Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016200.1 Corchorus olitorius cultivar O-4 contig16233, 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: 16553
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2961 original size:45 final size:45
Alignment explanation
Indices: 2886--2982 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
2876 AGTGCATTAC
* **
2886 CTAA-ATTCTAGTACTCCATCTATAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
* * *
2930 CTAATATTCTACTCCTCCATCTCTACATAATTCATTAAAATAAAG
1 CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
2975 CTAATATT
1 CTAATATT
2983 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (45 bp):
CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
Found at i:11389 original size:331 final size:329
Alignment explanation
Indices: 10739--13079 Score: 2282
Period size: 331 Copynumber: 7.1 Consensus size: 329
10729 TTTAATTTAA
* ***
10739 ATATATTTTTATGATTATTTT---CAAAAATTGAGGAGAAATCTTTCATATCAATTTTTGCAAAA
1 ATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAATCTTTCGGGTCAATTTTTGCAAAA
* * *
10801 TTTTAGCCGAAATTGTGTACTAACAAACCATCACGGTTTTTTTTGGCTAAAAACGCGTTCCGGGA
65 TTTTAGCCGAAATCGTG---TAA-TAACCATCAC-G--TTTTTTGGCTAAAAACGCGTTCCGGGG
* * * * * * *
10866 ACCCGGCTCAATTTTTCATGATTTTTGGCTCCGAGACTACTTGAAATATCTATATTCGTCTAATC
123 CCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC
* *
10931 AAATCTC-GCCCACATTAGATTTAATGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTA
188 AAATCTCAG-CCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTA
** * * * * *
10995 ATTAGAAATTAATTTGGAAAAATAGGAAAAACGATATTTGAAA-CGTCAAAAGCCCTTCAATCTT
252 ATTAGAAATTAATTCAGAAAAATATGAAAAACGATA-TTAAAAGCGTGAAAAGTCCTCCAATCTT
* *
11059 TTTGGTGTTGAGTT
316 TTTGGCGTTGAATT
* **
11073 ATATATTTTTTTGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTAACAAAA
1 ATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAAA
** * * *
11138 TTTTAGCCGAAATCGTGTAATAATGATCACAGTTTTTTGGATAAAAAAGCGTTCTGGGGCCCCGG
65 TTTTAGCCGAAATCGTGTAATAACCATCAC-GTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGG
* * * * *
11203 CTCAGTTTTGCATGATTGTTGGTGCCAAGACTTCTTGAGATATCTACATTCATCTAATCAAATCT
129 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
** * * ** *
11268 CAGCCACATTGGATTTAAAAATTTGTTTTTACAATTATCTAAATCTTATTTCGATTTAATTAGAA
194 CAGCCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
*
11333 ATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATC--TTTGCCGT
259 ATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGT
*
11396 TAAATT
324 TGAATT
* * * * *
11402 ATATATATTTTATGAGTATTTTATCCAAAAATTGAAGAAAATTTTTCGGTTCAGTTTTTGCAAAA
1 ATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATCTTTCGGGTCAATTTTTGCAAAA
* * * * ** *
11467 TTTTAGCCAAAATCGTATATTAACCAT-ACAG-TTTTTGGCTAAAAACGCGTTTCGGGGCAGCAG
65 TTTTAGCCGAAATCGTGTAATAACCATCAC-GTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGG
* * * * *
11530 CTCAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATGTATATATTCATCTAATAAAATCT
129 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* * * * *
11595 TAGCCACATTGCATTTAA-GATTT-TTTTTATGAGCATTTAAATCATGTTTCGATTTAATTAGAA
194 CAGCCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
* *
11658 ATTAATT-A-AAAAATATGAAAAACGATATTAAAAGCGTCAAAAG--C-CC-TTCTTTTTGGCGT
259 ATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGT
11717 TGAATT
324 TGAATT
* * * *
11723 ATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGAAATATCTTTTGGGTCAATTTTTGCAAA
1 ATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAA
* * * * * * **
11788 ATTTTAGACGAAATCGTGTAATAATCATCACGGTTTTTAGCTAAAAACGTGTTCAGGGG-CCCAT
64 ATTTTAGCCGAAATCGTGTAATAACCATCACGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGG
* * * * *
11852 TTTAGTTTTGAATGATTTTTGGC-CCTGAA-ACTCCTTGAAATATCTATATTCATCCAACCAAAT
129 CTCAGTTTTGCATGATTTTTGGCGCC--AAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
* * *
11915 CACAG-C-CATT-G-----AT--TTTA----TA--AGCATCTAAATCATGTTTCGTTTTAATTAG
192 CTCAGCCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAG
* * * * * *
11964 AAATTAATTCGGAAAAATAGGAAAAACGGTATTAGAAGCGTGAAAAG-CCTTTCAATCTATTTGG
257 AAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-TCCAATCTTTTTGG
*
12028 GGTTGAATT
321 CGTTGAATT
* * * * * * * *
12037 ATATGTTTTTTATAAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCATTTTTTACAAA
1 ATAT-ATTTTTATGAGTATTTTAGCCAAAAATTGAGG-AAAATCTTTCGGGTCAATTTTTGCAAA
* * * **** ***
12102 ATATTAGCCGAAATCGTGTAACATCACGATTTTTTTTTTTTGGCTAAAAACGCGTTCCGATACCC
64 ATTTTAGCCGAAATCGTGT-A-ATAACCA-TCACGTTTTTTGGCTAAAAACGCGTTCCGGGGCCC
* * * *
12167 CGGGTCAGTATTGCATGATTTTCGGCGCCAAGACTCCTTGAACTATCTATATTCATCTAATCAAA
126 CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
* * * *
12232 TCTCAGTCACATTGGATTTAATGATTTGTTTTTATGAGCATCAAAATCTTGTTTCGATTTAATTA
191 TCTCAGCCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA
* * ** * ** * *
12297 GAAATTAATTCGGAAAAAGTAGGAAAAACGATATTGGAAGCGTAAAAAACCCTTCAATATTTTTG
256 GAAATTAATTCAGAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTG
*
12362 CCGTTGAATGAT
320 GCGTTGAAT--T
* ** *
12374 ATATTATTTTTTTATGA-TAATTTAG-CAAAAACTTGAGGAAACATCTTTCCAGTCATTTTTTGC
1 ATA-TA--TTTTTATGAGTATTTTAGCCAAAAA-TTGAGGAAA-ATCTTTCGGGTCAATTTTTGC
* * ** *
12437 AAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAAAAATACGTTCCAGGGCCC
61 AAAATTTTAGCCGAAATCGTGTAATAACCATCACGTTTTTTGGCTAAAAACGCGTTCCGGGGCCC
* * * * * * * * *
12502 CGGGTCAGTTTTGCATGAGTTTTGGCGCTAAAACTACTAGAGATATCCATATTTATCTAATCAAA
126 CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
** * * * * * * *
12567 TCTCATTCACGTTGCATTTAAGGATTTATTTTAACGAGCATCTGAATCTTATTTCGATTTAATAA
191 TCTCAGCCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA
* * * *
12632 GAAATTAATTTAGAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTTTGA
256 GAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGG
* *
12697 CATTAAATT
321 CGTTGAATT
* * * ** *
12706 ATATATATTTCATGATTATTTTAGCCAAAAATTGAGAAAAAAAT-TTTCTAGTCATTTTTTGCAA
1 ATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAG--GAAAATCTTTCGGGTCAATTTTTGCAA
* * * * * *
12770 AATTTTAGGCGAAATCGTGTACTGACCATCACGATTTTTTTGCTAAAAACGCGTTTCGTGGCCCC
63 AATTTTAGCCGAAATCGTGTAATAACCATCACG-TTTTTTGGCTAAAAACGCGTTCCGGGGCCCC
* * * * * *
12835 AGCTCTGTTTTGCATGATTTTTGCCGCCAAGACTCTTTGAGATATCCATATTCATCTAATCAAAT
127 GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
* * * *
12900 CTCAGCTACATTGGACTTAA-GAATTTATTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTA
192 CTCAGCCACATTGGATTTAATG-ATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA
* * *
12964 GATATTAATTCTGAAAAATATAAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGG
256 GAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGG
*
13029 CGTTAAATT
321 CGTTGAATT
*
13038 ATATATATTTTATGAGTA-TTTATGCCAAAAAATGATGGAAAA
1 ATATAT-TTTTATGAGTATTTTA-GCCAAAAATTGA-GGAAAA
13080 AATTTTTACG
Statistics
Matches: 1651, Mismatches: 291, Indels: 133
0.80 0.14 0.06
Matches are distributed among these distances:
308 37 0.02
310 33 0.02
311 1 0.00
313 4 0.00
314 87 0.05
315 4 0.00
316 4 0.00
317 23 0.01
318 56 0.03
319 5 0.00
320 10 0.01
321 50 0.03
322 99 0.06
323 59 0.04
324 1 0.00
325 40 0.02
326 6 0.00
327 96 0.06
328 7 0.00
329 59 0.04
330 42 0.03
331 250 0.15
332 238 0.14
333 12 0.01
334 108 0.07
335 192 0.12
336 8 0.00
337 62 0.04
338 50 0.03
339 8 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (329 bp):
ATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATCTTTCGGGTCAATTTTTGCAAAAT
TTTAGCCGAAATCGTGTAATAACCATCACGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCT
CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
GCCACATTGGATTTAATGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAAT
TAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTG
AATT
Found at i:12562 original size:335 final size:327
Alignment explanation
Indices: 10730--13085 Score: 1981
Period size: 332 Copynumber: 7.2 Consensus size: 327
10720 TTATATTTAT
* * * * * * * *
10730 TTAATTTAAATATATTTTTATGA-TTATTT-TCAAAAATTGAGGAGAAATCTTT-CATATCAATT
1 TTAAATTATATATTTTTTTATGAGTAATTTAGCAAAAATTGAGGAAAAAT-TTTCCA-GTCATTT
* * *
10792 TTTGCAAAATTTTAGCCGAAATTGTGTACTAACAAACCATCACGGTTTTTTTTGGCTAAAAACGC
64 TTTGCAAAATTTTAGCCGAAATCGTG---TAA-TAATCATCAC-G--TTTTTTGGCTAAAAACGC
* * * * * * * *
10857 GTTCCG-GGAACCCGGCTCAATTTTTCATGATTTTTGGCTCCGAGACTACTTGAAATATCTATAT
122 GTTCCGAGG-CCCCGGGTCAGTTTTGCATGA-TTTTGGCGCCAAGACT-CTTGAGATATCCATAT
* * * *
10921 TCGTCTAATCAAATCTC-GCCCACATTAGATTTAATGATTTATTTTTACGAGCATCTGAATCTTG
184 TCATCTAATCAAATCTCAG-TCACATTGGATTTAA-GATTTATTTTTACGAGCATCTAAATCTTG
* * *
10985 TTTCGATTTAATTAGAAATTAATTTGGAAAAATAGGAAAAACGATATTTGAAA-CGTCAAAAGCC
247 TTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATA-TTAAAAGCGTGAAAAGCC
* *
11049 CTTCAATCTTTTTGGTG
311 CTCCAATCTTTTTGGCG
* * * * ** *
11066 TTGAGTTATATA-TTTTTT-TGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATT
1 TTAAATTATATATTTTTTTATGAGTAATTTAG-CAAAAATTGAGGAAAAAT-TTTCCAGTCATTT
** * * * *
11129 TTAACAAAATTTTAGCCGAAATCGTGTAATAATGATCACAGTTTTTTGGATAAAAAAGCGTTCTG
64 TTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCAC-GTTTTTTGGCTAAAAACGCGTTCCG
* * * * *
11194 GGGCCCCGGCTCAGTTTTGCATGATTGTTGGTGCCAAGACTTCTTGAGATATCTACATTCATCTA
128 AGGCCCCGGGTCAGTTTTGCATGATT-TTGGCGCCAAGAC-TCTTGAGATATCCATATTCATCTA
* * * * ** *
11259 ATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAATTATCTAAATCTTATTTCGATT
191 ATCAAATCTCAGTCACATTGGATTT-AAGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATT
* * *
11324 TAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATC-
255 TAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCT
*
11388 -TTTGCCG
320 TTTTGGCG
* * * * * * *
11395 TTAAATTATATA-TATTTTATGAGTATTTTATCCAAAAATTGAAG-AAAATTTTTCGGTTCAGTT
1 TTAAATTATATATTTTTTTATGAGTAATTTA-GCAAAAATTGAGGAAAAATTTTCCAG-TCATTT
* * * * *
11458 TTTGCAAAATTTTAGCCAAAATCGTATATTAACCAT-ACAG-TTTTTGGCTAAAAACGCGTTTCG
64 TTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCAC-GTTTTTTGGCTAAAAACGCGTTCCG
* ** * * * * * * **
11521 GGGCAGCAGCTCAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATGTATATATTCATCTA
128 AGGCCCCGGGTCAGTTTTGCATGA-TTTTGGCGCCAAGACT-CTTGAGATATCCATATTCATCTA
* * * * * * *
11586 ATAAAATCTTAGCCACATTGCATTTAAGATTT-TTTTTATGAGCATTTAAATCATGTTTCGATTT
191 ATCAAATCTCAGTCACATTGGATTTAAGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTT
* * *
11650 AATTAGAAATTAATT--AAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCCCT----TCTT
256 AATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTT
11709 TTTGGCG
321 TTTGGCG
* * * *** *
11716 TTGAATTATATA-TTTTTTATGAGT-ATTATGGCTAAAAATTGAGGAAATATCTTTTGGGTCAAT
1 TTAAATTATATATTTTTTTATGAGTAATT-TAGC-AAAAATTGAGGAAAAAT-TTTCCAGTCATT
* * * * *
11779 TTTTGCAAAATTTTAGACGAAATCGTGTAATAATCATCACGGTTTTTAGCTAAAAACGTGTTCAG
63 TTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGTTTTTTGGCTAAAAACGCGTTCCG
* *** * * * *
11844 -GGGCCCATTTTAGTTTTGAATGATTTTTGGC-CCTGAA-ACTCCTTGAAATATCTATATTCATC
128 AGGCCCCGGGTCAGTTTTGCATGA-TTTTGGCGCC--AAGACT-CTTGAGATATCCATATTCATC
* * * * *
11906 CAACCAAATCACAG-C-CATT-GA--T----TTTA----TA--AGCATCTAAATCATGTTTCGTT
189 TAATCAAATCTCAGTCACATTGGATTTAAGATTTATTTTTACGAGCATCTAAATCTTGTTTCGAT
* * * *
11956 TTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGGTATTAGAAGCGTGAAAAGCCTTTCAATC
254 TTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATC
* *
12021 TATTTGGGG
319 TTTTTGGCG
* * * * **
12030 TTGAATTATAT-GTTTTTTATAAGT-ATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCATT
1 TTAAATTATATATTTTTTTATGAGTAATT-TAGC-AAAAATTGAGGAAAAAT-TTTCCAGTCATT
* * * **
12093 TTTTACAAAATATTAGCCGAAATCGTGTAA-CATCA-CGATTTTTTTTTTTTGGCTAAAAACGCG
63 TTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATC-A----CGTTTTTTGGCTAAAAACGCG
** * *
12156 TTCCGATACCCCGGGTCAGTATTGCATGATTTTCGGCGCCAAGACTCCTTGA-ACTATCTATATT
123 TTCCGAGGCCCCGGGTCAGTTTTGCATGATTTT-GGCGCCAAGACT-CTTGAGA-TATCCATATT
* * *
12220 CATCTAATCAAATCTCAGTCACATTGGATTTAATGATTTGTTTTTATGAGCATCAAAATCTTGTT
185 CATCTAATCAAATCTCAGTCACATTGGATTTAA-GATTTATTTTTACGAGCATCTAAATCTTGTT
** * *
12285 TCGATTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTGGAAGCGTAAAAAACCCT
249 TCGATTTAATTAGAAATTAATTCGGAAAAA-TAGGAAAAACGATATTAAAAGCGTGAAAAGCCCT
* * *
12350 TCAATATTTTTGCCG
313 CCAATCTTTTTGGCG
* *
12365 TTGAATGATATATTATTTTTTTATGA-TAATTTAGCAAAAACTTGAGGAAACATCTTTCCAGTCA
1 TTAAAT--TATA-TATTTTTTTATGAGTAATTTAGCAAAAA-TTGAGGAAAAAT-TTTCCAGTCA
* **
12429 TTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAAAAATACGTTC
61 TTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGTTTTTTGGCTAAAAACGCGTTC
* * * *
12494 C-AGGGCCCCGGGTCAGTTTTGCATGAGTTTTGGCGCTAAAACTACTAGAGATATCCATATTTAT
126 CGA-GGCCCCGGGTCAGTTTTGCATGA-TTTTGGCGCCAAGACT-CTTGAGATATCCATATTCAT
* * * * * *
12558 CTAATCAAATCTCATTCACGTTGCATTTAAGGATTTATTTTAACGAGCATCTGAATCTTATTTCG
188 CTAATCAAATCTCAGTCACATTGGATTTAA-GATTTATTTTTACGAGCATCTAAATCTTGTTTCG
* ** * * * *
12623 ATTTAATAAGAAATTAATTTAGAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAA
252 ATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAA
* *
12688 TCTTTTTGACA
317 TCTTTTTGGCG
* * * * * *
12699 TTAAATTATATA-TATTTCATGATTATTTTAGCCAAAAATTGAGAAAAAAATTTTCTAGTCATTT
1 TTAAATTATATATTTTTTTATGAGTAATTTAG-CAAAAATTGAG-GAAAAATTTTCCAGTCATTT
* * * * * *
12763 TTTGCAAAATTTTAGGCGAAATCGTGTACTGACCATCACGATTTTTTTGCTAAAAACGCGTTTCG
64 TTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACG-TTTTTTGGCTAAAAACGCGTTCCG
* * * * *
12828 TGGCCCCAGCTCTGTTTTGCATGATTTTTGCCGCCAAGACTCTTTGAGATATCCATATTCATCTA
128 AGGCCCCGGGTCAGTTTTGCATGA-TTTTGGCGCCAAGACTC-TTGAGATATCCATATTCATCTA
* * *
12893 ATCAAATCTCAG-CTACATTGGACTTAAGAATTTATTTTTACGAGCATCTGAATTTTGTTTCGAT
191 ATCAAATCTCAGTC-ACATTGGATTTAAG-ATTTATTTTTACGAGCATCTAAATCTTGTTTCGAT
* * ** *
12957 TTAATTAGATATTAATTCTGAAAAATATAAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATC
254 TTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATC
13022 TTTTTGGCG
319 TTTTTGGCG
* *
13031 TTAAATTATATA-TATTTTATGAGT-ATTTATGCCAAAAAATGATGGAAAAAATTTT
1 TTAAATTATATATTTTTTTATGAGTAATTTA-G-CAAAAATTGA-GG-AAAAATTTT
13086 TACGCCAAGA
Statistics
Matches: 1664, Mismatches: 274, Indels: 167
0.79 0.13 0.08
Matches are distributed among these distances:
308 37 0.02
310 36 0.02
312 1 0.00
313 8 0.00
314 92 0.06
317 28 0.02
318 51 0.03
319 6 0.00
320 11 0.01
321 44 0.03
322 97 0.06
323 66 0.04
325 40 0.02
326 7 0.00
327 91 0.05
328 14 0.01
329 58 0.03
330 37 0.02
331 241 0.14
332 245 0.15
333 18 0.01
334 93 0.06
335 199 0.12
336 14 0.01
337 58 0.03
338 54 0.03
339 17 0.01
340 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (327 bp):
TTAAATTATATATTTTTTTATGAGTAATTTAGCAAAAATTGAGGAAAAATTTTCCAGTCATTTTT
TGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGTTTTTTGGCTAAAAACGCGTTCCGAGG
CCCCGGGTCAGTTTTGCATGATTTTGGCGCCAAGACTCTTGAGATATCCATATTCATCTAATCAA
ATCTCAGTCACATTGGATTTAAGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA
GAAATTAATTCGGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGG
CG
Found at i:13271 original size:229 final size:225
Alignment explanation
Indices: 12859--13284 Score: 568
Period size: 229 Copynumber: 1.9 Consensus size: 225
12849 TGATTTTTGC
* * * *
12859 CGCCAAGACTCTTTGAGATATCCATATTCATCTAATCAAATCTCAGCTACATTGGACTTAAGAAT
1 CGCCAAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGAACTTAAGAAT
* * * *
12924 TTATTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGATATTAATTCTGAAAAATATAAAA
66 TTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAAAA
* * *
12989 AACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAG
131 AACGATATTAAAAGCATGAAAAGTCCACCAATCTTTTTGGCG-T--ATT-TATATATTCTATGAG
13054 TATTTATGCCAAAAAATGATGGAAAAAATTTTTA
192 TATTTATGCCAAAAAATGATGGAAAAAATTTTTA
* * *
13088 CGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGAT
1 CGCCAAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGAACTTAAGAAT
* * * *
13153 TTGTTTTTACGAGTATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATCAA
66 TTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAAATAAA
* * * *
13218 AAACGATATTAAAAGCATGGAGAGTTCACCAACATTTTTTTTGGCG--TTTATATATTCTATGAG
130 AAACGATATTAAAAGCATGAAAAGTCCACC-A-A-TCTTTTTGGCGTATTTATATATTCTATGAG
13281 TATT
192 TATT
13285 GTGGCTAAAA
Statistics
Matches: 171, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
227 18 0.11
228 2 0.01
229 105 0.61
230 34 0.20
231 1 0.01
232 1 0.01
233 10 0.06
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (225 bp):
CGCCAAGACTCCTTGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGAACTTAAGAAT
TTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAAAA
AACGATATTAAAAGCATGAAAAGTCCACCAATCTTTTTGGCGTATTTATATATTCTATGAGTATT
TATGCCAAAAAATGATGGAAAAAATTTTTA
Found at i:13727 original size:329 final size:325
Alignment explanation
Indices: 13095--13769 Score: 833
Period size: 329 Copynumber: 2.1 Consensus size: 325
13085 TTACGCCAAG
* ** *
13095 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTT
1 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAATCTGTTTT
* * *
13160 TACGAGTATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATCAAAAACGAT
66 TACGAGCATCTTAATCATGTTTCAATTTAATTAGAAATTAATTCAGAAAAAAAATCAAAAACGAT
* * * * *
13225 ATTAAAAGCATGGAGAGTTCACCAACATTTTTTTTGGCGTTTATATATTCTATGAGTATTGTGGC
131 ATTAAAAGCATGAAAAG-TCACCAACAATCTTTTTGACGTTTATATATTCTATGAGTATTGTGGC
13290 TAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCATGTACCATC
195 TAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCATGTACCATC
* * *
13355 ACGGTTTTTTGGCTAAAAACGCGTTCTAAGGTCCTGAGTCAGTTTTGCATGATTTTTAGTGGCAA
260 ACGGTTTTTTAGCTAAAAACGCGTACTAAGGCCCTGAGTCAGTTTTGCATGATTTTTAGTGGCAA
13420 C
325 C
* * **
13421 ACTCTTTGAAATATCTATATTCATCTAACCAAATCTTAGCCACATTGGGTTTAAAAATCTGTTTT
1 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAATCTGTTTT
* *
13486 TACGAGCAT-TTGAATCATGTTTCAATTTAATTAGAAATTAATT-TGAAACAAAAATAGGAAAAA
66 TACGAGCATCTT-AATCATGTTTCAATTTAATTAGAAATTAATTCAGAAA-AAAAAT--CAAAAA
* * ** *
13549 CGATATTAGAAGCGTGAAAAG-C-CCTTCAATCTTTTTGACGTTGAATTATATATTTTTATGAGT
127 CGATATTAAAAGCATGAAAAGTCACCAACAATCTTTTTGACG-T---TTATATA-TTCTATGAGT
* * * *
13612 ATTGTGGCTAAAAATTGAG-AAAAATATTTCGGGTCAATTTTTTCAAAATTTTTGCCGAAATCGT
187 ATTGTGGCTAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCAT
* * * *
13676 GTACCATCATGGTTTTTTAGCTAAAAACGTGTAC-ATGGGCCCT-AGGTCAGTTTTGGATGATTT
252 GTACCATCACGGTTTTTTAGCTAAAAACGCGTACTA-AGGCCCTGA-GTCAGTTTTGCATGATTT
* * *
13739 TTGGCGGCAAG
315 TTAGTGGCAAC
* * *
13750 ACCCCTTGAAACATATATAT
1 ACTCCTTGAAATATCTATAT
13770 ATATATATAT
Statistics
Matches: 297, Mismatches: 41, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
325 19 0.06
326 102 0.34
328 24 0.08
329 124 0.42
330 28 0.09
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (325 bp):
ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAATCTGTTTT
TACGAGCATCTTAATCATGTTTCAATTTAATTAGAAATTAATTCAGAAAAAAAATCAAAAACGAT
ATTAAAAGCATGAAAAGTCACCAACAATCTTTTTGACGTTTATATATTCTATGAGTATTGTGGCT
AAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCATGTACCATCA
CGGTTTTTTAGCTAAAAACGCGTACTAAGGCCCTGAGTCAGTTTTGCATGATTTTTAGTGGCAAC
Found at i:13769 original size:2 final size:2
Alignment explanation
Indices: 13762--13813 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
13752 CCCTTGAAAC
* *
13762 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13804 TT AT AT AT AT
1 AT AT AT AT AT
13814 CATCTAACCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:14461 original size:332 final size:329
Alignment explanation
Indices: 13807--14563 Score: 923
Period size: 332 Copynumber: 2.3 Consensus size: 329
13797 TTTATATTTA
* * *
13807 TATATATCATCTAACCAAATCTTAGACACATTGTATTTAAGGATTTGTTTTTACGAGTTCTAAAT
1 TATAT-TCATCTAA-CAAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGATCTAAAT
* * *
13872 CTTGTTTCGATTTAATTAGAAATTAATTTTGAAATAAAATAGGAAAAACGATATTAGAAGTATGA
63 CTTGTTTCGATTTAATTAGAAATTAA-TTCGAAATAAAATAGGAAAAACAATATTAGAAGCATGA
* * * * * * * *
13937 AAAAGGCTTTTAATTTTTTTGGCGTTGAATTATATATTATTTATGAGTATTTTCACTAGAAATCG
127 AAAAGCCCTTCAATCTTTTTGACATTGAATTATATATTATTTATGAGTATTTTAACTAAAAATCG
* *
14002 AGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTAGCCGAAATCGTGTATTAACCATCATGGTT
192 AGGAAAAATCTTTCGGATCAATTTTTACAAAATTTAGCCGAAATCGTGTACTAACCATCATGGTT
* * * * **
14067 TTCGGCTAAAAACGCGTTCTGAGGCGCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
257 TTCGGCTAAAAACGCATTCAGAGGCACAACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTT
*
14132 GAAATATC
322 AAAATATC
14140 TATATTCATCTAACGAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTAAAT
1 TATATTCATCTAAC-AAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACGAG-ATCTAAAT
* * * * *
14205 CTTGTTTCGATTTAATTAAAAATTAATTCGGAA-AAAATAGGAAAAACAATATTAGATGCGT-TA
63 CTTGTTTCGATTTAATTAGAAATTAATTCGAAATAAAATAGGAAAAACAATATTAGAAGCATGAA
* * *
14268 AAAGCCCTTCAATCTTTTTGATATTGAATTATATATTTTTTATGAGTATTTTAAC-AAAAATTTG
128 AAAGCCCTTCAATCTTTTTGACATTGAATTATATATTATTTATGAGTATTTTAACTAAAAA-TCG
** * * *
14332 AGGAATTATCTTTTGGATCAATTTTTACAAAATTTTAGTCGAAATTGTGTACT-ACCATCATGGG
192 AGGAAAAATCTTTCGGATCAATTTTTACAAAA-TTTAGCCGAAATCGTGTACTAACCATCAT-GG
* * * *
14396 TTTTTGGCTAAAAACGCATT-AGAGGGCCACAACTCTGTTTTGCATGATTTTTGGCATCGAGACT
255 TTTTCGGCTAAAAACGCATTCAGA-GG-CACAACTCAGTTTTGCATGATTTTTGGCACCAAGACT
14460 CCTTAAAATATC
318 CCTTAAAATATC
* * * * * *
14472 TTTATTCATCTAATCAAATCTCAACCACATTGGATTTAAGG-TTTGCTTTTATGTATATCTGAAT
1 TATATTCATCTAA-CAAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACG-AGATCTAAAT
14536 CTTGTTTCGATTTAATTAGAAATTAATT
63 CTTGTTTCGATTTAATTAGAAATTAATT
14564 AAAAAAATAT
Statistics
Matches: 366, Mismatches: 48, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
329 4 0.01
330 87 0.24
331 108 0.30
332 128 0.35
333 39 0.11
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (329 bp):
TATATTCATCTAACAAATCTCAGCCACATTGATTTAAGGATTTGTTTTTACGAGATCTAAATCTT
GTTTCGATTTAATTAGAAATTAATTCGAAATAAAATAGGAAAAACAATATTAGAAGCATGAAAAA
GCCCTTCAATCTTTTTGACATTGAATTATATATTATTTATGAGTATTTTAACTAAAAATCGAGGA
AAAATCTTTCGGATCAATTTTTACAAAATTTAGCCGAAATCGTGTACTAACCATCATGGTTTTCG
GCTAAAAACGCATTCAGAGGCACAACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTAAAA
TATC
Found at i:16323 original size:14 final size:14
Alignment explanation
Indices: 16304--16330 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16294 ATTATAAATA
16304 AAAAATAAATTATG
1 AAAAATAAATTATG
16318 AAAAATAAATTAT
1 AAAAATAAATTAT
16331 TAATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
AAAAATAAATTATG
Found at i:16327 original size:18 final size:17
Alignment explanation
Indices: 16271--16327 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
16261 TCTCAATCTG
16271 AAATAAATTA-AATAAAT
1 AAATAAATTATAA-AAAT
* *
16288 AAATATATTATAAATAAA
1 AAATAAATTATAAA-AAT
16306 AAATAAATTATGAAAAAT
1 AAATAAATTAT-AAAAAT
16324 AAAT
1 AAAT
16328 TATTAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 10 0.30
18 20 0.61
19 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAATAAATTATAAAAAT
Found at i:16393 original size:16 final size:16
Alignment explanation
Indices: 16368--16404 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16358 ATCTTTCCAT
16368 AATT-AAAAAAGTTAA
1 AATTAAAAAAAGTTAA
*
16383 TATTAAAAAAAGTTAA
1 AATTAAAAAAAGTTAA
16399 AATTAA
1 AATTAA
16405 TACTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AATTAAAAAAAGTTAA
Done.