Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014391.1 Corchorus capsularis cultivar CVL-1 contig14412, 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: 40740
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2553 original size:38 final size:37
Alignment explanation
Indices: 2474--2553 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 37
2464 ATCAGCTTGA
* *
2474 AAAAAAAAAGTCGGCCCAAAACAAAATAGGAGCAAAAC
1 AAAAAAAAAGTCAGCCCAAAACAAAATA-GACCAAAAC
*
2512 AAAAAAAAAGTCAGCCCAAAACAGAAATA-TCCAAAAGC
1 AAAAAAAAAGTCAGCCCAAAACA-AAATAGACCAAAA-C
2550 AAAA
1 AAAA
2554 TATTTTGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 5 0.14
38 27 0.73
39 5 0.14
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (37 bp):
AAAAAAAAAGTCAGCCCAAAACAAAATAGACCAAAAC
Found at i:10102 original size:23 final size:22
Alignment explanation
Indices: 10075--10160 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 22
10065 ATTTGCACCT
*
10075 ATAAAATTATCCTAGGGAGGTTA
1 ATAAAATT-TCATAGGGAGGTTA
*
10098 ATAAAATTTCATTGGGAGGTT-
1 ATAAAATTTCATAGGGAGGTTA
10119 ATGGAAAATTT-AT-GGAGAGGTT-
1 AT--AAAATTTCATAGG-GAGGTTA
* *
10141 ATCAAAATTACATAGAGAGG
1 AT-AAAATTTCATAGGGAGG
10161 ATATCATCGT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 10 0.19
22 27 0.51
23 16 0.30
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (22 bp):
ATAAAATTTCATAGGGAGGTTA
Found at i:10117 original size:22 final size:23
Alignment explanation
Indices: 10075--10119 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
10065 ATTTGCACCT
*
10075 ATAAAATTATCCTAGGGAGGTTA
1 ATAAAATTATCATAGGGAGGTTA
*
10098 ATAAAATT-TCATTGGGAGGTTA
1 ATAAAATTATCATAGGGAGGTTA
10120 TGGAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (23 bp):
ATAAAATTATCATAGGGAGGTTA
Found at i:10220 original size:22 final size:22
Alignment explanation
Indices: 10195--10400 Score: 109
Period size: 22 Copynumber: 9.5 Consensus size: 22
10185 GAGGTTATTC
10195 AAATTTCATAGTGTGATTATCA
1 AAATTTCATAGTGTGATTATCA
* * *
10217 AAATTTTATGAG-GAGGTTATCA
1 AAATTTCAT-AGTGTGATTATCA
* *
10239 AAATTTTCATAGCGTGATTAGC-
1 AAA-TTTCATAGTGTGATTATCA
* * *
10261 -AATTTTATAGCGTGGTTATCA
1 AAATTTCATAGTGTGATTATCA
* *
10282 AAATTTTATAAG-GAGATTATCA
1 AAATTTCAT-AGTGTGATTATCA
* * ** *
10304 AAATTTCACACTCAGGTTATCA
1 AAATTTCATAGTGTGATTATCA
* *
10326 AAATTTCATAATATG-TTATCA
1 AAATTTCATAGTGTGATTATCA
* * * *
10347 AATTTTCACAATGTGGTTATC-
1 AAATTTCATAGTGTGATTATCA
* * * *
10368 CAATTCTCATAGGGAGATTATCG
1 AAATT-TCATAGTGTGATTATCA
10391 AAATTTCATA
1 AAATTTCATA
10401 ATAAAGTTAT
Statistics
Matches: 142, Mismatches: 32, Indels: 20
0.73 0.16 0.10
Matches are distributed among these distances:
20 15 0.11
21 24 0.17
22 84 0.59
23 19 0.13
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
AAATTTCATAGTGTGATTATCA
Found at i:10266 original size:43 final size:43
Alignment explanation
Indices: 10184--10288 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 43
10174 ATTCGCATAG
* *
10184 GGAGGTTATTC-AAA-TTTCATAGTGTGATTATCAAAATTTTATGA
1 GGAGGTTA-TCAAAATTTTCATAGCGTGATTAGC-AAATTTTAT-A
10228 GGAGGTTATCAAAATTTTCATAGCGTGATTAGC-AATTTTATA
1 GGAGGTTATCAAAATTTTCATAGCGTGATTAGCAAATTTTATA
*
10270 GCGTGGTTATCAAAATTTT
1 G-GAGGTTATCAAAATTTT
10289 ATAAGGAGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
42 2 0.04
43 26 0.47
44 11 0.20
45 16 0.29
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (43 bp):
GGAGGTTATCAAAATTTTCATAGCGTGATTAGCAAATTTTATA
Found at i:10355 original size:43 final size:44
Alignment explanation
Indices: 10274--10423 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 44
10264 TTTATAGCGT
*
10274 GGTTATCAAAATTTTATAAGGAGATTATCAAAATTTCACACTCA
1 GGTTATCAAAATTTCATAAGGAGATTATCAAAATTTCACACTCA
* * * **
10318 GGTTATCAAAATTTCATAA-TATG-TTATCAAATTTTCACAATGT
1 GGTTATCAAAATTTCATAAGGA-GATTATCAAAATTTCACACTCA
* * * * * *
10361 GGTTATC-CAATTCTCATAGGGAGATTATCGAAATTTCATAATAA
1 GGTTATCAAAATT-TCATAAGGAGATTATCAAAATTTCACACTCA
*
10405 AGTTATCAAAATTTTCATA
1 GGTTATCAAAA-TTTCATA
10424 GCATAGTTAT
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 4 0.05
43 30 0.36
44 41 0.49
45 7 0.08
46 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAGGAGATTATCAAAATTTCACACTCA
Found at i:10363 original size:87 final size:89
Alignment explanation
Indices: 10272--10441 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 89
10262 ATTTTATAGC
* * * *
10272 GTGGTTATCAAAATT-TTATAAGGAGATTATCAAAATTTCACACTCAGGTTATCAAAA-TTTCAT
1 GTGGTTATC-AAATTCTCATAAGGAGATTATCAAAATTTCACAATAAAGTTATCAAAATTTTCAT
10335 A-ATATGTTATCAA-ATTTTCACAAT
65 ACATA-GTTATCAATATTTTCACAAT
* * * *
10359 GTGGTTATCCAATTCTCATAGGGAGATTATCGAAATTTCATAATAAAGTTATCAAAATTTTCATA
1 GTGGTTATCAAATTCTCATAAGGAGATTATCAAAATTTCACAATAAAGTTATCAAAATTTTCATA
10424 GCATAGTTATCAATATTT
66 -CATAGTTATCAATATTT
10442 CCATGTTGGA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
86 4 0.06
87 44 0.63
88 7 0.10
89 8 0.11
90 7 0.10
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (89 bp):
GTGGTTATCAAATTCTCATAAGGAGATTATCAAAATTTCACAATAAAGTTATCAAAATTTTCATA
CATAGTTATCAATATTTTCACAAT
Found at i:10367 original size:65 final size:67
Alignment explanation
Indices: 10275--10421 Score: 149
Period size: 65 Copynumber: 2.2 Consensus size: 67
10265 TTATAGCGTG
* * * * * *
10275 GTTATCAAAATTTT-ATAAGGAGATTATCAAAATT-TCACACTCAGGTTATCAAAATTTCATAAT
1 GTTATCAAAATTTTCACAATGTGGTTATC-AAATTCTCACACGCAGATTATCAAAATTTCATAAT
*
10338 -AT
65 AAA
* * * * *
10340 GTTATC-AAATTTTCACAATGTGGTTATCCAATTCTCATAGGGAGATTATCGAAATTTCATAATA
1 GTTATCAAAATTTTCACAATGTGGTTATCAAATTCTCACACGCAGATTATCAAAATTTCATAATA
10404 AA
66 AA
10406 GTTATCAAAATTTTCA
1 GTTATCAAAATTTTCA
10422 TAGCATAGTT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
64 11 0.17
65 39 0.59
66 7 0.11
67 9 0.14
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (67 bp):
GTTATCAAAATTTTCACAATGTGGTTATCAAATTCTCACACGCAGATTATCAAAATTTCATAATA
AA
Found at i:13126 original size:25 final size:25
Alignment explanation
Indices: 13098--13147 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
13088 CTTTACTTCA
13098 TAAAATAAAATCGAGATAATGTGCC
1 TAAAATAAAATCGAGATAATGTGCC
13123 TAAAATAAAATCGAGATAATGTGCC
1 TAAAATAAAATCGAGATAATGTGCC
13148 CCATTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (25 bp):
TAAAATAAAATCGAGATAATGTGCC
Found at i:14625 original size:21 final size:21
Alignment explanation
Indices: 14599--14640 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14589 ATGGAGGAAA
14599 TTGTCCCGATTTTAATAGTTT
1 TTGTCCCGATTTTAATAGTTT
*
14620 TTGTCCCGGTTTTAATAGTTT
1 TTGTCCCGATTTTAATAGTTT
14641 ATGGAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (21 bp):
TTGTCCCGATTTTAATAGTTT
Found at i:15782 original size:34 final size:34
Alignment explanation
Indices: 15731--15816 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
15721 AATTTTTTTT
* * *
15731 TAGAAAAGATAGTTTTTTTTTTTCAGATTATTATTAG
1 TAGAAAAGAT-G-TTTTTTTATGCACATTATTATT-G
*
15768 -AGAAAAGATGTTTTTTTATGGACATTATTATTG
1 TAGAAAAGATGTTTTTTTATGCACATTATTATTG
*
15801 TAGATAAGATGTTTTT
1 TAGAAAAGATGTTTTT
15817 CAATTCAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 1 0.02
34 32 0.74
35 1 0.02
36 9 0.21
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (34 bp):
TAGAAAAGATGTTTTTTTATGCACATTATTATTG
Found at i:20527 original size:22 final size:22
Alignment explanation
Indices: 20492--20729 Score: 157
Period size: 22 Copynumber: 10.8 Consensus size: 22
20482 AAATAGAAGG
*
20492 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
20513 TTATCGAAATTTCATAGAGATCGGA
1 TTATCAAAATTTCATAGAG-T--GA
*
20538 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGAG-TGA
*
20559 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAG-TGA
* * * *
20581 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGAGTGA
*
20603 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
*
20625 TTATCAAAATTTCATAGAGGGA
1 TTATCAAAATTTCATAGAGTGA
* * * *
20647 TCAAT-AAAATTTTATAGAGAGG
1 T-TATCAAAATTTCATAGAGTGA
* * ** *
20669 TTATCGAAATTTCATAAAAAGG
1 TTATCAAAATTTCATAGAGTGA
* *
20691 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAGA-GTGA
*
20713 TTACCAAAATTTCATAG
1 TTATCAAAATTTCATAG
20730 TGGTATTTTT
Statistics
Matches: 172, Mismatches: 32, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
21 25 0.15
22 121 0.70
23 9 0.05
24 4 0.02
25 13 0.08
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:20966 original size:44 final size:43
Alignment explanation
Indices: 20810--21275 Score: 267
Period size: 44 Copynumber: 10.7 Consensus size: 43
20800 TTACGTAGTA
* * * * *
20810 ATCAAAATTTCAT-GGAGGATAACAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGTAGGTTATCAAAATTTCATAGGGAGGTT
* * *
20852 ATCAAAATTTCATAGTTTA-GTTTTCAAAATATCATA-AGAGGGTT
1 ATCAAAATTTCATAG--TAGGTTATCAAAATTTCATAGGGA-GGTT
* * *
20896 ATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTAGGT-TATCAAAATTTCATAGGGAGGTT
* * ** *
20940 AACAAAATTTCATAATGAGGTTATCAAAAAATCACAGGGAGGTT
1 ATCAAAATTTCATAGT-AGGTTATCAAAATTTCATAGGGAGGTT
* *
20984 ATCAAAA-TT--T-GTA-GTTATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGTAGGTTATCAAAATTTCATAGGGAGGTT
* * * * *
21022 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATATGAAGGTTT
1 ATCAAAATTTCATA-GTAGG-TTATCAAAATTTCATAGGGAGG-TT
* * * * *
21068 ATCAAAATTTCATAGCAAGGTTATCATAATTTCATAGTGTGATT
1 ATCAAAATTTCATAG-TAGGTTATCAAAATTTCATAGGGAGGTT
* * *
21112 ATCAAAATTTCAGAGT-GTGATTA-CTAACAA-TTCATATGAAGGTT
1 ATCAAAATTTCATAGTAG-G-TTATC-AA-AATTTCATAGGGAGGTT
* * * * * * *
21156 TTTAAATTTTCATAACGT-GGTTATCAATATATCATA-TGACCGTT
1 ATCAAAATTTCAT-A-GTAGGTTATCAAAATTTCATAGGGA-GGTT
* * * * *
21200 ATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATA--GTAGGTTATCAAAATTTCATAGGGAGGTT
21245 ATCAAAATTTCATAGTGAGGTCT-TCAAAATT
1 ATCAAAATTTCATAGT-AGGT-TATCAAAATT
21276 CCTTAAGCAT
Statistics
Matches: 321, Mismatches: 72, Indels: 60
0.71 0.16 0.13
Matches are distributed among these distances:
38 27 0.08
39 3 0.01
40 1 0.00
41 2 0.01
42 16 0.05
43 15 0.05
44 158 0.49
45 76 0.24
46 23 0.07
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
ATCAAAATTTCATAGTAGGTTATCAAAATTTCATAGGGAGGTT
Found at i:21050 original size:23 final size:22
Alignment explanation
Indices: 20810--21275 Score: 242
Period size: 22 Copynumber: 21.4 Consensus size: 22
20800 TTACGTAGTA
*
20810 ATCAAAATTTCAT--GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * *
20830 AACAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
20852 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
20874 TTCAAAATATCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
20896 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
20918 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
20940 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
20962 ATCAAAAAATCACAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
20984 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
21000 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
21022 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
21045 ATCAAAATTTTATATGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
**
21068 ATCAAAATTTCATAGCAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
21090 ATCATAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
21112 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
21134 A-CTAACAA-TTCATATGAAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
21156 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
21178 ATCAATATATCATA-TGACCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * **
21200 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
21223 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
21245 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
21268 -TCAAAATT
1 ATCAAAATT
21276 CCTTAAGCAT
Statistics
Matches: 337, Mismatches: 87, Indels: 42
0.72 0.19 0.09
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 1 0.00
20 13 0.04
21 8 0.02
22 240 0.71
23 62 0.18
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:22007 original size:22 final size:22
Alignment explanation
Indices: 21976--22029 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
21966 AAGGTTCTCG
* * * *
21976 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
21998 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
22020 AAATTTCATA
1 AAATTTCATA
22030 AGGAGGTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:22046 original size:23 final size:22
Alignment explanation
Indices: 21991--22044 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
21981 CCATAGTATC
*
21991 GTTATTAAAATTTCATAGGAAG
1 GTTATAAAAATTTCATAGGAAG
*
22013 GTTATCAAAATTTCATAAGG-AG
1 GTTATAAAAATTTCAT-AGGAAG
22035 GTTATAAAAA
1 GTTATAAAAA
22045 ATAGTGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (22 bp):
GTTATAAAAATTTCATAGGAAG
Found at i:28119 original size:35 final size:35
Alignment explanation
Indices: 28039--28177 Score: 208
Period size: 35 Copynumber: 3.9 Consensus size: 35
28029 GGTAAGGATA
* *
28039 AGCACAGACTTAAGTTCAC-AGAAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAG-AATTAAGT-AAATT
* *
28075 AGTAAAGACTTAATTTCACAAGAATTAAATAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAATT
*
28110 AGCACAGACTTAATTTCACAAGAATTAAGTAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAATT
28145 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
28178 ATCAGCAATG
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
35 69 0.73
36 23 0.24
37 2 0.02
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (35 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAATT
Found at i:28256 original size:11 final size:11
Alignment explanation
Indices: 28240--28476 Score: 366
Period size: 11 Copynumber: 21.0 Consensus size: 11
28230 AAATTAGGCA
28240 AAAGAAGACTG
1 AAAGAAGACTG
28251 AAAGAAGACTG
1 AAAGAAGACTG
*
28262 AAAAAAGACTG
1 AAAGAAGACTG
28273 AAAGAAAGACTG
1 AAAG-AAGACTG
28285 AAAGAAGACTG
1 AAAGAAGACTG
*
28296 AAAAAAGACTG
1 AAAGAAGACTG
28307 AAAGAAAGACTG
1 AAAG-AAGACTG
*
28319 AAAGAAGATTG
1 AAAGAAGACTG
28330 AAAGAAGACTG
1 AAAGAAGACTG
28341 AAAGAAGACTG
1 AAAGAAGACTG
*
28352 AAAAAAGACTG
1 AAAGAAGACTG
28363 AAAGAAAGACTG
1 AAAG-AAGACTG
28375 AAAGAAGACTG
1 AAAGAAGACTG
28386 AAAGAAGACTG
1 AAAGAAGACTG
*
28397 AAAAAAGACTG
1 AAAGAAGACTG
28408 AAAGAAAGACTG
1 AAAG-AAGACTG
28420 AAAGAAGACTG
1 AAAGAAGACTG
28431 AAAGAAGACTAG
1 AAAGAAGACT-G
*
28443 AAAAAAGACTG
1 AAAGAAGACTG
28454 AAAGAAAGACTG
1 AAAG-AAGACTG
28466 AAAGAAGACTG
1 AAAGAAGACTG
28477 GCTTAGTTTC
Statistics
Matches: 208, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
11 143 0.69
12 65 0.31
ACGTcount: A:0.58, C:0.08, G:0.24, T:0.09
Consensus pattern (11 bp):
AAAGAAGACTG
Found at i:28283 original size:34 final size:34
Alignment explanation
Indices: 28240--28476 Score: 374
Period size: 34 Copynumber: 7.0 Consensus size: 34
28230 AAATTAGGCA
28240 AAAG-AAGACTGAAAGAAGACTGAAAAAAGACTG
1 AAAGAAAGACTGAAAGAAGACTGAAAAAAGACTG
28273 AAAGAAAGACTGAAAGAAGACTGAAAAAAGACTG
1 AAAGAAAGACTGAAAGAAGACTGAAAAAAGACTG
* *
28307 AAAGAAAGACTGAAAGAAGATTGAAAGAAGACTG
1 AAAGAAAGACTGAAAGAAGACTGAAAAAAGACTG
*
28341 AAAG-AAGACTGAAAAAAGACTGAAAGAAAGACTG
1 AAAGAAAGACTGAAAGAAGACTGAAA-AAAGACTG
28375 AAAG-AAGACTGAAAGAAGACTGAAAAAAGACTG
1 AAAGAAAGACTGAAAGAAGACTGAAAAAAGACTG
*
28408 AAAGAAAGACTGAAAGAAGACTGAAAGAAGACTAG
1 AAAGAAAGACTGAAAGAAGACTGAAAAAAGACT-G
*
28443 AAA-AAAGACTGAAAGAAAGACTGAAAGAAGACTG
1 AAAGAAAGACTGAAAG-AAGACTGAAAAAAGACTG
28477 GCTTAGTTTC
Statistics
Matches: 192, Mismatches: 7, Indels: 9
0.92 0.03 0.04
Matches are distributed among these distances:
33 35 0.18
34 136 0.71
35 21 0.11
ACGTcount: A:0.58, C:0.08, G:0.24, T:0.09
Consensus pattern (34 bp):
AAAGAAAGACTGAAAGAAGACTGAAAAAAGACTG
Found at i:28304 original size:45 final size:45
Alignment explanation
Indices: 28240--28476 Score: 431
Period size: 45 Copynumber: 5.2 Consensus size: 45
28230 AAATTAGGCA
28240 AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
1 AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
* *
28285 AAAGAAGACTGAAAAAAGACTGAAAGAAAGACTGAAAG-AAGATTG
1 AAAGAAGACTGAAAGAAGACTGAAA-AAAGACTGAAAGAAAGACTG
28330 AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
1 AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
28375 AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
1 AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
28420 AAAGAAGACTGAAAGAAGACTAGAAAAAAGACTGAAAGAAAGACTG
1 AAAGAAGACTGAAAGAAGACT-GAAAAAAGACTGAAAGAAAGACTG
28466 AAAGAAGACTG
1 AAAGAAGACTG
28477 GCTTAGTTTC
Statistics
Matches: 185, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
44 12 0.06
45 126 0.68
46 47 0.25
ACGTcount: A:0.58, C:0.08, G:0.24, T:0.09
Consensus pattern (45 bp):
AAAGAAGACTGAAAGAAGACTGAAAAAAGACTGAAAGAAAGACTG
Found at i:28511 original size:36 final size:36
Alignment explanation
Indices: 28470--28841 Score: 473
Period size: 36 Copynumber: 10.4 Consensus size: 36
28460 AGACTGAAAG
* *
28470 AAGACTGGCTTAGTTTCAATGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* *
28506 AAGACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
*
28542 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* *
28578 AAGACTGGCTTAATCTCAAGGAAATTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* * *
28613 TAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* * * *
28649 AATACTGGCTCAATTTCAAGGAAATTAAGT-AA-AA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* * * *
28683 AGGACTAGCTTAGTTTCAAGGAAACTAGGTAAGGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
*
28719 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* * *
28755 AAGACTGGTTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* *
28791 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* * *
28826 GACACAGGCTTAATTT
1 AAGACTGGCTTAATTT
28842 TAGGAAAGGA
Statistics
Matches: 300, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
34 25 0.08
35 49 0.16
36 226 0.75
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
Found at i:28702 original size:177 final size:177
Alignment explanation
Indices: 28504--28823 Score: 588
Period size: 177 Copynumber: 1.8 Consensus size: 177
28494 CTAGGTAAAG
28504 AAAAGACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
1 AAAAGACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
*
28569 GGTAAAGAAAAGACTGGCTTAATCTCAAGGAAATTAGGTAAA-GATAGACTGGCTTAATTTCAAG
66 GGTAAAGAAAAGACTGGCTTAATCTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAAG
28633 GAAATTAAGTAAAGAAAATACTGGCTCAATTTCAAGGAAATTAAGTA
131 GAAATTAAGTAAAGAAAATACTGGCTCAATTTCAAGGAAATTAAGTA
*
28680 AAAAGGACTAGCTTAGTTTCAAGGAAACTAGGTAAGGAAAAGACTGGCTTAGTTTCAAGGAAACT
1 AAAA-GACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACT
* *
28745 AGGTAAAGAAAAGACTGGTTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAA
65 AGGTAAAGAAAAGACTGGCTTAATCTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAA
28810 GGAAATTAAGTAAA
130 GGAAATTAAGTAAA
28824 AAGACACAGG
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
176 4 0.03
177 100 0.72
178 34 0.25
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (177 bp):
AAAAGACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
GGTAAAGAAAAGACTGGCTTAATCTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAAG
GAAATTAAGTAAAGAAAATACTGGCTCAATTTCAAGGAAATTAAGTA
Found at i:28890 original size:213 final size:213
Alignment explanation
Indices: 28472--28891 Score: 583
Period size: 213 Copynumber: 2.0 Consensus size: 213
28462 ACTGAAAGAA
* *
28472 GACTGGCTTAGTTTCAATGAAACTAGGTAAAGAAAAGACTAGCTTAGTTTCAAGGAAACTAGGTA
1 GACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTAGCTTAGTTTCAAGGAAACTAGGTA
*
28537 AAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATCTCAAGGAAA
66 AAGAAAAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATCTCAAGGAAA
* * * * * ** * ** *
28602 TTAGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAATACTGGCTCAATTTCA
131 TTAAGTAAAAAGACACAGGCTTAATTTCAAGGAAAGGAAATAAAGAAAATAAAGACTCAATTTCA
28667 AGGAAATTAAGTAAAAAG
196 AGGAAATTAAGTAAAAAG
* *
28685 GACTAGCTTAGTTTCAAGGAAACTAGGTAAGGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTA
1 GACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTAGCTTAGTTTCAAGGAAACTAGGTA
* * * *
28750 AAGAAAAGACTGGTTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCTTAATTTCAAGGAAA
66 AAGAAAAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATCTCAAGGAAA
* * *
28815 TTAAGTAAAAAGACACAGGCTTAATTT-TAGGAAAGGAAATTAAGTAAAATAAAGAACTTAA-TT
131 TTAAGTAAAAAGACACAGGCTTAATTTCAAGGAAAGGAAATAAAG-AAAATAAAG-ACTCAATTT
* *
28878 CAGGGTAATTAAGT
194 CAAGGAAATTAAGT
28892 GGAGTCAATA
Statistics
Matches: 180, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
212 12 0.07
213 164 0.91
214 4 0.02
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (213 bp):
GACTAGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTAGCTTAGTTTCAAGGAAACTAGGTA
AAGAAAAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATCTCAAGGAAA
TTAAGTAAAAAGACACAGGCTTAATTTCAAGGAAAGGAAATAAAGAAAATAAAGACTCAATTTCA
AGGAAATTAAGTAAAAAG
Found at i:28911 original size:36 final size:35
Alignment explanation
Indices: 28862--28980 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 35
28852 AATTAAGTAA
*
28862 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTC
1 AATAAAGAGCTTAATTCAGGGTAATTAAGT-GAGTC
28898 AATAAA-AGGCTTAATTCAGGGTAATTAAGT-AG--
1 AATAAAGA-GCTTAATTCAGGGTAATTAAGTGAGTC
* *
28930 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAGCTTAATTCAGGGTAATTAAGTG-AGTC
28966 AATAAAGAGCTTAAT
1 AATAAAGAGCTTAAT
28981 CTAGAAAAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
32 26 0.36
33 1 0.01
34 4 0.05
35 1 0.01
36 41 0.56
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (35 bp):
AATAAAGAGCTTAATTCAGGGTAATTAAGTGAGTC
Found at i:28934 original size:68 final size:68
Alignment explanation
Indices: 28852--28980 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
28842 TAGGAAAGGA
* *
28852 AATTAAGTAAAATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA-AGGCTTAATTCA
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGA-GCTTAATTCA
28916 GGGT
65 GGGT
*
28920 AATTAAGTAGAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
28981 CTAGAAAAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 56 0.98
69 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAATTCAG
GGT
Found at i:28943 original size:32 final size:32
Alignment explanation
Indices: 28852--28959 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 32
28842 TAGGAAAGGA
*
28852 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
*
28884 AATTAAGTGGAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT--AG--AATAAAGA-ACTTAATTCAGGGT
*
28920 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
28952 AATTAAGT
1 AATTAAGT
28960 GAAGTCAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
32 34 0.52
33 1 0.02
34 3 0.05
35 1 0.02
36 27 0.41
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (32 bp):
AATTAAGTAGAATAAAGAACTTAATTCAGGGT
Found at i:32562 original size:28 final size:27
Alignment explanation
Indices: 32517--32577 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
32507 TAAAGAAAAC
32517 AATTAAACTAAAAATAAAAAC-AAAGCA
1 AATTAAACTAAAAAT-AAAACTAAAGCA
** *
32544 AATTAAATCTAAATCTAAATCTAAAGCA
1 AATTAAA-CTAAAAATAAAACTAAAGCA
32572 AATTAA
1 AATTAA
32578 TAAAGCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.23
Consensus pattern (27 bp):
AATTAAACTAAAAATAAAACTAAAGCA
Found at i:34130 original size:21 final size:21
Alignment explanation
Indices: 34091--34129 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34081 TAACAAAATA
34091 GGTAAAAACATATATAAAAGT
1 GGTAAAAACATATATAAAAGT
*
34112 GGTAAAAA-GTATATAAAA
1 GGTAAAAACATATATAAAA
34130 ATAGCTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.15, T:0.23
Consensus pattern (21 bp):
GGTAAAAACATATATAAAAGT
Done.