Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016002.1 Corchorus capsularis cultivar CVL-1 contig16023, 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: 25005
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1197 original size:8 final size:8
Alignment explanation
Indices: 1169--1202 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1159 GAATCAGTTA
1169 TGAATTTT
1 TGAATTTT
*
1177 TGAAGTTTC
1 TGAA-TTTT
1186 TGAATTTT
1 TGAATTTT
1194 TGAATTTT
1 TGAATTTT
1202 T
1 T
1203 AAGAAGGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:5328 original size:34 final size:34
Alignment explanation
Indices: 5280--5361 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
5270 AGGTAACTTC
*
5280 TAATCCTAAACCATTTTATATTTGTAGTTTTAGT
1 TAATTCTAAACCATTTTATATTTGTAGTTTTAGT
5314 TAATTCTAAACCATTTTATATTTGTAGTTTTAGT
1 TAATTCTAAACCATTTTATATTTGTAGTTTTAGT
5348 TAATTCTAAACCAT
1 TAATTCTAAACCAT
5362 GGGTTTTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (34 bp):
TAATTCTAAACCATTTTATATTTGTAGTTTTAGT
Found at i:5772 original size:58 final size:58
Alignment explanation
Indices: 5679--5791 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
5669 ACTTTTAATA
* * * ** *
5679 GAGTTATTGTGGAGGCTAGATAAAAGCATGTTATTTCAATGGTAGAGGACATTAGATG
1 GAGTTATTGTAGAGGCTAGAGAAAAACATGTTATTTCAATGCAAAAGGACATTAGATG
* *
5737 GAGTTATTGTAGAGGTTAGAGAAAAACCTGTTATTTCAATGCAAAAGGACATTAG
1 GAGTTATTGTAGAGGCTAGAGAAAAACATGTTATTTCAATGCAAAAGGACATTAG
5792 GAAGTATATG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (58 bp):
GAGTTATTGTAGAGGCTAGAGAAAAACATGTTATTTCAATGCAAAAGGACATTAGATG
Found at i:9068 original size:330 final size:330
Alignment explanation
Indices: 8090--9283 Score: 1312
Period size: 330 Copynumber: 3.6 Consensus size: 330
8080 TGTCATTGTC
* * * * * * *
8090 CGTTGTTA-CCAAAAACTGTGACAACTAATACACGATTTCGGTTAAAATTTTACAAAAATTTACC
1 CGTTTTTAGCCAAAAACTGTGATAATTAATACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
* * *
8154 CGAGAGAATTT-TCCTAAATTTTTTGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAA
66 CGAG-GAATTTCTCCTCAA-TTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAA
* *
8218 AGATTGAAAGGCTTTTCACGCTTCTAATATCGGTTTTCTTATTTTTTTTCCGAATTAATTTCTAA
129 AGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA--TTTTTTCCGAATTAATTTCTAA
* * * *
8283 TTAAATCGAAACATGCTTCAGATGCTCGTAAAAAAATAATCCTTAAATCCAATGTGGTTGAGAAT
192 TTAAATCGAAACATGATTCAGATGCTCGTAAAAACA-AATCCTTAAATCCAATGTGGCTGAGATT
*** * ** * *
8348 TGGTTAGATGGATATAGATAAAACAATGAGACTTGGCGCCAAAAATCATGCAAAACAAAGCCGAG
256 TGGTTAGATGGATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAACTGAGCGGGG
* * *
8413 ACCCCGAAACA
321 A-CTCGGAACG
** * *
8424 CGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACA
1 CGTTTTTAGCCAAAAACTGTGATAATTAATACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
* ** *
8489 CGA-AACATTTCTCCTCAATTTCCAGCCACCATATTCATAAAGAAATATATAATTCAACGCCAAA
66 CGAGGA-ATTTCTCCTCAATTT-TGGCCACCATACTCATAAA-AAATATATAATTCAACGCCAAA
* * * * * *
8553 AATATTGAAGGGCTTCTCACGCTTTTAATATTAGTTTTT-CTATTTTTTCTGAATTAATTTCTAA
128 AAGATTGAAAGGCTTTTCACGCTTCTAATA-TCGTTTTTCCTATTTTTTCCGAATTAATTTCTAA
* *
8617 TTAAATCGAAAC-TAGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATT
192 TTAAATCGAAACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* ** * * * ** *
8681 TCGTTAGATAAATATAAATATTTCAATAAGTCTTGATGTCAAAAATCATGAAAAACTGAGTCGGG
256 TGGTTAGATGGATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAACTGAG-CGGG
*
8746 GTCTCGGAACG
320 GACTCGGAACG
* * *
8757 CGTTTTTAGCCAAAAAC-GTGATAATTAATACACGATTTCGGCTAAAATTTTGTAAAAATTAACC
1 CGTTTTTAGCCAAAAACTGTGATAATTAATACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
* * ** *
8821 CGAAGGAGTTT-TCCTCAACTTTTGGCTATGATACTCATAAAAAATATATAATTCAACACCAAAA
66 CG-AGGAATTTCTCCTCAA-TTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAA
* * *
8885 AGATTGAAAGG-TTATTCACGCTTCTAATATCGTTTTTCCTATTTTTCCCAAATTAATTCCTAAT
129 AGATTGAAAGGCTT-TTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAAT
* * * *
8949 TGAATCGAAACATGATTCATATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGGTAAGATTTG
193 TAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
*
9013 GTTAGATGGATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAACTGAGCCGGGAC
258 GTTAGATGGATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAACTGAGCGGGGAC
*
9078 TCCAGAACG
323 T-CGGAACG
* * * * ** * * * *
9087 CGTTTTTAGTCAAAACCCGTAATGCTTAGTACATGATTTAAGATAAAATTTTGCAAAAATTGACC
1 CGTTTTTAGCCAAAAACTGTGATAATTAATACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
* * * * *
9152 CGAGAAATTTCTCCTCAATTTTGGGCCA-CATACTAATAAAAAACATATAACTCAACGTCAAAAA
66 CGAGGAATTTCTCCTCAATTTT-GGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAA
* * * ** * *
9216 GAATG-AAGGGTTTCTTACGCTTCTAATATCACTTTTCCTACCTTTTTCTGAATTAATTTCTAAT
130 GATTGAAAGGCTTT-TCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCGAATTAATTTCTAAT
9280 TAAA
193 TAAA
9284 AAATATATTT
Statistics
Matches: 713, Mismatches: 126, Indels: 45
0.81 0.14 0.05
Matches are distributed among these distances:
329 11 0.02
330 181 0.25
331 160 0.22
332 63 0.09
333 102 0.14
334 70 0.10
335 70 0.10
336 50 0.07
337 6 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (330 bp):
CGTTTTTAGCCAAAAACTGTGATAATTAATACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
CGAGGAATTTCTCCTCAATTTTGGCCACCATACTCATAAAAAATATATAATTCAACGCCAAAAAG
ATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAA
ATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
AGATGGATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAACTGAGCGGGGACTCG
GAACG
Found at i:9394 original size:27 final size:27
Alignment explanation
Indices: 9338--9403 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
9328 AAAAGTACAC
**
9338 AAAATTATATTTTAATAATGGTATAGTT
1 AAAA-TATATTTTAATAATGCAATAGTT
*
9366 AAAATATATTTTAATAATGACAAT-TTT
1 AAAATATATTTTAATAATG-CAATAGTT
9393 AAAATATATTT
1 AAAATATATTT
9404 GAAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 28 0.82
28 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (27 bp):
AAAATATATTTTAATAATGCAATAGTT
Found at i:9464 original size:96 final size:95
Alignment explanation
Indices: 9327--9504 Score: 245
Period size: 94 Copynumber: 1.9 Consensus size: 95
9317 TATATTTGAA
** *
9327 AAAAAGTACACAAAATTATATTTTAATAATGGTATAGTTAAAATATATTTTAATAATGAC-AATT
1 AAAAAGTACACAAAATTATATTTTAATAATGACATAATT-AAA-ATATTTTAATAATG-CTAA-T
*
9391 TTA-AAATATATTTGAAAAAAATAGTACAATGGG
62 TTAGAAAAATATTTGAAAAAAATAGTACAATGGG
*
9424 AAAAA-TACATAAAATTATATTTTAATAATGACATAATTAAAATATTTTAATAATGCTAATTTAG
1 AAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATTTTAATAATGCTAATTTAG
*
9488 AAAAATATTTGAGAAAA
66 AAAAATATTTGAAAAAA
9505 GGGATATAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
93 5 0.07
94 31 0.42
95 3 0.04
96 29 0.40
97 5 0.07
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (95 bp):
AAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATTTTAATAATGCTAATTTAG
AAAAATATTTGAAAAAAATAGTACAATGGG
Found at i:9915 original size:115 final size:117
Alignment explanation
Indices: 9712--9949 Score: 310
Period size: 115 Copynumber: 2.1 Consensus size: 117
9702 TTTTAAAATA
*
9712 GTATAAATAAAATATTTTATAAAGATTTAGATTTGATTAAAAAATAGAGTTTAAGTAGAGTAAAA
1 GTATAAATAAAATATTTTATAAAGATTTAGATTTAATTAAAAAATAGAGTTTAAGTAGAGTAAAA
*
9777 CTATAATAGTTTAAACAAAGGCAGTTTAGAAATAA-ATTAG-AAAA-ATAAGG
66 CTATAATACTTTAAACAAAGGCAGTTTAGAAA-AATATTAGTAAAATATAAGG
* *
9827 TTATAAATAAAATA-TTTATAAAGATTTAGATTTAATTTAAAAATAGAGTTTTTAA-TAGA-TAT
1 GTATAAATAAAATATTTTATAAAGATTTAGATTTAATTAAAAAATAGAG--TTTAAGTAGAGTA-
* * * *
9889 AACAGTTTAA-ACTTTAAACAATGGCAGTTTAGAAAAATGTTAGTAAAATATAAGG
63 AA-ACTATAATACTTTAAACAAAGGCAGTTTAGAAAAATATTAGTAAAATATAAGG
9944 GTATAA
1 GTATAA
9950 TGGTCGATTC
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
114 36 0.34
115 46 0.43
116 14 0.13
117 11 0.10
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (117 bp):
GTATAAATAAAATATTTTATAAAGATTTAGATTTAATTAAAAAATAGAGTTTAAGTAGAGTAAAA
CTATAATACTTTAAACAAAGGCAGTTTAGAAAAATATTAGTAAAATATAAGG
Found at i:10118 original size:30 final size:31
Alignment explanation
Indices: 10070--10128 Score: 111
Period size: 30 Copynumber: 1.9 Consensus size: 31
10060 TTATGTTTTC
10070 CGATTGTACCCTTTTTTTTAAAACATATTCT
1 CGATTGTACCCTTTTTTTTAAAACATATTCT
10101 CGATTGTACCC-TTTTTTTAAAACATATT
1 CGATTGTACCCTTTTTTTTAAAACATATT
10129 TCTAAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (31 bp):
CGATTGTACCCTTTTTTTTAAAACATATTCT
Found at i:10298 original size:37 final size:37
Alignment explanation
Indices: 10255--10349 Score: 136
Period size: 37 Copynumber: 2.6 Consensus size: 37
10245 TGTTTTTTTT
10255 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
* ** *
10292 TTTGTTTCCAATGTTGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
* *
10329 TTTGTCTCCAACGCCCTATTT
1 TTTGTTTCCAACGTCCTATTT
10350 GGGCTTAGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
Found at i:13166 original size:22 final size:22
Alignment explanation
Indices: 13140--13187 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
13130 AATTTATTCA
13140 ATATTAATTAACTATTAATTAG
1 ATATTAATTAACTATTAATTAG
*
13162 ATATTAATTAGCTATTAATTAG
1 ATATTAATTAACTATTAATTAG
13184 ATAT
1 ATAT
13188 ACAGTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATTAATTAACTATTAATTAG
Found at i:13183 original size:11 final size:11
Alignment explanation
Indices: 13141--13183 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
13131 ATTTATTCAA
*
13141 TATTAATTAAC
1 TATTAATTAGC
*
13152 TATTAATTAGA
1 TATTAATTAGC
13163 TATTAATTAGC
1 TATTAATTAGC
13174 TATTAATTAG
1 TATTAATTAG
13184 ATATACAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:14073 original size:74 final size:74
Alignment explanation
Indices: 13987--14143 Score: 244
Period size: 74 Copynumber: 2.1 Consensus size: 74
13977 TTAAGGAAGG
* * * * * *
13987 GAAATGTGTAATTACGAAAAAGGGTAGAAGGGAAAGGAATGGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGAGGAAACTCATAGAGGGACTTTT
14052 TAGTCATCC-
66 TAGTCA-CCT
14061 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGAGGAAACTCATAGAGGGACTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGAGGAAACTCATAGAGGGACTTTT
14126 TAGTCACCT
66 TAGTCACCT
14135 GAAAAGTGT
1 GAAAAGTGT
14144 GAAAAGACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
73 2 0.03
74 74 0.97
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.21
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGAAATAGAGGAAACTCATAGAGGGACTTTT
TAGTCACCT
Found at i:14238 original size:20 final size:20
Alignment explanation
Indices: 14213--14252 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14203 TAATTTTCTA
14213 TGTAGTTAAAAATAATATAT
1 TGTAGTTAAAAATAATATAT
14233 TGTAGTTAAAAATAATATAT
1 TGTAGTTAAAAATAATATAT
14253 AATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
TGTAGTTAAAAATAATATAT
Found at i:14266 original size:3 final size:3
Alignment explanation
Indices: 14243--14292 Score: 75
Period size: 3 Copynumber: 16.3 Consensus size: 3
14233 TGTAGTTAAA
14243 AAT AAT ATAT AAT -AT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14289 AAT A
1 AAT A
14293 TATATACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:14268 original size:12 final size:11
Alignment explanation
Indices: 14243--14298 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 11
14233 TGTAGTTAAA
14243 AATAATAT-AT
1 AATAATATAAT
14253 AATATATATAAT
1 AATA-ATATAAT
14265 AATAATAATAAT
1 AATAAT-ATAAT
14277 AATAATAATAAT
1 AATAAT-ATAAT
14289 AATATATATA
1 AATA-ATATA
14299 CACACACACA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.10
11 6 0.14
12 30 0.71
13 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAATATAAT
Found at i:22421 original size:288 final size:288
Alignment explanation
Indices: 21905--22475 Score: 1124
Period size: 288 Copynumber: 2.0 Consensus size: 288
21895 CACCCCCGTC
21905 AACCTTTTAAATGAGCTCCCTCATTCTCTTGATCACTACGCGGAACTTGGAATCTCGTGAATCAA
1 AACCTTTTAAATGAGCTCCCTCATTCTCTTGATCACTACGCGGAACTTGGAATCTCGTGAATCAA
21970 TATAATATACTCCCTCCGTTCCTTTTTAATTGTCACTTTTCCTTGTTCCTTTTTAATTGTCTCTC
66 TATAATATACTCCCTCCGTTCCTTTTTAATTGTCACTTTTCCTTGTTCCTTTTTAATTGTCTCTC
*
22035 ATATTTTCTTTCCAGAAATACCCTTCTTGAAAGAAAAGTTTAATTAAAATGTCAAACATACATTT
131 ATATTTTCTTTCCAGAAATAACCTTCTTGAAAGAAAAGTTTAATTAAAATGTCAAACATACATTT
*
22100 AATTAGAGAGAAGCAATGGCTTAAGGCCATTATAGGAAGATTAAGTGAAATTGTAATAGAATTTA
196 AATTAGAGAGAAGCAATGGCTTAAGGCCATTATAGGAAGATTAACTGAAATTGTAATAGAATTTA
22165 GGAAACTAACTGAAATTAACTACGCGTT
261 GGAAACTAACTGAAATTAACTACGCGTT
22193 AACCTTTTAAATGAGCTCCCTCATTCTCTTGATCACTACGCGGAACTTGGAATCTCGTGAATCAA
1 AACCTTTTAAATGAGCTCCCTCATTCTCTTGATCACTACGCGGAACTTGGAATCTCGTGAATCAA
22258 TATAATATACTCCCTCCGTTCCTTTTTAATTGTCACTTTTCCTTGTTCCTTTTTAATTGTCTCTC
66 TATAATATACTCCCTCCGTTCCTTTTTAATTGTCACTTTTCCTTGTTCCTTTTTAATTGTCTCTC
22323 ATATTTTCTTTCCAGAAATAACCTTCTTGAAAGAAAAGTTTAATTAAAATGTCAAACATACATTT
131 ATATTTTCTTTCCAGAAATAACCTTCTTGAAAGAAAAGTTTAATTAAAATGTCAAACATACATTT
22388 AATTAGAGAGAAGCAATGGCTTAAGGCCATTATAGGAAGATTAACTGAAATTGTAATAGAATTTA
196 AATTAGAGAGAAGCAATGGCTTAAGGCCATTATAGGAAGATTAACTGAAATTGTAATAGAATTTA
22453 GGAAACTAACTGAAATTAACTAC
261 GGAAACTAACTGAAATTAACTAC
22476 TTTTCTTAAA
Statistics
Matches: 281, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
288 281 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (288 bp):
AACCTTTTAAATGAGCTCCCTCATTCTCTTGATCACTACGCGGAACTTGGAATCTCGTGAATCAA
TATAATATACTCCCTCCGTTCCTTTTTAATTGTCACTTTTCCTTGTTCCTTTTTAATTGTCTCTC
ATATTTTCTTTCCAGAAATAACCTTCTTGAAAGAAAAGTTTAATTAAAATGTCAAACATACATTT
AATTAGAGAGAAGCAATGGCTTAAGGCCATTATAGGAAGATTAACTGAAATTGTAATAGAATTTA
GGAAACTAACTGAAATTAACTACGCGTT
Found at i:23113 original size:60 final size:59
Alignment explanation
Indices: 22966--23120 Score: 197
Period size: 60 Copynumber: 2.6 Consensus size: 59
22956 GGCTAATTGT
*
22966 TTAAATAGATCCCTAACGTATGTGAAAATGCTCAATTTAGGGCCAATGCTTTAAATTTGG
1 TTAAATAGA-CCCTAAAGTATGTGAAAATGCTCAATTTAGGGCCAATGCTTTAAATTTGG
* * *
23026 TTAGATAGAACCGTAAAGTATGTGAAAATGCTCAATTTAGGGTCC-ATGCTTTGAATTTGG
1 TTAAATAG-ACCCTAAAGTATGTGAAAATGCTCAATTTAGGG-CCAATGCTTTAAATTTGG
* *
23086 TTAAATATGACCCTAATGTAT-TAGAAAATACTCAA
1 TTAAATA-GACCCTAAAGTATGT-GAAAATGCTCAA
23121 ATAAAGACCT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 1 0.01
60 78 0.94
61 4 0.05
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (59 bp):
TTAAATAGACCCTAAAGTATGTGAAAATGCTCAATTTAGGGCCAATGCTTTAAATTTGG
Found at i:23274 original size:60 final size:59
Alignment explanation
Indices: 23178--23309 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 59
23168 GGGCCCTTAT
* * *
23178 TTGAGTATTTTCGCATACATTAGGACCTTGTTTAACCAAATTAGAAGT-AT-GAGCCCTAAA
1 TTGAGCATTTTCGCATACATTAGGACCTTATATAACCAAATTA-AA-TCATAGA-CCCTAAA
**
23238 TTGAGCATTTTCGCATACATTAGGGTCTTATATAACCAAATTAAATCCATAGACCCTAAA
1 TTGAGCATTTTCGCATACATTAGGACCTTATATAACCAAATTAAAT-CATAGACCCTAAA
23298 TTGAGCATTTTC
1 TTGAGCATTTTC
23310 ATATACGTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.02
59 2 0.03
60 59 0.92
61 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (59 bp):
TTGAGCATTTTCGCATACATTAGGACCTTATATAACCAAATTAAATCATAGACCCTAAA
Found at i:24317 original size:20 final size:20
Alignment explanation
Indices: 24292--24337 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
24282 ATCACCTACC
24292 AAGATCACCACAGGCGATCA
1 AAGATCACCACAGGCGATCA
24312 AAGATCACCACAGGCGATCA
1 AAGATCACCACAGGCGATCA
24332 AAGATC
1 AAGATC
24338 TCCCCAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.28, G:0.20, T:0.11
Consensus pattern (20 bp):
AAGATCACCACAGGCGATCA
Done.