Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008882.1 Corchorus capsularis cultivar CVL-1 contig08903, 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: 71779
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:9505 original size:41 final size:40
Alignment explanation
Indices: 9378--9995 Score: 535
Period size: 41 Copynumber: 15.8 Consensus size: 40
9368 CCTAGGTTTC
9378 TTTC-AAGTTGGCATCGGTTGGCCTTC--TAAAAT---GT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * * *
9412 TTTCAGAGTTGGTATCTGTTGGCCTTCTCTAAAAATCAAGCT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCT-TTAAAATCAAG-T
* * *
9454 TTTCAGAGTTGGCAACGGTTGGCCTTCTTTAAAGTCAAGTT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAG-T
*
9495 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAAT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* *
9535 TTTCAAAAGATGGCATCGGTAGGCCTTC--T-AAA--AAGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
*
9571 TTTCAAAGGTGGCATCGGTTGGCCTTCTTTAAAATCAAGTT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAG-T
* **
9612 TTTCAAAGTTGGCATCAGTTGGCCTTCTTTAAAATCAAAC
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* *
9652 TTTCAAAAGATGGCATCGGTTGGCATTC--T-AAAT-AAGT
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * *
9689 TTTCAAAGTTGGCATCGGGTGGCCGTCTTTAAAATCGAGTT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAG-T
* *
9730 TTTCAAAAGTTGGCATCGGTTGGCCCTT-TTTAAAAGCAA-A
1 TTTC-AAAGTTGGCATCGGTTGG-CCTTCTTTAAAATCAAGT
9770 TTTCAAAAGTTGGCATCGGTTGGCCTTC--T-AAA--AA-T
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * **
9805 TCTCAAAGTTGGCATCGGTTGGCCTTC-TTAAAGTTTTGAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGT
9846 TTTCAAAGTTGGCATCGGTTGGCCTTC--T--AA--AAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
* * * **
9880 TCTCAAAGTTGGCGTCGGTTGGCCTTC-TTAAAGTTTTGAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGT
* * * **
9921 TCTCGAAGTTGGCATCGGTTGGCCTTC-TTAAAGTTTTGAGT
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGT
* *
9962 TTTCAAAGTTGGCATCGGTTGACCTTCTTAAAAA
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAA
9996 AAAAATCTCG
Statistics
Matches: 489, Mismatches: 56, Indels: 72
0.79 0.09 0.12
Matches are distributed among these distances:
34 55 0.11
35 47 0.10
36 28 0.06
37 11 0.02
38 18 0.04
39 10 0.02
40 39 0.08
41 222 0.45
42 56 0.11
43 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (40 bp):
TTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGT
Found at i:9591 original size:117 final size:116
Alignment explanation
Indices: 9453--9995 Score: 608
Period size: 117 Copynumber: 4.7 Consensus size: 116
9443 AAAATCAAGC
* * *
9453 TTTTCAGAGTTGGCAACGGTTGGCCTTCTTTAAAGTCAAGTTTTTCAAAGTTGGCATCGGTTGGC
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
*
9518 CTTCTTTAAAATCAAATTTTCAAAAGATGGCATCGGTAGGCCTTCTAAAAAG
66 CTTCTTTAAAATCAAA-TTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
* *
9570 TTTTCAAAGGTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCAGTTGGC
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
*
9635 CTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCATTCTAAATAAG
66 CTTCTTTAAAATCAAA-TTTCAAAAGATGGCATCGGTTGGCCTTCTAAA-AAG
* * *
9688 TTTTCAAAGTTGGCATCGGGTGGCCGTCTTTAAAATCGAGTTTTTCAAAAGTTGGCATCGGTTGG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTC-AAAGTTGGCATCGGTTGG
* *
9753 CCCTT-TTTAAAAGCAAATTTCAAAAGTTGGCATCGGTTGGCCTTCTAAAAA-
65 -CCTTCTTTAAAATCAAATTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
* * **
9804 TTCTCAAAGTTGGCATCGGTTGGCCTTC-TTAAAGTTTTGAG-TTTTCAAAGTTGGCATCGGTTG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGTTTTTCAAAGTTGGCATCGGTTG
* * * *
9867 GCCTTC--TAAAAGT----TCTC-AAAGTTGGCGTCGGTTGGCCTTCTTAAAGTTTTGAG
64 GCCTTCTTTAAAA-TCAAATTTCAAAAGATGGCATCGGTTGGCCTTC-TAAA-----AAG
* * * **
9920 TTCTCGAAGTTGGCATCGGTTGGCCTTC-TTAAAGTTTTGAG-TTTTCAAAGTTGGCATCGGTTG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGTTTTTCAAAGTTGGCATCGGTTG
* *
9983 ACCTTCTTAAAAA
64 GCCTTCTTTAAAA
9996 AAAAATCTCG
Statistics
Matches: 382, Mismatches: 28, Indels: 31
0.87 0.06 0.07
Matches are distributed among these distances:
109 22 0.06
110 7 0.02
113 5 0.01
114 4 0.01
115 24 0.06
116 97 0.25
117 112 0.29
118 79 0.21
119 28 0.07
120 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (116 bp):
TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
CTTCTTTAAAATCAAATTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
Found at i:9774 original size:118 final size:117
Alignment explanation
Indices: 9453--9873 Score: 609
Period size: 117 Copynumber: 3.6 Consensus size: 117
9443 AAAATCAAGC
* * *
9453 TTTTCAGAGTTGGCAACGGTTGGCCTTCTTTAAAGTCAAGTTTTTCAAAGTTGGCATCGGTTGGC
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
* *
9518 CTTCTTTAAAATCAAATTTTCAAAAGATGGCATCGGTAGGCCTTCTAAAAAG
66 CTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
* *
9570 TTTTCAAAGGTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCAGTTGGC
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
*
9635 CTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCATTCTAAATAAG
66 CTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCCTTCTAAA-AAG
* * *
9688 TTTTCAAAGTTGGCATCGGGTGGCCGTCTTTAAAATCGAGTTTTTCAAAAGTTGGCATCGGTTGG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTC-AAAGTTGGCATCGGTTGG
* *
9753 CCCTT-TTTAAAAGCAAA-TTTCAAAAGTTGGCATCGGTTGGCCTTCTAAAAA-
65 -CCTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
* * **
9804 TTCTCAAAGTTGGCATCGGTTGGCCTTC-TTAAAGTTTTGAG-TTTTCAAAGTTGGCATCGGTTG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAA--ATCAAGTTTTTCAAAGTTGGCATCGGTTG
9867 GCCTTCT
64 GCCTTCT
9874 AAAAGTTCTC
Statistics
Matches: 277, Mismatches: 21, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
114 4 0.01
115 24 0.09
116 30 0.11
117 112 0.40
118 75 0.27
119 28 0.10
120 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (117 bp):
TTTTCAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCAAGTTTTTCAAAGTTGGCATCGGTTGGC
CTTCTTTAAAATCAAACTTTCAAAAGATGGCATCGGTTGGCCTTCTAAAAAG
Found at i:9864 original size:75 final size:75
Alignment explanation
Indices: 9770--9993 Score: 322
Period size: 75 Copynumber: 2.9 Consensus size: 75
9760 TAAAAGCAAA
*
9770 TTTCAAAAGTTGGCATCGGTTGGCCTTCTAAAAATTCTCAAAGTTGGCATCGGTTGGCCTTCTTA
1 TTTC-AAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGCATCGGTTGGCCTTCTTA
9835 AAGTTTTGAGT
65 AAGTTTTGAGT
*
9846 TTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGCGTCGGTTGGCCTTCTTAA
1 TTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGCATCGGTTGGCCTTCTTAA
9911 AGTTTTGAGT
66 AGTTTTGAGT
* * * *
9921 TCTCGAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGAGTTTTCAAAGTTGGCATCGGTTGACC
1 TTTCAAAGTTGGCATCGGTTGGCCTTC-TAAA------AGTTCTCAAAGTTGGCATCGGTTGGCC
9986 TTCTTAAA
59 TTCTTAAA
9994 AAAAAAATCT
Statistics
Matches: 134, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
75 94 0.70
76 8 0.06
82 32 0.24
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (75 bp):
TTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAGTTCTCAAAGTTGGCATCGGTTGGCCTTCTTAA
AGTTTTGAGT
Found at i:10890 original size:52 final size:52
Alignment explanation
Indices: 10763--10896 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
10753 TTTTCAAGTC
* *
10763 TTTTCAAGTCAGAGAGAAGA--AGAGCAAACAAAGTAAAATGATGAGCCTACA
1 TTTTCAAGTCAGAGAGAAGATCA-AGCAAATACAGTAAAATGATGAGCCTACA
* * *
10814 --TTCAAGTCAAAGGGAAGATCAAGCAAATACAGTAAAATGATGAGCCTAGA
1 TTTTCAAGTCAGAGAGAAGATCAAGCAAATACAGTAAAATGATGAGCCTACA
10864 TTTTCAAGTCAGAGAGAAGATCAAGCAAATACA
1 TTTTCAAGTCAGAGAGAAGATCAAGCAAATACA
10897 TGCATTAACA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
49 16 0.22
50 26 0.36
51 1 0.01
52 29 0.40
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (52 bp):
TTTTCAAGTCAGAGAGAAGATCAAGCAAATACAGTAAAATGATGAGCCTACA
Found at i:17591 original size:8 final size:7
Alignment explanation
Indices: 17558--17614 Score: 64
Period size: 8 Copynumber: 7.9 Consensus size: 7
17548 TATCATATTT
17558 TATATAA
1 TATATAA
17565 TATAT-A
1 TATATAA
17571 TATTATAA
1 TA-TATAA
17579 GTATATAGA
1 -TATATA-A
17588 TATATAA
1 TATATAA
17595 -ATATAA
1 TATATAA
17601 TATGATAA
1 TAT-ATAA
17609 TATATA
1 TATATA
17615 TTAAAATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 9 0.20
7 14 0.32
8 18 0.41
9 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:18701 original size:20 final size:22
Alignment explanation
Indices: 18667--18707 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
18657 TGTTTTCTAT
18667 TTTCTAATCTA-TTTTGATCAA
1 TTTCTAATCTATTTTTGATCAA
18688 TTTCTAAT-TATTTTTGATCA
1 TTTCTAATCTATTTTTGATCA
18708 CTGATCAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTCTAATCTATTTTTGATCAA
Found at i:18879 original size:21 final size:21
Alignment explanation
Indices: 18833--18890 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
18823 TGGTCTGTTA
18833 CTGTTTTGATCAATTTCTAAT
1 CTGTTTTGATCAATTTCTAAT
* * *
18854 ATGTTTTGATTAGTTTC-AATT
1 CTGTTTTGATCAATTTCTAA-T
* *
18875 CTGTTCTAATCAATTT
1 CTGTTTTGATCAATTT
18891 GGAATTGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
CTGTTTTGATCAATTTCTAAT
Found at i:21621 original size:13 final size:13
Alignment explanation
Indices: 21603--21628 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21593 TTCTGTCTTA
21603 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
21616 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
21629 GCTGCTGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (13 bp):
CTGTTTTTGAGTT
Found at i:26327 original size:20 final size:20
Alignment explanation
Indices: 26302--26341 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
26292 AATGACATGA
26302 CATGAAACT-CAAACCCTAAC
1 CATGAAA-TACAAACCCTAAC
26322 CATGAAATGACAAACCCTAA
1 CATGAAAT-ACAAACCCTAA
26342 GTGAGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 7 0.39
21 10 0.56
ACGTcount: A:0.47, C:0.30, G:0.07, T:0.15
Consensus pattern (20 bp):
CATGAAATACAAACCCTAAC
Found at i:26337 original size:21 final size:20
Alignment explanation
Indices: 26311--26365 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
26301 ACATGAAACT
26311 CAAACCCTAACCATGAAATGA
1 CAAACCCTAA-CATGAAATGA
* *
26332 CAAACCCTAA-GTGAGATGA
1 CAAACCCTAACATGAAATGA
26351 -AAACCCTAACTATGA
1 CAAACCCTAAC-ATGA
26366 CATTAAAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.31
19 7 0.24
20 3 0.10
21 10 0.34
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.16
Consensus pattern (20 bp):
CAAACCCTAACATGAAATGA
Found at i:26385 original size:25 final size:25
Alignment explanation
Indices: 26351--26398 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
26341 AGTGAGATGA
26351 AAACCCTAACTATGACAT-TAAAGCC
1 AAACCCTAAC-ATGACATCTAAAGCC
*
26376 AAACCCTAACATGTCATCTAAAG
1 AAACCCTAACATGACATCTAAAG
26399 TGAACATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (25 bp):
AAACCCTAACATGACATCTAAAGCC
Found at i:44955 original size:31 final size:30
Alignment explanation
Indices: 44887--44956 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
44877 AATTTGTAAA
* *
44887 TGGGTCTCTGAAGTGAATTTAGTGAGCAAT
1 TGGGTCCCTGAAGTGAATTAAGTGAGCAAT
** * *
44917 TAAGTCCCTGAAGTTGAGTTAATTGAGCAAT
1 TGGGTCCCTGAAG-TGAATTAAGTGAGCAAT
44948 TGGGTCCCT
1 TGGGTCCCT
44957 CACCAATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (30 bp):
TGGGTCCCTGAAGTGAATTAAGTGAGCAAT
Found at i:45005 original size:15 final size:16
Alignment explanation
Indices: 44985--45014 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44975 GAAAACTATA
44985 TATTTTTTAA-AAAAT
1 TATTTTTTAATAAAAT
45000 TATTTTTTAATAAAA
1 TATTTTTTAATAAAA
45015 AATATGACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTTTTAATAAAAT
Found at i:45726 original size:157 final size:157
Alignment explanation
Indices: 45429--45746 Score: 539
Period size: 157 Copynumber: 2.0 Consensus size: 157
45419 TCTGATCACC
45429 TTCTTGAATCCATTGAATTCTTGATTTTTGCTTATAAAAGCTTTCATAAGCCAACAAAAGCTCTT
1 TTCTTGAATCCATTGAATTCTTGATTTTTGCTTATAAAAGCTTTCATAAGCCAACAAAAGCTCTT
45494 TGAGTTCAAAGGTATTCTCATTCATCTCATCAATCAATTAAGAAGATGTAGAGTTTAACATAACT
66 TGAGTTCAAAGGTATTCTCATTCATCTCATCAATCAATTAAGAAGATGTAGAGTTTAACATAACT
*
45559 ATTTGAAGAAGTACAACCTCTTTTCGT
131 ATTTGAAGAAGTACAACCTCTTCTCGT
** *
45586 TTCTTGAATCCATTGGGTTCTTGATTTTTGCTTATAAAAGCTTTCCTAAGCCAACAAAAGCTCTT
1 TTCTTGAATCCATTGAATTCTTGATTTTTGCTTATAAAAGCTTTCATAAGCCAACAAAAGCTCTT
* *
45651 TGAGTTCAAAGGTATTCTCATTTATCTCATCAATCAATTGAGAAGATGTAGAGTTTAACATAGA-
66 TGAGTTCAAAGGTATTCTCATTCATCTCATCAATCAATTAAGAAGATGTAGAGTTTAACATA-AC
* * *
45715 TGTTTGTAGAAGTCCAACCTCTTCTCGT
130 TATTTGAAGAAGTACAACCTCTTCTCGT
45743 TTCT
1 TTCT
45747 ATTTTCTTAA
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
157 150 0.99
158 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (157 bp):
TTCTTGAATCCATTGAATTCTTGATTTTTGCTTATAAAAGCTTTCATAAGCCAACAAAAGCTCTT
TGAGTTCAAAGGTATTCTCATTCATCTCATCAATCAATTAAGAAGATGTAGAGTTTAACATAACT
ATTTGAAGAAGTACAACCTCTTCTCGT
Found at i:48054 original size:28 final size:29
Alignment explanation
Indices: 48018--48091 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
48008 GGGTCATCCA
48018 GGGGCATTTTGGTCATTTTCACATCTA-G
1 GGGGCATTTTGGTCATTTTCACATCTAGG
** *
48046 GGGGCATTTTGGTCATTTTTGCATTTAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
*
48075 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
48092 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 24 0.59
29 17 0.41
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.43
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCACATCTAGG
Found at i:51179 original size:23 final size:24
Alignment explanation
Indices: 51136--51180 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
51126 TTTTTCTCAC
*
51136 TTTGGGCCTTATCTCTTTTATGCA
1 TTTGGGCCTTATCCCTTTTATGCA
*
51160 TTTGGG-CTTGTCCCTTTTATG
1 TTTGGGCCTTATCCCTTTTATG
51181 TTCCATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.09, C:0.20, G:0.20, T:0.51
Consensus pattern (24 bp):
TTTGGGCCTTATCCCTTTTATGCA
Found at i:52240 original size:26 final size:26
Alignment explanation
Indices: 52211--52261 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
52201 ACAAATGGTA
52211 ATTAAATTCAA-AGAGTAAAAATAGTG
1 ATTAAATTCAAGAGAGT-AAAATAGTG
*
52237 ATTAAGTTCAAGAGAGTAAAATAGT
1 ATTAAATTCAAGAGAGTAAAATAGT
52262 AATCAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTG
Found at i:52276 original size:7 final size:7
Alignment explanation
Indices: 52266--52473 Score: 70
Period size: 7 Copynumber: 28.9 Consensus size: 7
52256 AATAGTAATC
52266 AGTAAAG
1 AGTAAAG
52273 AGTAAA-
1 AGTAAAG
52279 ATGGTAAAG
1 A--GTAAAG
52288 AGTAAAG
1 AGTAAAG
52295 AGTAATA-
1 AGTAA-AG
*
52302 AGTAAAA
1 AGTAAAG
52309 AGTAAAAG
1 AGT-AAAG
*
52317 AGAAAAG
1 AGTAAAG
52324 AGT-AAG
1 AGTAAAG
**
52330 AAGGTAATC
1 -A-GTAAAG
52339 AGTAAAG
1 AGTAAAG
52346 AGTAAA-
1 AGTAAAG
*
52352 ATGATAAAAA
1 A-G-T-AAAG
*
52362 AATAAAG
1 AGTAAAG
**
52369 AGTAATC
1 AGTAAAG
52376 AGTAAAAG
1 AGT-AAAG
*
52384 AAG-AATG
1 -AGTAAAG
*
52391 -GTAAAA
1 AGTAAAG
52397 AGTAAAG
1 AGTAAAG
**
52404 AGTAATC
1 AGTAAAG
52411 AGTAAAG
1 AGTAAAG
* *
52418 -GAAGAAT
1 AGTA-AAG
52425 AGTAAAG
1 AGTAAAG
52432 AGTAAAG
1 AGTAAAG
* **
52439 GGTAATC
1 AGTAAAG
*
52446 AGTAAAA
1 AGTAAAG
**
52453 AGATAATC
1 AG-TAAAG
52461 AGTAAAG
1 AGTAAAG
52468 AGTAAA
1 AGTAAA
52474 ATAGTAAAAG
Statistics
Matches: 145, Mismatches: 36, Indels: 40
0.66 0.16 0.18
Matches are distributed among these distances:
5 1 0.01
6 10 0.07
7 101 0.70
8 25 0.17
9 7 0.05
10 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:52276 original size:22 final size:22
Alignment explanation
Indices: 52249--52328 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
52239 TAAGTTCAAG
*
52249 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATAGTAAACAGTAA
* *
52271 AGAGTAAAATGGTAAAGAGTAA
1 AGAGTAAAATAGTAAACAGTAA
* *
52293 AGAGTAATA-AGTAAAAAGTAAA
1 AGAGTAAAATAGTAAACAGT-AA
*
52315 AGAG-AAAAGAGTAA
1 AGAGTAAAATAGTAA
52329 GAAGGTAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
21 11 0.22
22 38 0.78
ACGTcount: A:0.59, C:0.01, G:0.23, T:0.17
Consensus pattern (22 bp):
AGAGTAAAATAGTAAACAGTAA
Found at i:52328 original size:58 final size:56
Alignment explanation
Indices: 52265--52416 Score: 124
Period size: 58 Copynumber: 2.8 Consensus size: 56
52255 AAATAGTAAT
52265 CAGTAAAGAGTAAAATGGTAAAGAGTAAAGAGTAATAAGTAAAAAGTAAAAGAGAAAA
1 CAGTAAAGAGTAAAATGGTAAAGAGTAAAGAGTAATAAGTAAAAA-T-AAAGAGAAAA
* * * * *
52323 GAGT-AAGAAGGT--AATCAGTAAAGAGTAAA-A-TGATAA--AAAAATAAAGAGTAAT
1 CAGTAAAG-A-GTAAAAT-GGTAAAGAGTAAAGAGTAATAAGTAAAAATAAAGAGAAAA
* *
52375 CAGTAAA-AG-AAGAATGGTAAAAAGTAAAGAGTAATCAGTAAA
1 CAGTAAAGAGTAA-AATGGTAAAGAGTAAAGAGTAATAAGTAAA
52417 GGAAGAATAG
Statistics
Matches: 73, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
50 1 0.01
51 12 0.16
52 15 0.21
53 7 0.10
54 5 0.07
55 3 0.04
56 5 0.07
57 7 0.10
58 16 0.22
59 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.17
Consensus pattern (56 bp):
CAGTAAAGAGTAAAATGGTAAAGAGTAAAGAGTAATAAGTAAAAATAAAGAGAAAA
Found at i:52404 original size:35 final size:35
Alignment explanation
Indices: 52259--52452 Score: 191
Period size: 35 Copynumber: 5.4 Consensus size: 35
52249 AGAGTAAAAT
*
52259 AGTAATCAGTAAAGAGTAAAATGGTAAAGAGTAAAG
1 AGTAATCAGTAAA-AGTAAAATGGTAAAAAGTAAAG
*
52295 AGTAATAAGTAAAAAGTAAAA-GAG-AAAAGAGT-AAG
1 AGTAATCAGT-AAAAGTAAAATG-GTAAAA-AGTAAAG
* *
52330 AAGGTAATCAGTAAAGAGTAAAATGATAAAAAAATAAAG
1 -A-GTAATCAGTAAA-AGTAAAATGGT-AAAAAGTAAAG
52369 AGTAATCAGTAAAAG-AAGAATGGTAAAAAGTAAAG
1 AGTAATCAGTAAAAGTAA-AATGGTAAAAAGTAAAG
* * *
52404 AGTAATCAGT-AAAGGAAGAATAGTAAAGAGTAAAG
1 AGTAATCAGTAAAAGTAA-AATGGTAAAAAGTAAAG
*
52439 GGTAATCAGTAAAA
1 AGTAATCAGTAAAA
52453 AGATAATCAG
Statistics
Matches: 135, Mismatches: 10, Indels: 26
0.79 0.06 0.15
Matches are distributed among these distances:
34 4 0.03
35 56 0.41
36 34 0.25
37 30 0.22
38 4 0.03
39 7 0.05
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.18
Consensus pattern (35 bp):
AGTAATCAGTAAAAGTAAAATGGTAAAAAGTAAAG
Found at i:52461 original size:15 final size:15
Alignment explanation
Indices: 52441--52503 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
52431 GAGTAAAGGG
52441 TAATCAGTAAAAAGA
1 TAATCAGTAAAAAGA
*
52456 TAATCAGTAAAGAGTA
1 TAATCAGTAAAAAG-A
* *
52472 AAAT-AGT-AAAAGG
1 TAATCAGTAAAAAGA
*
52485 TAATCAGTAAAAACA
1 TAATCAGTAAAAAGA
52500 TAAT
1 TAAT
52504 GATAATCAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 7 0.18
15 24 0.63
16 4 0.11
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (15 bp):
TAATCAGTAAAAAGA
Found at i:52465 original size:29 final size:28
Alignment explanation
Indices: 52432--52495 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
52422 AATAGTAAAG
*
52432 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
52461 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
52490 AGTAAA
1 AGTAAA
52496 AACATAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 25 0.81
30 3 0.10
31 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:52471 original size:22 final size:21
Alignment explanation
Indices: 52446--52605 Score: 72
Period size: 22 Copynumber: 7.1 Consensus size: 21
52436 AAGGGTAATC
52446 AGTAAAAAGATAATCAGTAAA
1 AGTAAAAAGATAATCAGTAAA
52467 GAGTAAAATAGTAAAAGGTAATCAGTAAA
1 -AGTAAAA-AG----A--TAATCAGTAAA
** * *
52496 AACATAATGATAATCAGTAAA
1 AGTAAAAAGATAATCAGTAAA
* *
52517 AGGTAAATTAG-TAATCAGTAAG
1 A-GTAAA-AAGATAATCAGTAAA
* * *
52539 AGCAAAATGGTAATCAGTAAA
1 AGTAAAAAGATAATCAGTAAA
* * *
52560 ACGTAAGAAGGTAATCAATAAA
1 A-GTAAAAAGATAATCAGTAAA
*
52582 GAGTAAAATAG-TAATTAGTAAA
1 -AGTAAAA-AGATAATCAGTAAA
52604 AG
1 AG
52606 GTAATCAGTA
Statistics
Matches: 104, Mismatches: 21, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
20 1 0.01
21 29 0.28
22 50 0.48
23 7 0.07
27 2 0.02
28 4 0.04
29 11 0.11
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTAAAAAGATAATCAGTAAA
Found at i:52530 original size:65 final size:64
Alignment explanation
Indices: 52441--52725 Score: 193
Period size: 65 Copynumber: 4.5 Consensus size: 64
52431 GAGTAAAGGG
* * **
52441 TAATCAGTAAAAAG-ATAATCAGTAAAGAGTAAAATAGTAAAAGGTAATCAGTAAAAACATAATG
1 TAATCAGTAAAGAGTA-AATTAGTAATCAGT-AAATAGTAAAAGGTAATCAGTAAAAACATAATG
52505 A
64 A
* * *
52506 TAATCAGTAAA-AGGTAAATTAGTAATCAGT-AAGAGCAAAATGGTAATCAGT-AAAACGTAA-G
1 TAATCAGTAAAGA-GTAAATTAGTAATCAGTAAATAGTAAAA-GGTAATCAGTAAAAACATAATG
52567 AA
64 -A
* * * * *
52569 GGTAATCAATAAAGAGT--A--A--AAT-AGTAATTAGTAAAAGGTAATCAGTAAGAGCAAAATG
1 --TAATCAGTAAAGAGTAAATTAGTAATCAGTAAATAGTAAAAGGTAATCAGTAAAAACATAATG
*
52627 G
64 A
* * *
52628 TAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTA-AAAA
1 TAATCAGTAAAGAGTAAATTAGTAATCAGTAAATAGTAA-AAGGTAATCAGTAAA-A--ACATAA
* *
52692 AGG
62 TGA
* *
52695 TAATCAGT-AAGAGTAAAATAGTAATTAGTAA
1 TAATCAGTAAAGAGTAAATTAGTAATCAGTAA
52726 GAGCAAAATG
Statistics
Matches: 177, Mismatches: 22, Indels: 41
0.74 0.09 0.17
Matches are distributed among these distances:
57 14 0.08
58 13 0.07
59 16 0.09
60 1 0.01
61 2 0.01
62 1 0.01
63 21 0.12
64 21 0.12
65 49 0.28
66 25 0.14
67 14 0.08
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (64 bp):
TAATCAGTAAAGAGTAAATTAGTAATCAGTAAATAGTAAAAGGTAATCAGTAAAAACATAATGA
Found at i:52530 original size:122 final size:120
Alignment explanation
Indices: 52391--52660 Score: 276
Period size: 122 Copynumber: 2.2 Consensus size: 120
52381 AAGAAGAATG
* * * * ** **
52391 GTAAAAAGTAAAGAGTAATCAGTAAAGGAAGAATAGTAAAGAGTAAAGGGTAATCA-GTAAAAAG
1 GTAAAAGGTAAATAGTAATCAGTAAAGCAA-AATAGTAAACAGTAAAACGTAAGAAGGTAAAAA-
* *
52455 ATAATCAGT-AAAGAGTAAAATAGTAAAAGGTAATCAGTAAAAACATAATGATAATCA
64 ATAAACAGTAAAAGAGT-AAATAGTAAAAGGTAATCAGTAAAAACAAAATGATAATCA
* * **
52512 GTAAAAGGTAAATTAGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAACGTAAGAAGGTAATCA
1 GTAAAAGGTAAA-TAGTAATCAGTAA-AGCAAAATAGTAAACAGTAAAACGTAAGAAGGTAAAAA
* * * * * *
52577 ATAAAGAGTAAAATAGTAATTAGTAAAAGGTAATCAGTAAGAGCAAAATGGTAATCA
64 ATAAACAGTAAAAGAGTAAATAGTAAAAGGTAATCAGTAAAAACAAAATGATAATCA
52634 GT-AAAGAGTAAAATAGTAATCAGTAAA
1 GTAAAAG-GT-AAATAGTAATCAGTAAA
52661 AAGTAAGAAG
Statistics
Matches: 123, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
121 16 0.13
122 89 0.72
123 18 0.15
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (120 bp):
GTAAAAGGTAAATAGTAATCAGTAAAGCAAAATAGTAAACAGTAAAACGTAAGAAGGTAAAAAAT
AAACAGTAAAAGAGTAAATAGTAAAAGGTAATCAGTAAAAACAAAATGATAATCA
Found at i:52609 original size:22 final size:22
Alignment explanation
Indices: 52506--52776 Score: 125
Period size: 21 Copynumber: 12.9 Consensus size: 22
52496 AACATAATGA
*
52506 TAATCAGTAAAAGGTAAATTAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
52528 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* *
52549 TAATCAGTAAAACGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
*
52571 TAATCAAT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
*
52593 TAATTAGTAAAAGGT--AATCAG
1 TAATCAGTAAAAGGTAAAAT-AG
* *
52614 TAA-GAGCAAAATGGT--AATCAG
1 TAATCAGTAAAA-GGTAAAAT-AG
52635 TAA--AG----A-GTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* *
52650 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
*
52672 TAATCAGT-AAAGAGTAAAAAAGG
1 TAATCAGTAAAAG-GTAAAATA-G
*
52695 TAATCAGTAAGA-GTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * * *
52716 TAATTAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* * *
52737 TAATTAATAAGA-GTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
52758 TAATCAGT-AAAGAGTAAAA
1 TAATCAGTAAAAG-GTAAAA
52777 GGTGATCAGT
Statistics
Matches: 199, Mismatches: 27, Indels: 46
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.01
15 5 0.03
16 4 0.02
17 2 0.01
20 13 0.07
21 88 0.44
22 66 0.33
23 17 0.09
24 2 0.01
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:52616 original size:79 final size:78
Alignment explanation
Indices: 52527--52768 Score: 254
Period size: 79 Copynumber: 3.0 Consensus size: 78
52517 AGGTAAATTA
52527 GTAATCAGTAAGAGCAAAATGGTAATCAGTAAAACGTAAGAA-GGTAATCAATAAAGAGTAAAAT
1 GTAATCAGTAAGAGCAAAATGGTAATCAGTAAAA-GTAA-AATGGTAATCAATAAAGAGTAAAAT
*
52591 AGTAATTAGTAAAAG
64 AGTAATCAGTAAAAG
* * *
52606 GTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAG
1 GTAATCAGTAAGAGCAAAATGGTAATCAGTAAA-AGTAAAATGGTAATCAATAAAGAGT---AA-
**
52671 GTAATCAGTAAAGAGTAAAAAAG
61 --AAT-AGTAATCAGT--AAAAG
* * * * * *
52694 GTAATCAGTAAGAGTAAAATAGTAATTAGTAAGAGCAAAATGGTAATTAAT-AAGAGTAAAATAG
1 GTAATCAGTAAGAGCAAAATGGTAATCAGTAAAAGTAAAATGGTAATCAATAAAGAGTAAAATAG
52758 TAATCAGTAAA
66 TAATCAGTAAA
52769 GAGTAAAAGG
Statistics
Matches: 136, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
77 3 0.02
78 2 0.01
79 59 0.43
80 4 0.03
82 2 0.01
83 2 0.01
85 3 0.02
86 13 0.10
87 14 0.10
88 34 0.25
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.22
Consensus pattern (78 bp):
GTAATCAGTAAGAGCAAAATGGTAATCAGTAAAAGTAAAATGGTAATCAATAAAGAGTAAAATAG
TAATCAGTAAAAG
Found at i:52616 original size:101 final size:102
Alignment explanation
Indices: 52506--52784 Score: 287
Period size: 101 Copynumber: 2.7 Consensus size: 102
52496 AACATAATGA
* * * *
52506 TAATCAGTAAAAGGTAAATTAGTAATCAGT-AAGAGCAAAATGGTAATCAGTAAAACGTAAGAAG
1 TAATCAGTAAAA-GCAAAATAGTAATCAGTAAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAG
* *
52570 GTAATCAATAAAGAGTAAAATA-GTAATTAGTAAAAGG
65 GTAATCAATAAAGAGTAAAAAAGGTAATCAGTAAAAGG
* * *
52607 TAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGG
1 TAATCAGTAAAAGCAAAATAGTAATCAGTAAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGG
* *
52672 TAATCAGTAAAGAGTAAAAAAGGTAATCAGTAAGAGTAAAATAG
66 TAATCAATAAAGAGTAAAAAAGGTAATC------AGTAAAA-GG
* * * * * * *
52716 TAATTAGTAAGAGCAAAATGGTAATTAAT-AAGAGTAAAATAGTAATCAGTAAAGAGTAA-AAGG
1 TAATCAGTAAAAGCAAAATAGTAATCAGTAAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGG
*
52779 TGATCA
66 TAATCA
52785 GTGATTCAAA
Statistics
Matches: 153, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
100 14 0.09
101 62 0.41
102 5 0.03
107 9 0.06
108 36 0.24
109 27 0.18
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.22
Consensus pattern (102 bp):
TAATCAGTAAAAGCAAAATAGTAATCAGTAAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGG
TAATCAATAAAGAGTAAAAAAGGTAATCAGTAAAAGG
Found at i:52718 original size:21 final size:22
Alignment explanation
Indices: 52621--52776 Score: 185
Period size: 22 Copynumber: 7.2 Consensus size: 22
52611 CAGTAAGAGC
*
52621 AAAATGGTAATCAGTAAAGAGT
1 AAAATAGTAATCAGTAAAGAGT
*
52643 AAAATAGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGTAAAGAGT
*
52665 AAGAA-GGTAATCAGTAAAGAGT
1 AA-AATAGTAATCAGTAAAGAGT
*
52687 AAAAAAGGTAATCAGT-AAGAGT
1 AAAATA-GTAATCAGTAAAGAGT
* *
52709 AAAATAGTAATTAGT-AAGAGC
1 AAAATAGTAATCAGTAAAGAGT
* * *
52730 AAAATGGTAATTAAT-AAGAGT
1 AAAATAGTAATCAGTAAAGAGT
52751 AAAATAGTAATCAGTAAAGAGT
1 AAAATAGTAATCAGTAAAGAGT
52773 AAAA
1 AAAA
52777 GGTGATCAGT
Statistics
Matches: 116, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
21 45 0.39
22 60 0.52
23 11 0.09
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (22 bp):
AAAATAGTAATCAGTAAAGAGT
Found at i:52786 original size:21 final size:21
Alignment explanation
Indices: 52637--52786 Score: 151
Period size: 21 Copynumber: 7.0 Consensus size: 21
52627 GTAATCAGTA
*
52637 AAGAGTAAAATAGTAATCAGT
1 AAGAGTAAAATGGTAATCAGT
*
52658 AAAAAGTAAGAA-GGTAATCAGT
1 -AAGAGTAA-AATGGTAATCAGT
*
52680 AAAGAGTAAAAAAGGTAATCAGT
1 -AAGAGT-AAAATGGTAATCAGT
* *
52703 AAGAGTAAAATAGTAATTAGT
1 AAGAGTAAAATGGTAATCAGT
* * *
52724 AAGAGCAAAATGGTAATTAAT
1 AAGAGTAAAATGGTAATCAGT
*
52745 AAGAGTAAAATAGTAATCAGT
1 AAGAGTAAAATGGTAATCAGT
*
52766 AAAGAGTAAAA-GGTGATCAGT
1 -AAGAGTAAAATGGTAATCAGT
52787 GATTCAAAGA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
21 55 0.50
22 40 0.37
23 14 0.13
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.22
Consensus pattern (21 bp):
AAGAGTAAAATGGTAATCAGT
Found at i:52853 original size:9 final size:9
Alignment explanation
Indices: 52815--52855 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
52805 GTAGTCAGTA
52815 TAAGAA-AG
1 TAAGAAGAG
52823 -AAGAAGAG
1 TAAGAAGAG
*
52831 TAAAAAGTAG
1 TAAGAAG-AG
52841 TAAGAAGAG
1 TAAGAAGAG
52850 TAAGAA
1 TAAGAA
52856 AAGAGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
7 5 0.18
8 2 0.07
9 13 0.46
10 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (9 bp):
TAAGAAGAG
Found at i:55108 original size:6 final size:6
Alignment explanation
Indices: 55097--55122 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55087 TAATCTACTA
55097 TAGATT TAGATT TAGATT TAGATT TA
1 TAGATT TAGATT TAGATT TAGATT TA
55123 CTTTACTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TAGATT
Found at i:55450 original size:20 final size:19
Alignment explanation
Indices: 55421--55472 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
55411 TTTCTAAAAA
55421 AAAAAAAAAATTTGCGTCG
1 AAAAAAAAAATTTGCGTCG
*
55440 AGAAAAGAAAAA-TTGTGTCG
1 A-AAAA-AAAAATTTGCGTCG
55460 AAAAAAAAAATTT
1 AAAAAAAAAATTT
55473 TAGGGTTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 12 0.41
21 5 0.17
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (19 bp):
AAAAAAAAAATTTGCGTCG
Found at i:56570 original size:15 final size:15
Alignment explanation
Indices: 56550--56592 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
56540 CCTTGCTAAG
56550 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
56565 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
56580 CAAGAAGATGAGC
1 CCAGAAGATGAGC
56593 AACTTGGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.42, C:0.23, G:0.28, T:0.07
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:60906 original size:6 final size:6
Alignment explanation
Indices: 60895--60937 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
60885 TAATCTGCTA
60895 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
60938 CTTTGCTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:65948 original size:16 final size:16
Alignment explanation
Indices: 65929--66002 Score: 114
Period size: 16 Copynumber: 4.6 Consensus size: 16
65919 GGGTTCGGGT
*
65929 GGGTTTGGGTATTTTC
1 GGGTTCGGGTATTTTC
65945 GGGTTCGGG-ATTTTTC
1 GGGTTCGGGTA-TTTTC
*
65961 GGGTTCGGGTTTTTTC
1 GGGTTCGGGTATTTTC
65977 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
65993 GGGTTCGGGT
1 GGGTTCGGGT
66003 TCGGATCGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
15 1 0.02
16 52 0.98
ACGTcount: A:0.04, C:0.11, G:0.41, T:0.45
Consensus pattern (16 bp):
GGGTTCGGGTATTTTC
Found at i:66798 original size:16 final size:16
Alignment explanation
Indices: 66765--66834 Score: 79
Period size: 16 Copynumber: 4.3 Consensus size: 16
66755 TATTTTGATC
*
66765 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGG-CGGGT
66782 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
***
66798 TCGGGTTC-GGCTATAT
1 TCGGGTTCGGGC-GGGT
66814 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
66830 TCGGG
1 TCGGG
66835 ACGTTGACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.07
16 28 0.64
17 13 0.30
ACGTcount: A:0.03, C:0.20, G:0.50, T:0.27
Consensus pattern (16 bp):
TCGGGTTCGGGCGGGT
Found at i:66824 original size:6 final size:6
Alignment explanation
Indices: 66765--66807 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
66755 TATTTTGATC
*
66765 TCGGGC TCGGG- TCGGGT TCGGGT TCGGG- -CGGGT TCGGGT TCGG
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGG
66808 CTATATTCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.12
5 5 0.15
6 25 0.74
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (6 bp):
TCGGGT
Done.