Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020714.1 Corchorus olitorius cultivar O-4 contig20747, 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: 36758
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:325 original size:28 final size:28
Alignment explanation
Indices: 294--349 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
284 TAGTTTTTGT
294 TTAAGTGCTACACACTTTAGAGGAGGAA
1 TTAAGTGCTACACACTTTAGAGGAGGAA
322 TTAAGTGCTACACACTTTAGAGGAGGAA
1 TTAAGTGCTACACACTTTAGAGGAGGAA
350 ACAAAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (28 bp):
TTAAGTGCTACACACTTTAGAGGAGGAA
Found at i:455 original size:2 final size:2
Alignment explanation
Indices: 448--480 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
438 TAATATGTAG
448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
481 GCCTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13027 original size:24 final size:24
Alignment explanation
Indices: 12995--13044 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
12985 ATTTTTTTTG
12995 AGAATACTCTCTAGTGTATTAATT
1 AGAATACTCTCTAGTGTATTAATT
13019 AGAATACTCTCTAGTGTATTAATT
1 AGAATACTCTCTAGTGTATTAATT
13043 AG
1 AG
13045 TTTCTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (24 bp):
AGAATACTCTCTAGTGTATTAATT
Found at i:13654 original size:29 final size:30
Alignment explanation
Indices: 13604--13676 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
13594 GTTAGACTGA
13604 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
1 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
* **
13634 GGGGCAAAATGT-CCATTATTGAAGTTCAG
1 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
**
13663 GGAACAAAACGTCC
1 GGGGCAAAACGTCC
13677 AAATGCTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (30 bp):
GGGGCAAAACGTCCCAAAATTGAAGTTCAG
Found at i:15498 original size:15 final size:15
Alignment explanation
Indices: 15475--15523 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
15465 AAGGAACCCT
*
15475 TTTCCTTCCTTCCCC
1 TTTCTTTCCTTCCCC
15490 TTTCTTTCC-TCCCC
1 TTTCTTTCCTTCCCC
*
15504 TCTTCTTTCCTTCCCA
1 T-TTCTTTCCTTCCCC
15520 TTTC
1 TTTC
15524 CTTCTTACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.20
15 19 0.63
16 5 0.17
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTCTTTCCTTCCCC
Found at i:16518 original size:31 final size:31
Alignment explanation
Indices: 16393--16554 Score: 159
Period size: 31 Copynumber: 5.3 Consensus size: 31
16383 ATGGTGTCCG
*
16393 ACGTGGCATGCCATGTATACCAAAAAGCGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
* * * * *
16424 ATGTGACACGCCACGTGTACCAAAAATCGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
* * **
16455 ATGTGGCACGCCACATGTACCAAAAAGCGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
*
16486 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
* * * *
16517 ACGT-ACATGCCTTGTGCA-TAAAAAG-GAC
1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
*
16545 ACGTGCCATG
1 ACGTGGCATG
16555 TGTCATTTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.06
29 10 0.09
30 11 0.10
31 83 0.75
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (31 bp):
ACGTGGCATGCCATGTGTACCAAAAAGCGAC
Found at i:21601 original size:668 final size:650
Alignment explanation
Indices: 19869--21823 Score: 2272
Period size: 668 Copynumber: 3.0 Consensus size: 650
19859 CTTAGTATAT
* * * * *
19869 GATTTTGGCTAAAATTTTGCAAAAATTGACAAGAAATATATTTCCTCAATTTCTAGCGAAAAAAC
1 GATTTCGGCTAAAATTTTGCAAAAATTGACACGAAATATATTTTCTCAATTT-TAGCCAAAATAC
* * *
19934 TCATAAAAAATATATAATTCAAAGCCAAAAAAATTGTAAG-CCTTTTTCACGCATCTAATATCAT
65 TCATAAAAAATATATAATTCAAAGCCAAAAATATTG-AAGAAC-TTTTCACGCTTCTAATATCAT
* * *
19998 TTTTCCTATTTTATTTCCAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATACTCGTAAAA
128 TTTTCCTATTTT-TTT--GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
* * * * *
20063 ACAATTCCTTAAATACAATGTGGCTGAGATTTGTTTATATGAATATAGATATATTTTAAGGAGTC
190 ACAAATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGAAGTC
* ** * * *** ** * * * *
20128 TTGGCATAAAAAATCATGCAAAACTGACCCCAAGCTGCGGAACACATTTTTATCCAAAAAAC-CG
253 TCGGCGCAAAAAATCATGCAAAACTAAGCCGGGGCCCCAGAACGCATTTTTAACCAAAAAACGTG
* * * * * * * *
20192 -TGA-TAGTACTCGATTTCGGCTAAATTTTTGCAGAAATTGACTCGAAATATT-TTTCTCAAATT
318 ATGATTATTACACGATTTTGACTAAAATTTTGCAGAAATTGACCCG-AATGTTATTTCTCAATTT
* * * * * * * *
20254 TAGCCA-AATAACTTATAAAAATATATAATTCAATGCCAAAAAGATTGGAGGACTTCTCACGTTT
382 TAGCAACAAT-ACTCATAAAATTATATAATTCAAAGCCAAAAAGATTGAAGG-CTTATCATGCTT
* * * *
20318 TTAATATCGTTTTTCGTATTTTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGC
445 TTAATATCGTTTTTCCTATTATTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGC
* *** * * *
20383 TCGTAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATAATTCAAG
510 TTGTTTTACAAATCCTTAAATCCAATGT-GCTAAGATTTGGTTAGATAAATATAGATATTTCAAG
* * * * * *
20448 GAGTTTTGCTACCAAAAATCATGCAAAACTGACTTGGGGC-C----CG-TTTTAGCCAGAAAAAC
574 GAGTTTCGGTGCCAAAAATCATGCAACACTAAC-CGGGGCGCGAAGCGTTTTTAGCCAGAAAAAC
20507 CGTGATGATACAC
638 CGTGATGATACAC
* * *
20520 GATTTCGACTAAAATTTTGCAAAAATTGACCCGAAATAT-TTTTCCTCAATTTTTAGCCACAATA
1 GATTTCGGCTAAAATTTTGCAAAAATTGACACGAAATATATTTT-CTCAA-TTTTAGCCAAAATA
* * * *
20584 CTCATAAAACATATATTATTCAATGCCAAAAATATTG-AGAACTTTTCACGCTTTTAATATCATT
64 CTCATAAAAAATATATAATTCAAAGCCAAAAATATTGAAGAACTTTTCACGCTTCTAATATCATT
* * *
20648 TTTCATATTTTTTAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
129 TTTCCTATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAA
* * * * *
20713 ATCCTTAAATTCAATGTGACTGAGATTTAATTAGATGAATATGGATATTTCAAGAAGTCTCAGCG
194 ATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGCG
* * *
20778 CCAAAAATCGTGCAAAACTTAGCCGGGGCCCCA-AACGCATTTTTAACCAAAAAACCGTGATGAT
259 CAAAAAATCATGCAAAACTAAGCCGGGGCCCCAGAACGCATTTTTAACCAAAAAA-CGTGATGAT
* *
20842 TATTACACGATTTTGACTAAAATTTTGCAAAAATTGACCCGAAAGTTATTTTCTCAATTTTAGCA
323 TATTACACGATTTTGACTAAAATTTTGCAGAAATTGACCCGAATGTTA-TTTCTCAATTTTAGCA
* * * *
20907 ACAATACTGATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGTGCTTTTCATGCTTCTAAT
387 ACAATACTCAT-AAAATTATATAATTCAAAGCCAAAAAGATTGAAG-GCTTATCATGCTTTTAAT
*
20972 ATCGTTTTTCCTATTATTTTCTGAATTAATTTCTAATTAAATCGAAATATGATTCAGATGCTTGT
450 ATCGTTTTTCCTATTATTTTC-GAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT
*
21037 TTTACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGT
514 TTTACAAATCCTTAAATCCAATGTG-CTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGT
* *
21102 CTCGGTGCCAAAAATCATGCAACACTAAACCGGGGCCGCGGAATGCGTTTTTA-CTTTTTAGCCA
578 TTCGGTGCCAAAAATCATGCAACACT-AACCGGGG-CGC-GAA-GCGTTTTTAGC----CAG--A
21166 AAAACCGTGATGATTATTACAC
633 AAAACCGTGATG---A-TACAC
* * * * *
21188 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTTCTCAATTTTGGCTAAAATACA
1 GATTTCGGCTAAAATTTTGCAAAAATTGACACGAAATATATTTTCTCAATTTTAGCCAAAATACT
* * *** * *
21253 CATAAAAAATATATAATTCAACGCTAAAAATATTGAAGGGGTTTTAACGCTTCTAATATC-GTTT
66 CATAAAAAATATATAATTCAAAGCCAAAAATATTGAAGAACTTTTCACGCTTCTAATATCATTTT
* *
21317 TCCTACTTTTTTTGAATTAATTCCTAATTAAATCGAAACAAGATTTTGATGCTCGTAAAAACAAA
131 TCCTA-TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA
* *
21382 TCCTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGCGC
195 TCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGCGC
* * * * *
21447 GAAAAATCATGCAAAACTAAGCCGGGGCCCCAGAACGCGTTCTTAACCATAAATCGTGATGATTA
260 AAAAAATCATGCAAAACTAAGCCGGGGCCCCAGAACGCATTTTTAACCAAAAAACGTGATGATTA
* *
21512 TTACACGATTTTGAC-AAAATTTTGCAGAAATTGACCCGAATGTTATTTCCTTAATTTTTAGCGA
325 TTACACGATTTTGACTAAAATTTTGCAGAAATTGACCCGAATGTTATTT-CTCAA-TTTTAGCAA
* *
21576 CAATACTCATACACATTATATAATTCAAAGCCATAAAGATTGAAGGGCTTATCATGCTTTTAATA
388 CAATACTCATA-AAATTATATAATTCAAAGCCAAAAAGATTGAA-GGCTTATCATGCTTTTAATA
*
21641 TCTTTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTT
451 TCGTTTTTCCTATTATTTT-CGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTT
** *
21706 TTACAAATCCTCGAATCCAATGTTGCTAAGATTTGGTTAGATAAACATAGATATTTCAAGGAGTT
515 TTACAAATCCTTAAATCCAATG-TGCTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTT
* *
21771 TCGGTGCCAAAAATCATGCAACACTGAAGCAGGGTCGCGAAACGCGTTTTTAG
579 TCGGTGCCAAAAATCATGCAACACT-AA-CCGGGGCGCG-AA-GCGTTTTTAG
21824 TTGAAAACCG
Statistics
Matches: 1114, Mismatches: 143, Indels: 76
0.84 0.11 0.06
Matches are distributed among these distances:
643 19 0.02
644 39 0.04
645 1 0.00
646 91 0.08
647 34 0.03
648 22 0.02
649 99 0.09
650 125 0.11
651 84 0.08
652 4 0.00
658 3 0.00
659 5 0.00
662 2 0.00
664 13 0.01
666 3 0.00
667 85 0.08
668 456 0.41
669 29 0.03
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (650 bp):
GATTTCGGCTAAAATTTTGCAAAAATTGACACGAAATATATTTTCTCAATTTTAGCCAAAATACT
CATAAAAAATATATAATTCAAAGCCAAAAATATTGAAGAACTTTTCACGCTTCTAATATCATTTT
TCCTATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAAT
CCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGCGCA
AAAAATCATGCAAAACTAAGCCGGGGCCCCAGAACGCATTTTTAACCAAAAAACGTGATGATTAT
TACACGATTTTGACTAAAATTTTGCAGAAATTGACCCGAATGTTATTTCTCAATTTTAGCAACAA
TACTCATAAAATTATATAATTCAAAGCCAAAAAGATTGAAGGCTTATCATGCTTTTAATATCGTT
TTTCCTATTATTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTTTTACAA
ATCCTTAAATCCAATGTGCTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTTTCGGTGC
CAAAAATCATGCAACACTAACCGGGGCGCGAAGCGTTTTTAGCCAGAAAAACCGTGATGATACAC
Found at i:21785 original size:331 final size:329
Alignment explanation
Indices: 19877--21818 Score: 1846
Period size: 331 Copynumber: 5.9 Consensus size: 329
19867 ATGATTTTGG
** *
19877 CTAAAATTTTGCAAAAATTGACAAGAAA-TATATTTCCTCAATTTCTAGCGAA-AAAACTCATAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGT-TATTTCCTCAATTT-TAGC-AACAATACTCATAA
* * * * * * *
19940 AAAATATATAATTCAAAGCCAAAAAAATTGTAA-GCCTTTTTCACGCATCTAATATCATTTTTCC
63 AAATTATATAATTCAACGCCAAAAAGATTG-AAGGGC-TTTTCACGCTTTTAATATCGTTTTTCC
* * * * * *
20004 TATTTTATTTCCAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAATT
126 TA-TTT-TTT-CGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGT-AAAACAAAT
* * * * * * **
20069 CCTTAAATACAATGTGGCTGAGATTTGTTTATATGAATATAGATATATTTTAAGGAGTCTTGGCA
187 CCTTAAATCCAATGTTGCTGAGATTTGGTTAGATGAATATAG--ATATTTCAAGGAGTCTCGGTG
** * * *** * ** * * * *
20134 TAAAAAATCATGCAAAACTGACCCCAAGCTGCGGAACACATTTTTATCCAAAAAACC--G-TGA-
250 CCAAAAATCATGCAAAACTAAGCCGGGGC-CCCAAACGCGTTCTTAACCAAAAAACCGTGATGAT
* * *
20195 TAGTACTCGATTTCGG
314 TATTACACGATTTCGA
* * * * * * *
20211 CTAAATTTTTGCAGAAATTGACTCGAAA--TATTTTTCTCAAATTTAGCCA-AATAACTTATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTA-TTTCCTCAATTTTAGCAACAAT-ACTCATAAA
* * * * * *
20273 AA-TATATAATTCAATGCCAAAAAGATTGGAGGACTTCTCACGTTTTTAATATCGTTTTTCGTAT
64 AATTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA-
* * *
20337 TTTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCGTAAAAAAAATCCTTAA
128 TTTTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAACAAATCCTTAA
* * * * * * *
20402 ATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATAATTCAAGGAGTTTTGCTACCAAAAAT
193 ATCCAATGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
* * *
20467 CATGCAAAACTGA-CTTGGGG---C---C-CGTT-TTAGCCAGAAAAACCGTGATG---A-TACA
258 CATGCAAAACTAAGC-CGGGGCCCCAAACGCGTTCTTAACCA-AAAAACCGTGATGATTATTACA
20519 CGATTTCGA
321 CGATTTCGA
* *
20528 CTAAAATTTTGCAAAAATTGACCCGAAA-TATTTTTCCTCAATTTTTAGCCACAATACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGT-TATTTCCTCAA-TTTTAGCAACAATACTCATAAA
* * * ** * *
20592 ACA-TATATTATTCAATGCCAAAAATATTG-AGAACTTTTCACGCTTTTAATATCATTTTTCATA
64 A-ATTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA
* *
20655 TTTTTTAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
128 TTTTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGT-AAAACAAATCCTTA
* ** * * * *
20720 AATTCAATG-TGACTGAGATTTAATTAGATGAATATGGATATTTCAAGAAGTCTCAGCGCCAAAA
192 AATCCAATGTTG-CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAA
* * * *
20784 ATCGTGCAAAACTTAGCCGGGGCCCCAAACGCATTTTTAACCAAAAAACCGTGATGATTATTACA
256 ATCATGCAAAACTAAGCCGGGGCCCCAAACGCGTTCTTAACCAAAAAACCGTGATGATTATTACA
*
20849 CGATTTTGA
321 CGATTTCGA
* *
20858 CTAAAATTTTGCAAAAATTGACCCGAAAGTTATTTTCTCAATTTTAGCAACAATACTGATAAAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTATTTCCTCAATTTTAGCAACAATACTCATAAAAA
* * *
20923 TTATATAATTCAACGCCAAAAAGATTGAAGTGCTTTTCATGCTTCTAATATCGTTTTTCCTATTA
66 TTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATT-
* * ***
20988 TTTTCTGAATTAATTTCTAATTAAATCGAAATATGATTCAGATGCTTGTTTTACAAATCCTTAAA
130 TTTTC-GAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAACAAATCCTTAAA
*
21053 TCCAATG-TGACTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
194 TCCAATGTTG-CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
* * ** * *
21117 CATGCAACACTAAACCGGGGCCGCGGAATGCGTTTTTACTTTTTAGCC-AAAAACCGTGATGATT
258 CATGCAAAACTAAGCCGGGGCC-CCAAACGCG---TT-C---TTAACCAAAAAACCGTGATGATT
*
21181 ATTACACGATTTCGG
315 ATTACACGATTTCGA
* * * * *
21196 CTAAAATTTTGCAAAAATTGACTCGAAAGATATTTTCTCAATTTTGGCTAA-AATACACATAAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTATTTCCTCAATTTTAGC-AACAATACTCATAAAA
* * * * * *
21260 AATATATAATTCAACGCTAAAAATATTGAAGGGGTTTTAACGCTTCTAATATCG-TTTTCCTACT
65 ATTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA-T
* * * ** *
21324 TTTTTTGAATTAATTCCTAATTAAATCGAAACAAGATTTTGATGCTCGTAAAAACAAATCCTTAT
129 TTTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGT-AAAACAAATCCTTAA
* * * * *
21389 ATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGCGCGAAAAAT
193 ATCCAATGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
* *
21454 CATGCAAAACTAAGCCGGGGCCCCAGAACGCGTTCTTAACC-ATAAATCGTGATGATTATTACAC
258 CATGCAAAACTAAGCCGGGGCCCCA-AACGCGTTCTTAACCAAAAAACCGTGATGATTATTACAC
*
21518 GATTTTGA
322 GATTTCGA
* * * * * *
21526 C-AAAATTTTGCAGAAATTGACCCGAATGTTATTTCCTTAATTTTTAGCGACAATACTCATACAC
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTATTTCCTCAA-TTTTAGCAACAATACTCATAAAA
* * * * *
21590 ATTATATAATTCAAAGCCATAAAGATTGAAGGGCTTATCATGCTTTTAATATCTTTTTTCCTATT
65 ATTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATT
* *** **
21655 ATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTTTTACAAATCCTCGA
130 -TTTT-CGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAACAAATCCTTAA
* * * *
21720 ATCCAATGTTGCTAAGATTTGGTTAGATAAACATAGATATTTCAAGGAGTTTCGGTGCCAAAAAT
193 ATCCAATGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
* * * * *
21785 CATGCAACACTGAAGCAGGGTCGCGAAACGCGTT
258 CATGCAAAACT-AAGCCGGGGCCCCAAACGCGTT
21819 TTTAGTTGAA
Statistics
Matches: 1344, Mismatches: 212, Indels: 107
0.81 0.13 0.06
Matches are distributed among these distances:
316 6 0.00
317 46 0.03
318 57 0.04
319 126 0.09
320 31 0.02
322 1 0.00
324 1 0.00
325 37 0.03
326 16 0.01
327 51 0.04
328 40 0.03
329 82 0.06
330 201 0.15
331 216 0.16
332 109 0.08
333 11 0.01
334 26 0.02
335 2 0.00
336 38 0.03
337 105 0.08
338 135 0.10
339 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (329 bp):
CTAAAATTTTGCAAAAATTGACCCGAAAGTTATTTCCTCAATTTTAGCAACAATACTCATAAAAA
TTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTT
TTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAACAAATCCTTAAATC
CAATGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCAT
GCAAAACTAAGCCGGGGCCCCAAACGCGTTCTTAACCAAAAAACCGTGATGATTATTACACGATT
TCGA
Found at i:23706 original size:332 final size:328
Alignment explanation
Indices: 23076--23805 Score: 884
Period size: 332 Copynumber: 2.2 Consensus size: 328
23066 GCAATATTGT
*
23076 GGCTAAAATTTTGCAAAAAATTGACCCGAAA-ATTTTTTCCTCAATTTTTTGGAT-AAATACTCA
1 GGCTAAAATTTTG-AAAAAATTGACCCGAAAGA--TTTT-CTCAA--TTTTGGCTAAAATACTCA
* * *
23139 T--AATATATATAATTTAACGCCAAAAAGATTAGAGAACTTTTCACGCTTTGAATATCGTTTTTC
60 TAAAAAATATATAATTCAACGCCAAAAAGATTAGAGAACTTTTCACGCTTTGAATATCGTATTTC
* * *
23202 ATATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAAAATATTC
125 ATATTTTTTCGAATTAATTTCTAAATAAATCGAAACAAGATTTAAATACTCGTAAAAAAATATCC
* * ** * *
23267 TTAAATCCAATGGGGCTGAAATTTGTTTAGATGAATATGTATATCTCAAGGAGTCTTGGTGCAAA
190 TCAAATCCAATGGGGCTGAAATTTGATTAGATGAATATAAATATCTCAAGGAGTCTCGGAGCAAA
* * * *
23332 AAATCATTCAAAACTAAGCCCGGGCCCCAGAACGCTTTTTTAGCCAAAAACTGTGATGGTTATTA
255 AAATCATGCAAAACTAAGCCCGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
23397 CACGATTTC
320 CACGATTTC
*
23406 GGCTAAAATTTTGTAAAAATTGACCCGAAAGATAATTTCTCAATTTTGGCTAAAATACTCATAAA
1 GGCTAAAATTTTGAAAAAATTGACCCGAAAGAT--TTTCTCAATTTTGGCTAAAATACTCATAAA
** * * * * *
23471 AAATATATAATTCAACGCTGAAAAGGTT-GAAGGACTTTTGACG-TTTCTAATATCGTATTTCCT
64 AAATATATAATTCAACGCCAAAAAGATTAG-AGAACTTTTCACGCTTT-GAATATCGTATTTCAT
* *
23534 ATTTTTTTCCGAATTAATTTTTAAATAAATCGAAACAAGATTTAGATACTCGTAAAAACAA-ATC
127 A-TTTTTT-CGAATTAATTTCTAAATAAATCGAAACAAGATTTAAATACTCGTAAAAA-AATATC
* * * * *
23598 CTCAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGTAGTCTCGGAGCCA
189 CTCAAATCCAATGGGGCTGAAATTTGATTAGATGAATATAAATATCTCAAGGAGTCTCGGAGCAA
* * * *
23663 AAAATCATGCAAAATTGAG-CTGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
254 AAAATCATGCAAAACTAAGCCCGGG-CCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
*
23727 TACCCGATTTC
318 TACACGATTTC
* *
23738 AGCTAAAATTTT-ACAAAAATTGACACGAAAGATTTCTCTTCAATTTTCGGCTAAAATACTCATA
1 GGCTAAAATTTTGA-AAAAATTGACCCGAAAGATTT-TC-TCAATTTT-GGCTAAAATACTCATA
23802 AAAA
62 AAAA
23806 GAAGATTAGA
Statistics
Matches: 344, Mismatches: 40, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
327 7 0.02
328 11 0.03
329 25 0.07
330 68 0.20
331 12 0.03
332 199 0.58
333 22 0.06
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
GGCTAAAATTTTGAAAAAATTGACCCGAAAGATTTTCTCAATTTTGGCTAAAATACTCATAAAAA
ATATATAATTCAACGCCAAAAAGATTAGAGAACTTTTCACGCTTTGAATATCGTATTTCATATTT
TTTCGAATTAATTTCTAAATAAATCGAAACAAGATTTAAATACTCGTAAAAAAATATCCTCAAAT
CCAATGGGGCTGAAATTTGATTAGATGAATATAAATATCTCAAGGAGTCTCGGAGCAAAAAATCA
TGCAAAACTAAGCCCGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT
TTC
Found at i:24323 original size:15 final size:16
Alignment explanation
Indices: 24305--24334 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24295 ATAAATAATA
24305 ATATTATAAT-TAAAT
1 ATATTATAATATAAAT
24320 ATATTATAATATAAA
1 ATATTATAATATAAA
24335 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATATAAAT
Found at i:24333 original size:35 final size:34
Alignment explanation
Indices: 24294--24359 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
24284 GTTTCATGAC
* *
24294 TATAAATAATAA-TATTATAATTAAATATATTATAA
1 TATAAA-AATAATTATTAGAAGTAAAT-TATTATAA
24329 TATAAAAATAATTATTAGAAGTAAATTATTA
1 TATAAAAATAATTATTAGAAGTAAATTATTA
24360 ATTACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (34 bp):
TATAAAAATAATTATTAGAAGTAAATTATTATAA
Found at i:30422 original size:61 final size:60
Alignment explanation
Indices: 30305--30422 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
30295 GGGACATTTT
* * *
30305 CCCTAAAATTTTAATTTGGAACTTTCATCCATTAAAACTATCAAAATTAGGACAATTTCC
1 CCCTAAAATTTTAATTTGAAACTTTCATCCATTAAAACTATCAAAATCAAGACAATTTCC
* * * *
30365 CCCTTAAATTATTAATTTGAAATTTTCA-CCCTTTAAACTATCAAAATCAAGACCAATT
1 CCCTAAAATT-TTAATTTGAAACTTTCATCCATTAAAACTATCAAAATCAAGA-CAATT
30423 AATGCTGACG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 29 0.59
61 20 0.41
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (60 bp):
CCCTAAAATTTTAATTTGAAACTTTCATCCATTAAAACTATCAAAATCAAGACAATTTCC
Found at i:35347 original size:322 final size:318
Alignment explanation
Indices: 34755--35960 Score: 1196
Period size: 322 Copynumber: 3.8 Consensus size: 318
34745 GCATTGGCTG
* * *
34755 AGTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCAATGAACAAAATCCCAG
1 AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTC-ATGAACCAAATCCCAG
* ** *
34820 CCACGTTCGATTTAATTATTTGTTTTTACGAGACATCTGAATCTTGTTTCAATTTAATTA-AAAT
65 CCACATTCGATTTAAGGATTTGTTTTTACGAG-CATCTGAATCTTGTTTCGATTTAATTAGAAA-
* * * * * * * * *
34884 TTAATT-CGAAAAAAATGGAAAAACGATAATAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGT
128 TTAATTAGGAAAAAAATGGAAAAATGATATTAAAAGTGTGAAAAGACCTTCAATTTTTTTGGCGT
* * *
34948 TGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTTTT
193 TGAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAA-TATTCCGGTCAG-TTT
** *
35013 TTG-CTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTCCTGAGCCCCGACTC
256 TTGCCAAAAATCGTGTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTCC-GAGCCCCGACTC
* * * **
35077 AATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAG
1 AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCAT-GAACCAAATCCCAG
* * *
35142 TCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
65 CCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * *
35207 AATTAGGAAAAAATTGGAAAAATGATATTAAAAGTGTCAAAAGACCATCAATATTTTTGGTGTTG
130 AATTAGGAAAAAAATGGAAAAATGATATTAAAAGTGTGAAAAGACCTTCAATTTTTTTGGCGTTG
* *
35272 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAA-ATTCCTGGTCAGTTTTTA
195 AATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAATATTCC-GGTCAGTTTTT-
* * * *
35336 GCCAAAAATCGTGTACT---ATCATGATTTTTGGGCTAAAAACGCGTTTCGGGAGCCCCGGCTC
258 GCCAAAAATCGTGTACTAACATCACGGTTTTT-GGCTAAAAACGCG-TTC-CGAGCCCCGACTC
*
35397 AGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCAT----C---TCTCAG
1 AGTTTTGCATGATTTTTGGC-GTAAAGACTCCTTGAAATATCTATATTCATGAACCAAATCCCAG
* * * * *
35454 ACATATTAGATTTAAGGATTTGTTTTTACGAACATCTGAATATTGTTTCGATTTAATTAGAAA-T
65 CCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * * * * ** * *
35518 AGATTCGGAAAAAGATAGAACAATGATATTTAAAGAGAGAAAA-ATATTTTAATTTTTTTTGCGT
130 A-ATTAGGAAAAAAATGGAAAAATGATATTAAAAGTGTGAAAAGA-CCTTCAATTTTTTTGGCGT
* * * *
35582 TGAATTGTGTATTTTTTCTGACTATTGTGGCAAAAAAATTGAGAAAAAATTTTTCGGGTCAGTTT
193 TGAATTATATATTTTTTCTGACTATTGTGGC-AAAAAATTGAGAAAAAA-TATTCCGGTCAGTTT
* * * * * * *
35647 TTGCAAAACTTTCCCTGAAATCCTGTACTAAGCATCACGGTTTTTTGCGAAAACCACGTTCCGGG
256 TTGC-CAA---------AAATCGTGTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTCCGAG
35712 ACCCC-AGCTC
310 -CCCCGA-CTC
* *
35722 AGTTTTGCATGA-TTTTGGCGTAAAGTCTCCTTGAAATATCTATATTCATCGAACCAAATCCTAG
1 AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCAT-GAACCAAATCCCAG
* * ** * *
35786 CCAAATTCGATTTAACGATTTACTTTTACGAGGATCTGAATCTTGTTTCGTTTTAATTAGAAATT
65 CCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* *
35851 AATTCA--AAAAAAAAGGAAAAATGATATTAGAAGTGTGAAAA-ATCCTTCAATTTTTTTGGCGT
130 AATT-AGGAAAAAAATGGAAAAATGATATTAAAAGTGTGAAAAGA-CCTTCAATTTTTTTGGCGT
* * * * *
35913 TAAATTCTATATTATTTATGACTATTGTCGCAAAAAATTGAGAAAAAA
193 TGAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAA
35961 AAATTTCGTC
Statistics
Matches: 734, Mismatches: 108, Indels: 76
0.80 0.12 0.08
Matches are distributed among these distances:
311 3 0.00
312 134 0.18
313 18 0.02
314 13 0.02
315 4 0.01
318 10 0.01
319 12 0.02
320 70 0.10
321 41 0.06
322 191 0.26
323 12 0.02
324 36 0.05
325 22 0.03
326 9 0.01
327 10 0.01
329 1 0.00
330 17 0.02
331 69 0.09
332 60 0.08
333 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (318 bp):
AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATGAACCAAATCCCAGC
CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTAGGAAAAAAATGGAAAAATGATATTAAAAGTGTGAAAAGACCTTCAATTTTTTTGGCGTTGA
ATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAATATTCCGGTCAGTTTTTGCC
AAAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTCCGAGCCCCGACTC
Done.