Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024578.1 Corchorus olitorius cultivar O-4 contig24611, 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: 62576
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1643 original size:16 final size:15
Alignment explanation
Indices: 1613--1646 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1603 CTCTGGTTAT
*
1613 GATTTCTTTATATGC
1 GATTTCTTCATATGC
1628 GATTTGCTTCATATGC
1 GATTT-CTTCATATGC
1644 GAT
1 GAT
1647 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (15 bp):
GATTTCTTCATATGC
Found at i:2568 original size:25 final size:26
Alignment explanation
Indices: 2510--2558 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2500 TTTTTGGCTC
*
2510 TTAACGTTTTTTGCCTTTGAATACCA
1 TTAACGTTTTTAGCCTTTGAATACCA
2536 TTAACGTTTTTAG-CTTTGAATAC
1 TTAACGTTTTTAGCCTTTGAATAC
2559 TTGTAACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.47
Consensus pattern (26 bp):
TTAACGTTTTTAGCCTTTGAATACCA
Found at i:2574 original size:25 final size:25
Alignment explanation
Indices: 2524--2574 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2514 CGTTTTTTGC
**
2524 CTTTGAATACCATTAACGTTTTTAG
1 CTTTGAATACCATTAACGTTACTAG
*
2549 CTTTGAATA-CTTGTAACGTTACTAG
1 CTTTGAATACCAT-TAACGTTACTAG
2574 C
1 C
2575 CATAATTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (25 bp):
CTTTGAATACCATTAACGTTACTAG
Found at i:12218 original size:54 final size:54
Alignment explanation
Indices: 12154--12262 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
12144 CATCATATTT
*
12154 AATAAAATTGAATAACGTTAATATTCATATTGTGATATATAACGTTAAGAATTA
1 AATAAAATTGAATAACGTTAATATTCAAATTGTGATATATAACGTTAAGAATTA
* *
12208 AATAAAATTGAATAACGTTAATATTCAAATTGTGATTTTTAACGTTAAGAATTA
1 AATAAAATTGAATAACGTTAATATTCAAATTGTGATATATAACGTTAAGAATTA
12262 A
1 A
12263 CTAACAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.38
Consensus pattern (54 bp):
AATAAAATTGAATAACGTTAATATTCAAATTGTGATATATAACGTTAAGAATTA
Found at i:12237 original size:27 final size:27
Alignment explanation
Indices: 12154--12237 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
12144 CATCATATTT
12154 AATAAAATTGAATAACGTTAATATTCA
1 AATAAAATTGAATAACGTTAATATTCA
* *** *
12181 TATTGTGA-T-ATATAACGTTAAGAATT-A
1 -AATAAAATTGA-ATAACGTTAA-TATTCA
12208 AATAAAATTGAATAACGTTAATATTCA
1 AATAAAATTGAATAACGTTAATATTCA
12235 AAT
1 AAT
12238 TGTGATTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 11
0.66 0.16 0.18
Matches are distributed among these distances:
26 7 0.17
27 27 0.66
28 7 0.17
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.36
Consensus pattern (27 bp):
AATAAAATTGAATAACGTTAATATTCA
Found at i:18220 original size:22 final size:24
Alignment explanation
Indices: 18180--18228 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
18170 CTTGTCGACG
*
18180 ATTTGCTTCCTCTTAAGTCGACTA
1 ATTTGCTTCCTCTTAAGTCGACAA
*
18204 ATTT-CTT-CTCTTTAGTCGACAA
1 ATTTGCTTCCTCTTAAGTCGACAA
18226 ATT
1 ATT
18229 AGCTCTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 3 0.13
24 4 0.17
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (24 bp):
ATTTGCTTCCTCTTAAGTCGACAA
Found at i:18355 original size:16 final size:16
Alignment explanation
Indices: 18334--18366 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18324 CTTAAGTCGA
18334 TGCTTAAATCGACAAT
1 TGCTTAAATCGACAAT
*
18350 TGCTTAAGTCGACAAT
1 TGCTTAAATCGACAAT
18366 T
1 T
18367 CTTGCCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (16 bp):
TGCTTAAATCGACAAT
Found at i:25165 original size:52 final size:51
Alignment explanation
Indices: 25057--25296 Score: 311
Period size: 52 Copynumber: 4.6 Consensus size: 51
25047 AATTGAAAAC
* *
25057 TAAAACCTGATGGGAACTTTCCCAATTTGCAAAAGAGCTAGATTGAATACTT
1 TAAAAACTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTT
* *
25109 TGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATATTT
1 TAAAAAC-TGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
** *
25161 TGAAAATTTGATGGGAACTTTCCCAATTTAAAAAGAGCTAAATTGAATACTT
1 T-AAAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
* * * * *
25213 TAAAAACTGGTGGGAACTTTCTCGACTTGAAAAAGAGCTAAGTTGAATAC-T
1 TAAAAACTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTT
* *
25264 TAAAAACTGATGGGAGCTTTCCCAATTTAAAAA
1 TAAAAACTGATGGGAACTTTCCCAATTTGAAAA
25297 CTTAAACCTG
Statistics
Matches: 162, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
50 4 0.02
51 45 0.28
52 88 0.54
53 25 0.15
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (51 bp):
TAAAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
Found at i:28675 original size:25 final size:26
Alignment explanation
Indices: 28646--28695 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
28636 AGAAGGCCAA
28646 AGAAATGGACTTGAAC-AAAGATAAG
1 AGAAATGGACTTGAACAAAAGATAAG
*
28671 AGAAATGGACTTGACCAAAAGATAA
1 AGAAATGGACTTGAACAAAAGATAA
28696 AAGAGAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAAATGGACTTGAACAAAAGATAAG
Found at i:41422 original size:54 final size:54
Alignment explanation
Indices: 41338--41945 Score: 433
Period size: 54 Copynumber: 11.5 Consensus size: 54
41328 GACCTGGTGC
* * **
41338 GGTCATTCCAAAAAGTTTT-GACGATCAGAGTTGATCCCCAGAAGATCCAGTAC
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
* * * * * *
41391 AGTCATTTCAAGAAGTTTTTGATGGTCAGAGTTGATCTCCAGATGATCCAGTGT
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
** * * * * *
41445 GGTCGCTCCCAGAAATTTTCGACGATCAGAGTTGATCCCCAGAAGATCCAATGC
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
* * * * *
41499 GGCCATTTCAAGAAGTTTTTGATGGTCAGAGTTGATCTCCA-AATGATCCAGTGT
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAA-GATCCAGTGT
* * * * * * *
41553 GGTCGCTACC-AGAAATTTTCAATGGTCAGAGTTGATCCCCAGAAGATACAGTGC
1 GGTC-ATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
* * ** *
41607 GGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGTTGATCCACTGT
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
* * * *
41661 GGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTAT
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
* * * * *
41715 GGTCATTCC----A-------A-GATCAGAGTTGATCTCCAAATGGTCCAGTGC
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
* *** *
41757 GGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTTTA-AATGATCTAGTGT
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAA-GATCCAGTGT
* * * * * * *
41811 GGTCTTTCTAATAAGTTTTCAATGATCAGAGTTGATCGCCA-ATTGATCCAGTGC
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGA-AGATCCAGTGT
* ** * * * *
41865 AGTTGTTTCAAAAAGTTTTTGATGATCAGAGTTGATCTCCA-AATTGATCCAGTGT
1 GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAA--GATCCAGTGT
* * * *
41920 GGGCGTTCCAAGGAAGGTTTCCATGA
1 GGTCATTCCAA-GAAGTTTTCGATGA
41946 CCAAGGTTGC
Statistics
Matches: 434, Mismatches: 99, Indels: 41
0.76 0.17 0.07
Matches are distributed among these distances:
42 34 0.08
43 1 0.00
46 1 0.00
50 1 0.00
53 22 0.05
54 345 0.79
55 20 0.05
56 10 0.02
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (54 bp):
GGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCCCCAGAAGATCCAGTGT
Found at i:41546 original size:108 final size:108
Alignment explanation
Indices: 41358--41727 Score: 488
Period size: 108 Copynumber: 3.4 Consensus size: 108
41348 AAAAGTTTTG
* *
41358 ACGATCAGAGTTGATCCCCAGAAGATCCAGTACAGTCATTTCAAGAAGTTTTTGATGGTCAGAGT
1 ACGATCAGAGTTGATCCCCAGAAGATCCAGTGCGGTCATTTCAAGAAGTTTTTGATGGTCAGAGT
*
41423 TGATCTCCAGATGATCCAGTGTGGTCGCTCCCAGAAATTTTCG
66 TGATCTCCAGATGATCCAGTGTGGTCGCTCCCAGAAATTTTCA
* *
41466 ACGATCAGAGTTGATCCCCAGAAGATCCAATGCGGCCATTTCAAGAAGTTTTTGATGGTCAGAGT
1 ACGATCAGAGTTGATCCCCAGAAGATCCAGTGCGGTCATTTCAAGAAGTTTTTGATGGTCAGAGT
* *
41531 TGATCTCCAAATGATCCAGTGTGGTCGCTACCAGAAATTTTCA
66 TGATCTCCAGATGATCCAGTGTGGTCGCTCCCAGAAATTTTCA
* * * * * ** *
41574 ATGGTCAGAGTTGATCCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGT
1 ACGATCAGAGTTGATCCCCAGAAGATCCAGTGCGGTCATTTCAAGAAGTTTTTGATGGTCAGAGT
* * * ** * *
41639 TGATCCCCAGTTGATCCACTGTGGTCATTCCAAGAAGTTTTCA
66 TGATCTCCAGATGATCCAGTGTGGTCGCTCCCAGAAATTTTCA
* * * ** *
41682 ATGATCAGAGTTGATCCCCAGATGATCTAGTATGGTCATTCCAAGA
1 ACGATCAGAGTTGATCCCCAGAAGATCCAGTGCGGTCATTTCAAGA
41728 TCAGAGTTGA
Statistics
Matches: 229, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 229 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (108 bp):
ACGATCAGAGTTGATCCCCAGAAGATCCAGTGCGGTCATTTCAAGAAGTTTTTGATGGTCAGAGT
TGATCTCCAGATGATCCAGTGTGGTCGCTCCCAGAAATTTTCA
Found at i:41734 original size:42 final size:42
Alignment explanation
Indices: 41684--41769 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
41674 AGTTTTCAAT
* * *
41684 GATCAGAGTTGATCCCCAGATGATCTAGTATGGTCATTCCAA
1 GATCAGAGTTGATCCCCAAATGATCCAGTACGGTCATTCCAA
* * *
41726 GATCAGAGTTGATCTCCAAATGGTCCAGTGCGGTCATTCCAA
1 GATCAGAGTTGATCCCCAAATGATCCAGTACGGTCATTCCAA
41768 GA
1 GA
41770 AGTTTTCAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
GATCAGAGTTGATCCCCAAATGATCCAGTACGGTCATTCCAA
Found at i:41803 original size:96 final size:96
Alignment explanation
Indices: 41630--41814 Score: 271
Period size: 96 Copynumber: 1.9 Consensus size: 96
41620 AGTTTTCAAT
** *
41630 GATCAGAGTTGATCCCCAGTTGATCCACTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTG
1 GATCAGAGTTGATCCCCAAATGATCCACTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTG
*
41695 ATCCCCAGATGATCTAGTATGGTCATTCCAA
66 ATCCCCAAATGATCTAGTATGGTCATTCCAA
* * *
41726 GATCAGAGTTGATCTCCAAATGGTCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTG
1 GATCAGAGTTGATCCCCAAATGATCCACTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTG
*** *
41791 ATCTTTAAATGATCTAGTGTGGTC
66 ATCCCCAAATGATCTAGTATGGTC
41815 TTTCTAATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (96 bp):
GATCAGAGTTGATCCCCAAATGATCCACTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTG
ATCCCCAAATGATCTAGTATGGTCATTCCAA
Found at i:41858 original size:150 final size:150
Alignment explanation
Indices: 41578--41847 Score: 398
Period size: 150 Copynumber: 1.8 Consensus size: 150
41568 TTTTCAATGG
41578 TCAGAGTTGATCCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGAT
1 TCAGAGTTGATCCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGAT
**
41643 CCCCAGTTGATCCACTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGAT
66 CCCCAAATGATCCACTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGAT
41708 CTAGTATGGTCATTCCAAGA
131 CTAGTATGGTCATTCCAAGA
* * * *
41728 TCAGAGTTGATCTCCA-AATGGTCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGA
1 TCAGAGTTGATCCCCAGAA-GATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGA
*** * * * * *
41792 TCTTTAAATGATCTAGTGTGGTCTTTCTAATAAGTTTTCAATGATCAGAGTTGATC
65 TCCCCAAATGATCCACTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
41848 GCCAATTGAT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
149 2 0.02
150 103 0.98
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (150 bp):
TCAGAGTTGATCCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGAT
CCCCAAATGATCCACTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGAT
CTAGTATGGTCATTCCAAGA
Found at i:41883 original size:204 final size:204
Alignment explanation
Indices: 41524--41901 Score: 483
Period size: 204 Copynumber: 1.9 Consensus size: 204
41514 TTTTTGATGG
* * *
41524 TCAGAGTTGATCTCCAAATGATCCAGTGTGGTCGCTACCAGAAATTTTCAATGGTCAGAGTTGAT
1 TCAGAGTTGATCTCCAAATGATCCAGTGCGGTCGATACCAGAAATTTTCAATGATCAGAGTTGAT
*
41589 CCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGTTGAT
66 CCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAATTGAT
** *
41654 CCACTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTATGGTC
131 CCACTGCAGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTATGGTC
41719 ATTCCAAGA
196 ATTCCAAGA
* * *
41728 TCAGAGTTGATCTCCAAATGGTCCAGTGCGGTC-ATTCCAAGAAGTTTTCAATGATCAGAGTTGA
1 TCAGAGTTGATCTCCAAATGATCCAGTGCGGTCGATACC-AGAAATTTTCAATGATCAGAGTTGA
*** * ** * * *
41792 TCTTTA-AATGAT-CTAGTGTGGTCTTTCTAATAAGTTTTCAATGATCAGAGTTGATCGCCAATT
65 TCCCCAGAA-GATAC-AGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAATT
* ** * **
41855 GATCCAGTGCAGTTGTTTCAAAAAGTTTTTGATGATCAGAGTTGATC
128 GATCCACTGCAGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATC
41902 TCCAAATTGA
Statistics
Matches: 146, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
203 6 0.04
204 140 0.96
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (204 bp):
TCAGAGTTGATCTCCAAATGATCCAGTGCGGTCGATACCAGAAATTTTCAATGATCAGAGTTGAT
CCCCAGAAGATACAGTGCGGTCACTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAATTGAT
CCACTGCAGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTATGGTC
ATTCCAAGA
Found at i:45990 original size:41 final size:41
Alignment explanation
Indices: 45945--46024 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
45935 TAAAAGTGTT
*
45945 GCGCCAAAAATCTCTTGAGATTTAAGCAAAAAGAAATAGTA
1 GCGCCAAAAATCTCTTAAGATTTAAGCAAAAAGAAATAGTA
*
45986 GCGCCAAAAATCTCTTAAGATTTAAGCGAAAAGAAATAG
1 GCGCCAAAAATCTCTTAAGATTTAAGCAAAAAGAAATAG
46025 CAAGGGTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.21
Consensus pattern (41 bp):
GCGCCAAAAATCTCTTAAGATTTAAGCAAAAAGAAATAGTA
Found at i:56207 original size:53 final size:53
Alignment explanation
Indices: 56148--56296 Score: 235
Period size: 53 Copynumber: 2.8 Consensus size: 53
56138 TACTATTACC
* *
56148 TGGTGAACGGAACAATGTTTCAACAAAGTCTTTTGTTTATAGTTTATAGTACG
1 TGGTGAATGGAACAATGTTTCACCAAAGTCTTTTGTTTATAGTTTATAGTACG
* * *
56201 TGGTGAATGGAACAATGTTTCACCAAAGTCTTTTGTATCTAGTTTATAGTACT
1 TGGTGAATGGAACAATGTTTCACCAAAGTCTTTTGTTTATAGTTTATAGTACG
* *
56254 TGGTGAATTGAACAATGTTTCACCAAAATCTTTTGTTTATAGT
1 TGGTGAATGGAACAATGTTTCACCAAAGTCTTTTGTTTATAGT
56297 ACTTGCAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 87 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (53 bp):
TGGTGAATGGAACAATGTTTCACCAAAGTCTTTTGTTTATAGTTTATAGTACG
Found at i:58036 original size:125 final size:125
Alignment explanation
Indices: 57814--58063 Score: 455
Period size: 125 Copynumber: 2.0 Consensus size: 125
57804 TCAAATGTTC
* * *
57814 TCCCAAACTCCAACTTATATCACCATTCTTCCAAACCCAACCTCCAATTTCAAAAGCTAAAGCCT
1 TCCCAAACTCCAACTTATATCACCATTCTTCCAAAACCAAACTCCAATCTCAAAAGCTAAAGCCT
57879 CTCTAAGAAATCCCCAAATTTGAATCTAACCATATATTTTGAAAGAAAGAAAAACAAAAA
66 CTCTAAGAAATCCCCAAATTTGAATCTAACCATATATTTTGAAAGAAAGAAAAACAAAAA
* *
57939 TCCCAAACTCCAACTTATATCACGATTCTTCCAAAACCAAACTCCAATCTCAAAAGCTAAAGTCT
1 TCCCAAACTCCAACTTATATCACCATTCTTCCAAAACCAAACTCCAATCTCAAAAGCTAAAGCCT
58004 CTCTAAGAAATCCCCAAATTTGAATCTAACCATATATTTTGAAAGAAAGAAAAACAAAAA
66 CTCTAAGAAATCCCCAAATTTGAATCTAACCATATATTTTGAAAGAAAGAAAAACAAAAA
58064 CTCTTGGCTT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (125 bp):
TCCCAAACTCCAACTTATATCACCATTCTTCCAAAACCAAACTCCAATCTCAAAAGCTAAAGCCT
CTCTAAGAAATCCCCAAATTTGAATCTAACCATATATTTTGAAAGAAAGAAAAACAAAAA
Found at i:59916 original size:5 final size:5
Alignment explanation
Indices: 59900--59947 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
59890 TTATAAGTTA
*
59900 ATAAT AATAAT ATAAT ATAAC ATAATT ATCAAT ATATAT ATAAT ATAA
1 ATAAT -ATAAT ATAAT ATAAT ATAA-T AT-AAT ATA-AT ATAAT ATAA
59948 AGATTGAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
5 20 0.54
6 15 0.41
7 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:60164 original size:21 final size:20
Alignment explanation
Indices: 60139--60185 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
60129 TAAATAAATT
*
60139 AATTAATGCT-AATTAATACTA
1 AATTAATG-TAAATTAAAAC-A
*
60160 AATTATTGTAAATTAAAACA
1 AATTAATGTAAATTAAAACA
60180 AATTAA
1 AATTAA
60186 GCATTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (20 bp):
AATTAATGTAAATTAAAACA
Found at i:62172 original size:16 final size:15
Alignment explanation
Indices: 62148--62186 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
62138 AATTTTTTTT
62148 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
62163 AAAAAGAAAAAATAGA
1 AAAAA-AAAAAAAAGA
62179 ATAAAAAA
1 A-AAAAAA
62187 TGGGTGTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 12 0.57
17 4 0.19
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Done.