Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011979.1 Corchorus capsularis cultivar CVL-1 contig12000, 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: 25197
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:227 original size:2 final size:2
Alignment explanation
Indices: 222--255 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
212 TTTTGCGATG
*
222 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256 TTGAATATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1466 original size:652 final size:645
Alignment explanation
Indices: 281--2392 Score: 2656
Period size: 652 Copynumber: 3.2 Consensus size: 645
271 AAAAACATAG
* * *
281 GCATCTTAATCCGGTTTCAATTTAATTAGAAATTAATTTCGAAAAAATAGGAAAAATGATATTAG
1 GCATCTTAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
* * * **
346 AAATGTCAGAAGCGCTTCAATTTTTTTTGGCGTTTAGTCATATATACTTTAATGAGTATTGTGGC
66 AAATGTCAGAAGCCCTTCAA-TTTTTTTGGCGTTGAGT--TATATATTTTTTTGAGTATTGTGGC
* *
411 CAAAAATTGAGGAGAAAATTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAAATCGTGTACTA
128 CAAAAATTGAGGAGAAAATTTTTGGGTCAA-TTTTTGCAAAATTTTAGCCG-AAATCATGTACT-
* * *
476 AACCATCACGGGTTTTGACTAAAAACGTGTTTCGGGGCACCGGCTCTGTTTTGCTTGATTTTCGG
190 AACCATCAC-GGTTTT-A-T---AAC----TAC---GCAGCGGCTCTGTTTTGCTTGATTTTTGG
* *
541 CGCCAAGTCTCATTGAAATATTTATATTCATCTAACAAAATCTCACCCACATTGGATTTAAGGA-
242 CGCCAAGTCTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATT-GATTTAAGGAT
* * *
605 TTTGATTTTACAAACATCTCAATCTGGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAAATAT
306 TTTG-TTTTAC-AGCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGG--AAAAAATAG
* * * * *
670 GAAAAATGATATTAGAAATGTCAAAAGCGCTTCAATTTTTATGGCGTTGAGTT-TTTTTTATTA-
367 GAAAAACGATATTAGAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATTTTTTTTTAT
* * * *
733 TTATTATTGTGGCCGAAATATTGAG-AAAATTTTCGGGTCAATTTCTTGCAAAATTTTAGCCCAA
432 TTA-TGTTGTGGCC-AAAAATTGAGCAAAAATTTCGGGTCAATTT-TTGCAAAATTTTAGCCGAA
* * * *
797 ATCGTGTACTATAACCATCATC-ATTTTCGACTAAAAACGCGATCCGGGACAGCGGCTCTGTTTT
494 ATCGTGTAC--TAACCATCA-CGGTTTTTGACTAAAAACGCGTTCCGGGACACCGGCTCTGTTTT
*
861 GCTTGATTTTTGGCGCCAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACAT
556 GCTTGATTTTTGGCACCAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACAT
*
926 TGGATTTGAGGATTTGATTTTACAA
621 TGGATTTAAGGATTTGATTTTACAA
** * *
951 GCATCTTAATTTGGTTTCGATTTAATTAGAAATTAATTTGGAAGAAATAGGAAAAGCGATATTAG
1 GCATCTTAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
*
1016 AAATGTCAGAAACCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCA
66 AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTT-TGAGTATTGTGGCCA
* * *
1081 AATATTGAGCAGAAAATTTTTGGGTCAATTTTTGGCAAAATTTTAGCCGAAATCATGTAATAACC
130 AAAATTGAGGAGAAAATTTTTGGGTCAATTTTT-GCAAAATTTTAGCCGAAATCATGTACTAACC
* * * * * *
1146 ATCACGGTTTT-TAACTACGCAGCGGCTCTATGTTGCTTTATTTTTTGTGCCAAGTCTCATCGAA
194 ATCACGGTTTTATAACTACGCAGCGGCTCTGTTTTGCTTGATTTTTGGCGCCAAGTCTCATTGAA
* *
1210 ATATCTATATTCATCTAACAAAATCTCAGCCACAATTGATTTATGGATTTTGTTATACATGCATC
259 ATATCTATATTCATCTAACAAAATCTCAGCCAC-ATTGATTTAAGGATTTTGTTTTACA-GCATC
* *
1275 TCAATCCGGTTTTGATTTAATTAGAAATTAATTTGG-AAAAATAGGAAAAACGATATTAGAAATG
322 TCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAATG
1339 TCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATTTTATTTTTATTTAGTGTTGTGGCCAAAAA
387 TCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATTTT-TTTTTATTTA-TGTTGTGGCCAAAAA
1404 TTGAGCAAAAAAATTTCGGGTCAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
450 TTGAGC--AAAAATTTCGGGTC-AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
* * * *
1469 CGGTTTTTGACTAAAAACACGTTCCGGGGCACCGGCTCTGTTATGCTTGATTTTTGGAACCAAGT
512 CGGTTTTTGACTAAAAACGCGTTCCGGGACACCGGCTCTGTTTTGCTTGATTTTTGGCACCAAGT
*
1534 CTCATCGAAATATCTATATTCATCTAACAAAATCTCGGCCACATTGGATTTAAGGATTTGATTTT
577 CTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGATTTT
1599 ACAA
642 ACAA
*
1603 GCAT-TTCAATCCGGTTTCGATTTAATTAGAAATTAAATTGGAAAAAATAGGAAAAACGATATTA
1 GCATCTT-AATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTA
* *
1667 GAAATGTCAGAAGCCCTTCAATTTTTTTGGCATTGAGTT-T-T-TTTTTTT-AGTATT-TAGCCA
65 GAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTTGAGTATTGTGGCCA
*
1727 AAAATTGAGGAGAAAATTTTTGGGTCAATATTTTGCAAAATTTTAGCCGAAATCTTGTACTAACC
130 AAAATTGAGGAGAAAATTTTTGGGTCAAT-TTTTGCAAAATTTTAGCCGAAATCATGTACTAACC
* *
1792 ATCACGGTTTTTGACTAAATACGCGTTCCGGAGCACCGGCTCTGTTTTGCTTGATTTTTGGCACC
194 ATCACGG-TTTT-A-TAACTA--CG---C--AG---CGGCTCTGTTTTGCTTGATTTTTGGCGCC
* * *
1857 AAGACTCATTGAAATATCTATATTCATTTAACAAAATCTCAGCCACATCGAATTTAAGGATTTAT
246 AAGTCTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTG-ATTTAAGGATTT-T
* *
1922 -TTTTGCGAGCATCTCAATCTGGTTTCGATGTAATTA-AAACTTAATTTGGAAAAAAATAGGAAA
309 GTTTTAC-AGCATCTCAATCTGGTTTCGATTTAATTAGAAA-TTAATTTGG-AAAAAATAGGAAA
* * * * *
1985 AACGATATTAGAAATGTGAGAAGTCTTTCAA-TTTTTTGGTGTTGACTTACTTTGTTTTTT-TTT
371 AACGATATTAGAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTA-TTT-TTTTTTATTT
* * * *
2048 A-G--GT---CAAAAATTGAGGCGAAAACTTTTGGGTCAATTTTTGCAAAAATTTAGCCGAAATA
434 ATGTTGTGGCCAAAAATTGA-GC-AAAAATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
*
2107 GTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGACACCGGCTCTGTTTTTCTTGA
497 GTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGACACCGGCTCTGTTTTGCTTGA
* * * *
2172 TTTTTGACATCATGTCTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATT
562 TTTTTGGCACCAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATT
2237 TAAGGATTCT--TTTTACAA
627 TAAGGATT-TGATTTTACAA
* * * * *
2255 GCATCTTAATCTGGTTTCGATTTAATTAGAACTTAATTTAGAAATAAATGGGTAAAACGATATTA
1 GCATCTTAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAA-AAATAGGAAAAACGATATTA
* *
2320 GAAATGTGAGAAGCCCTTCAATTTTTTT-GCGTTGAGTTATATATTTTTTTTAGTATTGTGGCCA
65 GAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTTGAGTATTGTGGCCA
*
2384 AAAACTGAG
130 AAAATTGAG
2393 ATATCTCAAT
Statistics
Matches: 1280, Mismatches: 116, Indels: 105
0.85 0.08 0.07
Matches are distributed among these distances:
646 68 0.05
647 14 0.01
648 1 0.00
649 62 0.05
650 10 0.01
651 19 0.01
652 411 0.32
653 208 0.16
654 64 0.05
655 17 0.01
656 6 0.00
657 17 0.01
659 10 0.01
660 115 0.09
661 22 0.02
662 49 0.04
663 1 0.00
665 6 0.00
666 9 0.01
667 24 0.02
668 55 0.04
669 16 0.01
670 76 0.06
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (645 bp):
GCATCTTAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTTGAGTATTGTGGCCAA
AAATTGAGGAGAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCAT
CACGGTTTTATAACTACGCAGCGGCTCTGTTTTGCTTGATTTTTGGCGCCAAGTCTCATTGAAAT
ATCTATATTCATCTAACAAAATCTCAGCCACATTGATTTAAGGATTTTGTTTTACAGCATCTCAA
TCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAATGTCAG
AAGCCCTTCAATTTTTTTGGCGTTGAGTTATTTTTTTTTATTTATGTTGTGGCCAAAAATTGAGC
AAAAATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
ACTAAAAACGCGTTCCGGGACACCGGCTCTGTTTTGCTTGATTTTTGGCACCAAGTCTCATCGAA
ATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACAA
Found at i:1830 original size:327 final size:328
Alignment explanation
Indices: 281--2392 Score: 2640
Period size: 333 Copynumber: 6.4 Consensus size: 328
271 AAAAACATAG
* * * * *
281 GCATCTTAATCCGGTTTCAATTTAATTAGAAATTAATTTCGAAAAAATAGGAAAAATGATATTAG
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
* * ** *
346 AAATGTCAGAAGCGCTTCAATTTTTTTTGGCGTTTAGTCATATATACTTTAATGAGTATTGTGGC
66 AAATGTCAGAAGCCCTTCAA-TTTTTTTGGCGTTGAGT--TATAT--TTTTTTTAGTATTGTGGC
411 CAAAAATTGAGGAGAAAATTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAAATCGTGTACTA
126 CAAAAATTGAGGAGAAAATTTTCGGGTCAA-TTTTTGCAAAATTTTAGCCG-AAATCGTGTACT-
* * * *
476 AACCATCACGGGTTTTGACTAAAAACGTGTTTCGGGGCACCGGCTCTGTTTTGCTTGATTTTCGG
188 AACCATCACGGTTTTTGACTAAAAACGCG-TTCCGGGCACCGGCTCTGTTTTGCTTGATTTTTGG
* * * *
541 CGCCAAGTCTCATTGAAATATTTATATTCATCTAACAAAATCTCACCCACATTGGATTTAAGGAT
252 CACCAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGAT
606 TTGATTTTACAA
317 TTGATTTTACAA
* * * *
618 ACATCTCAATCTGGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAAATATGAAAAATGATATT
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGG--AAAAAATAGGAAAAACGATATT
* * * * *
683 AGAAATGTCAAAAGCGCTTCAATTTTTATGGCGTTGAGTT-TTTTTTATTATTATTATTGTGGCC
64 AGAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATTTT-TT-TTAGTATTGTGGCC
* *
747 GAAATATT---GAGAAAATTTTCGGGTCAATTTCTTGCAAAATTTTAGCCCAAATCGTGTACTAT
127 -AAAAATTGAGGAGAAAATTTTCGGGTCAATTT-TTGCAAAATTTTAGCCGAAATCGTGTAC--T
* * * *
809 AACCATCATC-ATTTTCGACTAAAAACGCGATCCGGGACAGCGGCTCTGTTTTGCTTGATTTTTG
188 AACCATCA-CGGTTTTTGACTAAAAACGCGTTCCGGG-CACCGGCTCTGTTTTGCTTGATTTTTG
* *
873 GCGCCAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTGAGGA
251 GCACCAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGA
938 TTTGATTTTACAA
316 TTTGATTTTACAA
* * * *
951 GCATCTTAATTTGGTTTCGATTTAATTAGAAATTAATTTGGAAGAAATAGGAAAAGCGATATTAG
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
*
1016 AAATGTCAGAAACCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCA
66 AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATAT-TTTTTT-T-AGTATTGTGGCCA
* * * * *
1081 AATATTGAGCAGAAAATTTTTGGGTCAATTTTTGGCAAAATTTTAGCCGAAATCATGTAATAACC
128 AAAATTGAGGAGAAAATTTTCGGGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTGTACTAACC
* * * * * * **
1146 ATCACGG-TTTT---T---AA--C--TAC--GCAGCGGCTCTATGTTGCTTTATTTTTTGTGCCA
192 ATCACGGTTTTTGACTAAAAACGCGTTCCGGGCACCGGCTCTGTTTTGCTTGATTTTTGGCACCA
*
1198 AGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACAATT-GATTTATGGATTTTG
257 AGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCAC-ATTGGATTTAAGGA-TTTG
* *
1262 -TTATACAT
320 ATTTTACAA
* *
1270 GCATCTCAATCCGGTTTTGATTTAATTAGAAATTAATTTGG-AAAAATAGGAAAAACGATATTAG
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
*
1334 AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATTTTATTTTTATTTAGTGTTGTGGCC
66 AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTA---TATTTTT-TTTAGTATTGTGGCC
* * *
1399 AAAAATTGAGCAAAAAAATTTCGGGTCAAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
127 AAAAATTGAGGAGAAAATTTTCGGGTC-AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
* * *
1464 CATCACGGTTTTTGACTAAAAACACGTTCCGGGGCACCGGCTCTGTTATGCTTGATTTTTGGAAC
191 CATCACGGTTTTTGACTAAAAACGCGTTCC-GGGCACCGGCTCTGTTTTGCTTGATTTTTGGCAC
*
1529 CAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCGGCCACATTGGATTTAAGGATTTG
255 CAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTG
1594 ATTTTACAA
320 ATTTTACAA
* * *
1603 GCATTTCAATCCGGTTTCGATTTAATTAGAAATTAAATTGGAAAAAATAGGAAAAACGATATTAG
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
* *
1668 AAATGTCAGAAGCCCTTCAATTTTTTTGGCATTGAGTT-T-TTTTTTTTAGTATT-TAGCCAAAA
66 AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATTTTTTTTAGTATTGTGGCCAAAA
* *
1730 ATTGAGGAGAAAATTTTTGGGTCAATATTTTGCAAAATTTTAGCCGAAATCTTGTACTAACCATC
131 ATTGAGGAGAAAATTTTCGGGTCAAT-TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
*
1795 ACGGTTTTTGACTAAATACGCGTTCCGGAGCACCGGCTCTGTTTTGCTTGATTTTTGGCACCAAG
195 ACGGTTTTTGACTAAAAACGCGTTCCGG-GCACCGGCTCTGTTTTGCTTGATTTTTGGCACCAAG
* * * * *
1860 ACTCATTGAAATATCTATATTCATTTAACAAAATCTCAGCCACATCGAATTTAAGGATTT-ATTT
259 TCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGA-TT
* *
1924 TTGCGA
323 TTACAA
*
1930 GCATCTCAATCTGGTTTCGATGTAATTA-AAACTTAATTTGGAAAAAAATAGGAAAAACGATATT
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAA-TTAATTTGG-AAAAAATAGGAAAAACGATATT
* * * * * * *
1994 AGAAATGTGAGAAGTCTTTCAA-TTTTTTGGTGTTGACTTACT-TTGTTTTTT--T-TT-AGGTC
64 AGAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTA-TATT-TTTTTTAGTATTGTGGCC
* * *
2053 AAAAATTGAGGCGAAAACTTTT-GGGTCAATTTTTGCAAAAATTTAGCCGAAATAGTGTACTAAC
127 AAAAATTGAGGAGAAAA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
* * *
2117 CATCACGGTTTTTGACTAAAAACGCGTTCCGGGACACCGGCTCTGTTTTTCTTGATTTTTGACAT
191 CATCACGGTTTTTGACTAAAAACGCGTTCCGGG-CACCGGCTCTGTTTTGCTTGATTTTTGGCAC
* *
2182 CATGTCTCATTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTCT
255 CAAGTCTCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATT-T
2247 --TTTTACAA
319 GATTTTACAA
* * * * *
2255 GCATCTTAATCTGGTTTCGATTTAATTAGAACTTAATTTAGAAATAAATGGGTAAAACGATATTA
1 GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAA-AAATAGGAAAAACGATATTA
*
2320 GAAATGTGAGAAGCCCTTCAATTTTTTT-GCGTTGAGTTATATATTTTTTTTAGTATTGTGGCCA
65 GAAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAG-T-TATATTTTTTTTAGTATTGTGGCCA
*
2384 AAAACTGAG
128 AAAATTGAG
2393 ATATCTCAAT
Statistics
Matches: 1560, Mismatches: 151, Indels: 135
0.85 0.08 0.07
Matches are distributed among these distances:
318 59 0.04
319 194 0.12
320 24 0.02
321 5 0.00
322 2 0.00
323 1 0.00
324 4 0.00
325 84 0.05
326 177 0.11
327 262 0.17
328 56 0.04
329 11 0.01
330 21 0.01
331 55 0.04
332 42 0.03
333 343 0.22
334 64 0.04
335 57 0.04
336 7 0.00
337 35 0.02
338 15 0.01
339 42 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (328 bp):
GCATCTCAATCTGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAG
AAATGTCAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATTTTTTTTAGTATTGTGGCCAAAA
ATTGAGGAGAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
CGGTTTTTGACTAAAAACGCGTTCCGGGCACCGGCTCTGTTTTGCTTGATTTTTGGCACCAAGTC
TCATCGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTA
CAA
Found at i:3671 original size:335 final size:333
Alignment explanation
Indices: 2395--3782 Score: 1805
Period size: 335 Copynumber: 4.2 Consensus size: 333
2385 AAACTGAGAT
*
2395 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACGATATTAG-
1 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACAATATTAGA
* * *
2459 AATGTCAGAAGTCCTTCAATTTTTTTGGCGTTGAGTT-T-T-TTTTTTTAGTATT-TTG-GCCAA
66 AATGTGAGAAGCCCTTCAATTTTTTTGGCGTTAAGTTATATATTTTTTT-G-ATTATTGTGCCAA
* * * *
2519 AAATTGAGGAGAAAAATTTT-GGGTCAATTTTTTGCAAAACTTTAGCCGGAATCGTGTAATAACC
129 AAATTGAGGAG-AAAATTTTAAGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
** * * * *
2583 ATCACGGTTTTT-GACCCAAAACGCGTTTCGGAGCACCGACTCTGTTTTGCTTGATTTTTGGCGC
193 ATCACGGTTTTTAG-CTAAAAACGCGTTCCGGAGCACCGGCTCAGTTTTGCATGATTTTTGGCGC
* *
2647 AAAGTCTCATTGAAATATCTATATTCATCTAACA-AAATCTCAGCCACATTGGATTTAAGGATTT
257 CAAGACTCATTGAAATATCTATATTCATCTAACACAAATCTCAGCCACATTGGATTTAAGGATTT
* *
2711 GATTTTACAAAC
322 GTTTTTACAAGC
* *
2723 ATC-CTAATCCGGTTTCGATTTAATTAGAAATTATTTTGGAAAAAAATAGGAAAAACAATATAAG
1 ATCTC-AATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACAATATTAG
* * * *
2787 AAATGTGAGAAGTCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTTTAGTATTGTGGCCAA
65 AAATGTGAGAAGCCCTTCAATTTTTTTGGCGTTAAGTTATATATTTTTTTGATTATTGT-GCCAA
* * *
2852 AAATTGAGGAGAAAATTTTCAGGTCAATTTTTTGTAAAA-TTTAGCCGAAATCGTGTACTAAACA
129 AAATTGAGGAGAAAATTTTAAGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
* *
2916 TCACGGTTTTTTA-CTAAAAACGCGTTCCGGAGCACCGGCTCTA-TTTTGC-TTATTTTTGGTGC
194 TCACGG-TTTTTAGCTAAAAACGCGTTCCGGAGCACCGGCTC-AGTTTTGCATGATTTTTGGCGC
* *
2978 CAAGTCTCATTGAAATATCTATATTCATCTAACAC--TTGCTCAGCCACATTGGATTTAAGGATT
257 CAAGACTCATTGAAATATCTATATTCATCTAACACAAAT-CTCAGCCACATTGGATTTAAGGATT
3041 TGTTTTTACAAGC
321 TGTTTTTACAAGC
*
3054 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAATAATAGGAAAAACGATATTAG
1 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAA-AATAGGAAAAACAATATTAG
* * *
3119 AAATGTGAGAAGCCCTTCATTTTTTTTTTTTTTGCGTCAAGTTATATATTTTTTTGATTATTGGT
65 AAATGTGAGAAGCCCTTCA-----ATTTTTTTGGCGTTAAGTTATATATTTTTTTGATTATT-GT
*
3184 GCCAAAATTTGAGGAG-AAATTTTAAGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACT
124 GCCAAAAATTGAGGAGAAAATTTTAAGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACT
* *
3248 AATCATCACGGTTTTTAGCTAAAAACGCGTTTC-GAGGTC-CCGGCTCAGTTTTGCAT-ATTTTT
189 AACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGA-G-CACCGGCTCAGTTTTGCATGA-TTTT
* * * *
3310 TTGCACCAAGACTCATTGAAATATCTATATTCATCTAACA-TAATCTTAGCCACATTGGATTTAA
251 TGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACACAAATCTCAGCCACATTGGATTTAA
* *
3374 GGATTTGTCTTTACGAGC
316 GGATTTGTTTTTACAAGC
* * *
3392 ATCTCAACCCGGTGTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAGGGAAAACAATATTAG
1 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGG-AAAAAAATAGGAAAAACAATATTAG
*** * *
3457 AAATGTGAGAAGCCGCTTTTTTTTTTTTTTGCGTTAAGTAATATA-TTTTTTGATTATTGGTGCC
65 AAATGTGAGAAGCC-C-TTCAATTTTTTTGGCGTTAAGTTATATATTTTTTTGATTATT-GTGCC
* * * *
3521 AAAAATTGAGGAGAAATTTTTAAGGTCAACTTTTTGCAAAATTTTAGTCGAAATCGTATACTAAC
127 AAAAATTGAGGAGAAAATTTTAAGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
* * **
3586 CATCACGGTTTTTAGCTAAAAACGTGTTCCGGGGTTCCGGCTCAGTTTTGCATGATTTTTGGCGC
192 CATCACGGTTTTTAGCTAAAAACGCGTTCCGGAGCACCGGCTCAGTTTTGCATGATTTTTGGCGC
* * **
3651 CAGGACTCATTGAAATATCTATATTCATCTAA-AGAAATCTCAAACACATTGGATTTAAGGATTT
257 CAAGACTCATTGAAATATCTATATTCATCTAACACAAATCTCAGCCACATTGGATTTAAGGATTT
*
3715 GTTTTTACGAGC
322 GTTTTTACAAGC
* *
3727 ATCTTAATCCGGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATAGGAAAAAC
1 ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAAC
3783 GATACTAACC
Statistics
Matches: 945, Mismatches: 76, Indels: 72
0.86 0.07 0.07
Matches are distributed among these distances:
327 1 0.00
328 59 0.06
329 36 0.04
330 4 0.00
331 125 0.13
332 110 0.12
333 38 0.04
334 48 0.05
335 225 0.24
336 36 0.04
337 106 0.11
338 148 0.16
339 7 0.01
340 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (333 bp):
ATCTCAATCCGGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACAATATTAGA
AATGTGAGAAGCCCTTCAATTTTTTTGGCGTTAAGTTATATATTTTTTTGATTATTGTGCCAAAA
ATTGAGGAGAAAATTTTAAGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
ACGGTTTTTAGCTAAAAACGCGTTCCGGAGCACCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
ACTCATTGAAATATCTATATTCATCTAACACAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
TTACAAGC
Found at i:14250 original size:18 final size:17
Alignment explanation
Indices: 14223--14256 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
14213 TTGGTTCAGA
14223 TTCTTGTCTTATTTTTTC
1 TTCTTGTCTT-TTTTTTC
*
14241 TTCTTTTCTTTTTTTT
1 TTCTTGTCTTTTTTTT
14257 GCCCATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (17 bp):
TTCTTGTCTTTTTTTTC
Found at i:20880 original size:2 final size:2
Alignment explanation
Indices: 20873--20898 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20863 AACTAGTAGC
20873 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20899 GCTACTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24025 original size:15 final size:15
Alignment explanation
Indices: 24001--24033 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23991 ATTTTAGTTG
24001 ATTTTCAATGTCTTA
1 ATTTTCAATGTCTTA
*
24016 ATTTTGAATGTCTTA
1 ATTTTCAATGTCTTA
24031 ATT
1 ATT
24034 AGATTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (15 bp):
ATTTTCAATGTCTTA
Found at i:24259 original size:11 final size:10
Alignment explanation
Indices: 24238--24267 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
24228 AATTTACTTT
*
24238 AAAATAAAAA
1 AAAACAAAAA
24248 AAAACAAAAA
1 AAAACAAAAA
24258 AAAACAAAAA
1 AAAACAAAAA
24268 GGGAATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:25052 original size:21 final size:21
Alignment explanation
Indices: 25028--25067 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25018 TGACTAAAAA
25028 ATAATTTTTTAAAAAAAATAT
1 ATAATTTTTTAAAAAAAATAT
*
25049 ATAATTTTTTTAAAAAAAT
1 ATAATTTTTTAAAAAAAAT
25068 TTGGTGAGGG
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATTTTTTAAAAAAAATAT
Done.