Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013538.1 Corchorus capsularis cultivar CVL-1 contig13559, 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: 85562
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:37960 original size:19 final size:19
Alignment explanation
Indices: 37931--37974 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
37921 ACTCAGACTC
37931 AAACT-AACTG-ACTCAAAA
1 AAACTGAACTGAACTC-AAA
37949 AAACTGAACTGAACTCAAA
1 AAACTGAACTGAACTCAAA
37968 AAACTGA
1 AAACTGA
37975 CTAAACCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.55, C:0.20, G:0.09, T:0.16
Consensus pattern (19 bp):
AAACTGAACTGAACTCAAA
Found at i:38217 original size:53 final size:53
Alignment explanation
Indices: 38154--38254 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
38144 TAAAAATTAA
38154 TTAGGGGAATGATACAAATGATACCAAAACAATTCTTTTATGTCCAATTTTAC
1 TTAGGGGAATGATACAAATGATACCAAAACAATTCTTTTATGTCCAATTTTAC
*
38207 TTAGGGGAATGATAGAAATGATACCAAAACAATTCTTTTATGTCCAAT
1 TTAGGGGAATGATACAAATGATACCAAAACAATTCTTTTATGTCCAAT
38255 GAGGGTGGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (53 bp):
TTAGGGGAATGATACAAATGATACCAAAACAATTCTTTTATGTCCAATTTTAC
Found at i:38523 original size:40 final size:41
Alignment explanation
Indices: 38453--38531 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
38443 TTATCAAAAC
*
38453 AATTCTTTTATTATAAAATTTCATTGCCATAAAAATATGTT
1 AATTCTTTTATTATAAAATTTCACTGCCATAAAAATATGTT
38494 AATTCTTTTATTAT-AAATTTCACTGCCATAAAAATATG
1 AATTCTTTTATTATAAAATTTCACTGCCATAAAAATATG
38532 ATATGAATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.44
Consensus pattern (41 bp):
AATTCTTTTATTATAAAATTTCACTGCCATAAAAATATGTT
Found at i:43859 original size:11 final size:12
Alignment explanation
Indices: 43837--43861 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43827 GTGCATGTTC
43837 TTTGATTTTTTT
1 TTTGATTTTTTT
43849 TTTGATTTTTTT
1 TTTGATTTTTTT
43861 T
1 T
43862 AAGTTTTATT
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTGATTTTTTT
Found at i:45298 original size:28 final size:28
Alignment explanation
Indices: 45233--45298 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 28
45223 GACAAAACGT
*
45233 ACATCCCAAAATTGAAGTTCAGGGGACAAA
1 ACAT-CCAAAATTGAAATTCA-GGGACAAA
* *
45263 ATAT-CAAAGTTGAAATTCA-GGATCAAA
1 ACATCCAAAATTGAAATTCAGGGA-CAAA
45290 ACATCCAAA
1 ACATCCAAA
45299 CGCTATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
26 3 0.10
27 7 0.23
28 17 0.57
30 3 0.10
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (28 bp):
ACATCCAAAATTGAAATTCAGGGACAAA
Found at i:48392 original size:18 final size:18
Alignment explanation
Indices: 48361--48395 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48351 GGTGAAATGG
*
48361 ATCGGTTGAGTCGGTTTT
1 ATCGGGTGAGTCGGTTTT
*
48379 ATCGGGTGATTCGGTTT
1 ATCGGGTGAGTCGGTTT
48396 GTGAAGTCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.11, G:0.34, T:0.43
Consensus pattern (18 bp):
ATCGGGTGAGTCGGTTTT
Found at i:48603 original size:22 final size:23
Alignment explanation
Indices: 48559--48606 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
48549 TATATATCCA
*
48559 AAAATTATTTTATTTTAATATAT
1 AAAATTATTTTATTTAAATATAT
48582 AAAA-TATTTTA-TTAAATAATAT
1 AAAATTATTTTATTTAAAT-ATAT
48604 AAA
1 AAA
48607 TGTAAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 14 0.61
23 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATTATTTTATTTAAATATAT
Found at i:48673 original size:20 final size:19
Alignment explanation
Indices: 48569--48685 Score: 71
Period size: 20 Copynumber: 6.2 Consensus size: 19
48559 AAAATTATTT
48569 TATTTTAATATATAA-A-A
1 TATTTTAATATATAATATA
* *
48586 TATTTTATTAAATAATATA
1 TATTTTAATATATAATATA
* * * *
48605 AATGTAAATA-AGAATATA
1 TATTTTAATATATAATATA
* * * *
48623 TA-TATATATATGTAAAAATTT
1 TATTTTA-ATATAT-AATA-TA
48644 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
48663 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
48683 TAT
1 TAT
48686 ATGTGTGTAA
Statistics
Matches: 72, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
17 14 0.19
18 12 0.17
19 12 0.17
20 23 0.32
21 8 0.11
22 3 0.04
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:51426 original size:13 final size:13
Alignment explanation
Indices: 51408--51454 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
51398 ATCATTTTTA
51408 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
51421 CTCTTTAC-TATTT
1 CTCTTTTCTTA-CT
51434 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
51448 CTCTTTT
1 CTCTTTT
51455 ATTGAATACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.07
13 15 0.56
14 8 0.30
15 2 0.07
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:51590 original size:21 final size:20
Alignment explanation
Indices: 51559--51608 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
51549 TCCTAATTGC
* *
51559 CATTTTGCTCTTACTGATTA
1 CATTTTACTCTTACCGATTA
51579 CTATTTTACTCTTACCGATTA
1 C-ATTTTACTCTTACCGATTA
*
51600 CCTTTTACT
1 CATTTTACT
51609 GATTAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.50
Consensus pattern (20 bp):
CATTTTACTCTTACCGATTA
Found at i:51725 original size:26 final size:26
Alignment explanation
Indices: 51691--51758 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
51681 CTCCTTACTG
*
51691 ATTACTATTTTACCTTC-TTGAACTTA
1 ATTACTATTTT-CATTCTTTGAACTTA
*
51717 ATTACTATTTTCATTCTTTGAATTTA
1 ATTACTATTTTCATTCTTTGAACTTA
* *
51743 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
51759 TTACTTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 4 0.11
26 27 0.75
27 5 0.14
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTACTATTTTCATTCTTTGAACTTA
Found at i:51902 original size:16 final size:16
Alignment explanation
Indices: 51881--52056 Score: 75
Period size: 16 Copynumber: 11.1 Consensus size: 16
51871 TTAATTACCA
51881 TTTTACTGATTACTTC
1 TTTTACTGATTACTTC
*
51897 TTTTACT--TTCACTCC
1 TTTTACTGATT-ACTTC
51912 ATTTTACTGATTACTTC
1 -TTTTACTGATTACTTC
* * *
51929 TTCTACGGGTTACTTC
1 TTTTACTGATTACTTC
*
51945 -TCT--TGATTAC--C
1 TTTTACTGATTACTTC
*
51956 ATTTTTCTGATTACTTC
1 -TTTTACTGATTACTTC
*
51973 TTTTGCTTTCG-TT-CTTTTAC
1 TTTTAC--T-GATTAC--TT-C
*
51993 TTTTACTGATTACTTT
1 TTTTACTGATTACTTC
* * **
52009 TTTTACT-TTTGCCCC
1 TTTTACTGATTACTTC
52024 TTTTACTGATTACTTC
1 TTTTACTGATTACTTC
* *
52040 CTTTACTGATTATTTC
1 TTTTACTGATTACTTC
52056 T
1 T
52057 CTTGATTACC
Statistics
Matches: 118, Mismatches: 23, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
11 1 0.01
13 7 0.06
14 2 0.02
15 24 0.20
16 57 0.48
17 9 0.08
18 8 0.07
19 4 0.03
20 6 0.05
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (16 bp):
TTTTACTGATTACTTC
Found at i:52060 original size:111 final size:115
Alignment explanation
Indices: 51846--52122 Score: 316
Period size: 111 Copynumber: 2.4 Consensus size: 115
51836 TACCGATTTA
51846 CTGATTACTTCTTTTACTCTTGCTCTTAATTACCATTTTACTGATTACTTCTTTTACTTTCACTC
1 CTGATTACTTCTTTTACTCTTGCTCTT-ATTACCATTTTACTGATTACTTCTTTTACTTTCACTC
*
51911 CATTTTACTGATTACTTCTTCTACGGGTTACTTCTCTTGATTACCATTTTT
65 CATTTTACTGATTACTTCTTCTACGGATTACTTCTCTTGATTACCATTTTT
* * * **
51962 CTGATTACTTCTTTTGCT-TTCGTTCTT-TTA-C-TTTTACTGATTACTTTTTTTACTTTTGC-C
1 CTGATTACTTCTTTTACTCTT-GCTCTTATTACCATTTTACTGATTACTTCTTTTACTTTCACTC
* * *
52022 CCTTTTACTGATTACTTCCTT-TACTGATTATTTCTCTTGATTACCATTTTT
65 CATTTTACTGATTACTT-CTTCTACGGATTACTTCTCTTGATTACCATTTTT
* * * *
52073 TTGATTATTTTGTTTTACT-TTGACTCTTTAATTACTGATTTTACTGATTA
1 CTGATTA-CTTCTTTTACTCTTG-CTC-TT-ATTAC-CATTTTACTGATTA
52123 ATCTCTTACC
Statistics
Matches: 136, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
111 51 0.38
112 40 0.29
113 3 0.02
114 3 0.02
115 5 0.04
116 22 0.16
118 12 0.09
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.55
Consensus pattern (115 bp):
CTGATTACTTCTTTTACTCTTGCTCTTATTACCATTTTACTGATTACTTCTTTTACTTTCACTCC
ATTTTACTGATTACTTCTTCTACGGATTACTTCTCTTGATTACCATTTTT
Found at i:52190 original size:34 final size:35
Alignment explanation
Indices: 52091--52337 Score: 172
Period size: 34 Copynumber: 6.8 Consensus size: 35
52081 TTTGTTTTAC
52091 TTTGACTCTTTAATTACTGATTTTACTGATTAATCTCT
1 TTTGAC-C-TTAATTACTGA-TTTACTGATTAATCTCT
* *
52129 TACCTTGACTCTTAATTA-TCAAATTACTGATTAATCTCT
1 T---TTGAC-CTTAATTACT-GATTTACTGATTAATCTCT
*
52168 TTTTA-CTTAATTACTGATTTACTGATTACTAT-TAC-
1 TTTGACCTTAATTACTGATTTACTGATTA--ATCT-CT
* * *
52203 CTTGACTCTTAATT-GTCAATTTACTGATTAATCTCT
1 TTTGAC-CTTAATTACT-GATTTACTGATTAATCTCT
*
52239 TTTTA-CTTAATTACTGATTTACTGATTACTAT-TAC-
1 TTTGACCTTAATTACTGATTTACTGATTA--ATCT-CT
* *
52274 CTTGACTCTTAATTA-TCAATTTACTGATTAATCTCT
1 TTTGAC-CTTAATTACT-GATTTACTGATTAATCTCT
*
52310 TTTTA-CTTAATTACTGATTTACTGATTA
1 TTTGACCTTAATTACTGATTTACTGATTA
52338 CTATTACTTT
Statistics
Matches: 167, Mismatches: 19, Indels: 50
0.71 0.08 0.21
Matches are distributed among these distances:
34 58 0.35
35 17 0.10
36 19 0.11
37 39 0.23
38 1 0.01
39 18 0.11
40 8 0.05
41 7 0.04
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (35 bp):
TTTGACCTTAATTACTGATTTACTGATTAATCTCT
Found at i:52212 original size:71 final size:71
Alignment explanation
Indices: 52100--52375 Score: 453
Period size: 71 Copynumber: 3.8 Consensus size: 71
52090 CTTTGACTCT
* *
52100 TTAATTACTGATTTTACTGATTAATCTCTTACCTTGACTCTTAATTATCAAATTACTGATTAATC
1 TTAATTACTGA-TTTACTGATT-A-CTATTACCTTGACTCTTAATTATCAATTTACTGATTAATC
52165 TCTTTTTAC
63 TCTTTTTAC
*
52174 TTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTGTCAATTTACTGATTAATCTCT
1 TTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCT
52239 TTTTAC
66 TTTTAC
52245 TTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCT
1 TTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCT
52310 TTTTAC
66 TTTTAC
* * * *
52316 TTAATTACTGATTTACTGATTACTATTACTTTGATTCTCAATTACTTAATTTACTGATTA
1 TTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTA-TCAATTTACTGATTA
52376 CTATTACTTT
Statistics
Matches: 193, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
71 157 0.81
72 15 0.08
73 10 0.05
74 11 0.06
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (71 bp):
TTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCT
TTTTAC
Found at i:52398 original size:45 final size:45
Alignment explanation
Indices: 52312--52398 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 45
52302 TAATCTCTTT
*
52312 TTACTTAATTACTGATTTACTGATTACTATTACTTTGATTCTCAA
1 TTACTTAATTACTGATTTACTGATTACTATTACTTTAATTCTCAA
52357 TTACTTAATTTACTGA-TTACT-ATTACT-TTGACTCTTAATTCT
1 TTACTTAA-TTACTGATTTACTGATTACTATT-ACT-TTAATTCT
52399 ATTGGGGTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
43 2 0.05
44 9 0.24
45 20 0.53
46 7 0.18
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.51
Consensus pattern (45 bp):
TTACTTAATTACTGATTTACTGATTACTATTACTTTAATTCTCAA
Found at i:53187 original size:51 final size:52
Alignment explanation
Indices: 53106--53218 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 52
53096 ATCAATATTC
* * * *
53106 AATTTTTATTGTTTAAAATTACTAGGACTCAACTCC-TACTATATAAAGATTT
1 AATTTTTATTGATTAAAATCACTAGAACTCAAC-CCTTACTACATAAAGATTT
*
53158 AATTTTTATT-ATTAAAATCATTAGAACTCAACCCTTACTACATAAAGATTT
1 AATTTTTATTGATTAAAATCACTAGAACTCAACCCTTACTACATAAAGATTT
53209 AATTTTTATT
1 AATTTTTATT
53219 TGCCAAAGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.04
51 43 0.78
52 10 0.18
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (52 bp):
AATTTTTATTGATTAAAATCACTAGAACTCAACCCTTACTACATAAAGATTT
Found at i:56147 original size:27 final size:26
Alignment explanation
Indices: 56074--56149 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
56064 GGTGAACTTA
* **
56074 AAAATGACTAAAATGCCCCTAAGTGC
1 AAAATGACCAAAATGCCCCTGGGTGC
56100 AAAATGACCAAAATGCCCCTGGGTGC
1 AAAATGACCAAAATGCCCCTGGGTGC
56126 TAAAATGACCAAAATGCCCCTGGG
1 -AAAATGACCAAAATGCCCCTGGG
56150 CGACCCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 23 0.50
27 23 0.50
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTGGGTGC
Found at i:57653 original size:3 final size:3
Alignment explanation
Indices: 57645--57679 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
57635 CCCAAAAATA
57645 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
57680 AGGCCAGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58173 original size:24 final size:24
Alignment explanation
Indices: 58127--58173 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
58117 AGAAGAGTCA
*
58127 AATACTGAACATACAGCAATTTGG
1 AATACTGAACATACAACAATTTGG
** *
58151 AATACTGAGTATACAACAGTTTG
1 AATACTGAACATACAACAATTTG
58174 AGGATAACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (24 bp):
AATACTGAACATACAACAATTTGG
Found at i:59917 original size:25 final size:26
Alignment explanation
Indices: 59883--59932 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
59873 ATGAAAGTAA
* * *
59883 AAGATTGTCACTTTTCATA-ACAAAG
1 AAGATGGTCAATTATCATATACAAAG
59908 AAGATGGTCAATTATCATATACAAA
1 AAGATGGTCAATTATCATATACAAA
59933 AATTTTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (26 bp):
AAGATGGTCAATTATCATATACAAAG
Found at i:61855 original size:3 final size:3
Alignment explanation
Indices: 61849--61874 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61839 AGAAGAAACG
61849 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
61875 GACGGGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:62515 original size:23 final size:24
Alignment explanation
Indices: 62489--62555 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 24
62479 TTCTAAGATT
62489 AAGAATCATGTAATTTA-TCAAAA
1 AAGAATCATGTAATTTACTCAAAA
62512 AAGAATCATGTAATTTATCTCTCAAAA
1 AAGAATCATGTAATTTA---CTCAAAA
62539 AAGAATCATGTAATTTA
1 AAGAATCATGTAATTTA
62556 AGGCATATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.43
27 23 0.57
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (24 bp):
AAGAATCATGTAATTTACTCAAAA
Found at i:64342 original size:18 final size:18
Alignment explanation
Indices: 64316--64362 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
64306 GTCCCTCACC
*
64316 AAATTTTTTTTTTTAAAA
1 AAATATTTTTTTTTAAAA
64334 AAATATTTTTTTTTAAAA
1 AAATATTTTTTTTTAAAA
64352 AAATATTTTTT
1 AAATATTTTTT
64363 AATCAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATATTTTTTTTTAAAA
Found at i:64370 original size:18 final size:18
Alignment explanation
Indices: 64329--64370 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
64319 TTTTTTTTTT
**
64329 TAAAAAAATATTTTTTTT
1 TAAAAAAATATTTTTTAA
64347 TAAAAAAATATTTTTTAA
1 TAAAAAAATATTTTTTAA
64365 TCAAAA
1 T-AAAA
64371 TGTATGACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAAAAATATTTTTTAA
Found at i:64971 original size:43 final size:44
Alignment explanation
Indices: 64887--64972 Score: 129
Period size: 43 Copynumber: 1.9 Consensus size: 44
64877 TTATTAAAAT
* *
64887 ATATATTTTAATTATGCAATTATTATTAAAATATATGAAATTGCCA
1 ATATATTTTAATTATGC-A-CATTATTAAAATATATAAAATTGCCA
64933 ATATATTTTAATTATGC-CATTATTAAAATATATAAAATTG
1 ATATATTTTAATTATGCACATTATTAAAATATATAAAATTG
64973 TCATTATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 21 0.55
46 17 0.45
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (44 bp):
ATATATTTTAATTATGCACATTATTAAAATATATAAAATTGCCA
Found at i:67056 original size:24 final size:24
Alignment explanation
Indices: 67021--67068 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
67011 TGAAAACGGA
67021 ATCAGACAGACAACGGAACGGAAT
1 ATCAGACAGACAACGGAACGGAAT
* *
67045 ATCAGACGGACAGCGGAACGGAAT
1 ATCAGACAGACAACGGAACGGAAT
67069 CACGGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.29, T:0.08
Consensus pattern (24 bp):
ATCAGACAGACAACGGAACGGAAT
Found at i:67261 original size:13 final size:13
Alignment explanation
Indices: 67243--67288 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
67233 ACTCGCGGAG
67243 GTCAACAGTCAAA
1 GTCAACAGTCAAA
*
67256 GTCAACAGTCAACG
1 GTCAACAGTCAA-A
*
67270 GTCAACAG-AAAA
1 GTCAACAGTCAAA
67282 GTCAACA
1 GTCAACA
67289 TTGACGTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 7 0.24
13 14 0.48
14 8 0.28
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (13 bp):
GTCAACAGTCAAA
Found at i:67265 original size:7 final size:7
Alignment explanation
Indices: 67243--67277 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
67233 ACTCGCGGAG
67243 GTCAACA
1 GTCAACA
67250 GTCAA-A
1 GTCAACA
67256 GTCAACA
1 GTCAACA
*
67263 GTCAACG
1 GTCAACA
67270 GTCAACA
1 GTCAACA
67277 G
1 G
67278 AAAAGTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (7 bp):
GTCAACA
Found at i:75186 original size:156 final size:156
Alignment explanation
Indices: 74775--75186 Score: 424
Period size: 156 Copynumber: 2.6 Consensus size: 156
74765 CATCTTGGTG
* ** *
74775 AAATTTCATCTCAAACAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
* * * * *
74840 GGGTGACAAACCAACTTCTCTATGCTA-GAGAGTTCGGTTTTACTTAGATTTTTTCCCATAGCCT
66 GGGTGAGAAACCAAGTTCACTATG-AAGGAGAGCTCGGTTTTACTTAGATTTTTTCCCATAGCCT
* **
74904 TATGGTGATAATCTAAGTATACTGGTG
130 TATGGTGATAATCTAAGTACACTGGAA
* * * ***
74931 GAATATCAGCTTCGTT--GCACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACC
1 AAATTTCAGC-TCATTCAG-ACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTT
* * * * * *
74994 TGGGGAGAGAAACCTAGTTCACCATCAAGGGGAGCTCGGTTTTACTTAGAATTTTTT-CCATAGT
64 TGGGGTGAGAAACCAAGTTCACTATGAAGGAGAGCTCGGTTTTACTTAG-ATTTTTTCCCATAGC
* * *
75058 CTTAT-ATGGATATTCTAAGT-CCCTTGGAA
128 CTTATGGT-GATAATCTAAGTACAC-TGGAA
*
75087 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
* * * *
75152 AGGTGAGAAGCTC-GGTTCACTATGAAGGAAAGCTC
66 GGGTGAGAAAC-CAAGTTCACTATGAAGGAGAGCTC
75187 AGATAAAGCC
Statistics
Matches: 205, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
155 8 0.04
156 186 0.91
157 11 0.05
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (156 bp):
AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
GGGTGAGAAACCAAGTTCACTATGAAGGAGAGCTCGGTTTTACTTAGATTTTTTCCCATAGCCTT
ATGGTGATAATCTAAGTACACTGGAA
Found at i:76770 original size:12 final size:12
Alignment explanation
Indices: 76753--76777 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
76743 TTGGAATCTC
76753 TGAGGTTTTCTT
1 TGAGGTTTTCTT
76765 TGAGGTTTTCTT
1 TGAGGTTTTCTT
76777 T
1 T
76778 TGAAGAGACT
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:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TGAGGTTTTCTT
Found at i:77421 original size:22 final size:21
Alignment explanation
Indices: 77377--77420 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
77367 TTGATCTGGA
77377 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
*
77398 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
77419 TT
1 TT
77421 TACACTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.43, G:0.09, T:0.30
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:77551 original size:24 final size:25
Alignment explanation
Indices: 77491--77549 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
77481 TTCAAACCCT
*
77491 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
77516 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
77540 AAA-TTCATTT
1 AAACTTCATTT
77550 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:77588 original size:26 final size:26
Alignment explanation
Indices: 77559--77626 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
77549 TTCCTTCATT
*
77559 TTAATCATAAACTAATTAAATACTGA
1 TTAATCATAAACTAATTAAATACTAA
* *
77585 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
77611 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
77627 AAACTAAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:77775 original size:21 final size:21
Alignment explanation
Indices: 77737--77777 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
77727 GGCTCCGCCA
*
77737 TTTTTTTTATTATTTTTTAAT
1 TTTTTTTTATAATTTTTTAAT
77758 TTTTTTTTA-AATTGTTTTAA
1 TTTTTTTTATAATT-TTTTAA
77778 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTTATAATTTTTTAAT
Found at i:80853 original size:23 final size:23
Alignment explanation
Indices: 80810--80853 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
80800 GAATAGAACA
* *
80810 TTAATTAGTAATATATATTATAC
1 TTAATTAATAATATAGATTATAC
80833 TTAATTAAT-ATATAGACTTAT
1 TTAATTAATAATATAGA-TTAT
80854 TAGTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (23 bp):
TTAATTAATAATATAGATTATAC
Found at i:83057 original size:128 final size:125
Alignment explanation
Indices: 82889--83136 Score: 365
Period size: 128 Copynumber: 2.0 Consensus size: 125
82879 ACCAACCTTG
82889 CAATTTAAAAGAGTGTGGAGGACAGAGAATGAGTAGGAGAAAGAGAATA-AGGATAAAAATAGAA
1 CAATTTAAAAGAGTGTGGAGGACAGAGAATGAGTAGGAGAAAGAGAATATAGG-TAAAAATAGAA
* * *
82953 GAAAAATTAGGTAAAAGTACATAAAATTTTGAATCTTAACTAA-TTTCCTTAATCTTGATTA
65 GAAAAATTAGGTAAAAGTACATAAAATTGTGAACCTTAACTAACTAT-CTTAATCTTGATTA
* * **
83014 CAATTTAAAAGAGTGTGTAGAATGAGAGAGAATGAGTAGGAGAAAGAGAATATAGGTAGGAATAG
1 CAATTTAAAAGAGTGTG--G-AGGACAGAGAATGAGTAGGAGAAAGAGAATATAGGTAAAAATAG
*
83079 AAGAAAAATTAGGTAAAAGTATATAAAATTGTGAACCTTAACTAACTATCTTAATCTT
63 AAGAAAAATTAGGTAAAAGTACATAAAATTGTGAACCTTAACTAACTATCTTAATCTT
83137 AATGATATAG
Statistics
Matches: 110, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
125 17 0.15
127 1 0.01
128 87 0.79
129 5 0.05
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (125 bp):
CAATTTAAAAGAGTGTGGAGGACAGAGAATGAGTAGGAGAAAGAGAATATAGGTAAAAATAGAAG
AAAAATTAGGTAAAAGTACATAAAATTGTGAACCTTAACTAACTATCTTAATCTTGATTA
Found at i:84893 original size:108 final size:104
Alignment explanation
Indices: 84752--85032 Score: 374
Period size: 108 Copynumber: 2.6 Consensus size: 104
84742 ATGGTAAAAA
84752 TAAAAAAAACT-A-TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
1 TAAAAAAAA-TAATTATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
84813 AAATTGTATATTAG-AAAAATTTTAATATATCCAAATTTTTT
64 AAATTGTATATTAGAAAAAATTTTAATATATCCAAA-TTTTT
84854 GGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
1 --TAAAAA-AAA-TAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAA
*
84919 TAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
62 TAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
** * *
84962 TATTAAAAATAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAAAAGAGTTTTTAGTAGA
1 TAAAAAAAATAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGA
85027 ATAAAA
61 ATAAAA
85033 CTATAATAGT
Statistics
Matches: 160, Mismatches: 6, Indels: 17
0.87 0.03 0.09
Matches are distributed among these distances:
104 30 0.19
105 9 0.06
106 6 0.04
107 6 0.04
108 60 0.38
109 49 0.31
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (104 bp):
TAAAAAAAATAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAA
ATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:85018 original size:109 final size:111
Alignment explanation
Indices: 84776--85032 Score: 377
Period size: 109 Copynumber: 2.4 Consensus size: 111
84766 TAAAATATTG
84776 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATAT
1 AATTTAATT-AATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATAT
84841 ATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
65 ATCCAAATTTTTT-GTAAAAATAAAGTAATTATAAAGATATTAGATTT
*
84889 AA-TT-A--AATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTAT
1 AATTTAATTAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG-AAAAATTTTAATAT
**
84950 ATCCAAA-TTTTT-TATTAA-AAA-TAATTATAAAGATATTAGATTT
65 ATCCAAATTTTTTGTAAAAATAAAGTAATTATAAAGATATTAGATTT
* *
84993 AATTTAATTGAATAAAAAAAGAGTTTTTAGTAGAATAAAA
1 AATTTAATT-AATGAAAATAGAGTTTTTAGTAGAATAAAA
85033 CTATAATAGT
Statistics
Matches: 133, Mismatches: 5, Indels: 16
0.86 0.03 0.10
Matches are distributed among these distances:
104 24 0.18
105 5 0.04
106 5 0.04
108 46 0.35
109 48 0.36
111 1 0.01
112 2 0.02
113 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (111 bp):
AATTTAATTAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATATA
TCCAAATTTTTTGTAAAAATAAAGTAATTATAAAGATATTAGATTT
Done.