Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022453.1 Corchorus olitorius cultivar O-4 contig22486, 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: 41754
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12 original size:3 final size:3
Alignment explanation
Indices: 5--84 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
1 GATT
5 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
85 GAAAACAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1363 original size:341 final size:328
Alignment explanation
Indices: 339--1817 Score: 1158
Period size: 332 Copynumber: 4.5 Consensus size: 328
329 AGTGTCTACA
* * ** * * * *
339 CATCTGAATCTTGTTTCGATTAAATTGGAAATTAA-TTCAGAAAAATATGAAAAAAGATATTAAA
1 CATCTGAATCTTATTTCGATTTAATCAGAAATTAATTTGAAAAAAATA-GAAAAACGATATTAGA
* * * ** * *
403 AGCGTGAAAAGTCCTCCAA--TATTTGGTGTTGAATTATATATATTTTATGAGTATTGTGGCTAA
65 AGCGTGAAAAGCCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCT-A
* *** * *
466 AAATTGAAGAAAAAAAATTAGAATCAATTTTTGCAAAATTGTAGCCGAAATCGTG---T-ACCAT
129 AAATTGAGGAAAAATCTTTCG-GTCAA-TTTTGCAAAATT-TAG-CGAAATCGTGTAATAACCAT
* * * * * **
527 CACGGT-TTTTTTGGCTAAAAATGCGTTCCAGAGCCCCA-GGTTAGTTTTACATGATTTTTTATG
190 CACAGTGTTTTTTGGCTAAAAACGCGTTTCAG-G-GCCATGGTTAGTTTTGCATGATTTTTGGTG
* * * * * * *
590 GCAA-AACTATTTGAAATATCTATATTCATCTAAACAAATCTTAGCCACATTGAATTTAAAGATT
253 CCAAGATC-CTTAGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATT
*
654 TGTTTTTGCGAG
317 TGTTTTTACGAG
* * * * * * * * * *
666 CATTTGAATAATATGTTTCGATTTAATTACAAATTCATTTAAAAGAAAAAAGAAAAACGATCTTT
1 CATCTGAAT-CT-TATTTCGATTTAATCAGAAATTAATTTGAAA-AAAATAGAAAAACGATATTA
* * * * *
731 GAAGCATGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTCTGGCT
63 GAAGCGTGAAAAGCCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCT
*
796 AAAAATTGA-GAAAAATATTTCCGGTCAATTTTTGCAAAATTTTAGACGAAATC---TAAT-ACC
128 -AAAATTGAGGAAAAATCTTT-CGGTCAA-TTTTGCAAAA-TTTAG-CGAAATCGTGTAATAACC
* * * * *
856 ATCA-TG-GTTTTTTGGCTAAAAACGCG-TTCTGTGGCCCTGGGTCAGTTTTGCATGAGTTTTGG
188 ATCACAGTGTTTTTTGGCTAAAAACGCGTTTCAG-GGCCAT-GGTTAGTTTTGCATGATTTTTGG
* * * *
918 TGCCAAGACTCCTTAAAATATATCTATATTCATTTAACCAAATCTCAGCTACATTGTATTTAAGG
251 TGCCAAGA-TCCTTAGAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGG
* *
983 ATTTATTTTTACGCG
314 ATTTGTTTTTACGAG
** * * * * *
998 TTTCTAAATCTTATTTCAATTTAATCAGAAACTAATTTGGAAATAAAATAGGAAAACGATTTTAG
1 CATCTGAATCTTATTTCGATTTAATCAGAAATTAATTT-GAAA-AAAATAGAAAAACGATATTAG
* * * * *
1063 AAGCGTGAAAAAGGCTTTCAATTTTTTTTGACGTTGAATTATATATTTTTTATGAGTATTTTCGC
64 AAGCGTG-AAAAGCCCTTCAA-TCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGC
* *
1128 TAGAAATCGAGGAAAAATCTTTCGGATCAATTTTCGCAAAATGTTAGCGGAAATCGTGTATTAAC
127 TA-AAATTGAGGAAAAATCTTTCGG-TCAATTTT-GCAAAAT-TTAGC-GAAATCGTGTAATAAC
* * * *
1193 CATCACAGTTTTCACTTTTCGGGTAAAAACGTGTTTC-GGGGCATGGCTTAGTTTTGCATGATTT
187 CATCACAGTGTT---TTTT-GGCTAAAAACGCGTTTCAGGGCCATGG-TTAGTTTTGCATGATTT
* * * *
1257 TTGGTGCTAAGATGCCTT-GAAATATCTATATTTATCTAACCAAATCCCAGCCACATTAAATTTA
247 TTGGTGCCAAGAT-CCTTAGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTA
*
1321 AGGATTTGTTTTTATGAG
311 AGGATTTGTTTTTACGAG
* * * *
1339 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACAATATTAG
1 CATCTGAATCTTATTTCGATTTAATCAGAAATTAATT-TGAAAAAAATA-GAAAAACGATATTAG
* * * * * * *
1404 AAGCGTTACAAGCCCTTCAAT-TTTTTTATGTCGAATTATATATTTTTTATGAGTATTTTAGCCA
64 AAGCGTGAAAAGCCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCTA
* * * * *
1468 AAATTTTAGGAAATATCTTTCGGGTCAA-TTT------TTTAACTGAAATTGTGTACTAACCAT-
129 AAA-TTGAGGAAAAATCTTTC-GGTCAATTTTGCAAAATTTAGC-GAAATCGTGTAATAACCATC
* * ** *
1525 -CA-TGGTTTTTGGCTAAAAACGCGTTCCAGGGCCATGG-T-GTTTTGCATGATTTTTGGCACCG
191 ACAGTGTTTTTTGGCTAAAAACGCGTTTCAGGGCCATGGTTAGTTTTGCATGATTTTTGGTGCCA
* * * * *
1586 AGA-CTCTTCGAAATATCTTTATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGA-TT-T
256 AGATC-CTTAGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGT
* *
1648 TTTTATGTG
320 TTTTACGAG
* ** *
1657 CATCTGAATCTTATTTCGATTCAATCAGAAATTAATTCAAAAAAAATATGAAAAACGATATTAAA
1 CATCTGAATCTTATTTCGATTTAATCAGAAATTAATTTGAAAAAAATA-GAAAAACGATATTAGA
* * * * *
1722 AGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTTGCCAA
65 AGCGTGAAAAGCCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAG-CTA
* * * *
1787 AAAGTGATGAAAAATATTTCGGGTCATTTTT
129 AAATTGAGGAAAAATCTTTC-GGTCAATTTT
1818 ACCATCATGT
Statistics
Matches: 934, Mismatches: 169, Indels: 106
0.77 0.14 0.09
Matches are distributed among these distances:
317 39 0.04
318 96 0.10
319 13 0.01
320 65 0.07
321 1 0.00
322 14 0.01
323 12 0.01
326 2 0.00
327 10 0.01
328 3 0.00
329 45 0.05
330 95 0.10
331 79 0.08
332 120 0.13
333 54 0.06
334 30 0.03
337 9 0.01
338 63 0.07
339 4 0.00
340 18 0.02
341 104 0.11
342 5 0.01
343 38 0.04
344 12 0.01
345 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (328 bp):
CATCTGAATCTTATTTCGATTTAATCAGAAATTAATTTGAAAAAAATAGAAAAACGATATTAGAA
GCGTGAAAAGCCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCTAAA
ATTGAGGAAAAATCTTTCGGTCAATTTTGCAAAATTTAGCGAAATCGTGTAATAACCATCACAGT
GTTTTTTGGCTAAAAACGCGTTTCAGGGCCATGGTTAGTTTTGCATGATTTTTGGTGCCAAGATC
CTTAGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTAC
GAG
Found at i:6021 original size:15 final size:16
Alignment explanation
Indices: 5987--6030 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
5977 TTTATTTCTA
* *
5987 ATAATTATTTTTAGATT
1 ATAA-TATTATTAAATT
6004 ATAATA-TATTAAATT
1 ATAATATTATTAAATT
6019 ATAATATTATTA
1 ATAATATTATTA
6031 TTTATAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATAATATTATTAAATT
Found at i:7062 original size:331 final size:332
Alignment explanation
Indices: 6367--11053 Score: 4008
Period size: 334 Copynumber: 14.1 Consensus size: 332
6357 ATACTTTACA
* * * ** * * *
6367 TCATCTAACCAAATCTCAGCAACATTTGATTTAAAAATGTATTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * *
6432 TTCGATTTAATTAGAAATTAATTTAGAAAAAAATAAGAAATATGATATTAAAAGCGTAAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAG-AAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTC
* * *
6497 CTCCAATATTTTTGGCGTTGAATTATATAT-TTTTACGAGTATTTTAGCCAAAAAAAAATTGAGG
130 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCC----AAAAATTGAGG
* * * *
6561 AGAAATTTTTC-GTATCAATTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACAAACCATCAC
191 AAAAATATTTCTG-GTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTG---TAAC-AACCATCAC
* ** ** * * * * * *
6625 GGTTTTTAACTAAAAACAAGTTAC-GGGGACCTGACTCAATTTTGCATGATTTTTGGCTCCGAGA
250 AGTTTTTGGCTAAAAACGCGTT-CTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* * *
6689 CTACATGAAATTTCTATAT
314 CTCCTTGAAATATCTATAT
* **
6708 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTAAAAATTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* ** * *
6773 TTCAATTTAATTAGAAATTAATTTTGAAAAAATA-G-AAAACGATATTAGATA-CGTCAAAAGTC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTA-AAAGCGTGAAAAGTC
*
6835 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTAAGGAAAA
130 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * * *
6900 ATCTTTCAGGTCAATTTTTACAAAATTTTAACCGAAATCGTGTAACAACCCATCACAGTTTTTAG
195 ATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAA-CCATCACAGTTTTTGG
* * * *
6965 CTAAAAAAGCGTTCTGGGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGTCAAGACTCCTTGAGA
259 CTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
*
7030 TATCAATAT
324 TATCTATAT
* ** *
7039 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* *
7104 TTCGATTTAATT-GAAAATTAATTCAG-AAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTC
66 TTCGATTTAATTAG-AAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTC
** * * *
7167 C-TCTAATCTTTTTAACATTAAATTATATATATATATTATGAGTATTTTATCCAAAAATTGAGAA
130 CTTC-AATCTTTTTGGCGTTGAATTATATATAT-T-TTATGAGTATTTTAGCCAAAAATTGAG--
* * * * *
7231 AAAAAAAATTT-TGGTCACTTTTTGCAAAATTTTAGCCAAAATCGTGT-ACAAACCATCACGGTT
190 GAAAAATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAC-AACCATCACAGTT
* * * * ** *
7294 TTTGGCTAAAAATGTGTT-TCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGTTCC-GGCACTC
254 TTTGGCTAAAAACGCGTTCT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG-ACTC
* *
7357 CTTGAATTATTTATAT
317 CTTGAAATATCTATAT
* * * * * *
7373 TCATCTAATAAAATCTTAGCCACATTGCATTTAACGATTTGTTTTTACGAACATCTAAATCTTTT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * *
7438 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATCAAAAGCGTGAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCC
** * * *
7503 TTCAATCTTTTTGGCACTGAATTTTATAT-TTTTAATGAGTATTATAGCTAAAAATTGA-GAAAA
131 TTCAATCTTTTTGGCGTTGAATTATATATATTTT-ATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * * ** * *
7566 TATCTTTCTGGTCAATATTTGTAAAATTTTAGCCGAAATCATGTAATTATCATCACGGTTTTTGG
195 -ATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCATCACAGTTTTTGG
* * *** ** * *
7631 CTAAAAACACGTTCCGGGG-CCCAATTCCA-TTTTAAATGATTTTTGACGCCGAGACTCCTTGAA
259 CTAAAAACGCGTTCTGGGGCCCCGGCT-CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
7694 ATATCTATAT
323 ATATCTATAT
* * * * **
7704 TCATCTAACCAAATCCCAG-C-C-------------A-TTGTTTTTACAAGCATCTGAATCAAGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * *
7753 TTTGTTTTAATTAGAAATTAATTCAGAAAAAAATAGG-AAATCGATA-T-AAA-TGTTAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAG-AAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * * * * *
7814 CTTCAATCTTTTGGGCGTTGAATTATAAATTTTTTATGAGTAATGTGGCTAAAAATTGAGGAAAA
130 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * *****
7879 ATATTTC-GCGTCAATTTTTGCAAAATATAAGCCGAAATCGTGTAACATTA-C-TGTTTTTTTTT
195 ATATTTCTG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACA--ACCATCACAGTTTTT
** ** * * * *
7941 CCCTAAAAACGCGTTCCAGGGCCCCGGGTCAGTTTTGCAT-ATTTTTGACACCAAGACTCCATGA
257 GGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
8005 AATATCTATAT
322 AATATCTATAT
* * * *
8016 TCATCTAATCAAATCTCAGCAACATTGGATTTAATGATTTGTTTTTACGTGCACCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTG-
* * * *
8081 TTTC-ATTTAATTAGAAATTAATTCAGAAAAAGTAGGAAAAACGATATT-AAAGCGTAAAAAATT
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTC
* * *
8144 CTTCAATATTTTTGGCGTTGAATTATAT-T-TTTTATGAGTATTTTAGCAAAAAAATTGAGTAAA
130 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGC-CAAAAATTGAGGAAA
* * * * * *
8207 TATCTTTCCGGTTAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGG
194 AATATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCATCACAGTTTTTGG
* * * * * * * **
8272 CTAAAAACGCGATCTAGGGCCCCGGGGTTAGTTTTGGATTATTTTTGGCGCTAAGACTCCTTGTG
259 CTAAAAACGCGTTCTGGGGCCCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
*
8337 ATATCCATAT
323 ATATCTATAT
* * * * *
8347 TCATCTAATCAAATCCCAGGCAGATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * *
8412 ATT-GATTTAATTAGAAATTAATTCA-AAAATCATATGAAAAACGATATGAAAATCGTGAAAACT
66 -TTCGATTTAATTAGAAATTAATTCAGAAAA-AATAGGAAAAACGATATTAAAAGCGTGAAAAGT
* * * * *
8475 CCTCCAATCTTTTTGGCGTTAAATTATATATATTTCATGATTATTTTATCCAAAAATTGAGGAAA
129 CCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * *
8540 AATATTTCTGCTCATTTTTTTGCAAAATTTTAGTCGAAATCGTGT----A-CGTCACAGTTTTTT
194 AATATTTCTGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCATCACAGTTTTTG
* * * * * * *
8600 GCTAAAAATGCGTT-TCGGGGCCCCAGCCCAGTTATGCATGATTTTTGACGTCAACACTCCTTGA
258 GCTAAAAACGCGTTCT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
8664 AATATCTATAT
322 AATATCTATAT
* * * * * * * *
8675 CCATCTAGTAAAATCTTAGCCACATTGCATTTAAGGATTTTTTTTTACGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * *
8740 TTCAATTTAATTAAAAATTAATTCTG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * *
8804 TCCAATCTTTTTGGAGTTGAATTATATATATTTTACGAGTATTTTAGACAAAAATTGAGGAAAAA
131 TTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
* * *
8869 TATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTAGTCAA-AATCACCGTTTT
196 TATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA---A--CAACCATCACAGTTTT
* * * * * * * * * * * *
8933 TGGCAAAAAAATGCATCCTAGGGCCCAGGTTCAATGTTGCATGATTTTTGACGGCCGAGAGTCCT
256 TGGC-TAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC-GCCAAGACTCCT
8998 TGAAATATCTATAT
319 TGAAATATCTATAT
* ** *** * *** * *
9012 TCATCTAACCAAATCTCAGCCACATTGGATTTTAAAAAAAAAAGAGTAAAACAAGCATCTGAATC
1 TCATCTAATCAAATCTCAGCCACATTGGA-TTT--AAGGATTTG-TTTTTACGAGCATCTAAATC
* * *
9077 ATGTTTCGATTTAATTAGAAATTAATTCAGAAAATAATAGGAAAAACGATATTAGAAGCATGAAA
62 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AATAGGAAAAACGATATTAAAAGCGTGAAA
* * * * * **
9142 AG-CAATTCAATCTTTTTGACATTGAATTATATCAT-TTTTATGAGTATTGTGGTTAAAAATTGA
126 AGTC-CTTCAATCTTTTTGGCGTTGAATTATAT-ATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * * * *
9205 -GAAAATAAATTTC-GAGT-AATTTTTTGCAAAATTCTAGACGAAATCGTGTAATAATCATTACG
189 GGAAAA-ATATTTCTG-GTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCATCAC-
* * ** *
9267 ATTTTTTTTTGGCTAAAAACGTGTTCCCGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAA
250 A---GTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAA
* * *
9332 GACTCTTTGAGATATCCATAT
312 GACTCCTTGAAATATCTATAT
* * * * * *
9353 TCATCTAATCAAACCTCAGCTACATTGGATTTAAGAATTAGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
*
9418 TTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAAACGATATTAAAAGCGTGAAAAGTC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATA-GGAAAAACGATATTAAAAGCGTGAAAAGTC
* * ** * **
9482 CTCCAATATTTTTACCGTTAAATTATATATATTTTATGAGTATTTTAGTAAAAAATTGACGGAAA
130 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA-GGAAA
* * * * *
9547 AA-ATTTTTCGGTTCACTTTTTTTTTTTTGCAAAATTTCAGCCGAAATCATGT-ACTAATCATCA
194 AATATTTCT-GG-TCA-------ATTTTTGCAAAATTTTAGCCGAAATCGTGTAAC-AACCATCA
* * * * *
9610 TAGTTTTTGG-TCGAAAACGCGTT-TCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGA
249 CAGTTTTTGGCT-AAAAACGCGTTCT-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAA
*
9673 GACTCCTTGAAATTTCTATAT
312 GACTCCTTGAAATATCTATAT
*
9694 TCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * *
9759 TTCGATTTAATTAGAAATTAATTCTGAAAAAAT--GAAAAACCATAGTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * * *
9822 TCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGT-TTGTGGCTAAAAATTGAGGGAAAA
131 TTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
* * * ** * *
9886 TATTTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATTGTGTTTC-A--ATCACGGCTTATTGGC
196 TATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCATCACAG-TTTTTGGC
* * * *
9948 TAAAAACGTGTTCTGGGGCCCCCATG-TCAGTTTTGCATGATTTTTTGTCG-CAAAACTCCTTGA
260 TAAAAACGCGTTCTGGGG-CCCC-GGCTCAGTTTTGCATGA-TTTTTGGCGCCAAGACTCCTTGA
*
10011 AATATCTAAAT
322 AATATCTATAT
* * * * * * * * *
10022 TCATATAATAAAATCTTAGCCACATTGAATTTAAGGATTT-TTTTTATGAGTATTTGAATCATGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * * * *
10086 TTCGATTTAATTAAAAATTAATTTTA-AAAAAATAGGGAAAACGAAATTAGATGCGTGATAAGCC
66 TTCGATTTAATTAGAAATTAA-TTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * * * *
10150 CTTCAATCTCTTTGGCGTTGAATTTTATATTTTTTATGAGTATTGT-GTCTAAAAACTGA-GAAA
130 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAG-CCAAAAATTGAGGAAA
* * * * * * * *****
10213 AATATATT-AGGTTAATTTTAGCAAAATTTTAACCGAAATCTTGT-ACCATCATGGTTTTTTTTT
194 AATAT-TTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCA---TCACAGTTT
** * * * * *
10276 TTTACTAAAAACGCGTTAC-AGGGCCCTGTG-TTAGTTTTGCATGATTTTTGGCGGCAAGCCTCC
255 TTGGCTAAAAACGCGTT-CTGGGGCCCCG-GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* *
10339 TTAAAATATATCTAAAT
318 TT-GAA-ATATCTATAT
* * * * **
10356 TCATCTAA-CTAATTCTCAGCCACATTGTATTTAAGTATTCG-TTTTACGAGTTTCTAAATCTTG
1 TCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTG
* ** * *
10419 TTTCGATTTAATCAGAAATTAATTTGGATATAAAATAAGAAAAATGATATTAGAAA-CGTGAAAA
65 TTTCGATTTAATTAGAAATTAATTCAGA-A-AAAATAGGAAAAACGATATTA-AAAGCGTG-AAA
* * * * * * * * *
10483 AGGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGATTGTTTTCGCTAAAAATCGAGG
126 AGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGG
* * *
10548 AAAAATCTTT-TGGATCAATTTTTGCAAAATTTTAGCAGAAATCGTAT-ACTAACCATCACA-TT
191 AAAAATATTTCTGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAC-AACCATCACAGTT
* ** * * *
10610 TTTCGGCTAAAAATGCGTT-TCGCAG-CCCGGCTCTGTTTTGCATGATTTTTTTGTGCCAAGACT
254 TTT-GGCTAAAAACGCGTTCT-GGGGCCCCGGCTCAGTTTTGCATGA-TTTTTGGCGCCAAGACT
10673 CCTTGAAATATCTATAT
316 CCTTGAAATATCTATAT
* * * * *
10690 TCATCTAACCAAATTTCAACCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * * * **
10755 CTCGATTTAATTAGAAATAAATACGGAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAACCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * *
10820 TTCAATCTTTTT---G--AAATTATATATTTTTTATGAGTATTCTAGCCAAATATTGAGCAAATA
131 TTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
* * * * *
10880 TCTTTCGGGTCAAGTTTTGCAAAATTTTAGCTGAAATCGTGT-ACTAACCATCAC--TGTTTGGC
196 TATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAC-AACCATCACAGTTTTTGGC
** ** * * ** *
10942 TAAAAACGCGTTCCAGGGCCACC-GCTTTGTTTTGCTTGATTTTTGACGCTGAGACTCCTTGAAT
260 TAAAAACGCGTTCTGGGGCC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
*
11006 TATCTTTAT
324 TATCTATAT
*
11015 TCATCTAATCAAATCTCAGCCACATTGTATTTAAGGATT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATT
11054 GTAATGACTC
Statistics
Matches: 3531, Mismatches: 648, Indels: 350
0.78 0.14 0.08
Matches are distributed among these distances:
311 1 0.00
312 166 0.05
313 23 0.01
314 2 0.00
315 53 0.02
316 10 0.00
325 76 0.02
326 51 0.01
327 263 0.07
328 263 0.07
329 253 0.07
330 84 0.02
331 346 0.10
332 192 0.05
333 94 0.03
334 371 0.11
335 198 0.06
336 178 0.05
337 160 0.05
338 120 0.03
339 90 0.03
340 16 0.00
341 315 0.09
342 52 0.01
343 118 0.03
344 4 0.00
345 32 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (332 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
TTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCC
TTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
TATTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACAACCATCACAGTTTTTGGCT
AAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
TCTATAT
Found at i:16985 original size:31 final size:30
Alignment explanation
Indices: 16943--17026 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 30
16933 ATAGGAGAAA
* *
16943 TTATCA-ATTGACCCCACTAAAATTGAAA-TT
1 TTATCACATTGACCCCA-TAAAA-TAAAAGAT
*
16973 TTATCACATTGACCCTTATAAAATAAAAGAT
1 TTATCACATTGACCC-CATAAAATAAAAGAT
*
17004 TTATAACATTGACCCCATTAAAA
1 TTATCACATTGACCCCA-TAAAA
17027 ACGTTGGATG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 11 0.24
31 33 0.73
32 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
TTATCACATTGACCCCATAAAATAAAAGAT
Found at i:29814 original size:12 final size:12
Alignment explanation
Indices: 29797--29821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29787 TTTGCCCATT
29797 GGATAGCTATAA
1 GGATAGCTATAA
29809 GGATAGCTATAA
1 GGATAGCTATAA
29821 G
1 G
29822 TATACTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (12 bp):
GGATAGCTATAA
Found at i:32890 original size:20 final size:20
Alignment explanation
Indices: 32861--32901 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
32851 ACATCTAATT
*
32861 TTAAAATAATAATACTATAA
1 TTAAAATAATAATACAATAA
* *
32881 TTAAAGTAATACTACAATAA
1 TTAAAATAATAATACAATAA
32901 T
1 T
32902 AAATCCTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAATAATAATACAATAA
Found at i:33273 original size:39 final size:39
Alignment explanation
Indices: 33209--33289 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
33199 TTTAATTCCT
*
33209 ATGTAATATATAAAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATAT-AAATAACTAAAATACTTACACTAATTAA
*
33249 ATGTAATACTAT-AATAACTGAAATACTTACACTAATTAA
1 ATGTAATA-TATAAATAACTAAAATACTTACACTAATTAA
33288 AT
1 AT
33290 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 27 0.71
40 8 0.21
41 3 0.08
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (39 bp):
ATGTAATATATAAATAACTAAAATACTTACACTAATTAA
Found at i:35094 original size:12 final size:12
Alignment explanation
Indices: 35077--35101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35067 ATGTAGTATA
35077 CTTATAGCTATC
1 CTTATAGCTATC
35089 CTTATAGCTATC
1 CTTATAGCTATC
35101 C
1 C
35102 AATGGGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CTTATAGCTATC
Done.