Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012647.1 Corchorus capsularis cultivar CVL-1 contig12668, 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: 78982
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:889 original size:408 final size:394
Alignment explanation
Indices: 55--1128 Score: 1228
Period size: 408 Copynumber: 2.7 Consensus size: 394
45 TTGGCACAAA
* ** * *
55 AACTTCTTAACCCGCTTATAAAAGTCCAAAAAATTTGACACTGACAATGTATTGTATGAATTAAT
1 AACTTCTTAACTCGCTTAT-GGAGTCC--AAAATTTTACACTGACAGTGTATTGTAT-AA-TAAT
* * * * * *
120 CATATAAGAAAAATTTATATAATACACCGTTCAGTGGAATTTAACAGACTGCACATGCAGGCTTT
61 CCTATAA-AAAAAATTATACAATACACCG-TCAGTGGAGTTTAGCAGACTGCACGTGCAGG----
* * *
185 AATTTTAAGGGTTGACATGTGTACACTTAGGGAATATGTATTAATATTAAATA--T-TTAATTAT
120 --GTTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTACTAATATTAAATATTTATTAATTAT
* * * *
247 GAAATAGGATATGTGTCAACTTCTTAACCCGTTTATGGAGTCCAAAATTTTACACTGACAGTATA
183 GAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA-TTTACACTGACAGTGTA
* * * * * * * * * *
312 ATGTATAATAATCCTATAAGAAAAATTATGCAATACCCGTTAGTGGATTTTAGGAGACTACACGT
247 TTGTATAATAATCATATAAAAAAAAATATACAATACCCGTCAATGGAGTTTAGCAGACTACACGC
* * * *
377 GCGGGATTGGGTTGACATGTGTCCCCTTACGAAATATGTATTAATATTAAATATTTAATTAATTA
312 GCGGGATAGGGTTGACATGTGTCACCTTACGAAAAATGTATTAATATTAAATATCTAATTAATTA
* * *
442 TGAAATGGGGTATGTGTT
377 TAAAATAGGGTATGTGTC
* *
460 AGCTTCTTAACTCGCTTATGGAGTCCAAAATTTATA-A-TGATAGTGTATTGTATAATAATCCTA
1 AACTTCTTAACTCGCTTATGGAGTCCAAAATTT-TACACTGACAGTGTATTGTATAATAATCCTA
* * *
523 TAAGAAAAATTATGCAATACACACAGTCAGTGGAGTTTAGCAGATTGCACGTGC-GGGTTTAAGG
65 TAAAAAAAATTATACAATACAC-C-GTCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGG
* *
587 GTTGACATGTAT-CCCTTAGGGAATATGT-GTAATATTAAATATTTAATTAATTATGAAATGGGG
128 GTTGACATGTGTACCCTTAGGGAATATGTACTAATATTAAATATTT-ATTAATTATGAAATGGGG
* *
650 TATGTGTCGATTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
192 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
*
715 ATCATATAAAACAAAAAAATATTACAATACACTGTCAATGGAGTTTAGCAGACTACACGCGCGGG
257 ATCATAT--AA-AAAAAAATA-TACAATAC-CCGTCAATGGAGTTTAGCAGACTACACGCGC-GG
* **
780 GCATAAGGGTTGACATGTGTCATCTTAGGCGTTAAGGAAAATGTATTAATATTTTATATCTAATT
316 G-AT-AGGGTTGACATGTGTCACCTTA--CG---A--AAAATGTATTAATATTAAATATCTAATT
845 AATTATAAAATAGGGTATGTGTC
372 AATTATAAAATAGGGTATGTGTC
* *
868 AACTTCTTAACTCGGTTATGGAGTTCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
1 AACTTCTTAACTCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
* * * *
933 AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGTAGACTGTACGTGCATGGTTTAAGGATT
66 AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTT
* * * * * *
998 GACATGTGTCCCCTTAAGGAATACGTACTAATATCAAATATTTAGTTAATTATGAGATGGAGTAT
131 GACATGTGTACCCTTAGGGAATATGTACTAATATTAAATATTTA-TTAATTATGAAATGGGGTAT
*
1063 GTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTTGTATAATAAT
195 GTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTA-TTGTATAATAAT
1128 C
259 C
1129 TTTATTATAG
Statistics
Matches: 572, Mismatches: 68, Indels: 52
0.83 0.10 0.08
Matches are distributed among these distances:
390 12 0.02
391 15 0.03
392 19 0.03
393 31 0.05
394 50 0.09
395 2 0.00
396 7 0.01
397 7 0.01
398 42 0.07
399 38 0.07
400 5 0.01
401 33 0.06
402 8 0.01
403 3 0.01
404 5 0.01
405 17 0.03
406 1 0.00
407 28 0.05
408 95 0.17
409 60 0.10
410 81 0.14
411 13 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (394 bp):
AACTTCTTAACTCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTT
GACATGTGTACCCTTAGGGAATATGTACTAATATTAAATATTTATTAATTATGAAATGGGGTATG
TGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCA
TATAAAAAAAAATATACAATACCCGTCAATGGAGTTTAGCAGACTACACGCGCGGGATAGGGTTG
ACATGTGTCACCTTACGAAAAATGTATTAATATTAAATATCTAATTAATTATAAAATAGGGTATG
TGTC
Found at i:1099 original size:200 final size:199
Alignment explanation
Indices: 55--1128 Score: 1143
Period size: 200 Copynumber: 5.3 Consensus size: 199
45 TTGGCACAAA
** * *
55 AACTTCTTAACCCGCTTATAAAAGTCCAAAAAATTTGACACTGACAATGTATTGTATGAATTAAT
1 AACTTCTTAACCCGCTTAT-GGAGTCC--AAAATTTTACACTGACAGTGTATTGTAT-AA-TAAT
* * * * * *
120 CATATAAGAAAAATTTATATAATACACCGTTCAGTGGAATTTAACAGACTGCACATGCAGGCTTT
61 CCTATAA-AAAAAATTATACAATACACCG-TCAGTGGAGTTTAGCAGACTGCACGTGC-GG----
* * * *
185 AATTTTAAGGGTTGACATGTGTACACTTAGGGAATATGTATTAATATTAAATA--T--TTAATTA
119 --GTTTAAGGGTTGACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTA
246 TGAAATAGGA-TATGTGTC
182 TGAAAT-GGAGTATGTGTC
* * *
264 AACTTCTTAACCCGTTTATGGAGTCCAAAATTTTACACTGACAGTATAATGTATAATAATCCTAT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
* * * * * * *
329 AAGAAAAATTATGCAATAC-CCGTTAGTGGATTTTAGGAGACTACACGTGCGGGATT--GGGTTG
66 AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGTTTAAGGGTTG
* * *
391 ACATGTGTCCCCTTACGAAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGGTATG
131 ACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGAGTATG
*
456 TGTT
196 TGTC
* * *
460 AGCTTCTTAACTCGCTTATGGAGTCCAAAATTTATA-A-TGATAGTGTATTGTATAATAATCCTA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTT-TACACTGACAGTGTATTGTATAATAATCCTA
* * *
523 TAAGAAAAATTATGCAATACACACAGTCAGTGGAGTTTAGCAGATTGCACGTGCGGGTTTAAGGG
65 TAAAAAAAATTATACAATACAC-C-GTCAGTGGAGTTTAGCAGACTGCACGTGCGGGTTTAAGGG
* * * *
588 TTGACATGTAT-CCCTTAGGGAATATGT-GTAATATTAAATATTTAATTAATTATGAAATGGGGT
128 TTGACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGAGT
651 ATGTGTC
193 ATGTGTC
* * *
658 GATTTCTTAACCCGCTTATGGAGTCCAAAA-TTTACACTGACAGTGTATTGTATAATAATCATAT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
* * * * * **
722 AAAACAAAAAAATATTACAATACACTGTCAATGGAGTTTAGCAGACTACACGCGCGGGGCATAAG
66 --AA-AAAAAATTA-TACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC-GGGTTTAAG
* * ** * *
787 GGTTGACATGTGTCATCTTAGGCGTTAAGGAAAATGTATTAATATTTTATATCTAATTAATTATA
126 GGTTGACATGTGTC--C-----CCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTATG
852 AAATAGG-GTATGTGTC
184 AAAT-GGAGTATGTGTC
* * *
868 AACTTCTTAACTCGGTTATGGAGTTCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
* * * *
933 AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGTAGACTGTACGTGCATGGTTTAAGGATT
66 AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGC-GGGTTTAAGGGTT
* * * * *
998 GACATGTGTCCCCTTAAGGAATACGTACTAATATCAAATATTTAGTTAATTATGAGATGGAGTAT
130 GACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGAGTAT
1063 GTGTC
195 GTGTC
*
1068 AACTTCTTAACCCGCTTATGGAGTCCAAAA-TTTACATTGACAGTGTATTTGTATAATAATC
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTA-TTGTATAATAATC
1129 TTTATTATAG
Statistics
Matches: 733, Mismatches: 101, Indels: 71
0.81 0.11 0.08
Matches are distributed among these distances:
192 41 0.06
194 3 0.00
195 45 0.06
196 54 0.07
197 6 0.01
198 121 0.17
199 32 0.04
200 127 0.17
201 48 0.07
202 12 0.02
203 13 0.02
204 11 0.02
205 3 0.00
206 24 0.03
207 53 0.07
208 13 0.02
209 32 0.04
210 60 0.08
211 35 0.05
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (199 bp):
AACTTCTTAACCCGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTATAATAATCCTAT
AAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGTTTAAGGGTTG
ACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGAGTATG
TGTC
Found at i:7748 original size:33 final size:33
Alignment explanation
Indices: 7706--7773 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
7696 TTGACACATG
7706 TCCATTTTTTTAAGTAATTAAGTTTTAAATATT
1 TCCATTTTTTTAAGTAATTAAGTTTTAAATATT
7739 TCCATTTTTTTAAGTAATTAAGTTTTAAATATT
1 TCCATTTTTTTAAGTAATTAAGTTTTAAATATT
7772 TC
1 TC
7774 AATCTAGTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.54
Consensus pattern (33 bp):
TCCATTTTTTTAAGTAATTAAGTTTTAAATATT
Found at i:11274 original size:6 final size:6
Alignment explanation
Indices: 11244--11284 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
11234 GTACTTTTTA
11244 ATATAG -TATAG ATAGATAG -TATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG AT--ATAG ATATAG ATATAG ATATAG ATATA
11285 CATTCATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 9 0.29
6 17 0.55
7 1 0.03
8 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:11612 original size:23 final size:24
Alignment explanation
Indices: 11562--11616 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
11552 ACACCAAGTG
11562 TAAAACTCATGTTTTACACCCATT
1 TAAAACTCATGTTTTACACCCATT
* *
11586 TAAAACTCAT-TTTT-GACCCTTT
1 TAAAACTCATGTTTTACACCCATT
11608 CTAAAACTC
1 -TAAAACTC
11617 GATCTTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 6 0.21
23 12 0.43
24 10 0.36
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAAACTCATGTTTTACACCCATT
Found at i:17224 original size:18 final size:19
Alignment explanation
Indices: 17183--17233 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
17173 CTGCAAAATT
17183 AACAAAAACACAAAAACGAAA
1 AACAAAAACA-AAAAACG-AA
*
17204 AACAAAAACAAAATACG-A
1 AACAAAAACAAAAAACGAA
17222 AAC-AAAACAAAA
1 AACAAAAACAAAA
17234 CTAAAGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.31
18 4 0.14
20 6 0.21
21 10 0.34
ACGTcount: A:0.76, C:0.18, G:0.04, T:0.02
Consensus pattern (19 bp):
AACAAAAACAAAAAACGAA
Found at i:20334 original size:16 final size:16
Alignment explanation
Indices: 20315--20373 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
20305 AGGTTCGGGC
20315 TTTTTCGGGTTCTGAT
1 TTTTTCGGGTTCTGAT
*
20331 TTTTTCGGGTT-TGAAC
1 TTTTTCGGGTTCTG-AT
* * *
20347 TTTTTCGGATTCGGGT
1 TTTTTCGGGTTCTGAT
20363 TTTTT-GGGTTC
1 TTTTTCGGGTTC
20374 GGGTTCGGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 7 0.20
16 27 0.77
17 1 0.03
ACGTcount: A:0.07, C:0.12, G:0.27, T:0.54
Consensus pattern (16 bp):
TTTTTCGGGTTCTGAT
Found at i:20575 original size:238 final size:238
Alignment explanation
Indices: 20137--20576 Score: 756
Period size: 238 Copynumber: 1.8 Consensus size: 238
20127 TGTTAATTCA
* * *
20137 GGTTCGGGTTCAGTTTGGTTTTTTGCCAGATTATTTACCTTTTTTATCTGGATGAATAATGTCAT
1 GGTTCGGGTTCAGTTTGGCTTTTTGCCAGATAATTTACCTTTTTTATCCGGATGAATAATGTCAT
20202 TATCTTTTTCAAATTTTATGTGTAATTTATTAATTTACCTTTTAAACATATTCATATGAAAAACT
66 TATCTTTTTCAAATTTTATGTGTAATTTATTAATTTACCTTTTAAACATATTCATATGAAAAACT
* ** * *
20267 ATAGGGCATAAATGAAATTTTCATACACTTCCAGATTCAGGTTCGGGCTTTTTCGGGTTCTGATT
131 ATAGGACATAAATGAAATTTTCATACACTTCCAGATTCAAATTCGGGCTTTTTCGGGTTCTAACT
20332 TTTTCGGGTTTGAACTTTTTCGGATTCGGGTTTTTTGGGTTCG
196 TTTTCGGGTTTGAACTTTTTCGGATTCGGGTTTTTTGGGTTCG
20375 GGTTCGGGTTCAGTTTGGCTTTTTGCCAGATAATTTACCTTTTTTATCCGGATGAATAATGTCAT
1 GGTTCGGGTTCAGTTTGGCTTTTTGCCAGATAATTTACCTTTTTTATCCGGATGAATAATGTCAT
*
20440 TATCTTTTTCAAATTTTATGTGTAATTTATTAATTTACCTTTTAAATATATTCATATGAAAAACT
66 TATCTTTTTCAAATTTTATGTGTAATTTATTAATTTACCTTTTAAACATATTCATATGAAAAACT
* * *
20505 ATAGGATATAAATGAAATTTTCATACACTTCCGGATTCAAATTCGGGTTTTTTCGGGTT-TAAAC
131 ATAGGACATAAATGAAATTTTCATACACTTCCAGATTCAAATTCGGGCTTTTTCGGGTTCT-AAC
20569 TTTTTCGG
195 TTTTTCGG
20577 ATTCGGGTTT
Statistics
Matches: 189, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
237 1 0.01
238 188 0.99
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (238 bp):
GGTTCGGGTTCAGTTTGGCTTTTTGCCAGATAATTTACCTTTTTTATCCGGATGAATAATGTCAT
TATCTTTTTCAAATTTTATGTGTAATTTATTAATTTACCTTTTAAACATATTCATATGAAAAACT
ATAGGACATAAATGAAATTTTCATACACTTCCAGATTCAAATTCGGGCTTTTTCGGGTTCTAACT
TTTTCGGGTTTGAACTTTTTCGGATTCGGGTTTTTTGGGTTCG
Found at i:30736 original size:18 final size:18
Alignment explanation
Indices: 30715--30765 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
30705 ATTAATTATT
*
30715 GTTAAATAGTTTATTAGG
1 GTTAATTAGTTTATTAGG
* *
30733 GTTAATTATTTTATTAGT
1 GTTAATTAGTTTATTAGG
*
30751 TTTAATTAGTTTATT
1 GTTAATTAGTTTATT
30766 TACAATTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
GTTAATTAGTTTATTAGG
Found at i:30912 original size:18 final size:18
Alignment explanation
Indices: 30886--30929 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
30876 GCCCGCAGGG
30886 AGAGAGAGACTAAGCTTC
1 AGAGAGAGACTAAGCTTC
* *
30904 AGAGGGAGA-GAGAGCTTC
1 AGAGAGAGACTA-AGCTTC
30922 AGAGAGAG
1 AGAGAGAG
30930 GCTCAGATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.39, C:0.11, G:0.39, T:0.11
Consensus pattern (18 bp):
AGAGAGAGACTAAGCTTC
Found at i:32721 original size:17 final size:17
Alignment explanation
Indices: 32699--32753 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
32689 TGTAAGTTGC
* *
32699 TTAAAATTTGTTTATGA
1 TTAAAACTTGTTTAGGA
*
32716 TTAAAACTTGTTTAGGC
1 TTAAAACTTGTTTAGGA
*
32733 TTTAAACTTGTTTAGGA
1 TTAAAACTTGTTTAGGA
32750 TTAA
1 TTAA
32754 GCAAATCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (17 bp):
TTAAAACTTGTTTAGGA
Found at i:34420 original size:2 final size:2
Alignment explanation
Indices: 34413--34445 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34403 ATAAGATAAG
34413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34446 GTTGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35288 original size:16 final size:17
Alignment explanation
Indices: 35262--35298 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
35252 TTGGGAAAGA
35262 TAAAAATGAAA-AAT-G
1 TAAAAATGAAATAATAG
35277 TAAAATATGAAATAATAG
1 TAAAA-ATGAAATAATAG
35295 TAAA
1 TAAA
35299 TGTATGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 3 0.16
18 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (17 bp):
TAAAAATGAAATAATAG
Found at i:41898 original size:33 final size:32
Alignment explanation
Indices: 41789--41898 Score: 107
Period size: 33 Copynumber: 3.4 Consensus size: 32
41779 GAAAGGTAAA
** *
41789 ATCATGACAACTTCAAGTGTCAATTAGAAATTT
1 ATCATGACAACTTCTGGTGTCAATT-GGAATTT
* * * *
41822 ATTATGACAACTTATGGTGTCAATTGTAA--G
1 ATCATGACAACTTCTGGTGTCAATTGGAATTT
* *
41852 ACCATGACAACTTCTGGTGTCATTTGGAGATTT
1 ATCATGACAACTTCTGGTGTCAATTGGA-ATTT
41885 ATCATGACAACTTC
1 ATCATGACAACTTC
41899 CGATGTCATT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 23 0.38
31 1 0.02
32 3 0.05
33 34 0.56
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
ATCATGACAACTTCTGGTGTCAATTGGAATTT
Found at i:48478 original size:6 final size:6
Alignment explanation
Indices: 48459--48554 Score: 53
Period size: 6 Copynumber: 15.8 Consensus size: 6
48449 AAGTCAACGT
48459 CCCGAA CCCG-- CCCGAA CCCGAAA TTACCCGAA CCCGAGA CAACCCGAA
1 CCCGAA CCCGAA CCCGAA CCCG-AA ---CCCGAA CCCGA-A C--C-CGAA
* *
48507 CCCG-- CCCGAA CCCGAA CCCG-- CCTGAA CCCGAA CCCG-A CCCGAG
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA
48550 CCCGA
1 CCCGA
48555 GATCAAAATA
Statistics
Matches: 72, Mismatches: 3, Indels: 30
0.69 0.03 0.29
Matches are distributed among these distances:
4 11 0.15
5 5 0.07
6 39 0.54
7 5 0.07
9 5 0.07
10 7 0.10
ACGTcount: A:0.28, C:0.50, G:0.19, T:0.03
Consensus pattern (6 bp):
CCCGAA
Found at i:48488 original size:16 final size:16
Alignment explanation
Indices: 48469--48510 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
48459 CCCGAACCCG
**
48469 CCCGAACCCGAAATTA
1 CCCGAACCCGAAACAA
*
48485 CCCGAACCCGAGACAA
1 CCCGAACCCGAAACAA
48501 CCCGAACCCG
1 CCCGAACCCG
48511 CCCGAACCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.45, G:0.17, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAAACAA
Found at i:48518 original size:16 final size:16
Alignment explanation
Indices: 48499--48554 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
48489 AACCCGAGAC
48499 AACCCGAACCCGCCCG
1 AACCCGAACCCGCCCG
*
48515 AACCCGAACCCGCCTG
1 AACCCGAACCCGCCCG
48531 AACCCGAACCCGACCCG
1 AACCCGAACCCG-CCCG
*
48548 AGCCCGA
1 AACCCGA
48555 GATCAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 27 0.75
17 9 0.25
ACGTcount: A:0.27, C:0.52, G:0.20, T:0.02
Consensus pattern (16 bp):
AACCCGAACCCGCCCG
Found at i:49305 original size:6 final size:6
Alignment explanation
Indices: 49294--49399 Score: 81
Period size: 6 Copynumber: 16.2 Consensus size: 6
49284 TACTCTAAGT
* *
49294 GAACCC GAACCC GAACCC G-ACCC GAACCC GAACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
49340 GAACCC GAAAATACCC GAACCC GAAAATACCC GAACCC GAAGTACCC GAACCC
1 GAACCC G---A-ACCC GAACCC G---A-ACCC GAACCC G-A--ACCC GAACCC
49393 GAACCC G
1 GAACCC G
49400 CCTGAACCCG
Statistics
Matches: 83, Mismatches: 4, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
5 9 0.11
6 53 0.64
7 3 0.04
8 1 0.01
9 7 0.08
10 10 0.12
ACGTcount: A:0.34, C:0.44, G:0.18, T:0.04
Consensus pattern (6 bp):
GAACCC
Found at i:49318 original size:17 final size:17
Alignment explanation
Indices: 49296--49347 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
49286 CTCTAAGTGA
49296 ACCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
49313 ACCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
* *
49330 ATCCGAGCCCGAACCCG
1 ACCCGAACCCGAACCCG
49347 A
1 A
49348 AAATACCCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.29, C:0.50, G:0.19, T:0.02
Consensus pattern (17 bp):
ACCCGAACCCGAACCCG
Found at i:49324 original size:23 final size:23
Alignment explanation
Indices: 49294--49348 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
49284 TACTCTAAGT
49294 GAACCCGAACCCGAACCCGA-CCC
1 GAACCCGAACCCG-ACCCGAGCCC
*
49317 GAACCCGAACCCGATCCGAGCCC
1 GAACCCGAACCCGACCCGAGCCC
49340 GAACCCGAA
1 GAACCCGAA
49349 AATACCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.31, C:0.47, G:0.20, T:0.02
Consensus pattern (23 bp):
GAACCCGAACCCGACCCGAGCCC
Found at i:49387 original size:15 final size:16
Alignment explanation
Indices: 49337--49395 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
49327 CCGATCCGAG
49337 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
49353 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
49369 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
49384 CCCGAACCCGAA
1 CCCGAACCCGAA
49396 CCCGCCTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 14 0.34
16 27 0.66
ACGTcount: A:0.39, C:0.41, G:0.15, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:49407 original size:31 final size:32
Alignment explanation
Indices: 49319--49409 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 32
49309 CCCGACCCGA
*
49319 ACCCGAACCCGATCCGAGCCCGAACCCGAAAAT
1 ACCCGAACCCGAACC-AGCCCGAACCCGAAAAT
* * *
49352 ACCCGAACCCGAA-AATACCCGAACCCG-AAGT
1 ACCCGAACCCGAACCA-GCCCGAACCCGAAAAT
* *
49383 ACCCGAACCCGAACCCGCCTGAACCCG
1 ACCCGAACCCGAACCAGCCCGAACCCG
49410 CCCAATTGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
31 26 0.54
32 10 0.21
33 12 0.25
ACGTcount: A:0.33, C:0.44, G:0.18, T:0.05
Consensus pattern (32 bp):
ACCCGAACCCGAACCAGCCCGAACCCGAAAAT
Found at i:50645 original size:16 final size:16
Alignment explanation
Indices: 50623--50671 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
50613 CAACATAATA
50623 AAAACAAAACGAAAAC
1 AAAACAAAACGAAAAC
* *
50639 GAAACAAAAACAAAAAC
1 AAAAC-AAAACGAAAAC
*
50656 AAAAAAAAACAGAAAA
1 AAAACAAAAC-GAAAA
50672 AACGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAACAAAACGAAAAC
Found at i:50665 original size:22 final size:22
Alignment explanation
Indices: 50622--50679 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
50612 ACAACATAAT
**
50622 AAAAACAAAACGAAAACGAAAC
1 AAAAACAAAACGAAAAAAAAAC
50644 AAAAACAAAAAC-AAAAAAAAAC
1 AAAAAC-AAAACGAAAAAAAAAC
*
50666 -AGAA-AAAACGAAAA
1 AAAAACAAAACGAAAA
50680 TGATATCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.16
20 4 0.13
21 3 0.10
22 14 0.45
23 5 0.16
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAAACAAAACGAAAAAAAAAC
Found at i:52046 original size:6 final size:6
Alignment explanation
Indices: 52029--52059 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
52019 CAGGCTGCAC
*
52029 CACAAT CGCAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT CACAAT C
52060 TTGCCAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:52114 original size:38 final size:38
Alignment explanation
Indices: 52058--52248 Score: 337
Period size: 38 Copynumber: 5.0 Consensus size: 38
52048 ACAATCACAA
*
52058 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
52096 TCTTACCAACAGCTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
52134 TCTTACCAACAGCTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
52172 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
52210 TCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
52248 T
1 T
52249 ATACACAGCC
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 149 1.00
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (38 bp):
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:65696 original size:219 final size:219
Alignment explanation
Indices: 65317--65761 Score: 881
Period size: 219 Copynumber: 2.0 Consensus size: 219
65307 TGGAATGTTT
65317 TTCTTTGCTTCTTTTTTGCTTTTCCCTTGTGTCATAGGGATAAGAATAGTTTTAGTAAAAGTATT
1 TTCTTTGCTTCTTTTTTGCTTTTCCCTTGTGTCATAGGGATAAGAATAGTTTTAGTAAAAGTATT
65382 TTTACTTCTTCTGATTTATTACAATCATTAAGAGAACTCAGCACTTCGTGTTCCACCTTATATGT
66 TTTACTTCTTCTGATTTATTACAATCATTAAGAGAACTCAGCACTTCGTGTTCCACCTTATATGT
65447 ATTATTTGGTGGCATAATTCATTTCTTGGTTGGCAGCTGCTTTTGGTAAGTAGGATTATATATCA
131 ATTATTTGGTGGCATAATTCATTTCTTGGTTGGCAGCTGCTTTTGGTAAGTAGGATTATATATCA
65512 CTGCATCCCTCGGAAACACTGTCA
196 CTGCATCCCTCGGAAACACTGTCA
65536 TTCTTTGCTTCTTTTTTGCTTTTCCCTTGTGTCATAGGGATAAGAATAGTTTTAGTAAAAGTATT
1 TTCTTTGCTTCTTTTTTGCTTTTCCCTTGTGTCATAGGGATAAGAATAGTTTTAGTAAAAGTATT
65601 TTTACTTCTTCTGATTTATTACAATCATTAAGAGAACTCAGCACTTCGTGTTCCACCTTATATGT
66 TTTACTTCTTCTGATTTATTACAATCATTAAGAGAACTCAGCACTTCGTGTTCCACCTTATATGT
65666 ATTATTTGGTGGCATAATTCATTTCTTGGTTGGCAGCTGCTTTTGGTAAGTAGGATTATATATCA
131 ATTATTTGGTGGCATAATTCATTTCTTGGTTGGCAGCTGCTTTTGGTAAGTAGGATTATATATCA
65731 CTGCATCCCTCGGAAACACTGTCA
196 CTGCATCCCTCGGAAACACTGTCA
*
65755 TTTTTTG
1 TTCTTTG
65762 TTTTCAACAA
Statistics
Matches: 225, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 225 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (219 bp):
TTCTTTGCTTCTTTTTTGCTTTTCCCTTGTGTCATAGGGATAAGAATAGTTTTAGTAAAAGTATT
TTTACTTCTTCTGATTTATTACAATCATTAAGAGAACTCAGCACTTCGTGTTCCACCTTATATGT
ATTATTTGGTGGCATAATTCATTTCTTGGTTGGCAGCTGCTTTTGGTAAGTAGGATTATATATCA
CTGCATCCCTCGGAAACACTGTCA
Found at i:74326 original size:45 final size:46
Alignment explanation
Indices: 74240--74331 Score: 168
Period size: 45 Copynumber: 2.0 Consensus size: 46
74230 ATTTTAATGC
74240 GAATACAGCCCCTTATATGGCTCTTTTTTTTTTTAGAACAAAAGAGT
1 GAATACAGCCCCTTATATGGC-CTTTTTTTTTTTAGAACAAAAGAGT
74287 GAATACAGCCCCTTATATGG-CTTTTTTTTTTTAGAACAAAAGAGT
1 GAATACAGCCCCTTATATGGCCTTTTTTTTTTTAGAACAAAAGAGT
74332 AATGGCAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 25 0.56
47 20 0.44
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (46 bp):
GAATACAGCCCCTTATATGGCCTTTTTTTTTTTAGAACAAAAGAGT
Found at i:74563 original size:5 final size:5
Alignment explanation
Indices: 74553--74579 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
74543 CCTCCCACAG
74553 AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AA
74580 CAGAGAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:77912 original size:25 final size:27
Alignment explanation
Indices: 77860--77912 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
77850 TTACTCAACT
**
77860 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
77887 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
77912 A
1 A
77913 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:78464 original size:20 final size:20
Alignment explanation
Indices: 78439--78476 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
78429 TTTAAGCAAT
*
78439 TGACCCGTTGAAAACCGGTG
1 TGACCCATTGAAAACCGGTG
*
78459 TGACCCATTGAAACCCGG
1 TGACCCATTGAAAACCGG
78477 ATTAACCCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (20 bp):
TGACCCATTGAAAACCGGTG
Done.