33845 TACCATTTTACTCTTCTCAATTTTT
1 TACCATTTTACTCTTCTCAATTAAT
*
33870 TACCATTTTACTCTT-TGAATTGAAT
1 TACCATTTTACTCTTCTCAATT-AAT
33895 TAC
1 TAC
33898 TGATTACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.51
Consensus pattern (25 bp):
TACCATTTTACTCTTCTCAATTAAT
Found at i:33944 original size:42 final size:42
Alignment explanation
Indices: 33894--33979 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 42
33884 TTGAATTGAA
*
33894 TTACTGATTACGATTACCATCT-TAA-TGATTACTC-TTTACTCT
1 TTACTGATTA--ATTACCAT-TAAAACTGATTACTCTTTTACTCT
33936 TTACTGATTAATTACCATTAAAACTGATTACTCTTTTACTCT
1 TTACTGATTAATTACCATTAAAACTGATTACTCTTTTACTCT
33978 TT
1 TT
33980 GAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
39 1 0.03
40 10 0.25
41 9 0.22
42 20 0.50
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.47
Consensus pattern (42 bp):
TTACTGATTAATTACCATTAAAACTGATTACTCTTTTACTCT
Found at i:34005 original size:95 final size:95
Alignment explanation
Indices: 33875--34127 Score: 300
Period size: 99 Copynumber: 2.6 Consensus size: 95
33865 TTTTTTACCA
* * * * *
33875 TTTTACTCTTTGAA-TTGAATTACTGATTACGATTACCATCTTAATGATTACTCTTTACTCTTTA
1 TTTTACTCTTTGAATTTTAATTACTGATTTCCATTACCATATTACTGATTACTCTTTACTCTTTA
*
33939 CTG-A-T-TAATTACCATTAAAACTGATTACT
66 CTGAATTATAATTACC-TT-AAACCGATTACT
33968 CTTTTACTCTTTGAATTTTAATTACTGATTTCCATTACCATATTACTGATTACTCTTTACTCTTT
1 -TTTTACTCTTTGAATTTTAATTACTGATTTCCATTACCATATTACTGATTACTCTTTACTCTTT
**
34033 ACTGAATTACTAATTACCTTTTACCGATTACT
65 ACTGAATTA-TAATTACCTTAAACCGATTACT
* * *
34065 GTTTAGC-CTTTGAATTTAATTAATTACTGATTTCTATTACCATTTTACTGATTACTCTTTACT
1 TTTTA-CTCTTTGAA-TT--TTAATTACTGATTTCCATTACCATATTACTGATTACTCTTTACT
34128 GAATTACTAA
Statistics
Matches: 139, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
94 14 0.10
95 48 0.35
96 12 0.09
97 13 0.09
98 2 0.01
99 50 0.36
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (95 bp):
TTTTACTCTTTGAATTTTAATTACTGATTTCCATTACCATATTACTGATTACTCTTTACTCTTTA
CTGAATTATAATTACCTTAAACCGATTACT
Found at i:34049 original size:22 final size:20
Alignment explanation
Indices: 34010--34064 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
34000 CATTACCATA
**
34010 TTACTGATTACTCTTTACTCT
1 TTACTGATTACTAATTAC-CT
34031 TTACTGAATTACTAATTACCTT
1 TTACTG-ATTACTAATTACC-T
*
34053 TTACCGATTACT
1 TTACTGATTACT
34065 GTTTAGCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.47
Consensus pattern (20 bp):
TTACTGATTACTAATTACCT
Found at i:34134 original size:22 final size:21
Alignment explanation
Indices: 34109--34213 Score: 79
Period size: 22 Copynumber: 4.9 Consensus size: 21
34099 TATTACCATT
34109 TTACTGATTACTCTTTACTGAA
1 TTACTGATTACTCTTTACTG-A
* *
34131 TTACTAATTACCCTTTTACTGA
1 TTACTGATTACTC-TTTACTGA
* ** *
34153 TTGCTCTTTTTCTCTTTACTGA
1 TTACT-GATTACTCTTTACTGA
34175 TTACT-ATTAC-CATTTTACTGA
1 TTACTGATTACTC--TTTACTGA
* *
34196 TTACTGTTTACTTTTTAC
1 TTACTGATTACTCTTTAC
34214 CATTACCATT
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 18 0.28
22 32 0.49
23 11 0.17
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (21 bp):
TTACTGATTACTCTTTACTGA
Found at i:34190 original size:80 final size:78
Alignment explanation
Indices: 34088--34239 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 78
34078 ATTTAATTAA
* *
34088 TTACTGATTTCTATTACCATTTTACTGATTACTCTTTACTGAATTACTAATTACCCTTTTACTGA
1 TTACTGATTACTATTACCATTTTACTGATTACTCTTTACT-AATTAC-AATTACCATTTTACTGA
*
34153 TTGCTCTTTTTCTCT
64 TTACTCTTTTTCTCT
* ** *
34168 TTACTGATTACTATTACCATTTTACTGATTACTGTTTACTTTTTACCATTACCATTTTACTGATT
1 TTACTGATTACTATTACCATTTTACTGATTACTCTTTACTAATTACAATTACCATTTTACTGATT
34233 ACTCTTT
66 ACTCTTT
34240 ACTCTTCATC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 23 0.35
79 4 0.06
80 38 0.58
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.51
Consensus pattern (78 bp):
TTACTGATTACTATTACCATTTTACTGATTACTCTTTACTAATTACAATTACCATTTTACTGATT
ACTCTTTTTCTCT
Found at i:34219 original size:35 final size:35
Alignment explanation
Indices: 34164--34269 Score: 142
Period size: 35 Copynumber: 3.1 Consensus size: 35
34154 TGCTCTTTTT
** *
34164 CTCTTTACTGATTACTATTACCATTTTACTGATTA
1 CTCTTTACTCTTTACCATTACCATTTTACTGATTA
* *
34199 CTGTTTACTTTTTACCATTACCATTTTACTGATTA
1 CTCTTTACTCTTTACCATTACCATTTTACTGATTA
* *
34234 CTCTTTACTCTTCATCATTACC-TTTTACTGATTA
1 CTCTTTACTCTTTACCATTACCATTTTACTGATTA
34268 CT
1 CT
34270 TTTTTTAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
34 14 0.22
35 49 0.78
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (35 bp):
CTCTTTACTCTTTACCATTACCATTTTACTGATTA
Done.