Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013693.1 Corchorus capsularis cultivar CVL-1 contig13714, 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: 157826
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:102 original size:32 final size:32
Alignment explanation
Indices: 28--134 Score: 178
Period size: 32 Copynumber: 3.3 Consensus size: 32
18 GCGGAGCCTC
* *
28 CCCCACTAGGACGGCTCTGCCACGGCGGAGCCT
1 CCCCACTAGGACGGCTCTGCCACGGC-TAGCCG
61 CCCCACTAGGACGGCTCTGCCACGGCTAGCCG
1 CCCCACTAGGACGGCTCTGCCACGGCTAGCCG
*
93 CCCCACTAGGACGGCTCTCCCACGGCTAGCCG
1 CCCCACTAGGACGGCTCTGCCACGGCTAGCCG
125 CCCCACTAGG
1 CCCCACTAGG
135 GCGACAAGGC
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 45 0.63
33 26 0.37
ACGTcount: A:0.16, C:0.45, G:0.27, T:0.12
Consensus pattern (32 bp):
CCCCACTAGGACGGCTCTGCCACGGCTAGCCG
Found at i:404 original size:32 final size:31
Alignment explanation
Indices: 359--475 Score: 135
Period size: 32 Copynumber: 3.6 Consensus size: 31
349 GACGGCCTGC
359 CCGCCCTCATGGGGCGGCTTGCCGTGGCGAAG
1 CCGCCC-CATGGGGCGGCTTGCCGTGGCGAAG
* * * *
391 CCGCCCCAGTGGGGCGGCCTGCCCATGGTGAAA
1 CCGCCCCA-TGGGGCGGCTTG-CCGTGGCGAAG
424 CCGCCCCATGAGGGCGGCTTGCCGTGGCGAAG
1 CCGCCCCATG-GGGCGGCTTGCCGTGGCGAAG
* *
456 CCTCCCAAGTGGGGCGGCTT
1 CCGCCCCA-TGGGGCGGCTT
476 CGCCACGGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.03
32 42 0.59
33 27 0.38
ACGTcount: A:0.12, C:0.35, G:0.38, T:0.15
Consensus pattern (31 bp):
CCGCCCCATGGGGCGGCTTGCCGTGGCGAAG
Found at i:6075 original size:31 final size:31
Alignment explanation
Indices: 6040--6134 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
6030 GACATGCCAT
*
6040 GTGTCACTTTTTGGTACACGTGGCGTGACAC
1 GTGTCGCTTTTTGGTACACGTGGCGTGACAC
6071 GTGTCGCTTTTTGGTACACGTGGCGTGACAC
1 GTGTCGCTTTTTGGTACACGTGGCGTGACAC
6102 GTGTCGCTTTTTGGTACACGTGGCGTGACAC
1 GTGTCGCTTTTTGGTACACGTGGCGTGACAC
6133 GT
1 GT
6135 CGGACACCGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.33
Consensus pattern (31 bp):
GTGTCGCTTTTTGGTACACGTGGCGTGACAC
Found at i:6091 original size:19 final size:19
Alignment explanation
Indices: 6067--6123 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
6057 ACGTGGCGTG
6067 ACACGTGTCGCTTTTTGGT
1 ACACGTGTCGCTTTTTGGT
*
6086 ACACGTG--GC---GT-G-
1 ACACGTGTCGCTTTTTGGT
6098 ACACGTGTCGCTTTTTGGT
1 ACACGTGTCGCTTTTTGGT
6117 ACACGTG
1 ACACGTG
6124 GCGTGACACG
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 7 0.24
13 1 0.03
14 3 0.10
17 3 0.10
18 1 0.03
19 14 0.48
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33
Consensus pattern (19 bp):
ACACGTGTCGCTTTTTGGT
Found at i:14946 original size:31 final size:31
Alignment explanation
Indices: 14906--14964 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
14896 ACGGTGTCCG
14906 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
14937 ATGTGGCACGCCACATGTACCAAAAAGT
1 ACGTGGCACGCCACGTGTACCAAAAAGT
14965 CGTGCCACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:15006 original size:31 final size:31
Alignment explanation
Indices: 14968--15053 Score: 163
Period size: 31 Copynumber: 2.8 Consensus size: 31
14958 AAAAAGTCGT
14968 GCCACGTGTACCAAAATGTGACACATGTCAC
1 GCCACGTGTACCAAAATGTGACACATGTCAC
14999 GCCACGTGTACCAAAATGTGACACATGTCAC
1 GCCACGTGTACCAAAATGTGACACATGTCAC
*
15030 GCCACGTGTACCAAAAAGTGACAC
1 GCCACGTGTACCAAAATGTGACAC
15054 GTGGCATGCC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (31 bp):
GCCACGTGTACCAAAATGTGACACATGTCAC
Found at i:17075 original size:2 final size:2
Alignment explanation
Indices: 17068--17096 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17058 TGCATAGATG
17068 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
17097 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23516 original size:33 final size:33
Alignment explanation
Indices: 23469--23543 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
23459 GATGACCCGT
23469 GCCGCCCCAGGAGGGCGGCTTACCATGGCTCAA
1 GCCGCCCCAGGAGGGCGGCTTACCATGGCTCAA
* *
23502 GCCGTCCCAGGAGGGTGGCTTACCATGGCTCAA
1 GCCGCCCCAGGAGGGCGGCTTACCATGGCTCAA
*
23535 GTCGCCCCA
1 GCCGCCCCA
23544 TTGCAGGCCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.17, C:0.36, G:0.32, T:0.15
Consensus pattern (33 bp):
GCCGCCCCAGGAGGGCGGCTTACCATGGCTCAA
Found at i:27550 original size:3 final size:3
Alignment explanation
Indices: 27542--27568 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27532 CTAACTCTTG
27542 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
27569 GGGGTCAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:33609 original size:42 final size:42
Alignment explanation
Indices: 33545--33628 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
33535 AACGTAGAAT
* **
33545 AACGTTAACGTGTTGTATTTTGATGACGATTTAAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
*
33587 AACGATAACGTGCCGTATTTTGATGACGATTTCAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
33629 CAATTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (42 bp):
AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
Found at i:34499 original size:27 final size:28
Alignment explanation
Indices: 34461--34522 Score: 117
Period size: 27 Copynumber: 2.2 Consensus size: 28
34451 TTTCACAACA
34461 AAATTTCATTTCTTAACTGAATTTTC-T
1 AAATTTCATTTCTTAACTGAATTTTCTT
34488 AAATTTCATTTCTTAACTGAATTTTCTT
1 AAATTTCATTTCTTAACTGAATTTTCTT
34516 AAATTTC
1 AAATTTC
34523 TTAAAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.76
28 8 0.24
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.52
Consensus pattern (28 bp):
AAATTTCATTTCTTAACTGAATTTTCTT
Found at i:34513 original size:14 final size:14
Alignment explanation
Indices: 34469--34517 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
34459 CAAAATTTCA
34469 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
* * **
34483 TTTCTAAATTTCA-
1 TTTCTTAACTGAAT
34496 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
34510 TTTCTTAA
1 TTTCTTAA
34518 ATTTCTTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (14 bp):
TTTCTTAACTGAAT
Found at i:34552 original size:22 final size:22
Alignment explanation
Indices: 34527--34570 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
34517 AATTTCTTAA
34527 AATAATTTATAAAATAAAACAG
1 AATAATTTATAAAATAAAACAG
34549 AATAATTTATAAAATAAAACAG
1 AATAATTTATAAAATAAAACAG
34571 CCGCACGCGA
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:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (22 bp):
AATAATTTATAAAATAAAACAG
Found at i:42066 original size:12 final size:12
Alignment explanation
Indices: 42045--42087 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
42035 TCTCTACTTC
*
42045 TTCTACTTCTTG
1 TTCTAGTTCTTG
*
42057 TTCTTGTTCTTG
1 TTCTAGTTCTTG
* *
42069 TCCTAGTTCTAG
1 TTCTAGTTCTTG
42081 TTCTAGT
1 TTCTAGT
42088 ATTATAATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.09, C:0.21, G:0.14, T:0.56
Consensus pattern (12 bp):
TTCTAGTTCTTG
Found at i:45662 original size:163 final size:163
Alignment explanation
Indices: 45381--45680 Score: 494
Period size: 163 Copynumber: 1.8 Consensus size: 163
45371 ATCTCATTAC
* *
45381 GCTCTAATTAATTCGGAGTCGAGTCGTGTTGGATTTCATATGAAGGAAAACTCTATCAGCACACG
1 GCTCTAATTAATTCGGAGTCGAGTCGCGTCGGATTTCATATGAAGGAAAACTCTATCAGCACACG
*
45446 ATTTTCACCATTTATAAGATTAGAATCCGATAACTTATTCATGGAGCATTGAATTTCCACTCAAT
66 ATTTTCACCATTTATAAGATTAGAATCCGATAACTTATTCAAGGAGCATTGAATTTCCACTCAAT
45511 CCAACAAGTCTTGGTTCAACTTAATCACATTGT
131 CCAACAAGTCTTGGTTCAACTTAATCACATTGT
* * *
45544 GCTCTAGTTAATTCGGAGTCGAGTCGCGTCGGATTTCATATGAAGGAAAACTCTATCGGCACATG
1 GCTCTAATTAATTCGGAGTCGAGTCGCGTCGGATTTCATATGAAGGAAAACTCTATCAGCACACG
* * * *
45609 GTTTTCGCCATTTATAAGACTT-GAATCCGATAACTTATTCAAGGAGTATTGAATTTTCACTCAA
66 ATTTTCACCATTTATAAGA-TTAGAATCCGATAACTTATTCAAGGAGCATTGAATTTCCACTCAA
45673 TCCAACAA
130 TCCAACAA
45681 ATGTTTATTC
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
163 124 0.98
164 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (163 bp):
GCTCTAATTAATTCGGAGTCGAGTCGCGTCGGATTTCATATGAAGGAAAACTCTATCAGCACACG
ATTTTCACCATTTATAAGATTAGAATCCGATAACTTATTCAAGGAGCATTGAATTTCCACTCAAT
CCAACAAGTCTTGGTTCAACTTAATCACATTGT
Found at i:48622 original size:18 final size:18
Alignment explanation
Indices: 48576--48622 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
48566 AAGAACTTTG
48576 ATTAAATTAAAGTGTTTA
1 ATTAAATTAAAGTGTTTA
* *
48594 AGTATAA-TAAAGTTTTTA
1 ATTA-AATTAAAGTGTTTA
*
48612 ATTAGATTAAA
1 ATTAAATTAAA
48623 CCAGTTAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.04
18 20 0.87
19 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTAAATTAAAGTGTTTA
Found at i:55514 original size:26 final size:26
Alignment explanation
Indices: 55485--55535 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
55475 CCATTTAACA
55485 AGTTAAAATTTAACCATGGTTAGCAG
1 AGTTAAAATTTAACCATGGTTAGCAG
55511 AGTTAAAATTTAACCATGGTTAGCA
1 AGTTAAAATTTAACCATGGTTAGCA
55536 TTAGGTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (26 bp):
AGTTAAAATTTAACCATGGTTAGCAG
Found at i:57053 original size:21 final size:21
Alignment explanation
Indices: 57016--57163 Score: 151
Period size: 21 Copynumber: 7.0 Consensus size: 21
57006 GTAACTCACG
*
57016 TGCTGGTCAGTCTTCAAACCC
1 TGCTGGTCAGTCATCAAACCC
* *
57037 TGCTGTTC-GATCATCAAAACC
1 TGCTGGTCAG-TCATCAAACCC
*
57058 TGCTGGTCAGTCTTCAAACCC
1 TGCTGGTCAGTCATCAAACCC
* * *
57079 TGCTGTTC-GATCGTCAAAACC
1 TGCTGGTCAG-TCATCAAACCC
*
57100 TGCTGGTCAGTCTTCAAACCC
1 TGCTGGTCAGTCATCAAACCC
57121 TGCTGGTC-GATCATCGAAA-CC
1 TGCTGGTCAG-TCATC-AAACCC
*
57142 TGCTGGTCACTCATCAAACCC
1 TGCTGGTCAGTCATCAAACCC
57163 T
1 T
57164 TCCTCATCTC
Statistics
Matches: 105, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
20 6 0.06
21 94 0.90
22 5 0.05
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCTGGTCAGTCATCAAACCC
Found at i:57063 original size:42 final size:42
Alignment explanation
Indices: 57016--57163 Score: 251
Period size: 42 Copynumber: 3.5 Consensus size: 42
57006 GTAACTCACG
57016 TGCTGGTCAGTCTTCAAACCCTGCTGTTCGATCATCAAAACC
1 TGCTGGTCAGTCTTCAAACCCTGCTGTTCGATCATCAAAACC
*
57058 TGCTGGTCAGTCTTCAAACCCTGCTGTTCGATCGTCAAAACC
1 TGCTGGTCAGTCTTCAAACCCTGCTGTTCGATCATCAAAACC
* *
57100 TGCTGGTCAGTCTTCAAACCCTGCTGGTCGATCATCGAAACC
1 TGCTGGTCAGTCTTCAAACCCTGCTGTTCGATCATCAAAACC
* *
57142 TGCTGGTCACTCATCAAACCCT
1 TGCTGGTCAGTCTTCAAACCCT
57164 TCCTCATCTC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (42 bp):
TGCTGGTCAGTCTTCAAACCCTGCTGTTCGATCATCAAAACC
Found at i:70134 original size:33 final size:33
Alignment explanation
Indices: 70092--70166 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
70082 TACACTGAGT
* *
70092 CTCCCCACTA-GGACGGCTCAGCCACGGCGGAGC
1 CTCCCCACTAGGGA-GGCTCAACCACAGCGGAGC
*
70125 CTCCCCACTAGGGAGTCTCAACCACAGCGGAGC
1 CTCCCCACTAGGGAGGCTCAACCACAGCGGAGC
70158 CTCCCCACT
1 CTCCCCACT
70167 GCGGCGGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.12
Consensus pattern (33 bp):
CTCCCCACTAGGGAGGCTCAACCACAGCGGAGC
Found at i:70139 original size:16 final size:17
Alignment explanation
Indices: 70118--70170 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
70108 CTCAGCCACG
70118 GCGGAGCCTCCCCACTA
1 GCGGAGCCTCCCCACTA
* *
70135 G-GGAGTCTCAACCAC-A
1 GCGGAGCCTC-CCCACTA
70151 GCGGAGCCTCCCCACT-
1 GCGGAGCCTCCCCACTA
70167 GCGG
1 GCGG
70171 CGGTTTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.19, C:0.42, G:0.28, T:0.11
Consensus pattern (17 bp):
GCGGAGCCTCCCCACTA
Found at i:75331 original size:19 final size:19
Alignment explanation
Indices: 75307--75349 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
75297 TTGAAAGTTA
*
75307 AAGAACCCATATGAGAAGG
1 AAGAACCCAGATGAGAAGG
75326 AAGAACCCAGATGAGAAGG
1 AAGAACCCAGATGAGAAGG
75345 AAGAA
1 AAGAA
75350 GATGGCGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.28, T:0.07
Consensus pattern (19 bp):
AAGAACCCAGATGAGAAGG
Found at i:76439 original size:22 final size:22
Alignment explanation
Indices: 76411--76453 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
76401 ATGGGAGCAT
76411 CAAATAGTATGAGAATTAAGAC
1 CAAATAGTATGAGAATTAAGAC
76433 CAAATAGTATGAGAATTAAGA
1 CAAATAGTATGAGAATTAAGA
76454 GCTGGATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (22 bp):
CAAATAGTATGAGAATTAAGAC
Found at i:82142 original size:23 final size:23
Alignment explanation
Indices: 82108--82154 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
82098 AGGGTTTGCC
82108 ATAATGCAATAAAGT-TGAAATAA
1 ATAATGCAATAAAGTGT-AAATAA
*
82131 ATAATGCTATAAAGTGTAAATAA
1 ATAATGCAATAAAGTGTAAATAA
82154 A
1 A
82155 CTCATAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (23 bp):
ATAATGCAATAAAGTGTAAATAA
Found at i:85785 original size:42 final size:42
Alignment explanation
Indices: 85739--85930 Score: 269
Period size: 42 Copynumber: 4.6 Consensus size: 42
85729 CATGATTAAC
*
85739 ACCATCTCCTGGATTCTCAACTCCTTCAGCTTCATTGTCAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATTGTCAAT
* * * *
85781 ACCATGTCTTGGATTTTCAACTCCTTCAGCTTCATCGTGAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATTGTCAAT
* *
85823 ACCATCTCTTGGATTTTCAACTCCTTCAGCTTCATTATCAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATTGTCAAT
* * *
85865 ACCATCTCCTGGATTTTCAACTCCTTCA-ATTGGATTTTCAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTT-CATTGTCAAT
*
85907 ACCAACTCCTGGATTTTCAACTCC
1 ACCATCTCCTGGATTTTCAACTCC
85931 ATCAACTGGC
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
41 2 0.01
42 133 0.99
ACGTcount: A:0.23, C:0.30, G:0.10, T:0.38
Consensus pattern (42 bp):
ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATTGTCAAT
Found at i:85939 original size:21 final size:21
Alignment explanation
Indices: 85832--85939 Score: 76
Period size: 21 Copynumber: 5.1 Consensus size: 21
85822 TACCATCTCT
* *
85832 TGGATTTTCAACTCCTTCAGC
1 TGGATTTTCAACTCCATCAAC
** * **
85853 TTCATTATCAA-TACCATCTCC
1 TGGATTTTCAACT-CCATCAAC
* *
85874 TGGATTTTCAACTCCTTCAAT
1 TGGATTTTCAACTCCATCAAC
* **
85895 TGGATTTTCAA-TACCAACTCC
1 TGGATTTTCAACT-CCATCAAC
85916 TGGATTTTCAACTCCATCAAC
1 TGGATTTTCAACTCCATCAAC
85937 TGG
1 TGG
85940 CCTCTGAACA
Statistics
Matches: 62, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.37
Consensus pattern (21 bp):
TGGATTTTCAACTCCATCAAC
Found at i:86594 original size:29 final size:29
Alignment explanation
Indices: 86556--86637 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
86546 TGAACAAACC
*
86556 CTAATTCCCAGAAACAATTCATACCCACT
1 CTAATACCCAGAAACAATTCATACCCACT
86585 CTAATACCCAGAAACAATTCATACCCACT
1 CTAATACCCAGAAACAATTCATACCCACT
86614 CTAATACCCAGAAACAATTCATAC
1 CTAATACCCAGAAACAATTCATAC
86638 ATATAACTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.41, C:0.33, G:0.04, T:0.22
Consensus pattern (29 bp):
CTAATACCCAGAAACAATTCATACCCACT
Found at i:101602 original size:66 final size:62
Alignment explanation
Indices: 101522--101678 Score: 217
Period size: 66 Copynumber: 2.5 Consensus size: 62
101512 GAAATATTCA
*
101522 TATGAAATTATGATAACTTTCCTATTAAATTATGATAATTAATTA-TACTATTTTTGATGACGTC
1 TATGAAATTTTGATAACTTTCCTATTAAATTATGATAATT-A-TACTA-T-TTTTTG-TGACGTC
101586 CT
61 CT
*
101588 TATGAAATTTTGATAACTTTCCTATGAAATTATGATAATTATACTATTTTTTGTGACGTCCT
1 TATGAAATTTTGATAACTTTCCTATTAAATTATGATAATTATACTATTTTTTGTGACGTCCT
* * *
101650 TATAAAATTTTGATAACCTTCGTATTAAA
1 TATGAAATTTTGATAACTTTCCTATTAAA
101679 ATTTCAATAA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
62 34 0.40
63 6 0.07
64 3 0.04
65 3 0.04
66 38 0.45
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (62 bp):
TATGAAATTTTGATAACTTTCCTATTAAATTATGATAATTATACTATTTTTTGTGACGTCCT
Found at i:101634 original size:22 final size:22
Alignment explanation
Indices: 101522--101634 Score: 63
Period size: 22 Copynumber: 5.1 Consensus size: 22
101512 GAAATATTCA
*
101522 TATGAAATTATGATAACTTTCC
1 TATGAAATTATGATAACTTTAC
* * *
101544 TATTAAATTATGATAA-TTAAT
1 TATGAAATTATGATAACTTTAC
* * * * *
101565 TAT-ACTATTTTTGATGAC-GTCC
1 TATGA--AATTATGATAACTTTAC
* *
101587 TTATGAAATTTTGATAACTTTCC
1 -TATGAAATTATGATAACTTTAC
101610 TATGAAATTATGATAA-TTATAC
1 TATGAAATTATGATAACTT-TAC
101632 TAT
1 TAT
101635 TTTTTGTGAC
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 7 0.10
22 53 0.78
23 6 0.09
24 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (22 bp):
TATGAAATTATGATAACTTTAC
Found at i:101658 original size:62 final size:66
Alignment explanation
Indices: 101526--101666 Score: 211
Period size: 62 Copynumber: 2.2 Consensus size: 66
101516 TATTCATATG
* *
101526 AAATTATGATAACTTTCCTATTAAATTATGATAATTAATTATACTATTTTTGATGACGTCCTTAT
1 AAATTTTGATAACTTTCCTATGAAATTATGATAATTAATTATACTATTTTTGATGACGTCCTTAT
*
101591 G
66 A
101592 AAATTTTGATAACTTTCCTATGAAATTATG---A-TAATTATACTATTTTTTG-TGACGTCCTTA
1 AAATTTTGATAACTTTCCTATGAAATTATGATAATTAATTATACTA-TTTTTGATGACGTCCTTA
101652 TA
65 TA
101654 AAATTTTGATAAC
1 AAATTTTGATAAC
101667 CTTCGTATTA
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
62 36 0.51
63 7 0.10
66 28 0.39
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (66 bp):
AAATTTTGATAACTTTCCTATGAAATTATGATAATTAATTATACTATTTTTGATGACGTCCTTAT
A
Found at i:101734 original size:22 final size:22
Alignment explanation
Indices: 101709--101756 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
101699 GATTTTCGAG
* * *
101709 AACCTTTTTATCAATTTTTTTT
1 AACCTTCTTATCAAATTTTATT
*
101731 AACCTTCTTATGAAATTTTATT
1 AACCTTCTTATCAAATTTTATT
101753 AACC
1 AACC
101757 ACCCTAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (22 bp):
AACCTTCTTATCAAATTTTATT
Found at i:101932 original size:22 final size:22
Alignment explanation
Indices: 101894--101953 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
101884 AAAACCTCCA
*
101894 TATG-AATTGTCAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
101916 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
101938 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
101954 CCTCGCTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:101962 original size:22 final size:21
Alignment explanation
Indices: 101920--102173 Score: 115
Period size: 22 Copynumber: 11.8 Consensus size: 21
101910 TCACACTCTG
* * *
101920 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTC-CTATA
*
101942 AAATTGTGATAACCTCGCTATA
1 AAATTTTGATAACCTC-CTATA
101964 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGAT-AACC-TCCTATA
*
101987 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCC-TATA
* * *
102009 ATATCTTGATAA----CTA-C
1 AAATTTTGATAACCTCCTATA
*
102025 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCT-CCTATA
** * * *
102047 ATTTTTTTATAACCTCATTATG
1 AAATTTTGATAACCTC-CTATA
* * *
102069 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCT-CCTATA
* * * * *
102091 AAATTCTGATCTACATACTATG
1 AAATTTTGAT-AACCTCCTATA
* * *
102113 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT--CCTATA
*
102135 AAATTTTGATAACCTTCATATA
1 AAATTTTGATAACC-TCCTATA
*
102157 AAATTTTGATATCCTCC
1 AAATTTTGATAACCTCC
102174 CTGAAATCTT
Statistics
Matches: 177, Mismatches: 39, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
18 1 0.01
20 2 0.01
21 9 0.05
22 125 0.71
23 25 0.14
24 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATA
Found at i:102174 original size:88 final size:82
Alignment explanation
Indices: 101959--102186 Score: 189
Period size: 88 Copynumber: 2.7 Consensus size: 82
101949 GATAACCTCG
* * * * *
101959 CTATAAAATTTTGATAAACCTTCCTATAAAATTTTGATAACCTCCTTATGATATCTTGATAACTA
1 CTATGAAATTTTGAT-AACCTTCATATAAAATTTTGATATCCTCCCTATGAAATCTTGATAACTA
* **
102024 CAAATTTTGATAACCTCC
65 CAAATTTTGATAAACTAA
** * * *
102042 CTATGATTTTTTTATAACC-TCATTATGAAATTTTGTTAAT-CTCCCTATGAAAT-TCTGATCTA
1 CTATGAAATTTTGATAACCTTCA-TATAAAATTTTGAT-ATCCTCCCTATGAAATCT-TGA--T-
*
102104 CATACTATGAAATTTTGA-AAACTAAA
60 -A-ACTA-CAAATTTTGATAAACT-AA
102130 CTATGAAATTTTGATAACCTTCATATAAAATTTTGATATCCTCCC--TGAAATCTTGAT
1 CTATGAAATTTTGATAACCTTCATATAAAATTTTGATATCCTCCCTATGAAATCTTGAT
102187 TACTTCATAA
Statistics
Matches: 113, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
81 3 0.03
82 30 0.27
83 12 0.11
84 2 0.02
86 10 0.09
87 11 0.10
88 42 0.37
89 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (82 bp):
CTATGAAATTTTGATAACCTTCATATAAAATTTTGATATCCTCCCTATGAAATCTTGATAACTAC
AAATTTTGATAAACTAA
Found at i:102326 original size:22 final size:22
Alignment explanation
Indices: 102294--102371 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
102284 TCACAATTTG
*
102294 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTCTAT
*
102315 AAAATTTTGATAACCTATCTAT
1 AAAATTTTGATAACCTCTCTAT
* * * *
102337 AAAATTTCGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
*
102359 GAAATTTTGATAA
1 AAAATTTTGATAA
102372 TCACATTATG
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 4 0.09
22 41 0.91
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:102409 original size:21 final size:22
Alignment explanation
Indices: 102268--102411 Score: 75
Period size: 22 Copynumber: 6.6 Consensus size: 22
102258 TAAATACCAC
*
102268 TATGAAATTTTGGTAATCACAAT
1 TATGAAATTTTGATAATCAC-AT
* * * *
102291 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
*
102312 TATAAAATTTTGATAA-C-CTAT
1 TATGAAATTTTGATAATCAC-AT
* * * * * *
102333 CTATAAAATTTCGTTGA-CCCCT
1 -TATGAAATTTTGATAATCACAT
102355 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* *
102378 TATGTAATTTTGATAACTCGC-T
1 TATGAAATTTTGATAA-TCACAT
102400 T-TGAAATTTTGA
1 TATGAAATTTTGA
102412 AGTTGGACAA
Statistics
Matches: 94, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 14 0.15
22 71 0.76
23 8 0.09
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:102527 original size:32 final size:31
Alignment explanation
Indices: 102491--102572 Score: 74
Period size: 38 Copynumber: 2.4 Consensus size: 31
102481 GGAGACGAAG
102491 ACAAAAAGCAAAATTAAATACAACGATTGGAA
1 ACAAAAAGCAAAATTAAATACAAC-ATTGGAA
**
102523 ACAAAGACAAAATGCAAAATTAAATAGGACATTGGAA
1 AC----A-AAAA-GCAAAATTAAATACAACATTGGAA
102560 ACAAAAAGACAAA
1 ACAAAAAG-CAAA
102573 TTGACTTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
31 1 0.02
32 10 0.24
33 1 0.02
36 1 0.02
37 13 0.32
38 15 0.37
ACGTcount: A:0.61, C:0.12, G:0.13, T:0.13
Consensus pattern (31 bp):
ACAAAAAGCAAAATTAAATACAACATTGGAA
Found at i:102725 original size:31 final size:32
Alignment explanation
Indices: 102680--102747 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
102670 TTTAGTAATG
* * *
102680 ACAATTTAGAAATATGTTTTTTAAAA-AATGGT
1 ACAATTGAGAAATATG-TTTTAAAAATAAGGGT
102712 ACAATTGA-AAATATGTTTTAAAAATAAGGGT
1 ACAATTGAGAAATATGTTTTAAAAATAAGGGT
102743 ACAAT
1 ACAAT
102748 CGGAAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.25
31 17 0.53
32 7 0.22
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.35
Consensus pattern (32 bp):
ACAATTGAGAAATATGTTTTAAAAATAAGGGT
Found at i:104296 original size:2 final size:2
Alignment explanation
Indices: 104289--104323 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
104279 TGATTATAGG
104289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104324 GTTTCTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:110401 original size:22 final size:22
Alignment explanation
Indices: 110345--110401 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
110335 AATATTTAAA
*
110345 GAAATTTTGTTAACCATACTAT
1 GAAATTTTGATAACCATACTAT
*
110367 GAAATTCTT-ATAACCCTACTAT
1 GAAATT-TTGATAACCATACTAT
*
110389 GACATTTTGATAA
1 GAAATTTTGATAA
110402 TCTCTTTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.07
22 26 0.87
23 2 0.07
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
GAAATTTTGATAACCATACTAT
Found at i:110501 original size:24 final size:22
Alignment explanation
Indices: 110419--110568 Score: 90
Period size: 22 Copynumber: 6.5 Consensus size: 22
110409 GATAACCTTT
*
110419 CTATGAAATTGTGATAATTAACCACC
1 CTATGAAATT-T--TAA-TAACCAAC
*
110445 CTATGAAATTTCAATAACCAAC
1 CTATGAAATTTTAATAACCAAC
* *
110467 CTAAGAGATTTTAATAA-CATGATC
1 CTATGAAATTTTAATAACCA--A-C
**
110491 CTATGAAATTTTGGTAACC-AC
1 CTATGAAATTTTAATAACCAAC
* * *
110512 ACTATGGAATTTTGATAACC-TC
1 -CTATGAAATTTTAATAACCAAC
* *
110534 CTCATGAAATTATAATAACCATC
1 CT-ATGAAATTTTAATAACCAAC
*
110557 TTATGAAATTTT
1 CTATGAAATTTT
110569 GATATCCACA
Statistics
Matches: 100, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.05
22 63 0.63
23 6 0.06
24 14 0.14
25 2 0.02
26 10 0.10
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCAAC
Found at i:110774 original size:19 final size:20
Alignment explanation
Indices: 110743--110780 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
110733 TATTGACATT
110743 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
110762 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
110781 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:122683 original size:2 final size:2
Alignment explanation
Indices: 122676--122704 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
122666 GTTTATAATC
122676 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
122705 CAGAAGTTTT
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:134993 original size:11 final size:11
Alignment explanation
Indices: 134970--135004 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
134960 CTGATAACGT
134970 AACAAAAATAA
1 AACAAAAATAA
* *
134981 AACGAAAACAA
1 AACAAAAATAA
134992 AACAAAAATAA
1 AACAAAAATAA
135003 AA
1 AA
135005 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.80, C:0.11, G:0.03, T:0.06
Consensus pattern (11 bp):
AACAAAAATAA
Found at i:136156 original size:24 final size:25
Alignment explanation
Indices: 136129--136175 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
136119 AAAAGCAAGG
136129 CTCTCCCTTTCCTT-TTTCTTCTTT
1 CTCTCCCTTTCCTTCTTTCTTCTTT
*
136153 CTCTCTCTTTCCTTCTTTCTTCT
1 CTCTCCCTTTCCTTCTTTCTTCT
136176 GTCCCTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (25 bp):
CTCTCCCTTTCCTTCTTTCTTCTTT
Found at i:148420 original size:19 final size:19
Alignment explanation
Indices: 148388--148426 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
148378 CACGAATAGT
*
148388 TGCTAGTTCACTTATTTGG
1 TGCTAATTCACTTATTTGG
*
148407 TGCTAATTCGCTTATTTGG
1 TGCTAATTCACTTATTTGG
148426 T
1 T
148427 CATTTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (19 bp):
TGCTAATTCACTTATTTGG
Done.