Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010654.1 Corchorus capsularis cultivar CVL-1 contig10675, 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: 27081
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:47 original size:35 final size:35
Alignment explanation
Indices: 1--299 Score: 379
Period size: 35 Copynumber: 8.5 Consensus size: 35
1 AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCT
1 AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCT
*
36 AATTTCCTTGAAATTAAGTCAGTCTATCTTTACCT
1 AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCT
*
71 AATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
1 AATTTCCTTGAAATTAAGCCAGTC-TATCTTTACCT
* * * *
107 AGTTTCCTTGAAACTAAGCCAGTCCT-TTTTTACTT
1 AATTTCCTTGAAATTAAGCCAGT-CTATCTTTACCT
*
142 AATTTCCTTGAAATTAAGCCAGTCTACTTTTTACCT
1 AATTTCCTTGAAATTAAGCCAGTCTA-TCTTTACCT
** * * *
178 AGCTTCCTTGAAACTAAGCCAGTCT-TGTTTTACTT
1 AATTTCCTTGAAATTAAGCCAGTCTAT-CTTTACCT
* * * *
213 AATTTCCCTGAAATTAAGTCACTCT-TCTTTACTT
1 AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCT
*
247 AATTTCCTTGAAATTAAGCCAGTCTATTTTTACCT
1 AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCT
*
282 AATTGCCTTGAAATTAAG
1 AATTTCCTTGAAATTAAG
300 TTAGTCAGTC
Statistics
Matches: 231, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
34 32 0.14
35 136 0.59
36 62 0.27
37 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (35 bp):
AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCT
Found at i:130 original size:71 final size:70
Alignment explanation
Indices: 1--299 Score: 390
Period size: 71 Copynumber: 4.3 Consensus size: 70
* * * *
1 AATTTCCTTGAAATTAAGCCAGTCT-ATCTTTACCTAATTTCCTTGAAATTAAGTCAGTCTATCT
1 AATTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TTT
65 TTACCT
65 TTACCT
* *
71 AATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTT
1 AATTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGT-CTTTT
*
136 TTACTT
65 TTACCT
**
142 AATTTCCTTGAAATTAAGCCAGTCTACTT-TTTACCTAGCTTCCTTGAAACTAAGCCAGTCTTGT
1 AATTTCCTTGAAATTAAGCCAGTCT-CTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT-T
*
206 TTTACTT
64 TTTACCT
* * * *
213 AATTTCCCTGAAATTAAGTCA--CTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTT
1 AATTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TTT
276 TTACCT
65 TTACCT
*
282 AATTGCCTTGAAATTAAG
1 AATTTCCTTGAAATTAAG
300 TTAGTCAGTC
Statistics
Matches: 206, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
68 3 0.01
69 53 0.26
70 29 0.14
71 117 0.57
72 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (70 bp):
AATTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTT
TACCT
Found at i:210 original size:106 final size:104
Alignment explanation
Indices: 1--299 Score: 420
Period size: 106 Copynumber: 2.8 Consensus size: 104
* * *
1 AATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAATTTCCTTGAAATTAAGTCAGTCTATCTT
1 AATTTCCTTGAAATTAAGCCAGTCT-TCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTTT
*
66 TACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCT
65 TACCTAA-TTCCTTGAAATTAAGCCAGTCTTGTCTTTACCT
* * *
107 AGTTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTACTTT
1 AATTTCCTTGAAATTAAGCCAGT-CTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTA-TTT
* * *
172 TTACCTAGCTTCCTTGAAACTAAGCCAGTCTTGT-TTTACTT
64 TTACCTA-ATTCCTTGAAATTAAGCCAGTCTTGTCTTTACCT
* * *
213 AATTTCCCTGAAATTAAGTCACTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTTTT
1 AATTTCCTTGAAATTAAGCCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTTTT
278 ACCTAATTGCCTTGAAATTAAG
66 ACCTAATT-CCTTGAAATTAAG
300 TTAGTCAGTC
Statistics
Matches: 171, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
103 2 0.01
104 22 0.13
105 36 0.21
106 77 0.45
107 34 0.20
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (104 bp):
AATTTCCTTGAAATTAAGCCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATTTTT
ACCTAATTCCTTGAAATTAAGCCAGTCTTGTCTTTACCT
Found at i:483 original size:35 final size:35
Alignment explanation
Indices: 379--538 Score: 194
Period size: 36 Copynumber: 4.5 Consensus size: 35
369 TCATCTTTGG
* * * *
379 ATTAAATCTTTGCTGACTCTACTTAATTTTTGTGGA
1 ATTAAGTCTTTGCT-AATTTACTTAATTTTTGTGAA
* *
415 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGCA
1 ATTAAGTCTTTGCTAA-TTTACTTAATTTTTGTGAA
451 ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAA
1 ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAA
* * **
486 ATTAAGTTTTTGCCAATTTACTTTTTTTTTTTGTGAA
1 ATTAAGTCTTTGCTAATTTAC--TTAATTTTTGTGAA
523 ATTAAGTCTTTGCTAA
1 ATTAAGTCTTTGCTAA
539 CTTCTTTCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
35 37 0.34
36 45 0.42
37 26 0.24
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (35 bp):
ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAA
Found at i:558 original size:12 final size:12
Alignment explanation
Indices: 539--638 Score: 127
Period size: 12 Copynumber: 8.7 Consensus size: 12
529 TCTTTGCTAA
539 CTTC-TTTCAGT
1 CTTCTTTTCAGT
550 CTTCTTTTCAGT
1 CTTCTTTTCAGT
* *
562 CTTATTTCCAGT
1 CTTCTTTTCAGT
*
574 CTTC-TTTCATT
1 CTTCTTTTCAGT
585 CTTCTTTTCAGT
1 CTTCTTTTCAGT
*
597 CTTC-CTTCAGT
1 CTTCTTTTCAGT
*
608 CTTCTTTTTAGT
1 CTTCTTTTCAGT
620 CTTC-TTTCAGT
1 CTTCTTTTCAGT
631 CTTCTTTT
1 CTTCTTTT
639 GCCTAATTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
11 33 0.44
12 42 0.56
ACGTcount: A:0.09, C:0.26, G:0.07, T:0.58
Consensus pattern (12 bp):
CTTCTTTTCAGT
Found at i:569 original size:23 final size:23
Alignment explanation
Indices: 539--638 Score: 139
Period size: 23 Copynumber: 4.3 Consensus size: 23
529 TCTTTGCTAA
539 CTTC-TTTCAGTCTTCTTTTCAGT
1 CTTCTTTTCAGTCTTC-TTTCAGT
* * *
562 CTTATTTCCAGTCTTCTTTCATT
1 CTTCTTTTCAGTCTTCTTTCAGT
*
585 CTTCTTTTCAGTCTTCCTTCAGT
1 CTTCTTTTCAGTCTTCTTTCAGT
*
608 CTTCTTTTTAGTCTTCTTTCAGT
1 CTTCTTTTCAGTCTTCTTTCAGT
631 CTTCTTTT
1 CTTCTTTT
639 GCCTAATTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
23 57 0.85
24 10 0.15
ACGTcount: A:0.09, C:0.26, G:0.07, T:0.58
Consensus pattern (23 bp):
CTTCTTTTCAGTCTTCTTTCAGT
Found at i:579 original size:35 final size:34
Alignment explanation
Indices: 539--633 Score: 129
Period size: 35 Copynumber: 2.8 Consensus size: 34
529 TCTTTGCTAA
*
539 CTTCTTTCAGTCTTCTTTTCAGTCTTATTTCCAGT
1 CTTCTTTCAGTCTTCTTTTCAGTCTTACTT-CAGT
* *
574 CTTCTTTCATTCTTCTTTTCAGTCTTCCTTCAGT
1 CTTCTTTCAGTCTTCTTTTCAGTCTTACTTCAGT
*
608 CTTCTTTTTAGTCTTC-TTTCAGTCTT
1 CTTC-TTTCAGTCTTCTTTTCAGTCTT
634 CTTTTGCCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 18 0.33
35 36 0.67
ACGTcount: A:0.09, C:0.26, G:0.07, T:0.57
Consensus pattern (34 bp):
CTTCTTTCAGTCTTCTTTTCAGTCTTACTTCAGT
Found at i:833 original size:31 final size:31
Alignment explanation
Indices: 795--856 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
785 ACTGTTGCTT
*
795 CCACTTAATTTCTATGAATTAAGTCTTTTGA
1 CCACTTAATTTCGATGAATTAAGTCTTTTGA
826 CCACTTAATTTCGATGAATTAAGTCTTTTGA
1 CCACTTAATTTCGATGAATTAAGTCTTTTGA
857 GTACTGTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (31 bp):
CCACTTAATTTCGATGAATTAAGTCTTTTGA
Found at i:2960 original size:40 final size:41
Alignment explanation
Indices: 2663--3273 Score: 588
Period size: 41 Copynumber: 14.9 Consensus size: 41
2653 GAATAAGACG
****
2663 AAACTAAACAACACCTTCCCACCGGGAAGGGCAAACTGGGAATA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG---A
* *
2707 AGCAACTAAACAACACCTTCCGGTGAGGAAGGACAAACTGGGA
1 A--AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * *
2750 AATCTAAACAACACCTTCCGGTGAGGAAGGGCAAAGTGGGA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * *
2791 AATCTAAACAACACCTTCCGGTGGGGAATGGCAAACTGGGG
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
2832 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACT-GG-
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * * *
2871 ----TAAAAAACACCTTCCGATGGGGAAGAGCGAACTGGGA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
*
2908 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACT-GGA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
2948 AAAGTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
*
2989 AAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG--A
3032 TGTAAACTTTAAACAACACCTTCCGGTGGGGAAGGGCAAAACT-GG-
1 ---AAAC--TAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGA
* * * *
3077 AATCTAAACAACACCTTCCGATTGGGAAGGGCAAGCTGGGA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* ** * *
3118 ATCGGCAACTAGACATTACCTTCCAGTGGGGAAGCGCAAACTGGGA
1 A-----AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * *
3164 GAACTAAACAACACCTTCTGGTGGGGAAAGGCAAACT-GG-
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* ** **
3203 ----TAAACAACACCTTCCGATGGGGAAGGGCAGGCTAAG-
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* **
3239 AAACTAGACAACACCTTCCAATGGGGAAGGGCAAA
1 AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAA
3274 ATTGGAAATT
Statistics
Matches: 479, Mismatches: 59, Indels: 62
0.80 0.10 0.10
Matches are distributed among these distances:
35 57 0.12
36 3 0.01
39 4 0.01
40 98 0.20
41 208 0.43
42 3 0.01
43 3 0.01
44 1 0.00
46 68 0.14
48 29 0.06
49 5 0.01
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (41 bp):
AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
Found at i:3110 original size:88 final size:86
Alignment explanation
Indices: 2871--3306 Score: 370
Period size: 81 Copynumber: 5.2 Consensus size: 86
2861 GGCAAACTGG
* * * * * *
2871 TAAAAAACACCTTCCGATGGGGAAGAGCGAACTGGGAAAAGTAAACAACACCTTCCGGTGGGGAA
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AAACTAAACAACACCTTCCGATGGGGAA
*
2936 GGGCAAACT-GG-A----AAAG
65 GGGCAAACTGGGAATCGGAAAC
*
2952 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAA
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AAACTAAACAACACCTTCCGATGGGGAA
*
3017 GGGCAAACTGGGAAAT-GTAAAC
65 GGGCAAACTGGG-AATCGGAAAC
* *
3039 TTTAAACAACACCTTCCGGTGGGGAAGGGCAAAACT-GGAATCTAAACAACACCTTCCGATTGGG
1 --TAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAAACTAAACAACACCTTCCGATGGGG
* *
3103 AAGGGCAAGCTGGGAATCGGCAAC
63 AAGGGCAAACTGGGAATCGGAAAC
* ** * * * *
3127 TAGACATTACCTTCCAGTGGGGAAGCGCAAACTGGGAGAACTAAACAACACCTTCTGGTGGGGAA
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA-AACTAAACAACACCTTCCGATGGGGAA
*
3192 AGGCAAAC------T-GG----
65 GGGCAAACTGGGAATCGGAAAC
* ** ** * *
3203 TAAACAACACCTTCCGATGGGGAAGGGCAGGCTAAGAAACTAGACAACACCTTCCAATGGGGAAG
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGGGGAAG
* * **
3268 GGCAAAATTGGAAATTTGACAAC
66 GGC-AAACTGGGAATCGGA-AAC
3291 TAAACAACACCTTCCG
1 TAAACAACACCTTCCG
3307 ACTGGGAAAG
Statistics
Matches: 288, Mismatches: 42, Indels: 43
0.77 0.11 0.12
Matches are distributed among these distances:
75 26 0.09
76 30 0.10
80 2 0.01
81 68 0.24
82 3 0.01
83 1 0.00
84 1 0.00
85 5 0.02
86 26 0.09
87 35 0.12
88 57 0.20
89 29 0.10
90 5 0.02
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (86 bp):
TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGGGGAAG
GGCAAACTGGGAATCGGAAAC
Found at i:3314 original size:48 final size:48
Alignment explanation
Indices: 3240--3337 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 48
3230 CAGGCTAAGA
* * *
3240 AACTAGACAACACCTTCCAATGGGGAAGGGCAAAATTGGAAATTTGAC
1 AACTAAACAACACCTTCCAATGGGGAAAGGCAAAATTGGAAATTAGAC
*
3288 AACTAAACAACACCTTCCGACT-GGGAAAGGCAAAATTGGAAATTAGAC
1 AACTAAACAACACCTTCC-AATGGGGAAAGGCAAAATTGGAAATTAGAC
3336 AA
1 AA
3338 AGCTAGTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (48 bp):
AACTAAACAACACCTTCCAATGGGGAAAGGCAAAATTGGAAATTAGAC
Found at i:9064 original size:26 final size:26
Alignment explanation
Indices: 8988--9073 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 26
8978 GAGTACTCTA
* *
8988 AAAAT-CCCCTTGTAGTATAAAGATGACA
1 AAAATACCCC-TG-AGTGTAAA-ATGACC
9016 AAAATACCCCTGAGTGTGAAAATGACC
1 AAAATACCCCTGAGTGT-AAAATGACC
9043 AAAATACCCCT-AGTGGTAAAATGACC
1 AAAATACCCCTGAGT-GTAAAATGACC
9069 AAAAT
1 AAAAT
9074 GCCCTTGGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
26 17 0.32
27 22 0.42
28 10 0.19
29 4 0.08
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (26 bp):
AAAATACCCCTGAGTGTAAAATGACC
Found at i:9342 original size:22 final size:22
Alignment explanation
Indices: 9317--9388 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
9307 GAAGCCCTGG
*
9317 GAAAGCCTGCCCTGAGATGGTT
1 GAAAGCCTGCCCTGAGATGCTT
* ** * *
9339 GAAAGTCTATCTTGAGACGCTT
1 GAAAGCCTGCCCTGAGATGCTT
*
9361 GAAAGCCTGCCCTGAGATGTTT
1 GAAAGCCTGCCCTGAGATGCTT
9383 GGAAAG
1 -GAAAG
9389 AAAGACCGCC
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
22 32 0.86
23 5 0.14
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (22 bp):
GAAAGCCTGCCCTGAGATGCTT
Found at i:15466 original size:36 final size:36
Alignment explanation
Indices: 15419--15542 Score: 134
Period size: 36 Copynumber: 3.5 Consensus size: 36
15409 TAATCTCTTT
*
15419 TTGAGATTAAGTTCTTTATTGATTTCACTTAATTACC
1 TTGA-ATTAAGTTCTTTATTGATCTCACTTAATTACC
*
15456 TTGAATTAAGTTCTTTA-T--TCT-ACGTAATTACC
1 TTGAATTAAGTTCTTTATTGATCTCACTTAATTACC
* * *
15488 CTGCATTAAG-TCTTTTATTGACCTCACTTAATTACAC
1 TTGAATTAAGTTC-TTTATTGATCTCACTTAATTAC-C
15525 -TGAATTAAGTTCTTTATT
1 TTGAATTAAGTTCTTTATT
15543 TTACTAAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
31 2 0.03
32 22 0.30
33 3 0.04
35 3 0.04
36 36 0.49
37 7 0.10
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (36 bp):
TTGAATTAAGTTCTTTATTGATCTCACTTAATTACC
Found at i:15639 original size:71 final size:70
Alignment explanation
Indices: 15556--15999 Score: 522
Period size: 71 Copynumber: 6.3 Consensus size: 70
15546 CTAAATTTCC
* * * *
15556 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCCTT
1 TTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTT--TT
15619 TACCTAA
64 TACCTAA
* * * *
15626 CTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCATTGAAACTAAGCCAGTCCTTTTTT
1 TTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGT-CTTTTTT
*
15691 ACTTAA
65 ACCTAA
* * *
15697 TTTCCTTGAAATTAAGCCAGTCT-ATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
1 TTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TTTTT
*
15761 ACCTAG
65 ACCTAA
* *
15767 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTTTT
1 TTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGT-CTTTTTT
*
15832 ACTTAA
65 ACCTAA
* **
15838 TTTCCTTGAAATTAAGTCAGTCTACTT-TTTACCTAGCTTCCTTGAAACTAAGCCAGTCTTGTTT
1 TTTCCTTGAAATTAAGCCAGTCT-CTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT-TTT
* *
15902 TACTTGA
64 TACCTAA
* * * * * *
15909 TTTCCATGAAATTAAGTCAG--TCTTCTTTACTTAATTTCCTTGAAATTAAGCTAGTCTATCTTT
1 TTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TTTTT
15972 ACCTAA
65 ACCTAA
*
15978 TTTCCTTGAAATTAAGTCAGTC
1 TTTCCTTGAAATTAAGCCAGTC
16000 AGTCTTTCAG
Statistics
Matches: 325, Mismatches: 37, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
68 3 0.01
69 56 0.17
70 68 0.21
71 164 0.50
72 30 0.09
73 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (70 bp):
TTTCCTTGAAATTAAGCCAGTCTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTTTTA
CCTAA
Found at i:15748 original size:177 final size:174
Alignment explanation
Indices: 15556--15999 Score: 536
Period size: 177 Copynumber: 2.5 Consensus size: 174
15546 CTAAATTTCC
15556 TTTCCTGAAATTAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCCTTTA
1 TTTCCTGAAATTAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTT-CTTTA
* * *
15621 CCTAACTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCATTGAAACTAAGCCAGTCCT
65 CCTAATTTCCTTGAAATTAAGCCAGTCCTTT-TTTACCTAATTTCATTGAAACTAAGCCAGT-CT
* * *
15686 -TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTTACCTAA
128 ATTTTTACCTAACTTCCTTGAAACTAAGCCAGTCT-TGCTTTACCTAA
* * * * * *
15732 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAATTAAGCCAGTCTTTTCTTT
1 TTTCC-TGAAATTAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAGTC-TTTCTTT
* * * * * *
15797 ACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTAAGTCAGTCTA
64 ACCTAATTTCCTTGAAATTAAGCCAGTCCTTTTTTACCTAATTTCATTGAAACTAAGCCAGTCTA
* * * *
15862 CTTTTTACCTAGCTTCCTTGAAACTAAGCCAGTCTTGTTTTACTTGA
129 -TTTTTACCTAACTTCCTTGAAACTAAGCCAGTCTTGCTTTACCTAA
** * *
15909 TTTCCATGAAATTAAG--TCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCTAGTCTATCTTT
1 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCTTT
*
15972 ACCTAATTTCCTTGAAATTAAGTCAGTC
64 ACCTAATTTCCTTGAAATTAAGCCAGTC
16000 AGTCTTTCAG
Statistics
Matches: 226, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
175 35 0.15
176 59 0.26
177 129 0.57
178 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (174 bp):
TTTCCTGAAATTAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCTTTAC
CTAATTTCCTTGAAATTAAGCCAGTCCTTTTTTACCTAATTTCATTGAAACTAAGCCAGTCTATT
TTTACCTAACTTCCTTGAAACTAAGCCAGTCTTGCTTTACCTAA
Found at i:16006 original size:35 final size:36
Alignment explanation
Indices: 15556--15999 Score: 504
Period size: 35 Copynumber: 12.6 Consensus size: 36
15546 CTAAATTTCC
* * * *
15556 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
15590 TTTCCTTGAAATTAAGCCAGTCT-TTCCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTATT-CTTTACCTAA
* * *
15626 CTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
* * *
15662 TTTCATTGAAACTAAGCCAGTCCT-TT-TTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-CTATTCTTTACCTAA
15697 TTTCCTTGAAATTAAGCCAGTCTA-TCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
*
15732 TTTCCTTGAAATTAAGCCAGTCTA-TCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
* *
15767 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
* *
15803 TTTCCTTGAAACTAAGCCAGTCCT-TT-TTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-CTATTCTTTACCTAA
* *
15838 TTTCCTTGAAATTAAGTCAGTCTACTT-TTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTA-TTCTTTACCTAA
* * * *
15874 CTTCCTTGAAACTAAGCCAGTCT-TGT-TTTACTTGA
1 TTTCCTTGAAATTAAGCCAGTCTAT-TCTTTACCTAA
* * *
15909 TTTCCATGAAATTAAGTCAGTC--TTCTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
*
15943 TTTCCTTGAAATTAAGCTAGTCTA-TCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
*
15978 TTTCCTTGAAATTAAGTCAGTC
1 TTTCCTTGAAATTAAGCCAGTC
16000 AGTCTTTCAG
Statistics
Matches: 356, Mismatches: 39, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
33 1 0.00
34 41 0.12
35 187 0.53
36 121 0.34
37 6 0.02
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTCCTTGAAATTAAGCCAGTCTATTCTTTACCTAA
Found at i:16113 original size:36 final size:35
Alignment explanation
Indices: 16073--16231 Score: 201
Period size: 36 Copynumber: 4.5 Consensus size: 35
16063 TCATCTTTGG
* * * *
16073 ATTAAATCTTTGCTGACTCTACTTAATTTTTGTGGA
1 ATTAAGTCTTTGCT-AATTTACTTAATTTTTGTGAA
* *
16109 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGCA
1 ATTAAGTCTTTGCTAA-TTTACTTAATTTTTGTGAA
16145 ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAA
1 ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAA
* * **
16180 ATTAAGTTTTTGCCAATTTACATTTTTTTTTGTGAA
1 ATTAAGTCTTTGCTAATTTAC-TTAATTTTTGTGAA
16216 ATTAAGTCTTTGCTAA
1 ATTAAGTCTTTGCTAA
16232 CTTCTTTCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
35 37 0.34
36 71 0.66
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.50
Consensus pattern (35 bp):
ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAA
Found at i:16185 original size:71 final size:71
Alignment explanation
Indices: 16073--16231 Score: 203
Period size: 71 Copynumber: 2.2 Consensus size: 71
16063 TCATCTTTGG
* * * *
16073 ATTAAATCTTTGCTGACTCTACTTAATTTTTGTGGAATTAAGTCTTTGCTAATTTTAC-TTAATT
1 ATTAAGTCTTTGCT-AATCTACTTAATTTTTGTGAAATTAAGTCTTTGCCAA-TTTACATTAATT
*
16137 CTTGTGCA
64 CTTGTGAA
* * ** *
16145 ATTAAGTCTTTGCTAATTTACTTAATTTTTGTGAAATTAAGTTTTTGCCAATTTACATTTTTTTT
1 ATTAAGTCTTTGCTAATCTACTTAATTTTTGTGAAATTAAGTCTTTGCCAATTTACATTAATTCT
16210 TGTGAA
66 TGTGAA
16216 ATTAAGTCTTTGCTAA
1 ATTAAGTCTTTGCTAA
16232 CTTCTTTCAG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
70 5 0.07
71 58 0.76
72 13 0.17
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.50
Consensus pattern (71 bp):
ATTAAGTCTTTGCTAATCTACTTAATTTTTGTGAAATTAAGTCTTTGCCAATTTACATTAATTCT
TGTGAA
Found at i:16251 original size:12 final size:12
Alignment explanation
Indices: 16232--16331 Score: 145
Period size: 12 Copynumber: 8.7 Consensus size: 12
16222 TCTTTGCTAA
16232 CTTC-TTTCAGT
1 CTTCTTTTCAGT
16243 CTTCTTTTCAGT
1 CTTCTTTTCAGT
*
16255 CTTCTTTCCAGT
1 CTTCTTTTCAGT
16267 CTTC-TTTCAGT
1 CTTCTTTTCAGT
16278 CTTCTTTTCAGT
1 CTTCTTTTCAGT
*
16290 CTTC-CTTCAGT
1 CTTCTTTTCAGT
*
16301 CTTCTTTTTAGT
1 CTTCTTTTCAGT
16313 CTTC-TTTCAGT
1 CTTCTTTTCAGT
16324 CTTCTTTT
1 CTTCTTTT
16332 GCCTAATTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
11 34 0.43
12 45 0.57
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.57
Consensus pattern (12 bp):
CTTCTTTTCAGT
Found at i:16331 original size:23 final size:23
Alignment explanation
Indices: 16232--16331 Score: 157
Period size: 23 Copynumber: 4.3 Consensus size: 23
16222 TCTTTGCTAA
16232 CTTC-TTTCAGTCTTCTTTTCAGT
1 CTTCTTTTCAGTCTTC-TTTCAGT
*
16255 CTTCTTTCCAGTCTTCTTTCAGT
1 CTTCTTTTCAGTCTTCTTTCAGT
*
16278 CTTCTTTTCAGTCTTCCTTCAGT
1 CTTCTTTTCAGTCTTCTTTCAGT
*
16301 CTTCTTTTTAGTCTTCTTTCAGT
1 CTTCTTTTCAGTCTTCTTTCAGT
16324 CTTCTTTT
1 CTTCTTTT
16332 GCCTAATTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
23 61 0.86
24 10 0.14
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.57
Consensus pattern (23 bp):
CTTCTTTTCAGTCTTCTTTCAGT
Found at i:20051 original size:27 final size:28
Alignment explanation
Indices: 20016--20092 Score: 113
Period size: 27 Copynumber: 2.8 Consensus size: 28
20006 CCTTCTAGTA
* *
20016 TAAAGATGACAAAAATACCCCTGAGT-G
1 TAAAAATGACCAAAATACCCCTGAGTGG
*
20043 TGAAAATGACCAAAATACCCCT-AGTGG
1 TAAAAATGACCAAAATACCCCTGAGTGG
20070 TAAAAATGACCAAAATACCCCTG
1 TAAAAATGACCAAAATACCCCTG
20093 GAAATTCCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (28 bp):
TAAAAATGACCAAAATACCCCTGAGTGG
Found at i:22332 original size:27 final size:27
Alignment explanation
Indices: 22302--22384 Score: 166
Period size: 27 Copynumber: 3.1 Consensus size: 27
22292 ATAAGCATGC
22302 TAGTTCTAAGAAAGTTGTTAAGGAGTG
1 TAGTTCTAAGAAAGTTGTTAAGGAGTG
22329 TAGTTCTAAGAAAGTTGTTAAGGAGTG
1 TAGTTCTAAGAAAGTTGTTAAGGAGTG
22356 TAGTTCTAAGAAAGTTGTTAAGGAGTG
1 TAGTTCTAAGAAAGTTGTTAAGGAGTG
22383 TA
1 TA
22385 TGTTAGCTAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.34
Consensus pattern (27 bp):
TAGTTCTAAGAAAGTTGTTAAGGAGTG
Found at i:26278 original size:33 final size:32
Alignment explanation
Indices: 26208--26315 Score: 119
Period size: 33 Copynumber: 3.3 Consensus size: 32
26198 AAAGGATCAT
* **
26208 GTGGCCGGTTGTGGCCGGGCATGGCCGAATCAT
1 GTGGCCGGTTGTGGCCGGGCATGTCC-AATCGC
*
26241 GTGGCCGGTTGTGGCCGGGCATGTCCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGTCCA-ATCGC
* *
26274 GTGGCC-GATGATGGCCGGGCATCTCCAAATCGC
1 GTGGCCGGTTG-TGGCCGGGCATGTCC-AATCGC
26307 GTGGCCGGT
1 GTGGCCGGT
26316 GTTGCGCGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
32 4 0.06
33 57 0.90
34 2 0.03
ACGTcount: A:0.11, C:0.27, G:0.41, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTTGTGGCCGGGCATGTCCAATCGC
Done.