Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016937.1 Corchorus olitorius cultivar O-4 contig16970, 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: 96519
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:709 original size:73 final size:73
Alignment explanation
Indices: 590--731 Score: 275
Period size: 73 Copynumber: 1.9 Consensus size: 73
580 TGTATAGATA
*
590 CTAATAATTTCCACTAGACCAATTTTGTGGATGAAATTTGGACCTTATAACTACTATTTTTGGTA
1 CTAATAATTTCCACTAGACCAATTTTGTAGATGAAATTTGGACCTTATAACTACTATTTTTGGTA
655 CATATACT
66 CATATACT
663 CTAATAATTTCCACTAGACCAATTTTGTAGATGAAATTTGGACCTTATAACTACTATTTTTGGTA
1 CTAATAATTTCCACTAGACCAATTTTGTAGATGAAATTTGGACCTTATAACTACTATTTTTGGTA
728 CATA
66 CATA
732 CATTTTTTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (73 bp):
CTAATAATTTCCACTAGACCAATTTTGTAGATGAAATTTGGACCTTATAACTACTATTTTTGGTA
CATATACT
Found at i:20940 original size:16 final size:17
Alignment explanation
Indices: 20914--20945 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20904 AGTGCAAATT
20914 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
20931 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
20946 ACGCAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:21238 original size:19 final size:18
Alignment explanation
Indices: 21183--21238 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
21173 CAATCAAGAA
21183 AATTAAAGAAAACAAT--T
1 AATT-AAGAAAACAATGAT
*
21200 AA-TAAGAAAACAGTGAAT
1 AATTAAGAAAACAATG-AT
21218 AATTAAGAAAACAATTGAT
1 AATTAAGAAAACAA-TGAT
21237 AA
1 AA
21239 AAACCTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.31
16 1 0.03
17 2 0.06
18 3 0.09
19 14 0.44
20 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.21
Consensus pattern (18 bp):
AATTAAGAAAACAATGAT
Found at i:23196 original size:42 final size:43
Alignment explanation
Indices: 23145--23238 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
23135 AGTCCATCAC
* * *
23145 CTAA-ATTCTA-CTCTATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCCAGATAATTCATCAAAATAAAG
*
23186 CTAATATTCTAGTCCTCCATCTCCAGATAATTCATCAAAATCAAG
1 CTAATATTCTA--CCTCCATCTCCAGATAATTCATCAAAATAAAG
23231 CTAATATT
1 CTAATATT
23239 AATTGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCCAGATAATTCATCAAAATAAAG
Found at i:32214 original size:22 final size:22
Alignment explanation
Indices: 32186--32232 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
32176 ATAATAAATA
* *
32186 CTTTTCAAGTTGTTTCCTTTCT
1 CTTTTCAACTTATTTCCTTTCT
* *
32208 CTTTTCATCTTATTTTCTTTCT
1 CTTTTCAACTTATTTCCTTTCT
32230 CTT
1 CTT
32233 CTAAACCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.04, T:0.64
Consensus pattern (22 bp):
CTTTTCAACTTATTTCCTTTCT
Found at i:34977 original size:36 final size:36
Alignment explanation
Indices: 34930--34999 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
34920 TTCAATAACC
* *
34930 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
34966 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
35000 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:35881 original size:206 final size:203
Alignment explanation
Indices: 35510--35925 Score: 667
Period size: 206 Copynumber: 2.0 Consensus size: 203
35500 GCTTAATAAC
* *
35510 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAATAAAGTTGTAGTAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
* * *
35575 ATACAACACATTATTATTATATATAAAACTATACCAAAAAAAATTAAGTTGGACATTAGTGGTTG
66 ATACAACACATTACTATTATATATAAAACTATAACAAAAAAAATTAAGTTGAACATTAGTGGTTG
*
35640 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-A-AAAGATATTAAAGA
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAAATATT-AAGA
35703 TCCGATTTA
195 TCCGATTTA
*
35712 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAATATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGT-AATAA
*
35777 GATACAACACATTACTATTATATATATAGAACTATGCAATAAAAAAAATT-AGTTGAACATTAGT
65 GATACAACACATTACTATTATATATA-A-AACTAT--AACAAAAAAAATTAAGTTGAACATTAGT
35841 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAATTAAAAATA
126 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-AA-TAAAAATA
35906 TTAAGATCCGATTTA
189 TTAAGATCCGATTTA
35921 TTTAT
1 TTTAT
35926 TATTGAGGAA
Statistics
Matches: 197, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
202 56 0.28
203 30 0.15
204 1 0.01
205 6 0.03
206 66 0.34
207 11 0.06
208 1 0.01
209 18 0.09
210 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
ATACAACACATTACTATTATATATAAAACTATAACAAAAAAAATTAAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAAATATTAAGAT
CCGATTTA
Found at i:40314 original size:16 final size:15
Alignment explanation
Indices: 40285--40339 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
40275 TTCAAATGTC
*
40285 GGGTCATTTAGGTTT
1 GGGTCATTTTGGTTT
*
40300 GGGTCAATTTTGGTTC
1 GGGTC-ATTTTGGTTT
*
40316 GGGTCCTTTTCGGTTT
1 GGGTCATTTT-GGTTT
40332 CGGGTCAT
1 -GGGTCAT
40340 ATGGTTCTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 9 0.28
16 17 0.53
17 6 0.19
ACGTcount: A:0.09, C:0.15, G:0.33, T:0.44
Consensus pattern (15 bp):
GGGTCATTTTGGTTT
Found at i:40689 original size:5 final size:5
Alignment explanation
Indices: 40670--40728 Score: 55
Period size: 5 Copynumber: 11.8 Consensus size: 5
40660 GGACCAGTAA
* * * * * *
40670 GGGAC GGGAT AGGAC GGGAC GGGAT AGGAC GGGAC GGGAT AGGAC GGGAC
1 GGGAC GGGAC GGGAC GGGAC GGGAC GGGAC GGGAC GGGAC GGGAC GGGAC
*
40720 GGGAT GGGA
1 GGGAC GGGA
40729 GGTCCTTTTA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.25, C:0.12, G:0.56, T:0.07
Consensus pattern (5 bp):
GGGAC
Found at i:40690 original size:15 final size:15
Alignment explanation
Indices: 40670--40724 Score: 110
Period size: 15 Copynumber: 3.7 Consensus size: 15
40660 GGACCAGTAA
40670 GGGACGGGATAGGAC
1 GGGACGGGATAGGAC
40685 GGGACGGGATAGGAC
1 GGGACGGGATAGGAC
40700 GGGACGGGATAGGAC
1 GGGACGGGATAGGAC
40715 GGGACGGGAT
1 GGGACGGGAT
40725 GGGAGGTCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.25, C:0.13, G:0.55, T:0.07
Consensus pattern (15 bp):
GGGACGGGATAGGAC
Found at i:41580 original size:14 final size:13
Alignment explanation
Indices: 41561--41597 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
41551 AAAATACCCT
41561 AAAAAAGAAAAGAA
1 AAAAAAGAAAA-AA
41575 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
41588 AAAAAAGAAA
1 AAAAAAGAAA
41598 TCACAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:44737 original size:14 final size:14
Alignment explanation
Indices: 44718--44749 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
44708 TATAGGTACA
44718 ATATTTTAGTATAT
1 ATATTTTAGTATAT
44732 ATATTTTAGTATAT
1 ATATTTTAGTATAT
44746 ATAT
1 ATAT
44750 CACACAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
ATATTTTAGTATAT
Found at i:46518 original size:30 final size:29
Alignment explanation
Indices: 46474--46530 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
46464 GCTCGAGGCT
*
46474 TTGGGTCACGGGTCAAT-CGGTTTAATCA
1 TTGGGTCACGGGTCAATACGGGTTAATCA
46502 TTGGGTCAATCGGGTCAATACGGGTTAAT
1 TTGGGTC-A-CGGGTCAATACGGGTTAAT
46531 AAATATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 1 0.04
30 9 0.36
31 8 0.32
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (29 bp):
TTGGGTCACGGGTCAATACGGGTTAATCA
Found at i:56779 original size:92 final size:93
Alignment explanation
Indices: 56683--56854 Score: 276
Period size: 92 Copynumber: 1.9 Consensus size: 93
56673 AATTAATAAT
* * * *
56683 ATGGTAAAAATAAAATAGGTATAAGGATATTTGATTTAATTAAAT-AAAATAGAGTTTTTGGTTG
1 ATGGTAAAAATAAAATAGGTAAAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTG
56747 AGC-AAAACTATAAAAGTAAAATAGTAAA
66 A-CTAAAACTATAAAAGTAAAATAGTAAA
*
56775 ATGGTAAAAATAAAATAGTTAAAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTG
1 ATGGTAAAAATAAAATAGGTAAAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTG
56840 ACTAAAACTATAAAA
66 ACTAAAACTATAAAA
56855 ATTTAAACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 43 0.59
93 30 0.41
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.31
Consensus pattern (93 bp):
ATGGTAAAAATAAAATAGGTAAAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTG
ACTAAAACTATAAAAGTAAAATAGTAAA
Found at i:58216 original size:288 final size:289
Alignment explanation
Indices: 57700--58268 Score: 1034
Period size: 288 Copynumber: 2.0 Consensus size: 289
57690 TTTTAAATTA
*
57700 AAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAGAATAGAGTTTTTAGTA
1 AAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAGAATAGAGCTTTTAGTA
57765 GAAAAAAACTGTATATTAAAAAAATTTAATATATCCAAATTTTTATTGAAAAATAGTAAAATGAT
66 GAAAAAAACTGTATATTAAAAAAATTTAATATATCCAAATTTTTATTGAAAAATAGTAAAATGAT
*
57830 AAAAAATAAAGTAATTATAAAGATGTTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATA
131 AAAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATA
*
57895 AAACTATAATAATTAAGCAATGGCATTTAAGAAATATATTTGAAAAATAAGGGTAT-AATGGTCG
196 AAACTATAATAATTAAGCAATGACATTTAAGAAATATATTTGAAAAATAAGGGTATAAATGGTCG
*
57959 ATTCAAAATTTTTACAAAACTTGTACTTT
261 ATTCAAAAGTTTTACAAAACTTGTACTTT
57988 AAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAGAATAGAGCTTTTAGTA
1 AAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAGAATAGAGCTTTTAGTA
* *
58053 GAATAAAACTGTATATTAAAAAAAGTTTAATATATCCAAATTTTTATTGTAAAATAGTAAAATGA
66 GAAAAAAACTGTATATTAAAAAAA-TTTAATATATCCAAATTTTTATTGAAAAATAGTAAAATGA
*
58118 T-AAACATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAGAAT
130 TAAAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAGAAT
* *
58182 AAAACTATAATATTTAAGCAATGATATTTAAGAAATATATTTGAAAAATAAGGGTATAAATGGTC
195 AAAACTATAATAATTAAGCAATGACATTTAAGAAATATATTTGAAAAATAAGGGTATAAATGGTC
58247 GATTCAAAAGTTTTACAAAACT
260 GATTCAAAAGTTTTACAAAACT
58269 CATATTTTTT
Statistics
Matches: 270, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
288 202 0.75
289 68 0.25
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (289 bp):
AAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAGAATAGAGCTTTTAGTA
GAAAAAAACTGTATATTAAAAAAATTTAATATATCCAAATTTTTATTGAAAAATAGTAAAATGAT
AAAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATA
AAACTATAATAATTAAGCAATGACATTTAAGAAATATATTTGAAAAATAAGGGTATAAATGGTCG
ATTCAAAAGTTTTACAAAACTTGTACTTT
Found at i:58223 original size:13 final size:14
Alignment explanation
Indices: 58191--58223 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58181 TAAAACTATA
*
58191 ATATTTAAGCAATG
1 ATATTTAAGAAATG
58205 ATATTTAAGAAAT-
1 ATATTTAAGAAATG
58218 ATATTT
1 ATATTT
58224 GAAAAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (14 bp):
ATATTTAAGAAATG
Found at i:58466 original size:2 final size:2
Alignment explanation
Indices: 58459--58485 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58449 GTGAATACTG
58459 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 A
58486 ATGAATCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59898 original size:19 final size:20
Alignment explanation
Indices: 59876--59913 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
59866 CTGTTTTTTT
59876 TTTTAATTT-AATATTTTAG
1 TTTTAATTTCAATATTTTAG
*
59895 TTTTAATTTCAATTTTTTA
1 TTTTAATTTCAATATTTTA
59914 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTAATTTCAATATTTTAG
Found at i:60182 original size:66 final size:67
Alignment explanation
Indices: 60076--60284 Score: 221
Period size: 66 Copynumber: 3.1 Consensus size: 67
60066 TCTTGTCTCT
* * * * * * *
60076 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATAAGG-AGGTTATCGGAATTCCA
1 GTGTGGTTAACCAAATTTCATAGGATAGTTATTAAAATTTCATAAGGAAGGTTATCGAAATTTCA
60140 TA
66 TA
* * * *
60142 GTGTGGTTAACCAAATTTCATATGGA-AGTTATCAAAATTTCAT-GGGAAGGTTATCAAAATTTG
1 GTGTGGTTAACCAAATTTCATA-GGATAGTTATTAAAATTTCATAAGGAAGGTTATCGAAATTTC
*
60205 AAA
65 ATA
* *
60208 GTGTGGTT-ACCAAAATTTCATAGGATCAGGTTATTAAAATTT-TTAAGGAAGGTTATTGAAATT
1 GTGTGGTTAACC-AAATTTCATAGGAT-A-GTTATTAAAATTTCATAAGGAAGGTTATCGAAATT
60271 TCATA
63 TCATA
60276 GTGTGGTTA
1 GTGTGGTTA
60285 TCACAATTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
65 8 0.07
66 66 0.57
67 4 0.03
68 38 0.33
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (67 bp):
GTGTGGTTAACCAAATTTCATAGGATAGTTATTAAAATTTCATAAGGAAGGTTATCGAAATTTCA
TA
Found at i:60189 original size:21 final size:23
Alignment explanation
Indices: 60080--60311 Score: 124
Period size: 22 Copynumber: 10.4 Consensus size: 23
60070 GTCTCTGTGT
* *
60080 GGTTATCAAAATTTCATA-AGAT
1 GGTTATCAAAATTTCATAGGGAA
* * *
60102 GGTTATTATAATTTCATAAGG-A
1 GGTTATCAAAATTTCATAGGGAA
** * * *
60124 GGTTATCGGAATTCCATAGTG-T
1 GGTTATCAAAATTTCATAGGGAA
* * *
60146 GGTTAACCAAATTTCATATGGAA
1 GGTTATCAAAATTTCATAGGGAA
60169 -GTTATCAAAATTTCAT-GGGAA
1 GGTTATCAAAATTTCATAGGGAA
* * * *
60190 GGTTATCAAAATTTGAAAGTG-T
1 GGTTATCAAAATTTCATAGGGAA
*
60212 GGTTACCAAAATTTCATA-GGATCA
1 GGTTATCAAAATTTCATAGGGA--A
* * *
60236 GGTTATTAAAATTT-TTAAGGAA
1 GGTTATCAAAATTTCATAGGGAA
** * *
60258 GGTTATTGAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATAGGGAA
* * *
60280 GGTTATCACAATTTTATA-GAAA
1 GGTTATCAAAATTTCATAGGGAA
60302 GGTTATCAAA
1 GGTTATCAAA
60312 GAGATTATCA
Statistics
Matches: 154, Mismatches: 46, Indels: 20
0.70 0.21 0.09
Matches are distributed among these distances:
21 5 0.03
22 126 0.82
23 8 0.05
24 15 0.10
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (23 bp):
GGTTATCAAAATTTCATAGGGAA
Found at i:60361 original size:22 final size:21
Alignment explanation
Indices: 60336--60477 Score: 108
Period size: 22 Copynumber: 6.5 Consensus size: 21
60326 ATCTTAACGA
60336 GGTTATAAGAATTTCATAGTGT
1 GGTTATAA-AATTTCATAGTGT
* *
60358 GGTTAACAAAATTTCATAAG-GA
1 GGTT-ATAAAATTTCAT-AGTGT
* * * * *
60380 GATTTCTAATATTTCATAGGGA
1 G-GTTATAAAATTTCATAGTGT
60402 GGTTATCAAAATTTCATAGTGT
1 GGTTAT-AAAATTTCATAGTGT
**
60424 GGTTATTAAAATTTTTTAGTGT
1 GGTTA-TAAAATTTCATAGTGT
*
60446 GGTTATCAAAATTTCATA-TGAA
1 GGTTAT-AAAATTTCATAGTG-T
60468 GGTTATAAAA
1 GGTTATAAAA
60478 GTCTCAATTT
Statistics
Matches: 96, Mismatches: 16, Indels: 17
0.74 0.12 0.13
Matches are distributed among these distances:
21 12 0.12
22 76 0.79
23 8 0.08
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGTGT
Found at i:60460 original size:66 final size:65
Alignment explanation
Indices: 60312--60477 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 65
60302 GGTTATCAAA
* * *
60312 GAGATTATCAAAATATCTTAACGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
1 GAGATTATCAAAATTTCATAAGGAGGTTATAA-AATTTCATAGTGTGGTTAACAAAATTTCATAA
60377 G
65 G
* * ** * *
60378 GAGATT-TCTAATATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATTAAAATTT-TTT
1 GAGATTATC-AAAATTTCATAAGGAGGTTAT-AAAATTTCATAGTGTGGTTAACAAAATTTCATA
60441 AG
64 AG
* * * *
60443 TGTGGTTATCAAAATTTCATATGAAGGTTATAAAA
1 -GAGATTATCAAAATTTCATAAGGAGGTTATAAAA
60478 GTCTCAATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
65 9 0.11
66 69 0.84
67 4 0.05
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (65 bp):
GAGATTATCAAAATTTCATAAGGAGGTTATAAAATTTCATAGTGTGGTTAACAAAATTTCATAAG
Found at i:60472 original size:44 final size:42
Alignment explanation
Indices: 60316--60477 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 42
60306 ATCAAAGAGA
* * *
60316 TTATCAAAATATCTTAACGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCAT-ATGAGGTTATAA-AATTTCATAGTGTGG
* * * * * * *
60360 TTAACAAAATTTCATAAGGAGATTTCTAATATTTCATAGGGAGG
1 TTATCAAAATTTCAT-ATGAG-GTTATAAAATTTCATAGTGTGG
* **
60404 TTATCAAAATTTCATAGTGTGGTTATTAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATA-TGAGGTTA-TAAAATTTCATAGTGTGG
60448 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATATG-AGGTTATAAAA
60478 GTCTCAATTT
Statistics
Matches: 94, Mismatches: 20, Indels: 9
0.76 0.16 0.07
Matches are distributed among these distances:
43 10 0.11
44 79 0.84
45 5 0.05
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (42 bp):
TTATCAAAATTTCATATGAGGTTATAAAATTTCATAGTGTGG
Found at i:60609 original size:22 final size:22
Alignment explanation
Indices: 60584--60710 Score: 98
Period size: 22 Copynumber: 5.8 Consensus size: 22
60574 TCATAGTATT
*
60584 GTTATCAAAATTTCAAAGCGAG
1 GTTATCAAAATTTCAAAGAGAG
*
60606 GTTATCAAAATTACATAATGA-A-
1 GTTATCAAAATTTCA-AA-GAGAG
** * *
60628 AATATCAAAATTTCATAGAGGG
1 GTTATCAAAATTTCAAAGAGAG
* * * * *
60650 GTCAACACAATTTTATAGAGAG
1 GTTATCAAAATTTCAAAGAGAG
60672 GTTATCAAAATTTCATAA-AGAG
1 GTTATCAAAATTTCA-AAGAGAG
*
60694 GTTATCAAATTTTCAAA
1 GTTATCAAAATTTCAAA
60711 ATGTGATTAC
Statistics
Matches: 80, Mismatches: 20, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.03
21 3 0.04
22 70 0.88
23 4 0.05
24 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (22 bp):
GTTATCAAAATTTCAAAGAGAG
Found at i:60839 original size:22 final size:22
Alignment explanation
Indices: 60814--61285 Score: 117
Period size: 22 Copynumber: 21.0 Consensus size: 22
60804 TTATGGAGTA
60814 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
60836 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
60858 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
60880 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
60902 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
60924 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
60946 ATCAGGGAGGTTATCAAAATTTGTA-GTT
1 ATCA---AAATT-TC---ATATGAAGGTT
* * *
60974 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
60996 ATCAAAATTTTATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
61018 -TAAATTAATTTTATAGGAAGGTTT
1 ATCAA--AATTTCATATGAAGG-TT
* *
61042 ATCCAAATTTCATA-GCAATGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
61064 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
61086 ATCAAAATTTAAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* *
61108 A-CTAACAA-TTCATGTGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
61130 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * * *
61152 ATCAATATATCGTATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
61174 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
61197 ATGAAAATTTTATTCTGAA-GTT
1 ATCAAAATTTCA-TATGAAGGTT
61219 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
61242 -TCAAAATTCCTTAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
61263 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
61285 A
1 A
61286 AAAAAAATTT
Statistics
Matches: 330, Mismatches: 85, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
21 20 0.06
22 229 0.69
23 52 0.16
24 6 0.02
25 9 0.03
26 2 0.01
28 9 0.03
29 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:60863 original size:44 final size:44
Alignment explanation
Indices: 60814--60937 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
60804 TTATGGAGTA
*
60814 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
* *
60856 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
* * * *
60902 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATA
60938 ATGAGGTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 65 0.94
45 1 0.01
46 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
Found at i:61050 original size:23 final size:23
Alignment explanation
Indices: 60972--61078 Score: 71
Period size: 23 Copynumber: 4.7 Consensus size: 23
60962 AAATTTGTAG
* *
60972 TTATCAAGATTTCATAAGG-AGG-
1 TTATCAAAATTTTAT-AGGAAGGT
*
60994 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
61017 TTA--AATTAATTTTATAGGAAGGT
1 TTATCAA--AATTTTATAGGAAGGT
* * * *
61040 TTATCCAAATTTCATAGCAATG-
1 TTATCAAAATTTTATAGGAAGGT
* *
61062 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
61079 TGTGATTATC
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
21 5 0.07
22 31 0.44
23 33 0.47
25 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:61286 original size:22 final size:23
Alignment explanation
Indices: 61243--61303 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
61233 TTGAGGTCTT
* * *
61243 CAAAATTCCTTAAGGAGGTT-AA
1 CAAAATTTCATAAGAAGGTTAAA
61265 CAAAATTTCATAAGAAGGTTAAA
1 CAAAATTTCATAAGAAGGTTAAA
*
61288 AAAAATTT-AT-AGAAGG
1 CAAAATTTCATAAGAAGG
61304 GTTCTCGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.18
22 19 0.56
23 9 0.26
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.26
Consensus pattern (23 bp):
CAAAATTTCATAAGAAGGTTAAA
Found at i:61467 original size:2 final size:2
Alignment explanation
Indices: 61460--61485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61450 TTAAAACTAG
61460 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
61486 ATTCATGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78065 original size:6 final size:6
Alignment explanation
Indices: 78054--78099 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
78044 TCTTTAATAC
*
78054 TCCTAT TCCTA- T-ATAT TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT
1 TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT
78100 GTATACATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
6 32 0.89
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCTAT
Found at i:80436 original size:105 final size:102
Alignment explanation
Indices: 80326--80529 Score: 320
Period size: 105 Copynumber: 2.0 Consensus size: 102
80316 TTGCTTAAAT
* *
80326 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATAAGTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTAT-A--A
80391 CTATTTTATTTTTACCATTTTACT-ATTTTAATTAAAATAA
63 CTATTTTATTTTTACCATTTTACTAATTTT-ATTAAAATAA
* *
80431 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAACTA
*
80496 TTTTATTTTTATCATTTTACTAATTTTATTAAAA
66 TTTTATTTTTACCATTTTACTAATTTTATTAAAA
80530 AACTTAGATA
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
102 30 0.32
103 5 0.05
104 1 0.01
105 57 0.61
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.51
Consensus pattern (102 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAACTA
TTTTATTTTTACCATTTTACTAATTTTATTAAAATAA
Found at i:80508 original size:23 final size:23
Alignment explanation
Indices: 80482--80525 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
80472 TTAAATCTAA
80482 TATCATTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
80505 TATCATTTTACTAATTTTATT
1 TATCATTATACTAATTTTATT
80526 AAAAAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Found at i:82201 original size:42 final size:41
Alignment explanation
Indices: 82148--82231 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 41
82138 TTACCTAAAC
*
82148 TCTACTACATCTCTAGGTAATTCATCAAAATAAAACTAATAT
1 TCTACTACATCTCTAGATAATTCATCAAAAT-AAACTAATAT
*
82190 TCTACTCCATCTCTAGATAATTCATCAAAATAAACTAATAT
1 TCTACTACATCTCTAGATAATTCATCAAAATAAACTAATAT
82231 T
1 T
82232 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 11 0.28
42 29 0.73
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.35
Consensus pattern (41 bp):
TCTACTACATCTCTAGATAATTCATCAAAATAAACTAATAT
Found at i:86920 original size:16 final size:17
Alignment explanation
Indices: 86899--86937 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
86889 ATGTTTAAGC
*
86899 TTACTTCCATTT-TTTT
1 TTACTTCCATTTCTTAT
*
86915 TTACTTGCATTTCTTAT
1 TTACTTCCATTTCTTAT
86932 TTACTT
1 TTACTT
86938 ATCGCTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.64
Consensus pattern (17 bp):
TTACTTCCATTTCTTAT
Found at i:90090 original size:45 final size:45
Alignment explanation
Indices: 89990--90102 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
89980 TAAAATGTGT
* *
89990 GAATTTAGCAGGTGCGAATTCAGCAGGTCCGAATATAGCAGGTGC
1 GAATTTAGCAGGTGCGAATTCAGCAGGTCCAAATATAGCAAGTGC
* * * *
90035 GAATCTAGCAGGTGCGAATTCAGCTGGTGCAAAT-TCAGCAAGTTC
1 GAATTTAGCAGGTGCGAATTCAGCAGGTCCAAATAT-AGCAAGTGC
*
90080 -AATTTCAGCAGGTGCAAATTCAG
1 GAATTT-AGCAGGTGCGAATTCAG
90103 GTTTACAGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 5 0.09
45 53 0.91
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (45 bp):
GAATTTAGCAGGTGCGAATTCAGCAGGTCCAAATATAGCAAGTGC
Found at i:90101 original size:15 final size:15
Alignment explanation
Indices: 89990--90102 Score: 115
Period size: 15 Copynumber: 7.5 Consensus size: 15
89980 TAAAATGTGT
*
89990 GAATTTAGCAGGTGC
1 GAATTCAGCAGGTGC
*
90005 GAATTCAGCAGGTCC
1 GAATTCAGCAGGTGC
90020 GAATAT-AGCAGGTGC
1 GAAT-TCAGCAGGTGC
90035 GAA-TCTAGCAGGTGC
1 GAATTC-AGCAGGTGC
*
90050 GAATTCAGCTGGTGC
1 GAATTCAGCAGGTGC
* * *
90065 AAATTCAGCAAGTTC
1 GAATTCAGCAGGTGC
90080 -AATTTCAGCAGGTGC
1 GAA-TTCAGCAGGTGC
*
90095 AAATTCAG
1 GAATTCAG
90103 GTTTACAGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
13 1 0.01
14 2 0.02
15 74 0.90
16 5 0.06
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (15 bp):
GAATTCAGCAGGTGC
Found at i:91959 original size:27 final size:27
Alignment explanation
Indices: 91905--91960 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
91895 ACCCCATCAC
**
91905 CTGCATCTTCAAATTTTGTTGAAAAAT
1 CTGCATCTTCAAATTTTGGAGAAAAAT
*
91932 CTGCATCTTCAAATTTTGGAGAAGAAT
1 CTGCATCTTCAAATTTTGGAGAAAAAT
91959 CT
1 CT
91961 ATGAGCAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (27 bp):
CTGCATCTTCAAATTTTGGAGAAAAAT
Found at i:92603 original size:2 final size:2
Alignment explanation
Indices: 92596--92620 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
92586 AATATTAATC
92596 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
92621 GATACTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.