Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014358.1 Corchorus capsularis cultivar CVL-1 contig14379, 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: 55002
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:361 original size:29 final size:29
Alignment explanation
Indices: 290--372 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 29
280 CCAAATGTCT
*
290 AATTGGAGTCTAAAACTTTCAAAAGTTGTTCA
1 AATT-GAGTCTAAAACTTT--AAAGTTGATCA
* *
322 ATTTGAATCTAAAACTTTAAA-TTGAATCA
1 AATTGAGTCTAAAACTTTAAAGTTG-ATCA
*
351 AATTGAGTCTAAACATTTTAAA
1 AATTGAGTCTAAA-ACTTTAAA
373 AAACACCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 7 0.16
31 13 0.30
32 3 0.07
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
AATTGAGTCTAAAACTTTAAAGTTGATCA
Found at i:589 original size:2 final size:2
Alignment explanation
Indices: 582--610 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
572 CCTTTCAATA
582 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 A
611 AACTTAAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:856 original size:3 final size:3
Alignment explanation
Indices: 848--887 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
838 TTTGGGGTTT
848 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
888 TTATTTTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1228 original size:30 final size:30
Alignment explanation
Indices: 1192--1250 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1182 GTTAATAAGC
*
1192 CATTAAAATTTGATGG-TATAAGAGAAAAGT
1 CATTAAAATTTGA-GGCAATAAGAGAAAAGT
1222 CATTAAAATTTGAGGCAATAAGAGAAAAG
1 CATTAAAATTTGAGGCAATAAGAGAAAAG
1251 CCAATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.25
Consensus pattern (30 bp):
CATTAAAATTTGAGGCAATAAGAGAAAAGT
Found at i:1747 original size:22 final size:22
Alignment explanation
Indices: 1722--1765 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1712 TTGGACATTT
1722 GCCTTACCTACGGTACTTTTTG
1 GCCTTACCTACGGTACTTTTTG
1744 GCCTTACCTACGGTACTTTTTG
1 GCCTTACCTACGGTACTTTTTG
1766 TTCGTGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (22 bp):
GCCTTACCTACGGTACTTTTTG
Found at i:2900 original size:7 final size:7
Alignment explanation
Indices: 2888--2913 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2878 GGCTTATTGC
2888 TCACAAG
1 TCACAAG
2895 TCACAAG
1 TCACAAG
2902 TCACAAG
1 TCACAAG
2909 TCACA
1 TCACA
2914 TCACTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15
Consensus pattern (7 bp):
TCACAAG
Found at i:5532 original size:33 final size:33
Alignment explanation
Indices: 5495--5648 Score: 202
Period size: 33 Copynumber: 4.7 Consensus size: 33
5485 CTTAGCCACA
* *
5495 CGGAGCCTCCCCACTATGATGGCTCTGCCACGG
1 CGGAGCCTCCCCACTAGGACGGCTCTGCCACGG
* *
5528 CGGAGCCTCCCCACTAGGGCGGCTCTGCCACAG
1 CGGAGCCTCCCCACTAGGACGGCTCTGCCACGG
* * *
5561 TGGAGCCTCCTCACTAGGGCGGCTCTGCCACGG
1 CGGAGCCTCCCCACTAGGACGGCTCTGCCACGG
*
5594 CGGAGCCGCCCCACTAGGACGGCTCTGCCACGG
1 CGGAGCCTCCCCACTAGGACGGCTCTGCCACGG
* * *
5627 C-TAGCCGCCCCACTAGGGCGGC
1 CGGAGCCTCCCCACTAGGACGGC
5649 AAAACATTTT
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
32 19 0.18
33 89 0.82
ACGTcount: A:0.14, C:0.41, G:0.31, T:0.14
Consensus pattern (33 bp):
CGGAGCCTCCCCACTAGGACGGCTCTGCCACGG
Found at i:5815 original size:33 final size:33
Alignment explanation
Indices: 5772--5834 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5762 ATGCCGTCCC
* *
5772 CCTAGTGCGGCATTACCATGGC-CAGGCCGCTCT
1 CCTAGGGCGGCACTACCATGGCTCA-GCCGCTCT
*
5805 CCTAGGGCGGCCCTACCATGGCTCAGCCGC
1 CCTAGGGCGGCACTACCATGGCTCAGCCGC
5835 CCCCTAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 24 0.92
34 2 0.08
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (33 bp):
CCTAGGGCGGCACTACCATGGCTCAGCCGCTCT
Found at i:7245 original size:57 final size:57
Alignment explanation
Indices: 7157--7271 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
7147 CACCAAAGTG
* *
7157 ACTCAATAATTCTGTGTTCAATATGGGATGTGATATGTTTTCAGATAAGCTTAATAT
1 ACTCAACAATTCTGTGTTCAATACGGGATGTGATATGTTTTCAGATAAGCTTAATAT
* *
7214 ACTCAACAATTTTGTGTTCAATACGGGATGTGATATGTTTTCAGATAAGTTTAATAT
1 ACTCAACAATTCTGTGTTCAATACGGGATGTGATATGTTTTCAGATAAGCTTAATAT
7271 A
1 A
7272 GAGTGGTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (57 bp):
ACTCAACAATTCTGTGTTCAATACGGGATGTGATATGTTTTCAGATAAGCTTAATAT
Found at i:11107 original size:21 final size:21
Alignment explanation
Indices: 11081--11125 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
11071 AGTCTTATCA
11081 CCCCTCAGTCATAAGCCTTCT
1 CCCCTCAGTCATAAGCCTTCT
11102 CCCCTCAGTCATAAGCCTTCT
1 CCCCTCAGTCATAAGCCTTCT
11123 CCC
1 CCC
11126 AATCATCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.47, G:0.09, T:0.27
Consensus pattern (21 bp):
CCCCTCAGTCATAAGCCTTCT
Found at i:16377 original size:23 final size:23
Alignment explanation
Indices: 16347--16396 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
16337 CTACTTAAGA
16347 AATGCTTATAGATGCATGATTAC
1 AATGCTTATAGATGCATGATTAC
16370 AATGCTTATAGATGCATGATTAC
1 AATGCTTATAGATGCATGATTAC
16393 AATG
1 AATG
16397 ATTTTTTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (23 bp):
AATGCTTATAGATGCATGATTAC
Found at i:18341 original size:27 final size:27
Alignment explanation
Indices: 18303--18384 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
18293 ATTTAATCAG
*
18303 AGGAAAAACCAATGACCTCCTTCTGAA
1 AGGAAAAACCAAGGACCTCCTTCTGAA
18330 AGGAAAAACCAAGGACCTCCTTCTGAA
1 AGGAAAAACCAAGGACCTCCTTCTGAA
* *
18357 AGGAAAAGCCAAGGACCTCCTTCCGAA
1 AGGAAAAACCAAGGACCTCCTTCTGAA
18384 A
1 A
18385 AAGCACCAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (27 bp):
AGGAAAAACCAAGGACCTCCTTCTGAA
Found at i:21259 original size:14 final size:15
Alignment explanation
Indices: 21229--21264 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
21219 TCGGTGTTGG
21229 TCGGTGTCGGTTTTTT
1 TCGGT-TCGGTTTTTT
21245 TCGGTTCGGTTTTTT
1 TCGGTTCGGTTTTTT
21260 T-GGTT
1 TCGGTT
21265 TTTATTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 11 0.55
16 5 0.25
ACGTcount: A:0.00, C:0.11, G:0.31, T:0.58
Consensus pattern (15 bp):
TCGGTTCGGTTTTTT
Found at i:24766 original size:14 final size:14
Alignment explanation
Indices: 24747--24775 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24737 TCCATTCATA
24747 AGATTTGATTTGAG
1 AGATTTGATTTGAG
24761 AGATTTGATTTGAG
1 AGATTTGATTTGAG
24775 A
1 A
24776 ATTGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (14 bp):
AGATTTGATTTGAG
Found at i:28027 original size:3 final size:3
Alignment explanation
Indices: 28021--28054 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28011 CTGAGAAAAA
28021 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
28055 GAAAAAGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33304 original size:1 final size:1
Alignment explanation
Indices: 33298--33338 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
33288 AAAGGTTAGG
*
33298 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33339 CTAAGCATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:36296 original size:21 final size:21
Alignment explanation
Indices: 36263--36305 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
36253 TTACTTTGTT
36263 TTTGCTTGCAGAT-ATTTCATA
1 TTTGCTTGCAGATCA-TTCATA
* *
36284 TTTGGTTGTAGATCATTCATA
1 TTTGCTTGCAGATCATTCATA
36305 T
1 T
36306 ATTGATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (21 bp):
TTTGCTTGCAGATCATTCATA
Found at i:36828 original size:42 final size:42
Alignment explanation
Indices: 36769--36854 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
36759 TATAGCATGA
36769 GCAAAACCCTCCATGGAATCAAGCTTTGATGTAAAAGTCTTG
1 GCAAAACCCTCCATGGAATCAAGCTTTGATGTAAAAGTCTTG
36811 GCAAAACCCTCCATGGAATCAAGCTTTGATGTAAAAGTCTTG
1 GCAAAACCCTCCATGGAATCAAGCTTTGATGTAAAAGTCTTG
36853 GC
1 GC
36855 GTTTGCGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
GCAAAACCCTCCATGGAATCAAGCTTTGATGTAAAAGTCTTG
Found at i:42667 original size:11 final size:11
Alignment explanation
Indices: 42647--42681 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
42637 AAGGAGGAGG
*
42647 AAGAAGAAGAA
1 AAGAAAAAGAA
42658 AAGAAAAAGAA
1 AAGAAAAAGAA
*
42669 GAGAAAAAGAA
1 AAGAAAAAGAA
42680 AA
1 AA
42682 AGAGGGTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:42669 original size:17 final size:17
Alignment explanation
Indices: 42647--42684 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
42637 AAGGAGGAGG
42647 AAGAAGA-AGAAAAGAAA
1 AAGAAGAGA-AAAAGAAA
42664 AAGAAGAGAAAAAGAAA
1 AAGAAGAGAAAAAGAAA
42681 AAGA
1 AAGA
42685 GGGTTCGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAGAGAAAAAGAAA
Found at i:43494 original size:35 final size:34
Alignment explanation
Indices: 43449--43754 Score: 256
Period size: 35 Copynumber: 8.6 Consensus size: 34
43439 AGAAATAAGC
* *
43449 AACTTAATTCAGGGTAATTAAGCAAGTCGGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* *
43483 CAACTTAATTCAGGGTAATTAAATGAGTCAGTAAT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * *
43518 CAACTTTAATTCAGGGTAATTAAGTGAGTTAATAAGT
1 -AAC-TTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
* *
43555 AACTTAATTCAGGGTAATCAAGT-AGTTCAATAAGT
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-T
* * * * *
43590 AACTTAATTTAGGGTAATCATGTGAA-TTAGAAGAT
1 AACTTAATTCAGGGTAATTAAGT-AAGTCAGTA-AT
*
43625 AACTTAATTCAGGGTAATTAAGTAAATCAGTAATGAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-A--A-T
* * * * * *
43663 AATTTCATTCAAGGTAATTAAGTGAGTTAATAAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
* * *
43698 AACTTAATTTAGGGTAATTAAGCAAGTCCGTAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
43733 AACTTAATTCAGGGTAATTAAG
1 AACTTAATTCAGGGTAATTAAG
43755 ATCGACTTAA
Statistics
Matches: 224, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
34 4 0.02
35 158 0.71
36 32 0.14
37 5 0.02
38 25 0.11
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (34 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
Found at i:43736 original size:108 final size:105
Alignment explanation
Indices: 43484--43754 Score: 296
Period size: 108 Copynumber: 2.5 Consensus size: 105
43474 GTCGGTAATC
* *** * * *
43484 AACTTAATTCAGGGTAATTAAATGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTTA
1 AACTTAATTTAGGGTAATTAAGCAAGTCAGTAATTAAC-TTAATTCAGGGTAATTAAGTAAATTA
*
43549 ATAAGTAACTTAATTCAGGGTAATCAAGTAGTTCAATAAGT
65 ATAAGTAACTTAATTCAAGGTAATCAAGTAGTTCAATAAGT
* * * * *
43590 AACTTAATTTAGGGTAATCATGTGAA-TTAG-AAGATAACTTAATTCAGGGTAATTAAGTAAATC
1 AACTTAATTTAGGGTAATTAAG-CAAGTCAGTAA-TTAACTTAATTCAGGGTAATTAAGTAAAT-
* * * *
43653 AGTAATGAGTAATTTCATTCAAGGTAATTAAGTGAGTT-AATAAGT
63 --TAATAAGTAACTTAATTCAAGGTAATCAAGT-AGTTCAATAAGT
*
43698 AACTTAATTTAGGGTAATTAAGCAAGTCCGTAATTAACTTAATTCAGGGTAATTAAG
1 AACTTAATTTAGGGTAATTAAGCAAGTCAGTAATTAACTTAATTCAGGGTAATTAAG
43755 ATCGACTTAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
105 24 0.18
106 24 0.18
107 3 0.02
108 78 0.58
109 6 0.04
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (105 bp):
AACTTAATTTAGGGTAATTAAGCAAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTAAATTAA
TAAGTAACTTAATTCAAGGTAATCAAGTAGTTCAATAAGT
Found at i:43736 original size:143 final size:141
Alignment explanation
Indices: 43484--43750 Score: 374
Period size: 143 Copynumber: 1.9 Consensus size: 141
43474 GTCGGTAATC
* * * *
43484 AACTTAATTCAGGGTAATTAAATGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTTA
1 AACTTAATTCAGGGTAATTAAATAAATCAGTAATCAAATTTAATTCAAGGTAATTAAGTGAGTTA
* *
43549 ATAAGTAACTTAATTCAGGGTAATCAAGTAGTTCAATAAGTAACTTAATTTAGGGTAATCATGTG
66 ATAAGTAACTTAATTCAGGGTAATCAAGAAGTTCAATAAGTAACTTAATTCAGGGTAATCATGTG
43614 AATTAGAAGAT
131 AATTAGAAGAT
* * *
43625 AACTTAATTCAGGGTAATTAAGTAAATCAGTAATGAGTAATTTCATTCAAGGTAATTAAGTGAGT
1 AACTTAATTCAGGGTAATTAAATAAATCAGTAATCA--AATTTAATTCAAGGTAATTAAGTGAGT
* * ** *
43690 TAATAAGTAACTTAATTTAGGGTAATTAAGCAAG-TCCGTAATTAACTTAATTCAGGGTAAT
64 TAATAAGTAACTTAATTCAGGGTAATCAAG-AAGTTCAATAAGTAACTTAATTCAGGGTAAT
43751 TAAGATCGAC
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
141 32 0.29
143 75 0.69
144 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.34
Consensus pattern (141 bp):
AACTTAATTCAGGGTAATTAAATAAATCAGTAATCAAATTTAATTCAAGGTAATTAAGTGAGTTA
ATAAGTAACTTAATTCAGGGTAATCAAGAAGTTCAATAAGTAACTTAATTCAGGGTAATCATGTG
AATTAGAAGAT
Found at i:50459 original size:33 final size:32
Alignment explanation
Indices: 50417--50604 Score: 129
Period size: 33 Copynumber: 5.7 Consensus size: 32
50407 AAGGTAATAG
50417 TAATCAGTAAATCAGTAATTAAGTAAAAGAGAT
1 TAATCAGTAAAT-AGTAATTAAGTAAAAGAGAT
* * *
50450 TAATCAGTAAATTGATAATTAAGAGTCAAGGTA-AT
1 TAATCAGTAAATAG-TAATT-A-AGTAAAAG-AGAT
* * *
50485 AGTAATCAATAAATCAATATTTAAGTAAAAGAGAT
1 --TAATCAGTAAAT-AGTAATTAAGTAAAAGAGAT
* *
50520 TAATCAGTAAATTGATAATTAAG-AGTCAAG-G--
1 TAATCAGTAAATAG-TAATTAAGTA--AAAGAGAT
50551 TAAT-AGT-AATAAGTAATTAAGTAAAAGAGAT
1 TAATCAGTAAAT-AGTAATTAAGTAAAAGAGAT
*
50582 TAATCAGTAAATTGATAATTAAG
1 TAATCAGTAAATAG-TAATTAAG
50605 AGTCAAGGTA
Statistics
Matches: 119, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
28 3 0.03
29 12 0.10
30 5 0.04
31 8 0.07
32 6 0.05
33 47 0.39
34 5 0.04
35 16 0.13
36 2 0.02
37 15 0.13
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (32 bp):
TAATCAGTAAATAGTAATTAAGTAAAAGAGAT
Found at i:50464 original size:70 final size:70
Alignment explanation
Indices: 50380--50641 Score: 423
Period size: 70 Copynumber: 3.9 Consensus size: 70
50370 AAAGTAATGG
*
50380 TAATCACTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
50445 GAGAT
66 GAGAT
* * *
50450 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAATAAATCAATATTTAAGTAAAA
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
50515 GAGAT
66 GAGAT
50520 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGT-A--A-T--A--AGTAATTAAGTAAAA
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
50577 GAGAT
66 GAGAT
*
50582 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTGATCAGTAAATCAGTAATTAAG
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAG
50642 AGTCAAGGTA
Statistics
Matches: 178, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
62 56 0.31
63 1 0.01
64 1 0.01
65 1 0.01
66 2 0.01
67 1 0.01
68 1 0.01
69 1 0.01
70 114 0.64
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (70 bp):
TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
GAGAT
Found at i:50630 original size:132 final size:137
Alignment explanation
Indices: 50380--50641 Score: 417
Period size: 132 Copynumber: 1.9 Consensus size: 137
50370 AAAGTAATGG
50380 TAATCACTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
1 TAATCACTAAATTGATAATTAAGAGTCAAGGTAATAGTAA-CAGT-AA-CAGTAATTAAGTAAAA
*
50445 GAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAATAAATCAATATTTAAG
63 GAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAATAAATCAATAATTAAG
50510 TAAAAGAGAT
128 TAAAAGAGAT
*
50520 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGT-A-A-T-A-AGTAATTAAGTAAAAGAG
1 TAATCACTAAATTGATAATTAAGAGTCAAGGTAATAGTAACAGTAACAGTAATTAAGTAAAAGAG
* * *
50580 ATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTGATCAGTAAATCAGTAATTAAG
66 ATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAATAAATCAATAATTAAG
50642 AGTCAAGGTA
Statistics
Matches: 117, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
132 76 0.65
134 1 0.01
136 1 0.01
137 1 0.01
139 1 0.01
140 37 0.32
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (137 bp):
TAATCACTAAATTGATAATTAAGAGTCAAGGTAATAGTAACAGTAACAGTAATTAAGTAAAAGAG
ATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAATAAATCAATAATTAAGTAA
AAGAGAT
Found at i:50678 original size:40 final size:39
Alignment explanation
Indices: 50582--50763 Score: 135
Period size: 40 Copynumber: 4.6 Consensus size: 39
50572 TAAAAGAGAT
*
50582 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATA--G-
1 TAATCAGTAAATTCATAATTAAGAGTCAAGGTAA-AGGGA
*
50619 TGATCAGTAAA-TCAGTAATTAAGAGTCAAGGTAAAGGGA
1 TAATCAGTAAATTCA-TAATTAAGAGTCAAGGTAAAGGGA
* * * *
50658 TTAATCAGTAAATTCATAATTAAAAGAG-GAA-GCAAAAGTA
1 -TAATCAGTAAATTCATAATT--AAGAGTCAAGGTAAAGGGA
* * * *
50698 GTAATCAGTAGA-CCAGTAATTAAGAGTCAAAGTAAATGGA
1 -TAATCAGTAAATTCA-TAATTAAGAGTCAAGGTAAAGGGA
* *
50738 TAGATCATTAAATTGATAATTAAGAG
1 TA-ATCAGTAAATTCATAATTAAGAG
50764 AGAAAGTAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 23
0.74 0.12 0.15
Matches are distributed among these distances:
36 3 0.03
37 29 0.25
38 6 0.05
39 6 0.05
40 59 0.52
41 6 0.05
42 5 0.04
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.26
Consensus pattern (39 bp):
TAATCAGTAAATTCATAATTAAGAGTCAAGGTAAAGGGA
Found at i:50697 original size:132 final size:129
Alignment explanation
Indices: 50430--50688 Score: 349
Period size: 132 Copynumber: 1.9 Consensus size: 129
50420 TCAGTAAATC
50430 AGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAAT
1 AGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAAT
* * * *
50495 AAATCAATATTTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAA
66 AAATCAATATTAAAGTAAAAGAGATTAATCAGTAAATTCATAATTAAAAG--AAGG-AATAGCAA
50560 TA
128 TA
* *
50562 AGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTGATCAGT
1 AGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAAT
* *
50627 AAATCAGTAATTAAGAGTCAAGGTAAAGGGATTAATCAGTAAATTCATAATTAAAAG-AGGAA
66 AAATCAAT-ATTAA-AGT--A---AAAGAGATTAATCAGTAAATTCATAATTAAAAGAAGGAA
50689 GCAAAAGTAG
Statistics
Matches: 113, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
132 70 0.62
133 4 0.04
134 3 0.03
135 2 0.02
136 4 0.04
139 30 0.27
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (129 bp):
AGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAAT
AAATCAATATTAAAGTAAAAGAGATTAATCAGTAAATTCATAATTAAAAGAAGGAATAGCAATA
Found at i:50727 original size:80 final size:78
Alignment explanation
Indices: 50569--50788 Score: 239
Period size: 80 Copynumber: 2.8 Consensus size: 78
50559 ATAAGTAATT
* * ** * *
50569 AAGTAAAAGAGATTAATCAGTAAATTGATAATT--AAGAGTCAAGGTAATAGTGATCAGTAAATC
1 AAGT-AAAGGGATTAATCAGTAAATTGATAATTAAAAGAG-AAAGAAAATAGTAATCAGTAAACC
50632 AGTAATTAAGAGTCA
64 AGTAATTAAGAGTCA
* * * *
50647 AGGTAAAGGGATTAATCAGTAAATTCATAATTAAAAGAGGAAGCAAAAGTAGTAATCAGTAGACC
1 AAGTAAAGGGATTAATCAGTAAATTGATAATTAAAAGAGAAAG-AAAA-TAGTAATCAGTAAACC
50712 AGTAATTAAGAGTCA
64 AGTAATTAAGAGTCA
* * *
50727 AAGTAAATGGA-TAGATCATTAAATTGATAATTAAGAGAGAAAGTAAAATTAGTAATCAGTAA
1 AAGTAAAGGGATTA-ATCAGTAAATTGATAATTAAAAGAGAAAG-AAAA-TAGTAATCAGTAA
50789 TTAAGAAAGG
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
77 26 0.22
78 6 0.05
79 9 0.08
80 78 0.66
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (78 bp):
AAGTAAAGGGATTAATCAGTAAATTGATAATTAAAAGAGAAAGAAAATAGTAATCAGTAAACCAG
TAATTAAGAGTCA
Found at i:51057 original size:21 final size:21
Alignment explanation
Indices: 50997--51059 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
50987 AGTAATCAGT
* *
50997 AAAGAGGAAAATGGTAAAGAGT
1 AAAGAGGAAAA-AGTAAAGAGA
* * ** *
51019 ATAGAGTAATCAGCAAAGAGA
1 AAAGAGGAAAAAGTAAAGAGA
51040 AAAGAGGAAAAAGTAAAGAG
1 AAAGAGGAAAAAGTAAAGAG
51060 TAATCAGTAA
Statistics
Matches: 29, Mismatches: 12, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.29, T:0.11
Consensus pattern (21 bp):
AAAGAGGAAAAAGTAAAGAGA
Found at i:51060 original size:35 final size:35
Alignment explanation
Indices: 50983--51086 Score: 129
Period size: 35 Copynumber: 2.9 Consensus size: 35
50973 GTAAGGGGTA
* *
50983 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGT
1 AAAGAGTAATCAGTAAAGA-GAAAATGGGAAAAAGT
* *
51019 ATAGAGTAATCAGCAAAGAGAAAA-GAGGAAAAAGT
1 AAAGAGTAATCAGTAAAGAGAAAATG-GGAAAAAGT
*
51054 AAAGAGTAATCAGTAAAGAGAAAAATGGTAAAA
1 AAAGAGTAATCAGTAAAGAG-AAAATGGGAAAA
51087 TGGTAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 30 0.52
36 26 0.45
37 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.25, T:0.14
Consensus pattern (35 bp):
AAAGAGTAATCAGTAAAGAGAAAATGGGAAAAAGT
Found at i:51133 original size:21 final size:22
Alignment explanation
Indices: 51104--51153 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
51094 TAAATTCAAG
* **
51104 AGAGTAAAATAGTAATTAGTAA
1 AGAGTAAAAGAGTAAAGAGTAA
51126 AGAG-AAAAGAGTAAAGAGTAA
1 AGAGTAAAAGAGTAAAGAGTAA
51147 AGAGTAA
1 AGAGTAA
51154 TCAGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (22 bp):
AGAGTAAAAGAGTAAAGAGTAA
Found at i:51134 original size:7 final size:7
Alignment explanation
Indices: 51121--51221 Score: 59
Period size: 7 Copynumber: 14.7 Consensus size: 7
51111 AATAGTAATT
51121 AGTAAAG
1 AGTAAAG
*
51128 AGAAAAG
1 AGTAAAG
51135 AGTAAAG
1 AGTAAAG
51142 AGTAAAG
1 AGTAAAG
**
51149 AGTAATC
1 AGTAAAG
51156 AGTAAA-
1 AGTAAAG
*
51162 A-AAAATG
1 AGTAAA-G
*
51169 -GTAAAA
1 AGTAAAG
51175 AGTAAAG
1 AGTAAAG
**
51182 AGTAATC
1 AGTAAAG
51189 AGTAAAGG
1 AGTAAA-G
*
51197 AAG-AATG
1 -AGTAAAG
51204 -GTAAAG
1 AGTAAAG
51210 AGTAAAG
1 AGTAAAG
*
51217 GGTAA
1 AGTAA
51222 TCAGTAAAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
5 4 0.06
6 4 0.06
7 58 0.83
8 2 0.03
9 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:51160 original size:35 final size:35
Alignment explanation
Indices: 51104--51229 Score: 161
Period size: 35 Copynumber: 3.6 Consensus size: 35
51094 TAAATTCAAG
* *
51104 AGAGTAAAATAGTAATTAGTAAAGAGAAAA-GAGTAA
1 AGAGT-AAAGAGTAATCAGTAAAGAGAAAATG-GTAA
51140 AGAGTAAAGAGTAATCAGTAAA-A-AAAATGGTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAAAATGGTAA
*
51173 AAAGTAAAGAGTAATCAGTAAAG-GAAGAATGGTAA
1 AGAGTAAAGAGTAATCAGTAAAGAGAA-AATGGTAA
*
51208 AGAGTAAAGGGTAATCAGTAAA
1 AGAGTAAAGAGTAATCAGTAAA
51230 ATGATAATCA
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
33 29 0.36
34 4 0.05
35 43 0.53
36 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (35 bp):
AGAGTAAAGAGTAATCAGTAAAGAGAAAATGGTAA
Found at i:51271 original size:22 final size:21
Alignment explanation
Indices: 51246--51409 Score: 145
Period size: 22 Copynumber: 7.6 Consensus size: 21
51236 ATCAATAAAG
*
51246 AGTAAAATAGTAAAAGGTATTC
1 AGTAAAA-AGTAAAAGGTAATC
*
51268 AGTAAAAA--AATAATGATAATC
1 AGTAAAAAGTAA-AA-GGTAATC
* **
51289 AGTAAAAGGTAAAATAATAATC
1 AGTAAAAAGTAAAA-GGTAATC
51311 AGT-AAAAGTAAGAAGGTAATC
1 AGTAAAAAGTAA-AAGGTAATC
* *
51332 AGTAAAGAGTAAAATAGTAATC
1 AGTAAAAAGTAAAA-GGTAATC
51354 AGTAAAAAGTAAGAAGGTAATC
1 AGTAAAAAGTAA-AAGGTAATC
* *
51376 AGTAAAGAGTAAAATAGTAATC
1 AGTAAAAAGTAAAA-GGTAATC
*
51398 AGTAAAAGGTAA
1 AGTAAAAAGTAA
51410 TCAGTAAGAG
Statistics
Matches: 118, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 32 0.27
22 78 0.66
23 4 0.03
ACGTcount: A:0.55, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTAAAAAGTAAAAGGTAATC
Found at i:51313 original size:43 final size:42
Alignment explanation
Indices: 51266--51481 Score: 218
Period size: 43 Copynumber: 5.2 Consensus size: 42
51256 TAAAAGGTAT
* * *
51266 TCAGTAAAAAAATAATGATAATCAGTAAA-AGGTAAAATAATAA
1 TCAGTAAAAAAAGAA-GGTAATCAGTAAAGA-GTAAAATAGTAA
*
51309 TCAGTAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
1 TCAGTAAAA-AAAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
51352 TCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
1 TCAGTAAAAA--AAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
51396 TCAGT-----AA-AAGGTAATCAGT-AAGAGTAAAATAGTAA
1 TCAGTAAAAAAAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
* * *
51431 TCAGTAAGAGCAAA-ATGGTAATTAGT-AAGAGTAAAAATAGTAA
1 TCAGTAA-A-AAAAGAAGGTAATCAGTAAAGAGT-AAAATAGTAA
*
51474 TCAATAAA
1 TCAGTAAA
51482 GAGTAAAAGG
Statistics
Matches: 153, Mismatches: 8, Indels: 25
0.82 0.04 0.13
Matches are distributed among these distances:
35 21 0.14
36 12 0.08
37 2 0.01
42 19 0.12
43 57 0.37
44 42 0.27
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAGTAAAAAAAGAAGGTAATCAGTAAAGAGTAAAATAGTAA
Found at i:51426 original size:35 final size:37
Alignment explanation
Indices: 51361--51439 Score: 144
Period size: 35 Copynumber: 2.2 Consensus size: 37
51351 ATCAGTAAAA
51361 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
51398 AGTAA-AAGGTAATCAGT-AAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
51433 AGTAAGA
1 AGTAAGA
51440 GCAAAATGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 23 0.56
36 13 0.32
37 5 0.12
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (37 bp):
AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:51430 original size:21 final size:21
Alignment explanation
Indices: 51417--51489 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
51407 TAATCAGTAA
51417 GAGTAAAATAGTAATCAGTAA
1 GAGTAAAATAGTAATCAGTAA
* * *
51438 GAGCAAAATGGTAATTAGTAA
1 GAGTAAAATAGTAATCAGTAA
*
51459 GAGTAAAAATAGTAATCAATAAA
1 GAGT-AAAATAGTAATCAGT-AA
51482 GAGTAAAA
1 GAGTAAAA
51490 GGTGATCAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.49
22 16 0.37
23 6 0.14
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.22
Consensus pattern (21 bp):
GAGTAAAATAGTAATCAGTAA
Found at i:51501 original size:43 final size:41
Alignment explanation
Indices: 51284--51501 Score: 223
Period size: 44 Copynumber: 5.2 Consensus size: 41
51274 AAAATAATGA
* * * *
51284 TAATCAGTAAAAGGTAAAATAATAATCAGTAAAAGTAAGAAGG
1 TAATCAGTAAGA-GTAAAATAGTAATCAATAAGAGTAA-AAGG
* *
51327 TAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGG
1 TAATCAGT-AAGAGTAAAATAGTAATCAAT-AAGAGTAA-AAGG
51371 TAATCAGTAAAGAGTAAAATAGTAATC------AGTAAAAGG
1 TAATCAGT-AAGAGTAAAATAGTAATCAATAAGAGTAAAAGG
* *
51407 TAATCAGTAAGAGTAAAATAGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGTAAAATAGTAATCAATAAGAGTAAAA-GG
*
51449 TAATTAGTAAGAGTAAAAATAGTAATCAATAAAGAGTAAAAGG
1 TAATCAGTAAGAGT-AAAATAGTAATCAAT-AAGAGTAAAAGG
*
51492 TGATCAGTAA
1 TAATCAGTAA
51502 TTCAAAGAGT
Statistics
Matches: 156, Mismatches: 8, Indels: 22
0.84 0.04 0.12
Matches are distributed among these distances:
35 18 0.12
36 12 0.08
37 5 0.03
41 6 0.04
42 15 0.10
43 48 0.31
44 52 0.33
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (41 bp):
TAATCAGTAAGAGTAAAATAGTAATCAATAAGAGTAAAAGG
Found at i:51583 original size:11 final size:11
Alignment explanation
Indices: 51567--51595 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
51557 TCAATAAAAG
51567 AGAGTAAGAAA
1 AGAGTAAGAAA
51578 AGAGTAAGAAA
1 AGAGTAAGAAA
51589 AGAGTAA
1 AGAGTAA
51596 AGATGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (11 bp):
AGAGTAAGAAA
Done.