Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010337.1 Corchorus capsularis cultivar CVL-1 contig10358, 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: 32849
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Found at i:688 original size:28 final size:28
Alignment explanation
Indices: 628--681 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
618 GAAAAAATAG
628 GAAAAACCATAAAATATAGATTTAATGC
1 GAAAAACCATAAAATATAGATTTAATGC
* *
656 CAAAAACCATTAAATATAGATTTAAT
1 GAAAAACCATAAAATATAGATTTAAT
682 CAGAAAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (28 bp):
GAAAAACCATAAAATATAGATTTAATGC
Found at i:1406 original size:331 final size:332
Alignment explanation
Indices: 699--3275 Score: 3311
Period size: 333 Copynumber: 7.7 Consensus size: 332
689 CTGAATTATA
* * * * * *
699 TCAGTTTTGAATGTTTTTTTGCATCGAGATTCCCTGAAATATCTATATTCATCTAATCAAATCTC
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* *
764 AGCCACATTCAATGTAATGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
* *
829 TTAATTTGAAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCTATAAATCTTTATGATG
131 TTAATTTG-AAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAG
* * * * * * * * *
894 -TGAATTATATATTTGTAATGAGTATTTTAGTCAAAATTTG-AGAAAAATCATATCGGGTCAGTT
195 TTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAAT-ATTTTGGTTCAATT
* * * * *
957 TTTCACAAAATTTTAGCCGAAATCGTGAACAAACCATCACGGTTTCTGGCTAAAAACGCGTTCTG
259 TTT-GCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGCGTTCTG
1022 GGGCCCCGGC
323 GGGCCCCGGC
* *
1032 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCAAATCAAATCTA
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
*
1097 AGCCATATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
* * *
1162 TTAATTTGAAAAAAATAGGAAAAA-AATATTTCAAGCATGAAAAGCCCATAAATCTTTTTGAAGT
131 TTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAGT
* *
1226 TGAATTATACATTTTTTATGAGTATTGTGGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTT
196 TGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTT
* * *
1291 TGCAAAGTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTCGCTGAAAACGCGGTAC-GGG
261 TGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGC-GTTCTGGG
*
1355 GCCCCGAC
325 GCCCCGGC
* * * * * *
1363 TTAGTTTTGCATGATTTTTGGCATCGAGATTCCTTCAAATATCTATATTCATCTAATTAAATCTA
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* *
1428 AGTCATATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
* * * * *
1493 TTAATTTGGAAAAAAAATAGGAAAAACTATATTTAAAGCATGAAAAGCCCGTAAATATTTTTGAA
131 TTAATTT-G-AAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAA
* *
1558 GTTG-ATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAAGAAAAATATTTTGGTTCAATT
194 GTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTTTGGTTCAATT
* * * *
1622 TTTGCAAAAATTTAGCCGAAATCGCGTACTAATCATCACGGTTTCTGGTTGAAAACGCGTTCCGG
259 TTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGCGTTCTGG
* **
1687 GACCCCGTT
324 GGCCCCGGC
* * * * *
1696 TCAGTTTTGCATGACTTTCGGTGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATTTC
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* * * *
1761 AGCCACATTGGATTTAAGTATTTGTTTTTACGAGCATC-AGAATCTTGTTTCGGTTTAATCAGAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTA-AATCTTGTTTCGATTTAATCAGAA
* * * * *
1825 ATTAACTTGAAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCACATAAGTCTTTACGAC
130 ATTAATTTG-AAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAA
* * * * * * ** *
1890 GTTGAATTATATAATTTTAATGAGTATTTTAGTCAAAAATTG-AGAAAAACCATATCAGATCAAT
194 GTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAA-TATTTTGGTTCAA-
* *
1954 TTTTTGCAAAATTTTAGCCGAAATCGTGTACAAATTACAAACCATCACAGTTTCTGGCTGAAAAC
257 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC----T---AATCATCACGGTTTCTGGCTGAAAAC
* *
2019 GCATTCAGGGGCCCCGGC
315 GCGTTCTGGGGCCCCGGC
* *
2037 TCAGTTTTGCATGATTTTTGGCATCGAGATTCCTTG-AA-A--TATATTCATCTAATCAAATCTC
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* * * * * *
2098 AGCCACATTGGATTTAAGGATTTGTTTTTATGAGCATTTGAATCTTGTTTCGATTTAATTAGAAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
* *
2163 TTAATTTGGAAAAAAATAGGAAAAACCATATTTGAATCATGAAAAGCCCATAAATCTTTTTGAAG
131 TTAATTT-GAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAG
* * * * * *
2228 -TGGATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTATGAAAAATGTTTTGGTTCAATTT
195 TTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTT
** * * * *
2292 TTGCAAAATTTTAGCCGAAATCGCATACTAATCCTCACAGTTTCTGGCTGAAAACGAGTTCT-AG
260 TTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGCGTTCTGGG
* *
2356 GACCCTGC
325 GCCCCGGC
* * *
2364 TCAGTTTTGCATGATTTTTGGCGTAGAAACTCCTTGAAATATATATATTCATCTAATCAAATCTC
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* *
2429 AGCAATATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAAAT-AGAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT-AATCAGAA
* ** *
2493 ATTAATTTGAAAAAAATAGGAAAAA-AATATTTCTAGCATGAAAAGCCCATAAATCTTTTTGAAG
130 ATTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAG
* * *
2557 TTGAATTAT-TCATTTTTTATGACTATTGTGGCCAAAAATTGAGGAAAAATATTTTGGTTCAATT
195 TTGAATTATAT-ATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTTTGGTTCAATT
* * *
2621 TTTGCAAAATTTTAGCCGAAATCGTATACTAATCATCACGGTTTCTAGCTGAAAACGCGTTCCGG
259 TTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGCGTTCTGG
2686 GGCCCCGGC
324 GGCCCCGGC
* * *
2695 TCAATTTTGCATGATTTTTAGTGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* * * * **
2760 AGCCATATTGGATTTAAGGATTTGTTTTTACGAGCATTTTGATCTTGTTTCGATTTAATCAGAAA
66 AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
* **
2825 TTAATTTGAAAAAAATAGGAAAAACCATATTTGAACCATGAAAAGCCCATAAATCTTTATGATTT
131 TTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAGT
* * * ** ***
2890 TGAATTCTATATTTTTTATGAGTATTTTAGTCAAAAATTGTGGAAATGCATTTCAT-G-TCAATT
196 TGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTT--TGGTTCAA-T
* * * *
2953 TTTTGCTAAATTTTAGCCGAAATCGTGTACAAATCATCACGGTTTATGGCTGAAAATGCGTTCTG
258 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGCGTTCTG
* *
3018 GGGCCCTGAC
323 GGGCCCCGGC
* * * * *
3028 TCAGTTTTACATGATTTTTGACGCCGAGACTCCTTGATATATCTATATTCATCTAATAAAATCTC
1 TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* * *
3093 AGCAACATTTGACT-TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAA
66 AGCCACATTCGA-TGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAA
* *
3157 ATTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCTATAAATCTTTATGACG
130 ATTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAG
* * * * * *
3222 TTGAATTTTATATTTTTTATGAGTATTTTAGTCAAAATTTGAGGAAAAACATTT
195 TTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTT
3276 CGGGGCCCCG
Statistics
Matches: 1969, Mismatches: 239, Indels: 72
0.86 0.10 0.03
Matches are distributed among these distances:
327 39 0.02
328 30 0.02
329 37 0.02
330 132 0.07
331 451 0.23
332 211 0.11
333 720 0.37
334 69 0.04
335 29 0.01
336 39 0.02
337 141 0.07
338 2 0.00
339 1 0.00
340 2 0.00
341 66 0.03
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (332 bp):
TCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
AGCCACATTCGATGTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAA
TTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATGAAGT
TGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAAGAAAAATATTTTGGTTCAATTTT
TGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTTCTGGCTGAAAACGCGTTCTGGGG
CCCCGGC
Found at i:3487 original size:260 final size:260
Alignment explanation
Indices: 3030--3538 Score: 779
Period size: 260 Copynumber: 2.0 Consensus size: 260
3020 GCCCTGACTC
* *
3030 AGTTTTACATGATTTTTGACGCCGAGACTCCTTGATATATCTATATTCATCTAATAAAATCTCAG
1 AGTTTTACATGATTTTTGACACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAG
* *
3095 CAACATTTGACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATT
66 CAACATTGGACTTAAGGATTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATT
* * *
3160 AATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCTATAAATCTTTATGACGTTG
131 AATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATAAAGTTG
* * *
3225 AATTTTATATTTTTTATGAGTATTTTAGTC-AAAATTTGAGGAAAAACATTTCGGGGCCCCGGCT
196 AATTATATATTTTTTATGAGTATTGTAGCCAAAAATTT-AGGAAAAACATTTCGGGGCCCCGGCT
3289 T
260 T
* * * * *
3290 AGTTTTGCATGATTTTTGCCACCGAGACTCCTTGAAATATCTATTTTGATCTAATCAAATCTCAG
1 AGTTTTACATGATTTTTGACACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAG
* * * *
3355 CCACATTGGA-TTCAAGGATTTGCTTTTATGAGTATCTGAATCTTGTTTCTATTTAATCAGAAAT
66 CAACATTGGACTT-AAGGATTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAAT
* *
3419 TAATTTGTAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTTTAAAGTT
130 TAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATAAAGTT
* *
3484 GAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTTAGGAAAAATATTTCGG
195 GAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTTAGGAAAAACATTTCGG
3539 TTCAATTTTT
Statistics
Matches: 224, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
259 2 0.01
260 215 0.96
261 7 0.03
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (260 bp):
AGTTTTACATGATTTTTGACACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAG
CAACATTGGACTTAAGGATTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATT
AATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAATCTTTATAAAGTTG
AATTATATATTTTTTATGAGTATTGTAGCCAAAAATTTAGGAAAAACATTTCGGGGCCCCGGCTT
Found at i:3901 original size:593 final size:588
Alignment explanation
Indices: 2719--4526 Score: 1482
Period size: 593 Copynumber: 3.0 Consensus size: 588
2709 TTTTTAGTGT
* * * *
2719 CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCATATTGGATTTAAGGATTTG
1 CGAGACTCCTTGAAATATCTATTTTGATCTAATCAAATCTCAGCCACATTGGATTCAAGGATTTG
*
2784 TTTTTACGAGCATTTTG-ATCTTGTTTCGATTTAATCAGAAATTAATTTGAAAAAAATAGGAAAA
66 TTTTTATGAGCA-TTTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGAAAAAAATAGGAAAA
* * * *
2848 ACCATATTTGAACCATGAAAAGCCCATAAATCTTTATGATTTTGAATTCTATATTTTTTATGAGT
130 ACCATATTTGAAGCATGAAAAGCCCATAAATCTTTTTGA-ATTGAATTATATATTTTTTATGAGT
* * * *** *
2913 ATTTTAGTCAAAAATTGT-GGAAATGCATTTC-ATGTCAATTTTTTGCTAAATTTTAGCCGAAAT
194 ATTGTGGCCAAAAATT-TAGGAAAAAAATTTCGGT-TCAA-TTTTTGC-AAATTTTAGCCGAAAT
* * * * * * * * * *
2976 CGTGTACAAATCATCACGGTTTATGGCTGAAAATGCGTTCTGGGGCCCTGACTCAGTTTTACATG
255 CGTGTACTAATCATCACAGTTTTTTGCTAAAAACGCTTTCCGGGGCCCCGGCTCAGTTTTACATG
* *** * ** * * *
3041 ATTTTTGACGCCGAGACTCCTTGATATATCTATATTCATCTAATAAAATCTCAGCAACATTTGAC
320 ATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCACACCAA-ATTCGA-
* * * *
3106 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATT-TGAAAA
383 TTAACGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* * * * * *
3170 AAATAGGAAAAACCATATTTGAAGCATG-AAAAGCCTATAAATC-TTTATGACGTTGAATTTTAT
448 AAAT-GGAAAAACGATATTAGAAGCGTGAAAAAGCCT-TCAACCGTTT-TGACATTGAA--TTAT
* * * * ** ** * ** **** *
3233 ATTTTTTATGAGTATTTTAGTCAAAATTT-GAGGAAAAACATTT--CGGGGCCCCG-G--CTTAG
508 ATTTTTTCTAAGTATTGT-GGCAATTTTTCG-GG-TCAA-TTTTCACCCGAAATCGTGTAC-TAA
** *
3292 TTTTGCA-TGATTTTTGCCA-C
568 CCTT-CACGGATTTTTGCCATC
3312 CGAGACTCCTTGAAATATCTATTTTGATCTAATCAAATCTCAGCCACATTGGATTCAAGGATTTG
1 CGAGACTCCTTGAAATATCTATTTTGATCTAATCAAATCTCAGCCACATTGGATTCAAGGATTTG
* * * * *
3377 CTTTTATGAGTATCTGAATCTTGTTTCTATTTAATCAGAAATTAATTTGTAAAAAATAGGAAAAA
66 TTTTTATGAGCATTTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGAAAAAAATAGGAAAAA
*
3442 CCATATTTGAAGCATGAAAAGCCCATAAATCTTTTTAAAGTTGAATTATATATTTTTTATGAGTA
131 CCATATTTGAAGCATGAAAAGCCCATAAATCTTTTTGAA-TTGAATTATATATTTTTTATGAGTA
*
3507 TTGTGGCCAAAAATTTAGGAAAAATATTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
195 TTGTGGCCAAAAATTTAGGAAAAAAATTTCGGTTCAATTTTTGC-AAATTTTAGCCGAAATCGTG
* * * * * * *
3572 TAGTAACCATCATAGTTTTTTGTTAAAAACGCTTTCCGGGGCCCCGGTTCGGTTTTGCA-GTATT
259 TACTAATCATCACAGTTTTTTGCTAAAAACGCTTTCCGGGGCCCCGGCTCAGTTTTACATG-ATT
* * * * * *
3636 TTTGGCATAAAGATTCTTTGAAATATCTGTATTCATCTAACCAAATCCCATCCAAATTCGATGTG
323 TTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCACA-CCAAATTCGAT-TA
*
3701 ACGATTTGTTTTTTCGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAA
386 ACGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAAA
* * *
3766 ATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAACCGTTTTGGCATTGAATTATATCTTTT
450 ATGGAAAAACGATATTAGAAGCGTGAAAAAGCCTTCAACCGTTTTGACATTGAATTATAT-TTTT
* *
3831 TCTTAGTATTGTGGCAATTTTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACGGCT
514 TCTAAGTATTGTGGCAATTTTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACGGAT
3896 TTTTGCTAAAACCACTTTC
579 TTTTG------CCA---TC
* * * *
3915 CAGGGCCTTGGCTCAGTTTTGCAAGATTTTTGACGTAAATACTCTTTGAAATATCTTATTCATCG
1 C-GAGAC-T--C-C----TTG-AA-A----T-A--T--CTA-T-TTTG----ATC-TAAT-----
* * * * *
3980 AACCAAATCCCAGCCTCATTCGATTCAACGATTTGTTTTTATGAGCATTTGAATTTTGTTTCGAT
34 ---CAAATCTCAGCCACATTGGATTCAAGGATTTGTTTTTATGAGCATTTGAATCTTGTTTCGAT
* * ** * ** * ** *
4045 TTAGTTAGAAATTAATTT-AAAAAAAT-GG-AAAATGATATTAGAAGCGCGAAAAACCTTTCAA-
96 TTAATCAGAAATTAATTTGAAAAAAATAGGAAAAACCATATTTGAAGCATGAAAAGCCCATAAAT
* * * * *
4106 CTGTTATTGCATTGAATTATATATTTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAAAAA
161 CT-TT-TTGAATTGAATTATATA-TTTTTTATGAGTATTGTGGCCAAAAATTTAG--GAAAAAAA
* * *
4171 TTTCGGGTCAA----T-----TTTTAGCCGAAATCGTGTACTAATTATTACAGTTTTTTGCTAAA
221 TTTCGGTTCAATTTTTGCAAATTTTAGCCGAAATCGTGTACTAATCATCACAGTTTTTTGCTAAA
* * * *
4227 AACACTTTCC-GAGACTCGGCTCAGTTTTACATGATTTTTGGCGTAAAGACTCCTTGAAATATCT
286 AACGCTTTCCGGGGCCCCGGCTCAGTTTTACATGATTTTTGGCGTAAAGACTCCTTGAAATATCT
* * * * *
4291 ATATTCATCGAACCAAATCACAGCCACATTCGATTTAACGATTTGTTTTTACGAGTATTCGGATC
351 ATATTCATCTAACCAAATCACA-CCAAATTCGA-TTAACGATTTGTTTTTACGAGCATTTGAATC
*
4356 TTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAATGGAAAAAGGATATTAGAAGCGTGAAAA
414 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAA
** *
4419 AAGCCTTCAACCGTTTTTTCATTGAATTATATTTTTTTCTAAGTATTGTGGCAATTTTTCAGGTC
478 AAGCCTTCAACCGTTTTGACATTGAATTATA-TTTTTTCTAAGTATTGTGGCAATTTTTCGGGTC
* *
4484 AATTTTCACCCGAGATCGTGTACTAACCTTCACGGTTTTTTGC
542 AATTTTCACCCGAAATCGTGTACTAACCTTCACGGATTTTTGC
4527 TAAAACCACT
Statistics
Matches: 985, Mismatches: 157, Indels: 120
0.78 0.12 0.10
Matches are distributed among these distances:
589 3 0.00
590 2 0.00
591 21 0.02
592 188 0.19
593 246 0.25
594 21 0.02
599 3 0.00
603 2 0.00
604 3 0.00
605 1 0.00
607 1 0.00
608 1 0.00
612 3 0.00
613 2 0.00
614 1 0.00
618 1 0.00
619 2 0.00
621 1 0.00
623 2 0.00
624 28 0.03
625 105 0.11
626 3 0.00
627 124 0.13
628 49 0.05
629 3 0.00
630 3 0.00
634 3 0.00
635 38 0.04
636 33 0.03
637 7 0.01
638 85 0.09
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (588 bp):
CGAGACTCCTTGAAATATCTATTTTGATCTAATCAAATCTCAGCCACATTGGATTCAAGGATTTG
TTTTTATGAGCATTTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGAAAAAAATAGGAAAAA
CCATATTTGAAGCATGAAAAGCCCATAAATCTTTTTGAATTGAATTATATATTTTTTATGAGTAT
TGTGGCCAAAAATTTAGGAAAAAAATTTCGGTTCAATTTTTGCAAATTTTAGCCGAAATCGTGTA
CTAATCATCACAGTTTTTTGCTAAAAACGCTTTCCGGGGCCCCGGCTCAGTTTTACATGATTTTT
GGCGTAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCACACCAAATTCGATTAACGAT
TTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAA
AAACGATATTAGAAGCGTGAAAAAGCCTTCAACCGTTTTGACATTGAATTATATTTTTTCTAAGT
ATTGTGGCAATTTTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACGGATTTTTGCC
ATC
Found at i:4452 original size:321 final size:321
Alignment explanation
Indices: 3850--4619 Score: 922
Period size: 321 Copynumber: 2.5 Consensus size: 321
3840 TGTGGCAATT
* *
3850 TTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACGGCTTTTTGCTAAAACCACTTTC
1 TTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACAGCTTTTTGCTAAAAACACTTTC
* * * * * *
3915 CAGGGCCTTGGCTCAGTTTTGCAAGATTTTTGACGTAAATACTCTTTGAAATATCTTATTCATCG
66 CAGAGACTCGGCTCAGTTTTACAAGATTTTTGACGTAAAGACTCCTTGAAATATCTTATTCATCG
* * * * *
3980 AACCAAATCCCAGCCTCATTCGATTCAACGATTTGTTTTTATGAGCATTTGAATTTTGTTTCGAT
131 AACCAAATCACAGCCACATTCGATTCAACGATTTGTTTTTACGAGCATTCGAATCTTGTTTCGAT
* * * *
4045 TTAGTTAGAAATTAATTTAAAAAAATGGAAAATGATATTAGAAGCGCGAAAAACCTTTCAACTGT
196 TTAATTAGAAATTAATTCAAAAAAATGGAAAAGGATATTAGAAGCGCGAAAAACCTTTCAACCGT
*
4110 TATTGCATTGAATTATATATTTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAAAAA
261 TATTGCATTGAATTATATATTTTTTTCTAAGTATTGTGGCAAAAAATTAAGAAAAAAAAAA
* * * * *
4171 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAA-TTATTACAGTTTTTTGCTAAAAACACTTT
1 TTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCT-TCACAGCTTTTTGCTAAAAACACTTT
* *
4235 CC-GAGACTCGGCTCAGTTTTACATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCAT
65 CCAGAGACTCGGCTCAGTTTTACAAGATTTTTGACGTAAAGACTCCTTGAAATATCT-TATTCAT
* * *
4299 CGAACCAAATCACAGCCACATTCGATTTAACGATTTGTTTTTACGAGTATTCGGATCTTGTTTCG
129 CGAACCAAATCACAGCCACATTCGATTCAACGATTTGTTTTTACGAGCATTCGAATCTTGTTTCG
** *
4364 ATTTAATTAGAAATTAATTCGGAAAAATGGAAAAAGGATATTAGAAGCGTGAAAAAAGCC-TTCA
194 ATTTAATTAGAAATTAATTCAAAAAAATGG-AAAAGGATATTAGAAGCGCG-AAAAA-CCTTTCA
* *
4428 ACCGTTTTTTCATTGAA-T-TATATTTTTTTCTAAGTATTGTGGC----AATT------------
256 ACCGTTATTGCATTGAATTATATATTTTTTTCTAAGTATTGTGGCAAAAAATTAAGAAAAAAAAA
4475 -
321 A
* * * * *
4475 TTTCAGGTCAATTTTCACCCGAGATCGTGTACTAACCTTCACGGTTTTTTGCTAAAACCACTTTC
1 TTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACAGCTTTTTGCTAAAAACACTTTC
** * * *
4540 CAG-GACCTCGGCTCAGTTTTGTAAGATTTTTTACGTAAAGACTCTTTTAAATA-CTATATTCAT
66 CAGAGA-CTCGGCTCAGTTTTACAAGATTTTTGACGTAAAGACTCCTTGAAATATCT-TATTCAT
4603 CGAACCAAATCACAGCC
129 CGAACCAAATCACAGCC
4620 TTGTAAAGAC
Statistics
Matches: 393, Mismatches: 48, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
304 85 0.22
305 42 0.11
317 4 0.01
320 47 0.12
321 171 0.44
322 19 0.05
323 23 0.06
324 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (321 bp):
TTTCGGGTCAATTTTCACCCGAAATCGTGTACTAACCTTCACAGCTTTTTGCTAAAAACACTTTC
CAGAGACTCGGCTCAGTTTTACAAGATTTTTGACGTAAAGACTCCTTGAAATATCTTATTCATCG
AACCAAATCACAGCCACATTCGATTCAACGATTTGTTTTTACGAGCATTCGAATCTTGTTTCGAT
TTAATTAGAAATTAATTCAAAAAAATGGAAAAGGATATTAGAAGCGCGAAAAACCTTTCAACCGT
TATTGCATTGAATTATATATTTTTTTCTAAGTATTGTGGCAAAAAATTAAGAAAAAAAAAA
Found at i:4645 original size:48 final size:48
Alignment explanation
Indices: 4574--4668 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
4564 GATTTTTTAC
4574 GTAAAGACTCTTTTAAATACTATATTCATCGAACCAAATCACAGCCTT
1 GTAAAGACTCTTTTAAATACTATATTCATCGAACCAAATCACAGCCTT
4622 GTAAAGACTCTTTTAAATACTATATTCATCGAACCAAATCACAGCCT
1 GTAAAGACTCTTTTAAATACTATATTCATCGAACCAAATCACAGCCT
4669 CGTTCGATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (48 bp):
GTAAAGACTCTTTTAAATACTATATTCATCGAACCAAATCACAGCCTT
Found at i:13088 original size:15 final size:15
Alignment explanation
Indices: 13064--13094 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13054 TACACGATGG
13064 AGAAAAAAAAATAAA
1 AGAAAAAAAAATAAA
*
13079 AGAAATAAAAATAAA
1 AGAAAAAAAAATAAA
13094 A
1 A
13095 ATTGAATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (15 bp):
AGAAAAAAAAATAAA
Found at i:24317 original size:2 final size:2
Alignment explanation
Indices: 24300--24367 Score: 65
Period size: 2 Copynumber: 36.0 Consensus size: 2
24290 CTAAAATTAT
* * *
24300 TA TA -A TA TA T- TT TA TA TA TA TA TA T- TA TA AA TCA GA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
24339 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24368 AATCAAATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
1 5 0.09
2 49 0.89
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24366 original size:39 final size:37
Alignment explanation
Indices: 24298--24372 Score: 123
Period size: 39 Copynumber: 2.0 Consensus size: 37
24288 CTCTAAAATT
*
24298 ATTATAATATATTTTATATATATATATTATAAATCAG
1 ATTATAATATATTATATATATATATATTATAAATCAG
24335 ATTATATATATATATATATATATATATATTATAAATCA
1 ATTATA-ATATAT-TATATATATATATATTATAAATCA
24373 AATCAGTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 6 0.17
38 6 0.17
39 23 0.66
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTATAATATATTATATATATATATATTATAAATCAG
Found at i:25696 original size:82 final size:81
Alignment explanation
Indices: 25555--25719 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 81
25545 TCCCCTTAAC
* *
25555 ATCCTTAACACAAGAGGAAAAAGGCTAATAAGCCTATGCAAAATCATAATGCAAAATCCTTGTTA
1 ATCCTTAACACAAGAGGAAAAAGGCTAATAAGCCTATGCAAAATCACAATGAAAAATCCTTGTTA
25620 TTGAAAAAAGTAATTG
66 TTGAAAAAAGTAATTG
* *
25636 ATCCTTTAACACAAGAGGGAAAAGGCTAATAAGCCTATGCGAAATCACAATGAAAAATCCTTGTT
1 ATCC-TTAACACAAGAGGAAAAAGGCTAATAAGCCTATGCAAAATCACAATGAAAAATCCTTGTT
25701 ATTGAAAAAAGTAATTG
65 ATTGAAAAAAGTAATTG
25718 AT
1 AT
25720 TAAAGAAAGG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 4 0.05
82 75 0.95
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.25
Consensus pattern (81 bp):
ATCCTTAACACAAGAGGAAAAAGGCTAATAAGCCTATGCAAAATCACAATGAAAAATCCTTGTTA
TTGAAAAAAGTAATTG
Found at i:32096 original size:1 final size:1
Alignment explanation
Indices: 32090--32114 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
32080 TAATAATAAT
32090 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
32115 GCTCTATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32347 original size:26 final size:27
Alignment explanation
Indices: 32288--32347 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
32278 TTCGCCACTT
**
32288 TAAATACATATCGAATAGAACGCTACTT
1 TAAATACATATCGAATAGAAC-CTACGG
32316 TAAATACATATCGAATAGAA-CTACGG
1 TAAATACATATCGAATAGAACCTACGG
*
32342 TGAATA
1 TAAATA
32348 GTATCTCACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 9 0.31
28 20 0.69
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (27 bp):
TAAATACATATCGAATAGAACCTACGG
Found at i:32635 original size:12 final size:10
Alignment explanation
Indices: 32607--32637 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
32597 CAAACTTTTC
32607 AATTCTCTCA
1 AATTCTCTCA
32617 AATTCTCTCA
1 AATTCTCTCA
32627 AATTCTCTCA
1 AATTCTCTCA
32637 A
1 A
32638 CCTTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTCTCTCA
Done.