Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013899.1 Corchorus capsularis cultivar CVL-1 contig13920, 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: 84233
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:363 original size:16 final size:16
Alignment explanation
Indices: 344--419 Score: 91
Period size: 16 Copynumber: 4.8 Consensus size: 16
334 TATTTTTGGG
344 TACCCGAACCCGAAAT
1 TACCCGAACCCGAAAT
* *
360 TACCCGAATCC-AAAC
1 TACCCGAACCCGAAAT
*
375 AACCCGAACCCGAAAT
1 TACCCGAACCCGAAAT
* *
391 TACCCAAACCCAAAAT
1 TACCCGAACCCGAAAT
*
407 GACCCGAACCCGA
1 TACCCGAACCCGA
420 TCAACCCGAC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
15 12 0.25
16 36 0.75
ACGTcount: A:0.41, C:0.39, G:0.11, T:0.09
Consensus pattern (16 bp):
TACCCGAACCCGAAAT
Found at i:380 original size:31 final size:31
Alignment explanation
Indices: 352--419 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
342 GGTACCCGAA
* *
352 CCCGAAATTACCCGAATCCAAACA-ACCCGAA
1 CCCGAAATTACCCAAACCCAAA-AGACCCGAA
383 CCCGAAATTACCCAAACCCAAAATGACCCGAA
1 CCCGAAATTACCCAAACCCAAAA-GACCCGAA
415 CCCGA
1 CCCGA
420 TCAACCCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 20 0.61
32 12 0.36
ACGTcount: A:0.41, C:0.40, G:0.10, T:0.09
Consensus pattern (31 bp):
CCCGAAATTACCCAAACCCAAAAGACCCGAA
Found at i:4096 original size:80 final size:80
Alignment explanation
Indices: 3963--4123 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
3953 CAACGTTTAA
* *
3963 CAATTCGATACCAAGATACAGCTGGAAACTTTGAGATAAAATCTTGTTTTATTCAGATTTTACCC
1 CAATTCGATACCAAGATACAACTGGAAACTTTGAGATAAAATCTTGATTTATTCAGATTTTACCC
4028 AAGTTTCATGGTCTG
66 AAGTTTCATGGTCTG
4043 CAATTCGATACCAAGATACAACTGGAAACTTTGAGATAAAATCTTGATTTATTCAGATTTTACCC
1 CAATTCGATACCAAGATACAACTGGAAACTTTGAGATAAAATCTTGATTTATTCAGATTTTACCC
4108 AAGTTTCATGGTCTG
66 AAGTTTCATGGTCTG
4123 C
1 C
4124 CTGGAGAAGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (80 bp):
CAATTCGATACCAAGATACAACTGGAAACTTTGAGATAAAATCTTGATTTATTCAGATTTTACCC
AAGTTTCATGGTCTG
Found at i:10025 original size:125 final size:125
Alignment explanation
Indices: 9803--10213 Score: 492
Period size: 125 Copynumber: 3.3 Consensus size: 125
9793 TCATCGGAAT
** ** * * * * *
9803 ATGTGAAGAACTTGTTCCGACATTTGTAATTGTCGG--TAGTGTTCTATAGCAAC-GTTTAATAA
1 ATGTGAA-AACTTGTTCCGACATTTACAAGGGTCGGTATAGTATTTTGTAGCGACTGTTTAATTA
*
9865 ATGTCACGATATAATATCTATACCAACACTTACAAATGTCGGAATACGTCGAAATCAAATG
65 TTGTCACGATATAATATCTATACCAACACTTACAAATGTCGGAATACGTCGAAATCAAATG
* * *
9926 ACGTGAACAACTTGTTTCGACATTTACAAGGGTCGGTATAGTATTTTGTTGCGA-TGTTTAATTA
1 ATGTGAA-AACTTGTTCCGACATTTACAAGGGTCGGTATAGTATTTTGTAGCGACTGTTTAATTA
* * *
9990 TTGTCACGATATAATATCTATACCAACACTTACAAATGTCAGAATATGTCAAAATCAAATG
65 TTGTCACGATATAATATCTATACCAACACTTACAAATGTCGGAATACGTCGAAATCAAATG
* * *
10051 ATATGAAAAACTTATTCCGGCATTTACAAGGGTCGGTATAGTATTTTGTAGCGACT-TTTAA-TA
1 ATGTG-AAAACTTGTTCCGACATTTACAAGGGTCGGTATAGTATTTTGTAGCGACTGTTTAATTA
* * ** * *
10114 TTGTCACAATATAATATCTAAACCAATGCTTACAAATGTCGGAATACTTCGAGATCAAATG
65 TTGTCACGATATAATATCTATACCAACACTTACAAATGTCGGAATACGTCGAAATCAAATG
* * **
10175 ATGTGAAAAATTGTTCCGACATTTATAAACGTCGGTATA
1 ATGTGAAAACTTGTTCCGACATTTACAAGGGTCGGTATA
10214 ATATATATAT
Statistics
Matches: 244, Mismatches: 39, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
123 57 0.23
124 58 0.24
125 126 0.52
126 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (125 bp):
ATGTGAAAACTTGTTCCGACATTTACAAGGGTCGGTATAGTATTTTGTAGCGACTGTTTAATTAT
TGTCACGATATAATATCTATACCAACACTTACAAATGTCGGAATACGTCGAAATCAAATG
Found at i:10373 original size:1 final size:1
Alignment explanation
Indices: 10367--10407 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
10357 AGAAATGAAG
10367 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10408 CCTTCTCTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12879 original size:8 final size:8
Alignment explanation
Indices: 12866--12890 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12856 TGGATCTTAA
12866 AAAAAAAC
1 AAAAAAAC
12874 AAAAAAAC
1 AAAAAAAC
12882 AAAAAAAC
1 AAAAAAAC
12890 A
1 A
12891 TCCCAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:15503 original size:405 final size:382
Alignment explanation
Indices: 14808--15663 Score: 1112
Period size: 405 Copynumber: 2.2 Consensus size: 382
14798 GCAACATGTT
* * ** *
14808 GAATCTTATCGGCATC-TTTG-GACTGATCTAAAGTTGGAAGTAAGGCGCATTTTCCATCCAATT
1 GAATCCTATCCGCATCTTTTGAGACTGATCTAAAGTTGG-AGTAAGGCGCATTTGACATCCAGTT
*
14871 GGAATCCACACTTGGCGCAGCTATAGGCCAGGCTTGAGACATGTTCATCATCACAACCCGCACAC
65 GGAATCCACACTTGGCGCAGCTATAGGCCAGGCTTGAGACATGTTCATCATCACAACCCGAACAC
* * *
14936 TTAAAGGAAGATGGAGTTTTGAGCAGAATGAGAGGGCATGATGGGTGGAAAGAATGATTGATGAT
130 TTAAAGGAAGATGGAGTGTGGAGCAGAATAAGAGGGCATGATGGGTGGAAAGAATGATTGATGAT
* *
15001 CTCTGGTGGAGTGTTCATCATGCAGGATTTATGGAGAAAAAGGTCGCATCTTTTACAAACAAAAC
195 CTCTGGTGGAATGTTCATCATGCAGGACTTATGGAGAAAAAGGTCGCATCTTTTACAAACAAAAC
* * *
15066 ATGGATCCTCATCTAATATTTCTAATGAGCACTTTTCTCCGCATACTCCGCATCCATGATCAACT
260 AAGGATCCTCATCTAATATTTCTAATGAGCACTTTTCTCCGCATAATCCACATCCATGATCAACT
*
15131 TCACTTGCAATAATATCATCATCAGCCTTGTTGTTGTTACGGAGTGCTAGAAGTGAATGC-GTGT
325 TCACTTGCAATAATAT--T-AT----C-----------ACGGAGTGCTACAAGTGAATGCTG-GT
*
15195 GCCCAATATACA
371 GCCCAATAAACA
*
15207 GAATCCTATCCGCATCTTTTGAAGACTGATCTAAAGTTGGAGCTAAGGCGCATTTGACATCTAGT
1 GAATCCTATCCGCATCTTTTG-AGACTGATCTAAAGTTGGAG-TAAGGCGCATTTGACATCCAGT
* *
15272 TGGAATCCACACTT-TCTGCAGCTATAGGCCAGGTTTGAGACATGTTCATCATCACAACCCGAAC
64 TGGAATCCACACTTGGC-GCAGCTATAGGCCAGGCTTGAGACATGTTCATCATCACAACCCGAAC
** *
15336 ACTTGTAGGAAGATGGTTGTGGTGGAAGCAGAATAAGAGGGCATGATGGGTGGAACA-AATGATT
128 ACTTAAAGGAAGATGG-AGT-GTGG-AGCAGAATAAGAGGGCATGATGGGTGGAA-AGAATGATT
* *
15400 -ATTGATCTGTTGTGGAATGTTCATCATGCAGGACTTATGGAGAAAAAGGTCGCATCTTTTACAA
189 GA-TGATCTCTGGTGGAATGTTCATCATGCAGGACTTATGGAGAAAAAGGTCGCATCTTTTACAA
* * * **
15464 CCAAAACAAGGATCTTCATCTGATATTTCTAATGAGCACTTTTCTCCGCATAATCCACATGTATG
253 ACAAAACAAGGATCCTCATCTAATATTTCTAATGAGCACTTTTCTCCGCATAATCCACATCCATG
*
15529 ATCAACTTCACTTGCAATAATATTATCACGGAGTGCTACAAGTGGATGCTGGTGCCCAATAAACA
318 ATCAACTTCACTTGCAATAATATTATCACGGAGTGCTACAAGTGAATGCTGGTGCCCAATAAACA
* *
15594 GAATCCTATCCACATCTTTGGAGGACTGATCTAAAGTTGGAGTTAAGGCGCATTTGACATCCAGT
1 GAATCCTATCCGCATCTTTTGA-GACTGATCTAAAGTTGGAG-TAAGGCGCATTTGACATCCAGT
15659 TGGAA
64 TGGAA
15664 GGAATGCTTT
Statistics
Matches: 411, Mismatches: 34, Indels: 36
0.85 0.07 0.07
Matches are distributed among these distances:
386 1 0.00
387 97 0.24
388 1 0.00
398 1 0.00
399 14 0.03
400 4 0.01
401 3 0.01
402 110 0.27
403 3 0.01
404 3 0.01
405 173 0.42
406 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (382 bp):
GAATCCTATCCGCATCTTTTGAGACTGATCTAAAGTTGGAGTAAGGCGCATTTGACATCCAGTTG
GAATCCACACTTGGCGCAGCTATAGGCCAGGCTTGAGACATGTTCATCATCACAACCCGAACACT
TAAAGGAAGATGGAGTGTGGAGCAGAATAAGAGGGCATGATGGGTGGAAAGAATGATTGATGATC
TCTGGTGGAATGTTCATCATGCAGGACTTATGGAGAAAAAGGTCGCATCTTTTACAAACAAAACA
AGGATCCTCATCTAATATTTCTAATGAGCACTTTTCTCCGCATAATCCACATCCATGATCAACTT
CACTTGCAATAATATTATCACGGAGTGCTACAAGTGAATGCTGGTGCCCAATAAACA
Found at i:19073 original size:2 final size:2
Alignment explanation
Indices: 19066--19095 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19056 ACTCTTTGAA
19066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19096 TCAAATATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21964 original size:320 final size:319
Alignment explanation
Indices: 19931--22286 Score: 2300
Period size: 320 Copynumber: 7.3 Consensus size: 319
19921 GAGTATTGTG
* *
19931 GCTAAAAA-TGCGTTTCGGGGGCTCGACTCTA-TTTTGCATGGTTTTTGGCATAAAGACTCCTTG
1 GCTAAAAACT-CGTTTCGGGGCCTCGACTC-AGTTTTGCATGATTTTTGGCATAAAGACTCCTTG
* * * * * * * *
19994 AAATATCTATTTTCATTTAAATAAATCTCAGTCACATTAGATTTAAGAATTTATTTTTACAAGCA
64 AAATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * *
20059 TCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTGGGAAAAATGGAAAAACGATATGAGAAGC
129 TCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGG-AAAACGATATTAGAAGC
* * ** * *
20124 GTGACAAGCCGGTCAATCTTTTTGG-CTTGAAATTATATA-TTTTCTGAGTATTGTGGCAAAAAT
193 GTGAAAAACCCTTCAATCTTTTTGGTATTG-AATTATATATTTTTCTGAGTATTGTGGCAAAAAA
* * * * *
20187 TTTAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAAACATGTACTAATCATCACGGTTTTTGT
257 TTGAGAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-T
* * * * * * * *
20251 TCTAAAAACGCGTTCCGGGGCC-CGGCTCAGGTTTGCATGATTTTTGACGTAAACACGT-CTTGA
1 GCTAAAAACTCGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGAC-TCCTTGA
* * * * * * * *
20314 AATATATATATTCATCGAACCAAATCCCAGTCACATTGAATTTAAGGATTTGTTTGTACGAGCGT
65 AATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * **
20379 CTGAATCCTGTTTCGATTTCATTAGAAATAAATTCGGGAAAAAA-GAAAAACAATAAAAGAAGCG
130 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAATGGAAAACGATATTAGAAGCG
* * * * * *
20443 TGAAAAGCTCGTCAATCTTTTTGGCATTGAATTATATATTATTCTGAGTATTGTGGCAAAAATTT
194 TGAAAAACCCTTCAATCTTTTTGGTATTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATT
* *** * * *
20508 CAGAAAAAA-AAAT--GGTCAATTTTTAGCCGAAATCATATACTAACCATCACGGTTTTTT
259 GAGAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTT
* * * *
20566 GACCAAAAACTCG-TTCTGGGGCCCCTG-CTCAGTTTTGCATAATTTTTGGCAGAAAGA-TACCT
1 G-CTAAAAACTCGTTTC-GGGGCCTC-GACTCAGTTTTGCATGATTTTTGGCATAAAGACT-CCT
* *
20628 TGAAATATCTATATTCATCTAACCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAG
62 TGAAATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* *
20693 CATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTCGGATTTAAAAAAATGGAAAAACGATAT
127 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-----AAAAAATGG-AAAACGATAT
* * * ** *
20758 TAGAAGCGTGAAAAAACCTTCATTTTTTTTGCG--TTGAATTATATATTTTTCTGAAAATTGTGA
186 TAGAAGCGTGAAAAACCCTTCAATCTTTTTG-GTATTGAATTATATATTTTTCTGAGTATTGTGG
* * *
20821 CAAAAAATTGAG-GAAAACTCTTTCAAGTCAGTTTCTGTAAAATTTTACGCGAAATCGTGTACTA
250 CAAAAAATTGAGAAAAAACT-TTTCAGGTCAGTTT-T-T---A----GC-CGAAATCGTGTACTA
*
20885 ACCATCACAGTTTTTT
304 ACCATCACGGTTTTTT
* * * * * ** *
20901 ACTAAAAACGCGTTCCGGGGTCC-CGGCTCAGTTTTGCATGATTTTCGGTGTAAAGACTTCTTGA
1 GCTAAAAACTCGTTTCGGGG-CCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGA
* * * *
20965 AATATCTATATTCATCGAATCAAATCCCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCAT
65 AATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * *** *
21030 CTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGATAACGATATTAGTTTCA
130 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAATGGAAAACGATATTAGAAGCG
* * *
21095 TGAAAAACCCTTCAATCTTTTTTGG-AGTTGAATTATATATTTTTTATGAGTATTGGGGTAAAAA
194 TGAAAAACCCTTCAATC-TTTTTGGTA-TTGAATTATATA-TTTTTCTGAGTATTGTGG-CAAAA
* * * * * * *
21159 AACTGAGAAAAAACTTTTCAGGTAAGTTTTTAGCCGAAATAGGGCACTAACCGTCACGGTTTTTG
255 AATTGAGAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTT
* * * *
21224 GCTATAAAAGCT--TTTTGGTGCCTCGACTCAGTTTTGCATGATTTTTGGTATAAAGATTCCTTG
1 GCTA-AAAA-CTCGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTG
* *
21287 AAATATCTATATTCATCT-AACTAAATCTCAGCCACATTGGATTTAAGGATTTTTTTTTACGAGA
64 AAATATCTATATTCATCTAAAC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * ** * * **
21351 ATCTTAATCTTATTTCGATTT-ATTATTAATAAATTCGGAAAAATTTGAAAATTATATTAGAAGC
128 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAACGATATTAGAAGC
* * *
21415 GTGAAAAACCCTTCAATTTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGCGGCAAAAAA
193 GTGAAAAACCCTTCAATCTTTTTGGTATTGAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAA
* ** * ** * * * ***
21480 TTGAGGAAAAACTTTTGGGGTCAGTTTTT-G-CAAAATTTTAGT-CGAA--AT---TGTGTACC
257 TTGAGAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGT-GTACTAACCATCACGGTTTTTT
* * * * * * *
21536 GCT-AAAAGT-GCTTTCTGGAGCCCCGACTCCGTTTTGCATAATTTTTGGCGTAAAAACTCCTTG
1 GCTAAAAACTCG-TTTC-GGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTG
* * * *
21599 AAATATCTATATTCAT-TAAACCAAATCTCAACCAAATTCGATTTAAGAATTTGTTTTTACGAGC
64 AAATATCTATATTCATCTAAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * *
21663 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATGGAAAATGATATTAGAAGC
128 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAACGATATTAGAAGC
* * * *
21728 GTGAAAAATCCTTCAATCTTTTTGGTAATGAATTATATATTTTTATGAGTATTGTGGCAAAAATT
193 GTGAAAAACCCTTCAATCTTTTTGGTATTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAAT
* * *
21793 TGAGAAAAAAATTTTCAGGTCAGTTTTTAGCGGAAATCGTGTACTAACCAATTACGGTTTTTT
258 TGAGAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACC-ATCACGGTTTTTT
* * *
21856 GCTAAAAACTCGTTTCGAGGCCTCGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCTTTGAA
1 GCTAAAAACTCGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAA
* * * * *
21921 ATATCTATATTCATCTAAATAAATCTCAGCCACATTAGATTTAAGAATGTATTTTTACGAGCATC
66 ATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * *
21986 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAATGATATTAGAAGCGT
131 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAT-GGAAAACGATATTAGAAGCGT
* * * * * *
22051 GAAAAATCGTTTAATCTTTTTGGCATTGAATTATATATTTTTTATGATTATTGTGGCAAAAAATT
195 GAAAAACCCTTCAATCTTTTTGGTATTGAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAATT
* *
22116 GAGAAAAAA-TTTTCGGGTCAGTTTTTAGAAAATTTTAGTCGAAATCGTGTACTAACCATCACGG
259 GAGAAAAAACTTTTCAGGTCAG----T------TTTTAGCCGAAATCGTGTACTAACCATCACGG
*
22180 TTTTTG
314 TTTTTT
* * * * * *
22186 GCT-AAAACGCGTTTCAGGGCCTCAACTTAGTTTTGCATGGTTTTTGCCATAAAGACTCACTT-A
1 GCTAAAAACTCGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTC-CTTGA
* *
22249 AATATCTATAATCATCTAACCAAATCTCAGCCACATTG
65 AATATCTATATTCATCTAAACAAATCTCAGCCACATTG
22287 AAAAGCCCGT
Statistics
Matches: 1685, Mismatches: 270, Indels: 153
0.80 0.13 0.07
Matches are distributed among these distances:
309 1 0.00
310 4 0.00
311 4 0.00
312 165 0.10
313 75 0.04
314 8 0.00
315 5 0.00
316 57 0.03
317 128 0.08
318 50 0.03
319 181 0.11
320 204 0.12
321 122 0.07
322 91 0.05
323 176 0.10
324 6 0.00
325 9 0.01
326 1 0.00
327 1 0.00
328 1 0.00
329 112 0.07
330 33 0.02
331 36 0.02
332 14 0.01
333 23 0.01
334 145 0.09
335 33 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (319 bp):
GCTAAAAACTCGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAA
ATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
TGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAACGATATTAGAAGCGTG
AAAAACCCTTCAATCTTTTTGGTATTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGA
GAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTT
Found at i:24610 original size:72 final size:72
Alignment explanation
Indices: 24489--24626 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
24479 CACCCTGCGA
* *
24489 GATATCCAATGATCTCATAACATTGATCTTTTGTATGCCCCGTCATTTGACAATGTCCACACCTT
1 GATATCCAATGATCTCATAACATTGATCTTTCGTATGCCCCATCATTTGACAATGTCCACACCTT
24554 GCAGCAG
66 GCAGCAG
* * * * *
24561 GATATCCAATGATCTCATAGCATTGGTCTTTCGTGTGCCCCATCTTTTGACAATGTTCACACCTT
1 GATATCCAATGATCTCATAACATTGATCTTTCGTATGCCCCATCATTTGACAATGTCCACACCTT
24626 G
66 G
24627 GCTTGTCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (72 bp):
GATATCCAATGATCTCATAACATTGATCTTTCGTATGCCCCATCATTTGACAATGTCCACACCTT
GCAGCAG
Found at i:25712 original size:12 final size:12
Alignment explanation
Indices: 25695--25720 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25685 CACGATTTAC
25695 GGCTTCAATCTT
1 GGCTTCAATCTT
25707 GGCTTCAATCTT
1 GGCTTCAATCTT
25719 GG
1 GG
25721 ATCCTGCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (12 bp):
GGCTTCAATCTT
Found at i:26470 original size:6 final size:6
Alignment explanation
Indices: 26459--26493 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
26449 AGCCATAGGC
*
26459 AGCAGA AGCAGA AGCAGA AGCAGA ATCA-A AGCAGA
1 AGCAGA AGCAGA AGCAGA AGCAGA AGCAGA AGCAGA
26494 TCAATTTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.51, C:0.17, G:0.29, T:0.03
Consensus pattern (6 bp):
AGCAGA
Found at i:29868 original size:40 final size:40
Alignment explanation
Indices: 29823--29904 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
29813 AAAAGACAAG
29823 ATTACTCTTTAATTTTAAAAAGTAGAATCTTTCAATTGAC
1 ATTACTCTTTAATTTTAAAAAGTAGAATCTTTCAATTGAC
29863 ATTACTCTTTAATTTTAAAAAGTAGAATCTTTCAATTGAC
1 ATTACTCTTTAATTTTAAAAAGTAGAATCTTTCAATTGAC
29903 AT
1 AT
29905 CAATATGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (40 bp):
ATTACTCTTTAATTTTAAAAAGTAGAATCTTTCAATTGAC
Found at i:32376 original size:19 final size:17
Alignment explanation
Indices: 32340--32378 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
32330 TTTAGTTTAG
32340 TTTAATTTAGTTATTGT
1 TTTAATTTAGTTATTGT
*
32357 TTTACATTTATTTAATTGT
1 TTTA-ATTTAGTT-ATTGT
32376 TTT
1 TTT
32379 TTAATTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (17 bp):
TTTAATTTAGTTATTGT
Found at i:36718 original size:24 final size:24
Alignment explanation
Indices: 36655--36718 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
36645 AACAGAGGAA
*
36655 GAGCATAACTCCGACAAAGCGGAG
1 GAGCATAACTCCGACGAAGCGGAG
*
36679 GAGCATAACTCCGACGAAGTGGAG
1 GAGCATAACTCCGACGAAGCGGAG
*
36703 GAGCTTAACTCCGACG
1 GAGCATAACTCCGACG
36719 TATATAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (24 bp):
GAGCATAACTCCGACGAAGCGGAG
Found at i:41791 original size:41 final size:41
Alignment explanation
Indices: 41734--41815 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
41724 CCTCCTATTG
41734 TGTAGCCCATTTCAATATTATGTTCATGAATAATAAAAAAA
1 TGTAGCCCATTTCAATATTATGTTCATGAATAATAAAAAAA
41775 TGTAGCCCATTTCAATATTATGTTCATGAATAATAAAAAAA
1 TGTAGCCCATTTCAATATTATGTTCATGAATAATAAAAAAA
41816 ATGAATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (41 bp):
TGTAGCCCATTTCAATATTATGTTCATGAATAATAAAAAAA
Found at i:49294 original size:2 final size:2
Alignment explanation
Indices: 49287--49322 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
49277 TACATAAGAA
49287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
49323 CTAAATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51362 original size:36 final size:36
Alignment explanation
Indices: 51245--51364 Score: 107
Period size: 36 Copynumber: 3.2 Consensus size: 36
51235 CAGACAGTTC
* * * *
51245 AACCCAAGAGATCATAAGTGAAGAAAACGACCAAGACAA
1 AACCCAAGAGATC--AA-CGAAGAAGACGATCAAGGCAA
* * * * *
51284 TACCCAGGAGATGAAGGAAGAAGACGATGAAGG-AA
1 AACCCAAGAGATCAACGAAGAAGACGATCAAGGCAA
*
51319 ATTCCCAAGAGATCAACGAAGAAGACGATCAAGGCAA
1 A-ACCCAAGAGATCAACGAAGAAGACGATCAAGGCAA
51356 AACCCAAGA
1 AACCCAAGA
51365 CCAAGAGATC
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
35 2 0.03
36 47 0.73
37 5 0.08
39 10 0.16
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.08
Consensus pattern (36 bp):
AACCCAAGAGATCAACGAAGAAGACGATCAAGGCAA
Found at i:60449 original size:2 final size:2
Alignment explanation
Indices: 60442--60475 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
60432 TCAAGACCAC
60442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60476 CTTAGGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61710 original size:6 final size:6
Alignment explanation
Indices: 61699--61723 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61689 TTTCTTCACT
61699 ATCTCC ATCTCC ATCTCC ATCTCC A
1 ATCTCC ATCTCC ATCTCC ATCTCC A
61724 ATTGATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (6 bp):
ATCTCC
Found at i:75502 original size:10 final size:9
Alignment explanation
Indices: 75484--75527 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 9
75474 TGAGATAAAT
75484 AAATAAAAA
1 AAATAAAAA
75493 AAAGTAAAAA
1 AAA-TAAAAA
75503 AAACTAAAAA
1 AAA-TAAAAA
75513 AAA-AAAAA
1 AAATAAAAA
75521 AAA-AAAA
1 AAATAAAA
75528 CTTGAATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 12 0.36
9 3 0.09
10 18 0.55
ACGTcount: A:0.89, C:0.02, G:0.02, T:0.07
Consensus pattern (9 bp):
AAATAAAAA
Found at i:75516 original size:22 final size:22
Alignment explanation
Indices: 75483--75529 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
75473 ATGAGATAAA
*
75483 TAAATAAAAAAAAGTAAAAAAAAC
1 TAAA-AAAAAAAA-AAAAAAAAAC
75507 TAAAAAAAAAAAAAAAAAAAAC
1 TAAAAAAAAAAAAAAAAAAAAC
75529 T
1 T
75530 TGAATGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 8 0.36
24 4 0.18
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (22 bp):
TAAAAAAAAAAAAAAAAAAAAC
Found at i:81492 original size:30 final size:30
Alignment explanation
Indices: 81458--81522 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
81448 ATTTTGATTT
*
81458 TATTAGAAATATTTA-TTAATATGTAATAAA
1 TATTAG-AATATTTATTTAATATGCAATAAA
81488 TATTAGAATATTTATTTAATATGCAATAAA
1 TATTAGAATATTTATTTAATATGCAATAAA
81518 TATTA
1 TATTA
81523 TTAGAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (30 bp):
TATTAGAATATTTATTTAATATGCAATAAA
Found at i:83801 original size:18 final size:19
Alignment explanation
Indices: 83778--83816 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
83768 CTTTTATTTA
*
83778 TTTA-TTTATTAGTTTTTT
1 TTTATTTTATTAATTTTTT
*
83796 TTTATTTTTTTAATTTTTT
1 TTTATTTTATTAATTTTTT
83815 TT
1 TT
83817 GCATCATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTATTTTATTAATTTTTT
Found at i:83915 original size:21 final size:22
Alignment explanation
Indices: 83891--83934 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
83881 TAGGATATAG
*
83891 AAATGGAATTATAAGAAG-AAT
1 AAATGGAATTAAAAGAAGCAAT
*
83912 AAATGTAATTAAAAGAAGCAAT
1 AAATGGAATTAAAAGAAGCAAT
83934 A
1 A
83935 CTTTCACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (22 bp):
AAATGGAATTAAAAGAAGCAAT
Done.