Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012503.1 Corchorus olitorius cultivar O-4 contig12536, 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: 37574
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:17617 original size:2 final size:2
Alignment explanation
Indices: 17610--17636 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17600 AATTACCTTT
17610 TA 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 TA T
17637 GAATAAACTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25249 original size:26 final size:25
Alignment explanation
Indices: 25214--25265 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
25204 GGGGCGTTTA
25214 TATTTGTAATATTGACCATTTTTCAT
1 TATTTGTAATATTGACCA-TTTTCAT
*
25240 TATTTGTAATATTGACGATTTTCAT
1 TATTTGTAATATTGACCATTTTCAT
25265 T
1 T
25266 GGATTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (25 bp):
TATTTGTAATATTGACCATTTTCAT
Found at i:25808 original size:19 final size:19
Alignment explanation
Indices: 25772--25808 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25762 CTTATCTGTA
**
25772 ACCGTTTCATCATTGTTTG
1 ACCGTTTCATCACCGTTTG
25791 ACCGTTTCATCACCGTTT
1 ACCGTTTCATCACCGTTT
25809 TGGGACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (19 bp):
ACCGTTTCATCACCGTTTG
Found at i:25884 original size:21 final size:21
Alignment explanation
Indices: 25858--25897 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25848 CGCTGCTCTA
*
25858 ATAATCTCATCTGTACAGTAC
1 ATAATCTAATCTGTACAGTAC
25879 ATAATCTAATCTGTACAGT
1 ATAATCTAATCTGTACAGT
25898 GTATTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAATCTAATCTGTACAGTAC
Found at i:28100 original size:338 final size:338
Alignment explanation
Indices: 27466--28143 Score: 1252
Period size: 338 Copynumber: 2.0 Consensus size: 338
27456 TCCCAACCAA
27466 TCATTAATTCAATTTTTTTATCACAATGTATTATTTTAGATGAGTGAAAATATTTATATGTAGTC
1 TCATTAATTCAATTTTTTTATCACAATGTATTATTTTAGATGAGTGAAAATATTTATATGTAGTC
27531 AATGTGAAAGCAATTTTCCCAACCAATCAACTTTGGACAAATGTCAGCAGGAAAATAACCAAATA
66 AATGTGAAAGCAATTTTCCCAACCAATCAACTTTGGACAAATGTCAGCAGGAAAATAACCAAATA
27596 CCGAGCATACAACAGTTTGGATAACTTTAATAATAAGGTATATATATAGGTCAATGTAGATATAG
131 CCGAGCATACAACAGTTTGGATAACTTTAATAATAAGGTATATATATAGGTCAATGTAGATATAG
* *
27661 TTAAATTATTATAAAAGAGAAATCATGTTAGGTTGAGTGGAAAAAGCTCAATGCTCCTTAAGTAA
196 TTAAATTATTATAAAACAGAAAACATGTTAGGTTGAGTGGAAAAAGCTCAATGCTCCTTAAGTAA
27726 GGTTTCGGATTAGAGTCTTGTGTATGGCGAAAATAGGTGCTGGGAGAGTATGCCCCTTAAGTAAA
261 GGTTTCGGATTAGAGTCTTGTGTATGGCGAAAATAGGTGCTGGGAGAGTATG-CCCTTAAGTAAA
*
27791 GTTTCGGATTAGAG
325 GTTTCAGATTAGAG
* *
27805 TCATTAATTCAA-TTTTTTATCGCAATGTATTATTTTGGATGAGTGAAAATATTTATATGTAGTC
1 TCATTAATTCAATTTTTTTATCACAATGTATTATTTTAGATGAGTGAAAATATTTATATGTAGTC
* *
27869 AATGTGAAAGCAATTTTCCCAATCAATCAACTTTGGACAAATGTCAGCAGGAAAATAGCCAAATA
66 AATGTGAAAGCAATTTTCCCAACCAATCAACTTTGGACAAATGTCAGCAGGAAAATAACCAAATA
*
27934 CTGAGCATACAACAGTTTGGATAACTTTAATAATAAGGTATATATATAGGTCAATGTAGATATAG
131 CCGAGCATACAACAGTTTGGATAACTTTAATAATAAGGTATATATATAGGTCAATGTAGATATAG
27999 TTAAATTATTATAAAACAGAAAACATGTTAGGTTGAGTGGAAAAAAGCTCAATGCTCCTTAAGTA
196 TTAAATTATTATAAAACAGAAAACATGTTAGGTTGAGTGG-AAAAAGCTCAATGCTCCTTAAGTA
28064 AGGTTTCGGATTAGAGTCTTGTGTATGGCG-AAATAGGTGCTGGGAGAGTATGCCCTTAAGTAAA
260 AGGTTTCGGATTAGAGTCTTGTGTATGGCGAAAATAGGTGCTGGGAGAGTATGCCCTTAAGTAAA
28128 GTTTCAGATTAGAG
325 GTTTCAGATTAGAG
28142 TC
1 TC
28144 TTGTGTATGG
Statistics
Matches: 330, Mismatches: 8, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
337 27 0.08
338 237 0.72
339 66 0.20
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (338 bp):
TCATTAATTCAATTTTTTTATCACAATGTATTATTTTAGATGAGTGAAAATATTTATATGTAGTC
AATGTGAAAGCAATTTTCCCAACCAATCAACTTTGGACAAATGTCAGCAGGAAAATAACCAAATA
CCGAGCATACAACAGTTTGGATAACTTTAATAATAAGGTATATATATAGGTCAATGTAGATATAG
TTAAATTATTATAAAACAGAAAACATGTTAGGTTGAGTGGAAAAAGCTCAATGCTCCTTAAGTAA
GGTTTCGGATTAGAGTCTTGTGTATGGCGAAAATAGGTGCTGGGAGAGTATGCCCTTAAGTAAAG
TTTCAGATTAGAG
Found at i:28152 original size:62 final size:64
Alignment explanation
Indices: 28050--28171 Score: 194
Period size: 62 Copynumber: 1.9 Consensus size: 64
28040 AAAAAGCTCA
* * * *
28050 ATGCTCCTTAAGTAAGGTTTCGGATTAGAGTCTTGTGTATGGC-GAAATAGGTGCTGGGAGAGT
1 ATGCTCCTTAAGTAAAGTTTCAGATTAGAGTCTTGTGTATGGCAAAAATAAGTGCTGGGAGAGT
28113 ATGC-CCTTAAGTAAAGTTTCAGATTAGAGTCTTGTGTATGGCAAAAATAAGTGCTGGGA
1 ATGCTCCTTAAGTAAAGTTTCAGATTAGAGTCTTGTGTATGGCAAAAATAAGTGCTGGGA
28172 AAGTTTCCCC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 36 0.67
63 18 0.33
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (64 bp):
ATGCTCCTTAAGTAAAGTTTCAGATTAGAGTCTTGTGTATGGCAAAAATAAGTGCTGGGAGAGT
Found at i:29691 original size:337 final size:328
Alignment explanation
Indices: 28952--30517 Score: 1422
Period size: 328 Copynumber: 4.8 Consensus size: 328
28942 ATACTTTACA
* * * * * * *
28952 TCATCCAACCAAATCTCAACAATATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTC-ACCACATTGAATTTAAGAATTTGTTTTTACGAACATCTGAATCTTGT
* * * **
29017 TTCGATTTAATTAGAAATTAATTTAGAAAAAAATAAGAAATACGATATTAAAAACGTGAAAAGCC
65 TTCGATTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAACGATATT-AAAA-GCAAAAAGCC
* * * *
29082 CTCCAATCTTTTTGACGTTGAAT-TATATATTTTTATGAGTATTTTAGCCAATAATTGAGGAGAA
127 CTCCAATCTTTTTGGCGTTAAATATATAT-TTTTTATGAGTATTTTAGTCAAAAATTGAGGA-AA
* * * **
29146 -ATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCCGTGTACTAACTAACCATTATGGTT
190 TATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAAT-CGTG---TAA-TAACCATCACAGTT
* * ** * * * *
29210 TTTT-GCTAAAAACGCATTTCGGGGATCCGCCTCAATTTTGCATGATTTTTGAC-TCAAGACTAC
250 TTTTGGCTAAAAACGCGTTCCGGGGCCCCG-ATCAGTTTTGCATGATTTTTGGCGTCAAGACTCC
29273 TTGAAATATCTATAT
314 TTGAAATATCTATAT
* * * *
29288 CCATCTAATCAAATCTCAACCACTTTAAATTTAAGAATTTGTTTTTAC-AAGTATCTGAATCTTG
1 TCATCTAATCAAATCTC-ACCACATTGAATTTAAGAATTTGTTTTTACGAA-CATCTGAATCTTG
* *
29352 TTTTGATTTAATTAGAAATTAATTCAGAAAAAAATAGGTAAAAACGATATTAGAAATGTCAAAAA
64 TTTCGATTTAATTAGAAATTAATTCAG-AAAAAATATG-AAAAACGATATTA-AAA-G-CAAAAA
** *
29417 G-CCTTTAATCTTTTTAGCGTTGAAATATATATTTTTTATGAGTATTTTAGTCAAAAATTGAGGA
124 GCCCTCCAATCTTTTTGGCGTT-AAATATATATTTTTTATGAGTATTTTAGTCAAAAATTGAGGA
* * ** *
29481 AATATCTTTCGGGTCAACTTTTACAAAATTTTAGCTGAAATTGTGTAATAACCATCACAGTTTTT
188 AATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTT
* *
29546 TGGCTAAAAAAGCGTTCCGGGGCCCCGATACAGTTTTACATGATTTTTGGCGTCAAGACTCCTTG
253 TGGCTAAAAACGCGTTCCGGGGCCCCGAT-CAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTG
* *
29611 AGATATCCATAT
317 AAATATCTATAT
* * ** * * *
29623 TCATCTAATCAAATCTCGACTACATTGGATTTAAAGTTTTTTTTTTTTACGAATATCGGAATCTT
1 TCATCTAATCAAATCTC-ACCACATTGAATTT-AAG-AATTTGTTTTTACGAACATCTGAATCTT
* * * * *
29688 GTTTCGATTTAATTAAAAATTAATTCAGAAAAAGTATGAAAAACAATATTAAAAGCATGGAAAGT
63 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCA--AAAAGC
* * * * *
29753 CCTCCAATCTTTTTGGTGTTAAAT-TATATATATTATTATTATTTTA-TCCAAAAATTGAGGAAA
126 CCTCCAATCTTTTTGGCGTTAAATATATATTTTTTATGAGTATTTTAGT-CAAAAATTGAGG-AA
* * * * *
29816 AAAT-TTTTGGGT-AATTTTTTGCAAAATTTTAGTCAAAATCGT-T--T-ATCATCATAG-TTTT
189 ATATCTTTCGGGTCAA-TTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTT
* * ** **
29874 TGGCTAAAAACGCGTTTCAGGGCTTCGACTCAGTTTTGCATGATTTTTGGCGTTGAGACTCCTTG
253 TGGCTAAAAACGCGTTCCGGGGCCCCGA-TCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTG
29939 AAATATCTATAT
317 AAATATCTATAT
* * * ** * *
29951 TCATCTAATAAAATCTCAGCCACATTGCATTTGAGGCTTTGTTTTTACGAGCATCTGAATCTTAT
1 TCATCTAATCAAATCTCA-CCACATTGAATTTAAGAATTTGTTTTTACGAACATCTGAATCTTGT
* ***
30016 TTCGATTTAATTAGAAATTAGTTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGGAAGCCCT
65 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGC-AAAAAGCCCT
* * * * * ** *
30081 TCATTATTTTTGGTGTTAAATTATATATTTTTTATGCGTA-TTGGGGCTAAAAATTGAGGAAATA
129 CCAATCTTTTTGGCGTTAAA-TATATATTTTTTATGAGTATTTTAGTC-AAAAATTGAGGAAATA
* *
30145 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAATCATCAC-GATTTTTGGC
192 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTTGGC
* * * * *
30209 TAAAAACGCGTTCCGGGGCCCGGTTCAGTTTTGCATTAGTTTTGGCGCCAAGACTCCTTGAAATA
257 TAAAAACGCGTTCCGGGGCCCCGATCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATA
30274 TCTATAT
322 TCTATAT
* * *
30281 TCATCTAACCAAA--TCA--A-A--G------CG-A-TTGTTTTTAC-AAGCATCTGAAT-TATA
1 TCATCTAATCAAATCTCACCACATTGAATTTAAGAATTTGTTTTTACGAA-CATCTGAATCT-TG
* * * *
30329 TTTTGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCC
64 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGC--AAAAAGCC
* * * * * * * * *
30394 CTTCAATTTTTTTGGCGTTGAAT-TATATTTTTTTTTAGTATTGT-GGCTAAAAATTAAGGAAAA
127 CTCCAATCTTTTTGGCGTTAAATATATATTTTTTATGAGTATTTTAGTC-AAAAATTGAGGAAAT
* * * * * *
30457 ATATTTCGCGTCAATTTTTGCAAAATATTAGCCGAAATCGTATAATAATCATCACAGTTTT
191 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTT
30518 CGACTAAAAA
Statistics
Matches: 1029, Mismatches: 163, Indels: 98
0.80 0.13 0.08
Matches are distributed among these distances:
313 83 0.08
314 78 0.08
315 23 0.02
316 1 0.00
322 1 0.00
324 1 0.00
325 25 0.02
326 82 0.08
327 59 0.06
328 102 0.10
329 9 0.01
330 57 0.06
331 33 0.03
332 6 0.01
333 75 0.07
334 57 0.06
335 77 0.07
336 98 0.10
337 83 0.08
338 74 0.07
339 5 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (328 bp):
TCATCTAATCAAATCTCACCACATTGAATTTAAGAATTTGTTTTTACGAACATCTGAATCTTGTT
TCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCAAAAAGCCCTCC
AATCTTTTTGGCGTTAAATATATATTTTTTATGAGTATTTTAGTCAAAAATTGAGGAAATATCTT
TCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTTGGCTAAA
AACGCGTTCCGGGGCCCCGATCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTA
TAT
Found at i:30568 original size:314 final size:314
Alignment explanation
Indices: 29989--30558 Score: 808
Period size: 313 Copynumber: 1.8 Consensus size: 314
29979 ATTTGAGGCT
* * *
29989 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAGTTCAGAAAAAATATGAA
1 TTGTTTTTACAAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAA
* * *
30054 AAACGATATTAAAAGCGTGGAAGCCCTTCATTATTTTTGGTGTTAAATTATATATTTTTTATGCG
66 AAACGATATTAAAAGCGTGAAAGCCCTTCATTATTTTTGGCGTTAAATTATATATTTTTTATGAG
* * * * *
30119 TATTGGGGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCG
131 TATTGGGGCTAAAAATTAAGGAAAAATATTTCGCGTCAATTTTTGCAAAATATTAGCCAAAATCG
* * * * * * *
30184 TGTAATAATCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCGGTTCAGTTTTGCATTAGT
196 TATAATAATCATCACGATTTTCGACTAAAAACGCATTCCAGGCCCCGGTTCAGTGTTGCATTAGT
30249 TTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCAAAGCGA
261 TTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCAAAGCGA
*
30303 TTGTTTTTACAAGCATCTGAAT-TATATTTTGATTTAATTAGAAATTAATTCAGAAAAAATAGGA
1 TTGTTTTTACAAGCATCTGAATCT-TATTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGA
* *
30367 AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATT-TTTTTGGCGTTGAATTATAT-TTTTTT-T
65 AAAACGATATTAAAAGCGTG-AAAGCCCTTC-ATTATTTTTGGCGTTAAATTATATATTTTTTAT
* * *
30429 TAGTATTGTGGCTAAAAATTAAGGAAAAATATTTCGCGTCAATTTTTGCAAAATATTAGCCGAAA
128 GAGTATTGGGGCTAAAAATTAAGGAAAAATATTTCGCGTCAATTTTTGCAAAATATTAGCCAAAA
** * *
30494 TCGTATAATAATCATCAC-AGTTTTCGACTAAAAACTTATTCCAGGCCCCAGTTTGAGTGTTGCA
193 TCGTATAATAATCATCACGA-TTTTCGACTAAAAACGCATTCCAGGCCCC-GGTTCAGTGTTGCA
30558 T
256 T
30559 GTTTTTTGGC
Statistics
Matches: 223, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
312 1 0.00
313 97 0.43
314 95 0.43
315 27 0.12
316 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (314 bp):
TTGTTTTTACAAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAA
AAACGATATTAAAAGCGTGAAAGCCCTTCATTATTTTTGGCGTTAAATTATATATTTTTTATGAG
TATTGGGGCTAAAAATTAAGGAAAAATATTTCGCGTCAATTTTTGCAAAATATTAGCCAAAATCG
TATAATAATCATCACGATTTTCGACTAAAAACGCATTCCAGGCCCCGGTTCAGTGTTGCATTAGT
TTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCAAAGCGA
Found at i:31829 original size:334 final size:330
Alignment explanation
Indices: 31063--32074 Score: 907
Period size: 333 Copynumber: 3.1 Consensus size: 330
31053 TGTTTCGATT
* * * * *
31063 TATGAAAAACGATATTAAAAGCATGAAAAATCCTCCAATC-TTTTTGGACTTAAATTATATATAT
1 TATGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTTGG-CTTGAATTATATATTT
* * * *
31127 TTTATGAGTATT-TTATTCAAAATTTGAGAAAAAAAATTTTCGAGTCAGTTTTTGCAAAATTTTA
65 TTTATGAGTATTGTGA--AAAAAATTGAGAAAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTA
*
31191 GTCGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAAAGCATTTCGGACCCCGACTCAATT
128 GCCGAAATCGTGTA-TAATCATCACAGTTTTTGGCTAAAAAAGCATTTCGGACCCCGACTCAATT
* * ** * *
31256 TTGCATGATTTTTGGTAGAAAGACTCTTTGAAATATTGATATTCATCTAACCAAATCTCAACCAC
192 TTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCCCAACCAC
31321 AATTGATTTAAAGATTTGTTTTTACGAACATTTGAATCTTGTTTCATTTTAATTAGAAATAAATT
257 AATTGATTTAAAGATTTGTTTTTACGAACATTTGAATCTTGTTTCATTTTAATTAGAAATAAATT
31386 GGAAAAAAAA
322 GG-AAAAAAA
* * ** *
31396 TATGACAAATGATATTAGATTCGTGAAAAATCCTTCAAT-TTTTTTGGCATTGAATTGTATATTT
1 TATGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTTGGC-TTGAATTATATATTT
* * * * **
31460 TTTCTGAGTATTGTGGCAAAGAATTGTAG--AAAAATTTTTCGGGTCTTTTTTTGCAAAATTTTA
65 TTTATGAGTATTGT-GAAAAAAATTG-AGAAAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTA
* * ** * * *
31523 GCCGAAATCGT-T-TACTCATCACGGTTTTTGGCTAAAACCGCTTTTTTGGGGCCCCTG-CT-AA
128 GCCGAAATCGTGTATAATCATCACAGTTTTTGGCTAAAAAAGC--ATTTCGGACCCC-GACTCAA
* * *
31584 GTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCAATATTCATCGAATCAAATCCCAGC
190 -TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCCCAAC
*
31649 C-C-ATTCGATTTAACGATTTGTTTTTACGAGCATGCATTTGAATCTTGTTTCGA-TTTAATTAG
254 CACAATT-GATTTAAAGATTTGTTTTTACGA--A--CATTTGAATCTTGTTTC-ATTTTAATTAG
* * *
31711 AATTTAATTCGG-GAAAAA
313 AAATAAATT-GGAAAAAAA
*
31729 TA-GAAAAACGATATTAGAAGCGTGAAAAAAAT-CTTCAATCTTTTTTTGCGTTGAATTATATAT
1 TATGAAAAACGATATTAGAAGCGTG--AAAAATCCTTCAATCTTTTTTGGC-TTGAATTATATAT
*
31792 TTTTTATGAGTATTGTGAAAAAAATTGAGAAAAAAA-TTTTCGAGTTAG----T------TTTTA
63 TTTTTATGAGTATTGTGAAAAAAATTGAGAAAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTA
* * * * * * ** ** * *
31846 GCCGAAATTGTGTAGTAACCATCACATTTTTTTTGCTGAAAACGCATTTCGGGGTCTTGACTGAG
128 GCCGAAATCGTGTA-TAATCATCACA-GTTTTTGGCTAAAAAAGCATTTC-GGACCCCGACTCAA
* * * * ** * **
31911 TTTTGCATGGTTTTTGACATAAAGACTCCTTGAAATATCTATATTCATCTTACCAAATCTCAGTC
190 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCCCAACC
* * * * * *
31976 AC-ATTGGATTGAAGGATTTTTTTTTACGGGA-ATCTGAATCTTCTTTCGA-TTTAATTAGAAAT
255 ACAATT-GATTTAAAGATTTGTTTTTAC-GAACATTTGAATCTTGTTTC-ATTTTAATTAGAAAT
* *
32038 AAATTCG--TAAAA
317 AAATTGGAAAAAAA
32050 TATGAAAAACGATATTAGAAGCGTG
1 TATGAAAAACGATATTAGAAGCGTG
32075 TAATAACCTT
Statistics
Matches: 560, Mismatches: 88, Indels: 73
0.78 0.12 0.10
Matches are distributed among these distances:
321 6 0.01
322 23 0.04
323 47 0.08
324 1 0.00
325 4 0.01
326 72 0.13
327 37 0.07
328 1 0.00
329 29 0.05
330 25 0.04
331 68 0.12
332 63 0.11
333 99 0.18
334 82 0.15
335 3 0.01
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (330 bp):
TATGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTTGGCTTGAATTATATATTTT
TTATGAGTATTGTGAAAAAAATTGAGAAAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTAGCC
GAAATCGTGTATAATCATCACAGTTTTTGGCTAAAAAAGCATTTCGGACCCCGACTCAATTTTGC
ATGATTTTTGGCAGAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCCCAACCACAATT
GATTTAAAGATTTGTTTTTACGAACATTTGAATCTTGTTTCATTTTAATTAGAAATAAATTGGAA
AAAAA
Found at i:32674 original size:541 final size:533
Alignment explanation
Indices: 31585--32639 Score: 1232
Period size: 541 Copynumber: 2.0 Consensus size: 533
31575 CCCTGCTAAG
* * *
31585 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCAATATTCATCGAATCAAATCCCAGCC
1 TTTTGCATGATTTTTGGCA-AAACACTCCTTGAAATATCAATATTCAGCGAACCAAATCCCAGCC
* * *
31650 CATTCGATTTAACGATTTGTTTTTACGAGCATGCATTTGAATCTTGTTTCGATTTAATTAGAATT
65 CATTCGATATAACGATTTGTTTTTACGAG-A-GCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* *
31715 TAATTCGGGAAAAATAGAAAAACGATATTAGAAGCGTGAAAAAAATCTTCAATCTTTTTTTGCGT
128 TAATTCGGGAAAAATAGAAAAACGATATTAGAAGCGTGAAAAAAACCGTCAATCTTTTTTTGCGT
*
31780 TGAATTATATATTTTTTATGAGTATTGTGAAAAAAATTGAGAAAAAAATTTTCGAGTTAGTTTTT
193 TGAATTATATATTTTTTATGAGTATTGTGAAAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTT
* * * * * *
31845 AGCCGAAATTGTGTAGTAACCATCACATTTTTTTTGCTGAAAACGCATTTCGGGGTCTTGACTGA
258 AGCCGAAATCGTGTACTAACCATCACA-TGTTTTTGCTAAAAACG-ATTTCGGGGTCCTGACTCA
* * * * * * *
31910 GTTTTGCATGGTTTTTGACATAAAGACTCCTTGAAATATCTATATTCATCTTACCAAATCTCAGT
321 GCTTTGCATGATTTTTGACACAAAGACTACTTGAAATATCTATATTCATCTAACCAAATATCAGA
* *
31975 CACATTGGATTGAAGGATTTTTTTTTACGGGAATCTGAATCTTCTTTCGATTTAATTAGAAATAA
386 CACATTGGATTGAAGAATTTGTTTTTACGGGAATCTGAATCTTCTTTCGATTTAATTAGAAATAA
* * * * * * **
32040 ATTCGTAAAATATGAAAAACGATATTAGAAGCGTGTAATAACCTTCACGGTTTTTGACTAAAAAC
451 ATTCGAAAAATATGAAAAACGATATTAAAAACGTGTAAAAACATTCAAGCCTTTTGACTAAAAAC
* *
32105 GCATTGCGGAGCCCCGGCTCAA
516 ACATT-CGGAG---CAGCTCAA
* *
32127 TTTTGCATGATTTTTTGTGC-AAACACTCCTTGAAATATCTATATTCAGCGAACCAAATCTCAGC
1 TTTTGCATGA-TTTTTG-GCAAAACACTCCTTGAAATATCAATATTCAGCGAACCAAATCCCAGC
* * * * *
32191 CATATTGGATATAAGGATTTGTTTTTACG-G-GTATCTGAATCTTGTTTCTATTTAATTAGAAAT
64 C-CATTCGATATAACGATTTGTTTTTACGAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * **
32254 TAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGTGTG-AAAAGCCCGTCAATC-TTTTTTGC
128 TAATTCGGG--AAAAATAGAAAAACGATATTAGAAGCGTGAAAAAAACCGTCAATCTTTTTTTGC
* * * *
32317 GTTGAATTATATATTTTTTCTTAGTATTGTCGCAAAAAATTGAGAAAAAAACTTCTT-GAGTCGG
191 GTTGAATTATATATTTTTTATGAGTATTGT-GAAAAAAATTGAGAAAAAAA-TT-TTCGAGTCAG
32381 TTTTTAGCCGAAATCGTGTACTAACCATCACA-GTTTTTGACTAAAAACG-TGTTCTGGGGTCAC
253 TTTTTAGCCGAAATCGTGTACTAACCATCACATGTTTTTG-CTAAAAACGAT-TTC-GGGGTC-C
* * ** * *
32444 T-ACTCTGCTTTGCATGATTTTTGGCACCGAGACTACTTGAAATATCTTTATTTATCTAATCCAA
314 TGACTCAGCTTTGCATGATTTTTGACACAAAGACTACTTGAAATATCTATATTCATCTAA-CCAA
* * * *
32508 ATATCA-ACAACATTGGATTTAAGAATTTGTTTTTACGTGTATCTGAATCTTGTTTCGATTTAAT
378 ATATCAGAC-ACATTGGATTGAAGAATTTGTTTTTACGGGAATCTGAATCTTCTTTCGATTTAAT
* * * *
32572 TAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAACTTG-AAAAATCATTTAATCCTT
442 TAGAAATAAATTC-G-AAAAATATGAAAAACGATATTAAAAACGTGTAAAAA-CATTCAAGCCTT
32636 TTGA
504 TTGA
32640 AATTGAATTA
Statistics
Matches: 435, Mismatches: 61, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
538 1 0.00
539 83 0.19
540 91 0.21
541 135 0.31
542 58 0.13
543 65 0.15
544 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (533 bp):
TTTTGCATGATTTTTGGCAAAACACTCCTTGAAATATCAATATTCAGCGAACCAAATCCCAGCCC
ATTCGATATAACGATTTGTTTTTACGAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCGGGAAAAATAGAAAAACGATATTAGAAGCGTGAAAAAAACCGTCAATCTTTTTTTGCGTTGA
ATTATATATTTTTTATGAGTATTGTGAAAAAAATTGAGAAAAAAATTTTCGAGTCAGTTTTTAGC
CGAAATCGTGTACTAACCATCACATGTTTTTGCTAAAAACGATTTCGGGGTCCTGACTCAGCTTT
GCATGATTTTTGACACAAAGACTACTTGAAATATCTATATTCATCTAACCAAATATCAGACACAT
TGGATTGAAGAATTTGTTTTTACGGGAATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCG
AAAAATATGAAAAACGATATTAAAAACGTGTAAAAACATTCAAGCCTTTTGACTAAAAACACATT
CGGAGCAGCTCAA
Found at i:34928 original size:21 final size:21
Alignment explanation
Indices: 34898--34938 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34888 CGATATATAC
34898 ATTTGATGAGAAAATGAATTT
1 ATTTGATGAGAAAATGAATTT
*
34919 ATTTGGTGAGAAAATGAATT
1 ATTTGATGAGAAAATGAATT
34939 AATTAGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (21 bp):
ATTTGATGAGAAAATGAATTT
Found at i:36876 original size:39 final size:40
Alignment explanation
Indices: 36820--36900 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
36810 TTTAATTCCT
36820 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
36860 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
36899 AT
1 AT
36901 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:37255 original size:204 final size:202
Alignment explanation
Indices: 37017--37413 Score: 670
Period size: 204 Copynumber: 1.9 Consensus size: 202
37007 TTAATAATAA
*
37017 ATAAATCGGATCATAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
1 ATAAATCAGATCATAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
* **
37082 AATAAATCAACCACTAATGTTTAACTAATTTTTTTTGG-TATAGTTCTATATATATAATAGTAAT
66 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTTATAGTT-T-TATATATAATAACAAT
37146 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGAC
129 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGAC
37211 CATTGATAT
194 CATTGATAT
*
37220 ATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
1 ATAAATCAGATC-ATAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
*
37285 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATTTATAGTTTTATATATAATAACA
65 TAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGG---TTATAGTTTTATATATAATAACA
*
37350 ATGTGTTGTATCTTATTCACTGCAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
127 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
37414 CATCATCGAT
Statistics
Matches: 182, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
203 11 0.06
204 88 0.48
206 75 0.41
207 1 0.01
208 7 0.04
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (202 bp):
ATAAATCAGATCATAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTTATAGTTTTATATATAATAACAATGT
GTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGACCA
TTGATAT
Done.