Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007484.1 Corchorus capsularis cultivar CVL-1 contig07505, 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: 70524
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1781 original size:21 final size:21
Alignment explanation
Indices: 1745--1800 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
1735 GTGCATGGGC
*
1745 ATGGCCAGGTCATGCGATGGTG
1 ATGGCC-GGACATGCGATGGTG
* *
1767 ATGGTCGGGCATGCGATGGTG
1 ATGGCCGGACATGCGATGGTG
1788 ATGGCCGGACATG
1 ATGGCCGGACATG
1801 TGGCCGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.18, C:0.18, G:0.43, T:0.21
Consensus pattern (21 bp):
ATGGCCGGACATGCGATGGTG
Found at i:33222 original size:30 final size:30
Alignment explanation
Indices: 33149--33223 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
33139 TAGTTAAGAA
* * *
33149 GGTAATTAAAAAAAGTAGGTTTTAATTCAG
1 GGTAATTAAGAAAAGTAAGCTTTAATTCAG
* *
33179 TGTAATTAAGAAAAGTAAGCTTTAATTTAG
1 GGTAATTAAGAAAAGTAAGCTTTAATTCAG
*
33209 GGTAATTAGGAAAAG
1 GGTAATTAAGAAAAG
33224 AAAGAAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (30 bp):
GGTAATTAAGAAAAGTAAGCTTTAATTCAG
Found at i:33232 original size:17 final size:18
Alignment explanation
Indices: 33212--33245 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33202 AATTTAGGGT
*
33212 AATTAGGAAAAG-AAAGA
1 AATTAAGAAAAGTAAAGA
33229 AATTAAGAAAAGTAAAG
1 AATTAAGAAAAGTAAAG
33246 TCGTAATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (18 bp):
AATTAAGAAAAGTAAAGA
Found at i:33236 original size:47 final size:48
Alignment explanation
Indices: 33182--33275 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
33172 AATTCAGTGT
* ** *
33182 AATTAAGAAAAGT-AAG-CTTTAATTTAGGGTAATTAGGAAAAGAAAGA
1 AATTAAGAAAAGTAAAGTC-GTAATGCAGGGTAATTAAGAAAAGAAAGA
33229 AATTAAGAAAAGTAAAGTCGTAATGCAGGGTAATTAAGAAAAGAAAG
1 AATTAAGAAAAGTAAAGTCGTAATGCAGGGTAATTAAGAAAAGAAAG
33276 CACCGTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 13 0.32
48 27 0.66
49 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.22, T:0.22
Consensus pattern (48 bp):
AATTAAGAAAAGTAAAGTCGTAATGCAGGGTAATTAAGAAAAGAAAGA
Found at i:33302 original size:40 final size:39
Alignment explanation
Indices: 33256--33419 Score: 166
Period size: 40 Copynumber: 4.3 Consensus size: 39
33246 TCGTAATGCA
* * * *
33256 GGGTAATTAAGAAAAGAAAGCACCGTCAAAGTCTTAATTT
1 GGGTAATTAAGAAAAGAAAG-ACAGTCAAGGTCCTAAGTT
33296 GGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTT
1 GGGTAATTAAGAAAAGAAAG-ACAGTCAAGGTCCTAAGTT
* *
33336 GGGTAATT-----AAG-AA-A-AGT-AAGGTCTTAATTT
1 GGGTAATTAAGAAAAGAAAGACAGTCAAGGTCCTAAGTT
33366 AGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTT
1 -GGGTAATTAAGAAAAGAAAG-ACAGTCAAGGTCCTAAGTT
*
33407 GGATAATTAAGAA
1 GGGTAATTAAGAA
33420 GAGTAAAGGC
Statistics
Matches: 103, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
30 11 0.11
31 11 0.11
32 1 0.01
34 2 0.02
35 3 0.03
36 3 0.03
37 2 0.02
39 1 0.01
40 58 0.56
41 11 0.11
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (39 bp):
GGGTAATTAAGAAAAGAAAGACAGTCAAGGTCCTAAGTT
Found at i:33357 original size:30 final size:31
Alignment explanation
Indices: 33323--33382 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
33313 AAGTACAGTC
33323 AAGGTCCTAAGTT-GGGTAATTAAGAAAAGT
1 AAGGTCCTAAGTTAGGGTAATTAAGAAAAGT
* *
33353 AAGGTCTTAATTTAGGGTAATTAAGAAAAG
1 AAGGTCCTAAGTTAGGGTAATTAAGAAAAG
33383 AAAGTACAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (31 bp):
AAGGTCCTAAGTTAGGGTAATTAAGAAAAGT
Found at i:33371 original size:71 final size:71
Alignment explanation
Indices: 33283--33871 Score: 821
Period size: 71 Copynumber: 8.4 Consensus size: 71
33273 AAGCACCGTC
*
33283 AAAGTCTTAATT-TGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
*
33347 AAAAGT
66 AAGAGT
* * *
33353 AAGGTCTTAATTTAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGATAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
33418 AAGAGT
66 AAGAGT
* *
33424 AAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
33489 AAGAGT
66 AAGAGT
* *
33495 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCATAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
33560 AAGAGT
66 AAGAGT
***
33566 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACA-TCAAGGTCCTAA-TCT-GGCCGTTAA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGT-TGGGTAATTAA
33628 GAAGAGT
65 GAAGAGT
* * * *
33635 AAAGTCTTAATTCAGGGTAGTTAAGAAAAGAGAGTACAGTCAAGGTCCTAATTTGGGCAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
33700 AAGAGT
66 AAGAGT
* * * * * * *
33706 GAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAATACAGTCAGGGTCTTAA-TTTGGCAACTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
33770 AAGAGT
66 AAGAGT
* * * * * * * *
33776 AAAGTTTTAATTCAGGGTAATTAAGAAAAGTAAGCACGGTCATGTTCTTAA-TTTGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
*
33840 AAAAGT
66 AAGAGT
* *
33846 GAAGGCTTAATTCAGGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGA
33872 GAAGTAAGCA
Statistics
Matches: 472, Mismatches: 42, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
69 50 0.11
70 136 0.29
71 286 0.61
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.26
Consensus pattern (71 bp):
AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
AAGAGT
Found at i:33442 original size:142 final size:141
Alignment explanation
Indices: 33283--33871 Score: 817
Period size: 140 Copynumber: 4.2 Consensus size: 141
33273 AAGCACCGTC
* *
33283 AAAGTCTTAATT-TGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAA-TTGGGCAATTAAG
* * * * *
33347 AAAAGTAAGGTCTTAATTTAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGATA
65 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTA
33412 ATTAAGAAGAGT
130 ATTAAGAAGAGT
* * *
33424 AAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAA-TTGGGCAATTAAG
*
33489 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCATAGTCAAGGTCCTAAGTTGGGTA
65 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTA
33554 ATTAAGAAGAGT
130 ATTAAGAAGAGT
**
33566 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACA-TCAAGGTCCTAATCT-GGCCGTTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAT-TGGGCAATTAAG
* * * * *
33629 AAGAGTAAAGTCTTAATTCAGGGTAGTTAAGAAAAGAGAGTACAGTCAAGGTCCTAATTTGGGCA
65 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTA
33694 ATTAAGAAGAGT
130 ATTAAGAAGAGT
* * * * * *
33706 GAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAATACAGTCAGGGTCTTAATTTGGCAACTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAATTGGGCAATTAAGA
* * * * * * *
33771 AGAGTAAAGTTTTAATTCAGGGTAATTAAGAAAAGTAAGCACGGTCATGTTCTTAA-TTTGGTAA
66 AGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTAA
*
33835 TTAAGAAAAGT
131 TTAAGAAGAGT
* *
33846 GAAGGCTTAATTCAGGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGA
33872 GAAGTAAGCA
Statistics
Matches: 404, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
140 157 0.39
141 90 0.22
142 157 0.39
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.26
Consensus pattern (141 bp):
AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAATTGGGCAATTAAGA
AGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTGGGTAA
TTAAGAAGAGT
Found at i:33841 original size:211 final size:211
Alignment explanation
Indices: 33283--33881 Score: 842
Period size: 211 Copynumber: 2.8 Consensus size: 211
33273 AAGCACCGTC
*
33283 AAAGTCTTAATT-TGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
* * * *
33347 AAAAGTAAGGTCTTAATTTAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGATA
66 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTAC-GTCAAGGTCCTAATTTGG-TA
33412 ATTAAGAAGAGTAAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGT
129 ATTAAGAAGAGTAAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGT
*
33477 TGGGTAATTAAGAAGAGT
194 TGGGCAATTAAGAAGAGT
* *
33495 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGCATAGTCAAGGTCCTAAGTTGGGTAATTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
* * ***
33560 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACATCAAGGTCCTAATCTGGCCGT
66 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACGTCAAGGTCCTAATTTGGTAAT
* * * * *
33625 TAAGAAGAGTAAAGTCTTAATTCAGGGTAGTTAAGAAAAGAGAGTACAGTCAAGGTCCTAATTTG
131 TAAGAAGAGTAAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTG
33690 GGCAATTAAGAAGAGT
196 GGCAATTAAGAAGAGT
* * * * * * *
33706 GAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAATACAGTCAGGGTCTTAA-TTTGGCAACTAAG
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
* * * * * *
33770 AAGAGTAAAGTTTTAATTCAGGGTAATTAAGAAAAGTAAGCACGGTCATGTTCTTAATTTGGTAA
66 AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTAC-GTCAAGGTCCTAATTTGGTAA
* * * *
33835 TTAAGAAAAGTGAAGGCTTAATTCAGGGTAATTAAGAGAAGTAAGCA
130 TTAAGAAGAGTAAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCA
33882 TAGTAAATGA
Statistics
Matches: 339, Mismatches: 46, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
210 50 0.15
211 173 0.51
212 27 0.08
213 89 0.26
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (211 bp):
AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAG
AAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACGTCAAGGTCCTAATTTGGTAAT
TAAGAAGAGTAAAGGCTTAATTCAGGGTAATTAAGAAAAGAAAGCACAGTCAAGGTCCTAAGTTG
GGCAATTAAGAAGAGT
Found at i:34214 original size:19 final size:18
Alignment explanation
Indices: 34190--34225 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34180 TGAAGATTTC
34190 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
34209 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
34226 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:42906 original size:19 final size:18
Alignment explanation
Indices: 42882--42917 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42872 TGAAGATTTC
42882 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
42901 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
42918 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:44480 original size:39 final size:39
Alignment explanation
Indices: 44417--44506 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
44407 ACGACCGATC
*
44417 ATTAAGTTAAAACAGCAGTCAAAGTACTGAATTCTTAGAA
1 ATTAAG-TAAAAAAGCAGTCAAAGTACTGAATTCTTAGAA
* * *
44457 ATTAAGTAAAAAATCAGTTAAAGTACTTAATTCTTAGAA
1 ATTAAGTAAAAAAGCAGTCAAAGTACTGAATTCTTAGAA
44496 ATTAAGTAAAA
1 ATTAAGTAAAA
44507 GCAACAGTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 40 0.87
40 6 0.13
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (39 bp):
ATTAAGTAAAAAAGCAGTCAAAGTACTGAATTCTTAGAA
Found at i:44569 original size:41 final size:41
Alignment explanation
Indices: 44519--44747 Score: 293
Period size: 41 Copynumber: 5.6 Consensus size: 41
44509 AACAGTCAAA
44519 AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAAGCAC
1 AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAAGCAC
* **
44560 AGACTTAATTTCAAGGAAGGAAATT-AGGTAAAAAAAGGCAC
1 AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAA-GCAC
* * *
44601 AGACCTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAC
1 AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAAGCAC
*
44642 AGACTTAATTTCAAGGAAGGAAATT-AGGTAATGTAAAGCAC
1 AGACTTAATTTCAAGGAAGGAAATTAAGTTAA-GTAAAGCAC
* * * * * *
44683 AAACTTAATTGCAAGGAAGCAAATTAGGTAAAG-AAAGGCTC
1 AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAA-GCAC
44724 AGACTTAATTTCAAGGAAGGAAAT
1 AGACTTAATTTCAAGGAAGGAAAT
44748 AGTTAAAGTC
Statistics
Matches: 160, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 14 0.09
41 137 0.86
42 9 0.06
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (41 bp):
AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAAGCAC
Found at i:44618 original size:82 final size:82
Alignment explanation
Indices: 44519--44747 Score: 345
Period size: 82 Copynumber: 2.8 Consensus size: 82
44509 AACAGTCAAA
* *
44519 AGACTTAATTTCAAGGAAGGAAATTAAGTTAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAAT
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAAT
44584 TAGGTAA-AAAAAGGCAC
66 TAGGTAATAAAAA-GCAC
*
44601 AGACCTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAAT
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAAT
**
44666 TAGGTAATGTAAAGCAC
66 TAGGTAATAAAAAGCAC
* * * *
44683 AAACTTAATTGCAAGGAAGCAAATTAGGTAAAG-AAAGGCTCAGACTTAATTTCAAGGAAGGAAA
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAA-GCACAGACTTAATTTCAAGGAAGGAAA
44747 T
65 T
44748 AGTTAAAGTC
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
81 3 0.02
82 129 0.96
83 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (82 bp):
AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAAT
TAGGTAATAAAAAGCAC
Found at i:44658 original size:123 final size:122
Alignment explanation
Indices: 44519--44756 Score: 379
Period size: 123 Copynumber: 1.9 Consensus size: 122
44509 AACAGTCAAA
* * * *
44519 AGACTTAATTTCAAGGAAGGAAATTAAGTTAA-GTAAAGCACAGACTTAATTTCAAGGAAGGAAA
1 AGACTTAATTTCAAGGAAGGAAATT-AGGTAATGTAAAGCACAAACTTAATTGCAAGGAAGCAAA
44583 TTAGGTAAAAAAAGGCACAGACCTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCAC
65 TTAGGTAAAAAAAGGCACAGACCTAATTTCAAGGAAGGAAA-TAGGTAAAGTAAAGCAC
44642 AGACTTAATTTCAAGGAAGGAAATTAGGTAATGTAAAGCACAAACTTAATTGCAAGGAAGCAAAT
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAATGTAAAGCACAAACTTAATTGCAAGGAAGCAAAT
* * * *
44707 TAGGTAAAGAAAGGCTCAGACTTAATTTCAAGGAAGGAAATAGTTAAAGT
66 TAGGTAAAAAAAGGCACAGACCTAATTTCAAGGAAGGAAATAGGTAAAGT
44757 CAATAAAAGG
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
122 14 0.13
123 92 0.87
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (122 bp):
AGACTTAATTTCAAGGAAGGAAATTAGGTAATGTAAAGCACAAACTTAATTGCAAGGAAGCAAAT
TAGGTAAAAAAAGGCACAGACCTAATTTCAAGGAAGGAAATAGGTAAAGTAAAGCAC
Found at i:44840 original size:36 final size:35
Alignment explanation
Indices: 44754--44928 Score: 169
Period size: 36 Copynumber: 4.9 Consensus size: 35
44744 AAATAGTTAA
44754 AGTCAATAAAAGGGCTTAATTCAGGGTAATTAAGT--
1 AGTCAAT-AAA-GGCTTAATTCAGGGTAATTAAGTGG
* *
44789 AG--AATAAAGAACTTAATTCAGGGAAATTAAGTGG
1 AGTCAATAAAG-GCTTAATTCAGGGTAATTAAGTGG
* **
44823 AGTCAATAAGAGGCTTAATTCAGGGTAATTGAGCAG
1 AGTCAATAA-AGGCTTAATTCAGGGTAATTAAGTGG
* * * * *
44859 AATTAATAAAGAACTTAATTCAAGGTAATTAGGTGG
1 AGTCAATAAAG-GCTTAATTCAGGGTAATTAAGTGG
*
44895 AGTTAATAAAAGGCTTAATTCAGGGTAATTAAGT
1 AGTCAAT-AAAGGCTTAATTCAGGGTAATTAAGT
44929 AGAATAAAGA
Statistics
Matches: 113, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
31 1 0.01
32 23 0.20
33 3 0.03
34 2 0.02
35 4 0.04
36 74 0.65
37 6 0.05
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (35 bp):
AGTCAATAAAGGCTTAATTCAGGGTAATTAAGTGG
Found at i:44895 original size:72 final size:70
Alignment explanation
Indices: 44754--44946 Score: 259
Period size: 72 Copynumber: 2.8 Consensus size: 70
44744 AAATAGTTAA
* *
44754 AGTCAATAAAAGGGCTTAATTCAGGGTAATTA-AGTA-GAATAAAGAACTTAATTCAGGGAAATT
1 AGTCAATAAAA-GGCTTAATTCAGGGTAATTAGAGAATGAATAAAGAACTTAATTCAAGGAAATT
44817 AAGTGG
65 AAGTGG
* * *
44823 AGTCAATAAGAGGCTTAATTCAGGGTAATTGAGCAGAATTAATAAAGAACTTAATTCAAGGTAAT
1 AGTCAATAAAAGGCTTAATTCAGGGTAATT-AG-AGAATGAATAAAGAACTTAATTCAAGGAAAT
*
44888 TAGGTGG
64 TAAGTGG
* *
44895 AGTTAATAAAAGGCTTAATTCAGGGTAATTA-AGTA-GAATAAAGAACTTAATT
1 AGTCAATAAAAGGCTTAATTCAGGGTAATTAGAGAATGAATAAAGAACTTAATT
44947 TCGGATAATT
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
68 35 0.32
69 14 0.13
71 4 0.04
72 57 0.52
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (70 bp):
AGTCAATAAAAGGCTTAATTCAGGGTAATTAGAGAATGAATAAAGAACTTAATTCAAGGAAATTA
AGTGG
Found at i:46992 original size:21 final size:21
Alignment explanation
Indices: 46916--46990 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
46906 GCATAGGCAA
46916 GGCCGGGTCATGCGATGGTGAT
1 GGCCGGG-CATGCGATGGTGAT
**
46938 GGTTGGGCATGCGATGGTGAT
1 GGCCGGGCATGCGATGGTGAT
*
46959 GGCCGGGCATGTGATGGTGAT
1 GGCCGGGCATGCGATGGTGAT
46980 GGCCGGGCATG
1 GGCCGGGCATG
46991 TGGCCGGTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 43 0.90
22 5 0.10
ACGTcount: A:0.13, C:0.16, G:0.48, T:0.23
Consensus pattern (21 bp):
GGCCGGGCATGCGATGGTGAT
Found at i:53467 original size:21 final size:21
Alignment explanation
Indices: 53433--53486 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
53423 GCATGGACAA
53433 GGCCGGGTCATGCGATAGTGAT
1 GGCCGGG-CATGCGATAGTGAT
*
53455 GGCCGGGCATGCGATGGTGAT
1 GGCCGGGCATGCGATAGTGAT
53476 GGCCGGGCATG
1 GGCCGGGCATG
53487 TGGCCGGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.15, C:0.20, G:0.46, T:0.19
Consensus pattern (21 bp):
GGCCGGGCATGCGATAGTGAT
Found at i:60541 original size:34 final size:37
Alignment explanation
Indices: 60503--60577 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 37
60493 AATAAAAAAA
* *
60503 TTAAAAAGCAAAAATAG-AAA-ATAAAAT-ATTTTTT
1 TTAAAAAGCAAAAACAGAAAAGAAAAAATAATTTTTT
* *
60537 TTAAAAAGGAAAAACGGAAAAGAAAAAATAATTTTTT
1 TTAAAAAGCAAAAACAGAAAAGAAAAAATAATTTTTT
60574 TTAA
1 TTAA
60578 TATCGACGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 14 0.41
35 3 0.09
36 6 0.18
37 11 0.32
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (37 bp):
TTAAAAAGCAAAAACAGAAAAGAAAAAATAATTTTTT
Found at i:60987 original size:27 final size:27
Alignment explanation
Indices: 60949--61008 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
60939 ATAAGAAAAC
60949 AATTAAACTAAAAATC-AAAGC-AAAGCA
1 AATTAAACT--AAATCTAAAGCTAAAGCA
* *
60976 AATTAAATTAAATCTAAATCTAAAGCA
1 AATTAAACTAAATCTAAAGCTAAAGCA
61003 AATTAA
1 AATTAA
61009 TAAAGCAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 4 0.14
27 20 0.69
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (27 bp):
AATTAAACTAAATCTAAAGCTAAAGCA
Found at i:63029 original size:27 final size:27
Alignment explanation
Indices: 62997--63093 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 27
62987 GGCCGAATTA
* * * *
62997 GCATTTTGGTCTTTTTTGCATTTAGGG
1 GCATTTTGGTCATTTTTACACTAAGGG
* *
63024 GTATTTTGGTCATTCTTACACTAAGGG
1 GCATTTTGGTCATTTTTACACTAAGGG
* * *
63051 GCATTTTGGTCATTTTGCACATTCAGGG
1 GCATTTTGGTCATTTT-TACACTAAGGG
* *
63079 ACATTTTGGACATTT
1 GCATTTTGGTCATTT
63094 CAAATTCCAA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
27 35 0.62
28 21 0.38
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (27 bp):
GCATTTTGGTCATTTTTACACTAAGGG
Found at i:63087 original size:28 final size:26
Alignment explanation
Indices: 63026--63093 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
63016 ATTTAGGGGT
*
63026 ATTTTGGTCATTCTTACACTAAGGGGC
1 ATTTTGGTCATT-TTACACTAAGGGAC
* *
63053 ATTTTGGTCATTTTGCACATTCAGGGAC
1 ATTTTGGTCATTTT--ACACTAAGGGAC
*
63081 ATTTTGGACATTT
1 ATTTTGGTCATTT
63094 CAAATTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.06
27 12 0.34
28 21 0.60
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (26 bp):
ATTTTGGTCATTTTACACTAAGGGAC
Found at i:67127 original size:24 final size:27
Alignment explanation
Indices: 67100--67152 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
67090 TTCTAGTGAT
*
67100 GAGAAT-AAG-GAAGGAAAA-GAGGAG
1 GAGAATCAAGAGAAGGAAAATAAGGAG
67124 GAGAATCAAGAGAAGGAAAATAAGGAG
1 GAGAATCAAGAGAAGGAAAATAAGGAG
67151 GA
1 GA
67153 ATTTCATCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 9 0.36
27 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.38, T:0.06
Consensus pattern (27 bp):
GAGAATCAAGAGAAGGAAAATAAGGAG
Found at i:68942 original size:21 final size:19
Alignment explanation
Indices: 68918--68964 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
68908 AAAGTTCGTG
68918 TTTGAAGATTTTTGAAGATAA
1 TTTGAAGA--TTTGAAGATAA
*
68939 TTTGAAGATTTGAAGATCA
1 TTTGAAGATTTGAAGATAA
68958 -TTGAAGA
1 TTTGAAGA
68965 ATTATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
21 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (19 bp):
TTTGAAGATTTGAAGATAA
Done.