Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022394.1 Corchorus olitorius cultivar O-4 contig22427, 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: 80438
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1151 original size:23 final size:23
Alignment explanation
Indices: 1125--1191 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1115 TTGATTGTTT
1125 CTTGTGAATTGTGTTGCCATGTG
1 CTTGTGAATTGTGTTGCCATGTG
* * *
1148 CTTGT--CTTG-ATTG---T-TT
1 CTTGTGAATTGTGTTGCCATGTG
1164 CTTGTGAATTGTGTTGCCATGTG
1 CTTGTGAATTGTGTTGCCATGTG
1187 CTTGT
1 CTTGT
1192 TGTTGCTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 14
0.61 0.12 0.27
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 3 0.10
19 3 0.10
20 3 0.10
21 3 0.10
22 1 0.03
23 11 0.35
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.49
Consensus pattern (23 bp):
CTTGTGAATTGTGTTGCCATGTG
Found at i:1153 original size:39 final size:39
Alignment explanation
Indices: 1110--1191 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
1100 TTGTCCATGA
1110 TTGTCTTGATTGTTTCTTGTGAATTGTGTTGCCATGTGC
1 TTGTCTTGATTGTTTCTTGTGAATTGTGTTGCCATGTGC
1149 TTGTCTTGATTGTTTCTTGTGAATTGTGTTGCCATGTGC
1 TTGTCTTGATTGTTTCTTGTGAATTGTGTTGCCATGTGC
1188 TTGT
1 TTGT
1192 TGTTGCTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.10, C:0.12, G:0.26, T:0.52
Consensus pattern (39 bp):
TTGTCTTGATTGTTTCTTGTGAATTGTGTTGCCATGTGC
Found at i:1697 original size:52 final size:52
Alignment explanation
Indices: 1619--2055 Score: 745
Period size: 52 Copynumber: 8.4 Consensus size: 52
1609 ATTTAAAAAG
1619 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
1671 TTTAAAAAATTTAGTAATTAGGGAGA-CGTATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCG-ATGAGGGCTGTCCCTCCAAACAT
*
1723 TTTAAAAAATTTAGTAATTAGGGAGACCTATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
* *
1775 TTTAAAAAACTTAGTAATTAGGGAGA-CGTATGAGGGCTGTCCCTCCAAATAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCG-ATGAGGGCTGTCCCTCCAAACAT
* *
1827 TTTAAAAAATTTGGTAATTAGGGAAACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
*
1879 TTTAAAAAATTTAGTAATTAGGGAGACCTATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
*
1931 TTTAAAAAAGTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACA-
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
* *
1982 TTTAAAAAGATCTAGTAATTAGGGAGACCGATGAGGGATGTCCCTCCAAACAT
1 TTTAAAAA-ATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
2035 TTTAAAAAATTTAGTAATTAG
1 TTTAAAAAATTTAGTAATTAG
2056 CATAGTGACA
Statistics
Matches: 362, Mismatches: 17, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
51 11 0.03
52 340 0.94
53 11 0.03
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (52 bp):
TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
Found at i:3271 original size:30 final size:30
Alignment explanation
Indices: 3235--3293 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3225 TAAAAAGGTC
3235 TGATGAGTTGGGTTTTAGAGCTAAGACTTG
1 TGATGAGTTGGGTTTTAGAGCTAAGACTTG
*
3265 TGATGAGTTGGGTTTTAGAGTTAAGACTT
1 TGATGAGTTGGGTTTTAGAGCTAAGACTT
3294 TTGAAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (30 bp):
TGATGAGTTGGGTTTTAGAGCTAAGACTTG
Found at i:5805 original size:334 final size:327
Alignment explanation
Indices: 4942--6290 Score: 1458
Period size: 334 Copynumber: 4.1 Consensus size: 327
4932 TATTTCAACG
* * * * * * *
4942 TTTTT-GGGATAG-TTTTACAAAATTTTGGCTGAAATCATGTAC--TAACCATCACTGTTTTTTG
1 TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTGTTA-CATCACAGTTTTTGG
*** * * * *
5003 CTAAAAACGCGTGTT-CTGGGCCCCGATTTAGTTTTGCATGA-TTTTGACAGTAGGACTCCTTTA
65 CTAAAAA--CGTGTTCCTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAA
* * * * * *
5066 AATATTTATATTCATCTAACTAAAACTCAGCCACAATGGATTTAAGGATAATTCTTTTACAAGCA
128 AATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAA-GCTTTTACGAGCA
* * * *
5131 TCTGAATTTTGTTTCGATTTAATTAGAAATTTATTCGGAAAAAT-G--ATAT--TAGAAGCCTAA
192 TCTGAATTATGTTTCGATTTAATTAGAAATTAATT-GGAAAAATAGAAATATAATTGAAGCCTGA
* ** *
5191 AAATCCCTTAAATTTTATTGTTGTTGAGTTAAATATTTTTTATGAGTATTGTGGCCAAAAATTGA
256 AAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGA
5256 GGAAAAA
321 GGAAAAA
* *
5263 TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTAC--TAACCATCACAGTTTTGGG
1 TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTGTTA-CATCACAGTTTTTGG
* * * * ** * *
5326 CTAAAAACGTGTTCTTTGGCCCTGACACAGTTTTGCATGATCTTTGGC-GCCAAGTGTCATTGAA
65 CTAAAAACGTGTTCCTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAG-CAAGACTCCTTAAA
* * * * * ** *
5390 GTATCTATATTCATCTAACCAATTCTCAGCCACATTGGACTGAAGGATTTGCTTTTAGGAGCATC
129 ATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAAGCTTTTACGAGCATC
*
5455 TGAATCATGTTTCGATTTAATTA-AGAATTAATTAGGAAAAAAATAGCAAATATGAAAATTGAAG
194 TGAATTATGTTTCGATTTAATTAGA-AATTAATT-GG--AAAAATAG-AAATAT---AATTGAAG
* ** * * ** * * *
5519 CATCTAAAGCCCTTCAGTCTTT-TTGGATTTGAATTATAAATTTTTTATGAGTTTTGTGGCCAAA
251 CCTGAAAAGCCCTTAAAT-TTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAA
5583 AATTGAGGAAAAA
315 AATTGAGGAAAAA
* * *
5596 TTTTTCGGGAGAGTTTTAGCAAAATTTTGGCCGAAATCGTGTACTGTTACATCACAGTTTTTGCC
1 TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTGTTACATCACAGTTTTTGGC
5661 TAAAAACGTGTTCCTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAAT
66 TAAAAACGTGTTCCTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAAT
* * * * * *
5726 ATCTATTTTCATCTAACCAAATATTAGACACAATGGATTAAAGGATAAGGTTTTACGAGCATCTA
131 ATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAAGCTTTTACGAGCATCTG
* * *
5791 AATTTTGTTTCGATTTAATTAGAAATTAATTCGAAAAATAGGAAAAATTATATTAGAAGCCTGAA
196 AATTATGTTTCGATTTAATTAGAAATTAATTGGAAAAATA-GAAATA-TA-ATT-GAAGCCTGAA
* * *
5856 AAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGAGGCAAAAAATTGAG
257 AAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAG
5921 GAAAAA
322 GAAAAA
* * ****
5927 ATTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATC--G---TG-TACATCTGTTTTTTTGGC
1 TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTGTTACATCACAGTTTTTGGC
* ** *
5986 TAAAAACGCGCATT-CTAGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACGCCTTAA
66 TAAAAACGTG--TTCCT-GGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAA
* * * * **
6050 AATATTTATATTCATCTATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGAGCAT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAAGCTTTTACGAGCAT
* *
6115 CTGAATTATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAT-G--ATAT--TAGAAGCCTGAA
193 CTGAATTATGTTTCGATTTAATTAGAAATTAATT-GGAAAAATAGAAATATAATTGAAGCCTGAA
*
6175 AAGCCCTTAAATTTTATTGGCGTAGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAG
257 AAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAG
6240 GAAAAA
322 GAAAAA
*
6246 TTTTCCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACT
1 TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACT
6291 TGGGCCCCGA
Statistics
Matches: 861, Mismatches: 131, Indels: 69
0.81 0.12 0.07
Matches are distributed among these distances:
319 112 0.13
320 1 0.00
321 13 0.02
322 69 0.08
323 104 0.12
324 9 0.01
325 23 0.03
326 5 0.01
327 132 0.15
328 11 0.01
329 2 0.00
330 6 0.01
331 110 0.13
332 2 0.00
333 108 0.13
334 150 0.17
335 4 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (327 bp):
TTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTGTTACATCACAGTTTTTGGC
TAAAAACGTGTTCCTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAAT
ATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAAGCTTTTACGAGCATCTG
AATTATGTTTCGATTTAATTAGAAATTAATTGGAAAAATAGAAATATAATTGAAGCCTGAAAAGC
CCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAA
AA
Found at i:6843 original size:607 final size:611
Alignment explanation
Indices: 5675--7552 Score: 2311
Period size: 655 Copynumber: 3.0 Consensus size: 611
5665 AACGTGTTCC
* * *
5675 TGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTCATCT
1 TGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGAAAGACGCCTTAAAATATCTATTTTCTTCT
* * * * *
5740 AACCAAATATTAGACACAATGGATTAAAGGATAAGGTTTTACGAGCATCTAAATTTTGTTTCGAT
66 AACTAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAA---T-TATCGA-
5805 TTAATTAGAAATTAATTCG-AAAAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATT
126 TT-ATT---AA-TAATTCGAAAAAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATT
* *
5869 TTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGAGGCAAAAAATTGAGGAAAAAATTTTCG
186 TTATTGACGTTGAGTTACATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCG
* * *
5934 GGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTAC-ATCTGT--TT-TTTTGGCTAAAAACGC
251 GGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACTATCATTGTTTTTGCTAAAAACGC
* * *
5995 GCATTCTAGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACGCCTTAAAATATTTATA
316 GCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATA
6060 TTCATCTATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGAGCATCTGAATTATG
381 TTCATCTATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGAGCATCTGAATTATG
*
6125 TTTCGATTTAATCAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTT
446 TTTCGATTTAATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTT
* * *
6190 ATTGGCGTAGAGTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTCCGGG
511 ATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTTTTCGGG
6255 ACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACT
576 ACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACT
6291 TGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGAAAGACGCCTTAAAATATCTATTTTCTTCT
1 TGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGAAAGACGCCTTAAAATATCTATTTTCTTCT
*
6356 AACTAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTACATTAT-G-TT-TT
66 AACTAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATCGATTATT
6418 -A-AA-TCGAAAAAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGACGT
131 AATAATTCGAAAAAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGACGT
*
6480 TGAGTTACATATTTTTTATGAGTATTGTGGCTAAAAAATT-AGCAAAAAATTTTCGGGATAGTTT
196 TGAGTTACATATTTTTTATGAGTATTGTGGC-AAAAAATTGAGGAAAAAATTTTCGGGATAGTTT
* * ** *
6544 TTGAAAAAATTTGGCCGAAATCGTACACTAACTATCATTGTTTATTGCAAAAAAACGCGCGTTCT
260 TTGCAAAATTTTGGCCGAAATCGTGTACTAACTATCATTGTTT-TTGC-TAAAAACGCGCGTTCT
* *
6609 GGGGCCCCGACTTAGTTTTGTATGATTTTTGGCAGCAATACTCCTTAAAATATTTATATTCATCT
323 GGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCT
*
6674 ATCCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGAGCATCTGAATTATGTTTCGAT
388 ATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGAGCATCTGAATTATGTTTCGAT
* * *
6739 TTAATTAGAAATTAATTCGGAAAAATGATATTAAAAGCCTGAAAAGCCCTTAAAGTTTATTGGTG
453 TTAATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCG
* *
6804 TTGAGTTATATATTTTTTATGAGTATTGTTGCAAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
518 TTGAGTTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
*
6869 TTGCAAAATTTTGGCTGAAATCGTGTAC-
583 TTGCAAAATTTTGGCCGAAATCGTGTACT
** * * * * * * *
6897 T---AACC-ATCACAGTTTTTGGTTAAAAACGCGTTCTTGGGCCCCGGCACAATTTTGCATGATT
1 TGGGCCCCGA-CACAG-TTTT-G-----CATG-ATT-TTTGG---CAG-A-AA----G-ACG--C
* * * * **
6958 TTTGGCAGCAATACTCCTTAAAATATCTATTTTCT-TCTAACCAAATCTCAGATGCAATGGATTT
44 CTT---A-AAATA-T-C-T---AT-T-T-TCTTCTAACT-A---AATCTCAGACACAATGGATTT
*
7022 AAGTATAAGGTTTTACGAGCATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCGAAAAAAT
92 AAGGATAAGGTTTTACGAGCATCTAAATTA----TCGA-TT-ATT---AA-TAATTCGAAAAAAT
* * * *
7087 A-GAAAAATCATATTAGAAGCCTGAAAAGCCCTAAAATTTTACTGCCGTTGAGTTACATATTTTT
147 AGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGACGTTGAGTTACATATTTTT
* * *
7151 TATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAGTTTTTTGCAAAATTTTGGCT
212 TATGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGATAG-TTTTTGCAAAATTTTGGCC
* * * * *
7216 GAAATCGTGTACTAACCATCACTGTTTTTTGCTAAAAACGCGTGTTCTGGGGTCTCGACTTAGTT
276 GAAATCGTGTACTAACTATCATTG-TTTTTGCTAAAAACGCGCGTTCTGGGGCCCCGACTTAGTT
* * *
7281 CTGCATGATTTTTGTCAGCAAGACTCCTTAAAAT-TTATATATTCATCTAACCAAATCTCAGCCA
340 TTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATT-TATATTCATCTATCCAAATCTCAGCCA
* * * *
7345 CAATGGATTTAAGAATAAATTTTTATGAGCATCTGAATTATTTTTCGATTTAATTAGAAATTATT
404 CAATGGATTTAAGAATAATTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAAT
* * *
7410 TCGAAAAAATGATACTAGAAGCCTGAAAAACCCTTAAATTTTATTGGCGTTGAGTTATATATTTT
469 TCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTT
* * * * * *
7475 ATATGAGTATTATAGCCTAAAATTAAGGAAAAATTTTTTGGGACAATTTTTGCAAAATTTTGGCC
534 TTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCC
7540 GAAATCGTGTACT
599 GAAATCGTGTACT
7553 AACCATCACA
Statistics
Matches: 1099, Mismatches: 95, Indels: 96
0.85 0.07 0.07
Matches are distributed among these distances:
600 3 0.00
601 133 0.12
602 13 0.01
603 8 0.01
604 6 0.01
605 4 0.00
606 4 0.00
607 290 0.26
609 2 0.00
610 2 0.00
611 3 0.00
612 6 0.01
613 1 0.00
615 2 0.00
616 111 0.10
617 2 0.00
621 1 0.00
622 2 0.00
624 2 0.00
627 1 0.00
628 4 0.00
629 1 0.00
630 1 0.00
631 1 0.00
634 2 0.00
635 1 0.00
636 3 0.00
637 6 0.01
640 47 0.04
644 1 0.00
645 1 0.00
647 2 0.00
649 2 0.00
653 1 0.00
654 9 0.01
655 367 0.33
656 51 0.05
657 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (611 bp):
TGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGAAAGACGCCTTAAAATATCTATTTTCTTCT
AACTAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATCGATTATT
AATAATTCGAAAAAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGACGT
TGAGTTACATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGATAGTTTT
TGCAAAATTTTGGCCGAAATCGTGTACTAACTATCATTGTTTTTGCTAAAAACGCGCGTTCTGGG
GCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCTATC
CAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGAGCATCTGAATTATGTTTCGATTTA
ATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGTTG
AGTTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTG
CAAAATTTTGGCCGAAATCGTGTACT
Found at i:7527 original size:655 final size:653
Alignment explanation
Indices: 6289--8727 Score: 2684
Period size: 655 Copynumber: 3.7 Consensus size: 653
6279 AAATCGTGTA
* * * *
6289 CTTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGAAAGACGCCTTAAAATATCTATTTTCTT
1 CTTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATATTCAT
* *
6354 CTAACTAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTACATTA----T-G
66 CTAACCAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATGTTTCG
*
6414 --TT--TT----A--AA-TCGAAAAAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAA
131 ATTTAATTAGAAATTAATTCGAAAAAATA-GAAAAATCATATTAGAAGCCTGAAAAGCCCTTAAA
* * *
6468 TTTTATTGACGTTGAGTTACATATTTTTTATGAGTATTGTGGCTAAAAAATT-AGCAAAAAATTT
195 TTTTACTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGC-AAAAAATTGAGGAAAAAATTT
* * * ** * ** *
6532 TCGGGATAGTTTTTGAAAAAATTTGGCCGAAATCGTACACTAACTATCATTGTTTATT-GCAAAA
259 TCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTT-TTGGC-TAA
* * *
6596 AAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGTATGATTTTTGGCAGCAATACTCCTTAAAATA
322 AAACGCGTGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAAT-
* *
6661 TTTATATTCATCTATCCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGAGCATCTGA
386 TTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAATTTTTACGAGCATCTGA
* *
6726 ATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATGATATTAAAAGCCTGAAAAGCCCTTA
451 ATTATGTTTCGATTTAATTAGAAATTAATTCGAAAAAATGATATTAGAAGCCTGAAAAGCCCTTA
* * * *
6791 AAGTTTATTGGTGTTGAGTTATATATTTTTTATGAGTATTGTTGCAAAAAATTGAGGAAAAATTT
516 AATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTT
*
6856 TTCGGGACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACTAACCATCACAGTTTTTGGTTAAA
581 TTCGGGACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAA
6921 AACGCGTT
646 AACGCGTT
* * * * *
6929 CTTGGGCCCCGGCACAATTTTGCATGATTTTTGGCAGCAATACTCCTTAAAATATCTATTTTCTT
1 CTTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATATTCAT
** *
6994 CTAACCAAATCTCAGATGCAATGGATTTAAGTATAAGGTTTTACGAGCATCTAAATTATGTTTCG
66 CTAACCAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATGTTTCG
*
7059 ATTTAATTAGAAATTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGCCCTAAAAT
131 ATTTAATTAGAAATTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGCCCTTAAAT
* * *
7124 TTTACTGCCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTC
196 TTTACTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTC
* * * *
7189 GGGATAGTTTTTTGCAAAATTTTGGCTGAAATCGTGTACTAACCATCACTGTTTTTTGCTAAAAA
261 GGGACAG-TTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
* * * *
7254 CGCGTGTTCTGGGGTCTCGACTTAGTTCTGCATGATTTTTGTCAGCAAGACTCCTTAAAATTTAT
325 CGCGTGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATTT-T
* *
7319 ATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATAAATTTTTATGAGCATCTGAATT
389 ATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAATTTTTACGAGCATCTGAATT
* * * *
7384 ATTTTTCGATTTAATTAGAAATTATTTCGAAAAAATGATACTAGAAGCCTGAAAAACCCTTAAAT
454 ATGTTTCGATTTAATTAGAAATTAATTCGAAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAAT
* * * * *
7449 TTTATTGGCGTTGAGTTATATATTTTATATGAGTATTATAGCCTAAAATTAAGGAAAAATTTTTT
519 TTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTTTTC
* *
7514 GGGACAATTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC
584 GGGACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC
7579 GCGTT
649 GCGTT
* * * * *
7584 CTTGGGCTCCGACACAGTTTTGCATGATTTATGGC-GCCAA-ATTTCATTGAAATATCTATATTC
1 CTTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAG-CAAGA-CTCCTTAAAATATCTATATTC
** * * ** * * *
7647 ATCTAACCACTTCTCAG-CGACATTGGATTGAAGGATTTGTTTTTACGAGCATCTGAATCATGTT
64 ATCTAACCAAATCTCAGAC-ACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATGTT
* * * * * **
7711 TCGATTTAATTAGAAATTAATTTGGAAAAAAATCG-GAAATACGAAAATT-GAAGCATCTAAAGC
128 TCGATTTAATTAGAAATTAA-TTCG-AAAAAATAGAAAAAT-C--ATATTAGAAGCCTGAAAAGC
* * ** * * * * * *
7774 CCTTCAGTCTTT-CTGGATTTGAATTATATATCTTTTATGAGTGTTGTGGCCAAAAATTGAGAAA
188 CCTTAAAT-TTTACTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAA
*
7838 AAAATTTTCGGGACAGTTTTTGCAAAATTTTGCCCGAAATCGTGTACGT-----T-ACAGTTTTT
252 AAAATTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTAC-TAACCATCACAGTTTTT
* * * **
7897 GGTTAAAAACGC--GTTCTTGGGCCCCGGCACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTT
316 GGCTAAAAACGCGTGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTT
* * * * *** ** *
7960 AAAATATCTATTTTCTTCTAACCAAACCTCAGATGCAATGGATTTAAGGATAAGGTTTTACGAGT
381 AAAAT-TTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAATTTTTACGAGC
*
8025 ATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAATTATATTAGAAG
445 ATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGAAAAAAT--G-------ATATTAGAAG
* * * * * *
8090 CCTGATAAGCCCTAAAATTTTACTGCCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAAAA
501 CCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTAGCCAAAA
* * *
8155 ATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGG-TCGAAATCGTGCAGTAACCATC
566 ATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCT-GAAATCGTGTACTAACCATC
** *
8219 ATTGTTTTTTGCTAAAAACGCGCGTT
630 ACAGTTTTTGGCTAAAAA--CGCGTT
* ** * * *
8245 CTAGGGCCCCGACTTAGTTTTGCATAATTTTTGGCAGTAAGACTCCTTAAAATATTTATATTCAT
1 CTTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATATTCAT
* * * ** * *** **
8310 CTATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACAATTTTGCCCGAATTATGTTT
66 CTAACCAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCAT--CTAAATTATGTTT
* *
8375 CGATTTAATTAGAAATTAATTCG--------GAAAAATGATATTAGAAGGCTGAAAAGCCCTTAA
129 CGATTTAATTAGAAATTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGCCCTTAA
* * * *
8432 ATTTTATTGGTGTTGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATTTT
194 ATTTTACTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAATTT
*
8497 TCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGTTAAAA
259 TCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAA
** * * ** * *
8562 ACGC--GTTCTTCGGCCCATGCAC--AGTTTTGCATGATCTTTGGC-GCCAAGTGTCATTTAAAT
324 ACGCGTGTTCTGGGGCCC-CG-ACTTAGTTTTGCATGATTTTTGGCAG-CAAGACTCCTTAAAAT
* ** * * * *** * *
8622 ATCTATATTCATCTAACTGATTCTCAGCCACATTGGATTTAATGATTTGTTTTTATGAGCATTTG
386 -TTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAATTTTTACGAGCATCTG
* * * *
8687 AATTTTGTTTCAATTTAATTAGAAAGTAATTTGGAAAAAAT
450 AATTATGTTTCGATTTAATTAGAAATTAA-TTCGAAAAAAT
8728 AGGAAATGCG
Statistics
Matches: 1518, Mismatches: 220, Indels: 104
0.82 0.12 0.06
Matches are distributed among these distances:
640 113 0.07
644 1 0.00
645 1 0.00
647 2 0.00
649 2 0.00
650 136 0.09
651 9 0.01
652 124 0.08
653 3 0.00
654 15 0.01
655 521 0.34
656 61 0.04
657 174 0.11
658 86 0.06
659 143 0.09
661 91 0.06
662 6 0.00
663 30 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (653 bp):
CTTGGGCCCCGACACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATATTCAT
CTAACCAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATGTTTCG
ATTTAATTAGAAATTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGCCCTTAAAT
TTTACTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTC
GGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC
GCGTGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATTTTAT
ATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAATTTTTACGAGCATCTGAATTAT
GTTTCGATTTAATTAGAAATTAATTCGAAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTT
TATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATTTTTCGG
GACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGC
GTT
Found at i:8831 original size:983 final size:973
Alignment explanation
Indices: 6292--8869 Score: 3358
Period size: 983 Copynumber: 2.6 Consensus size: 973
6282 TCGTGTACTT
** * * * * * * * *
6292 GGGCCCCGACACAGTTTTGCATGATTTTTGGCAGAAAGACGCCTTAAAATATCTATTTTCTTCTA
1 GGGCCCCGACTTAGTTCTGCATAATTTTTGGCAGCAAGACTCCTTAAAATTTATATATTCATCTA
* * * ** * *
6357 ACTAAATCTCAGACACAATGGATTTAAGGATAAGGTTTTACGAGCAT-CTACATTATG--T---T
66 ACCAAATCTCAGCCACAATGGATTTAAGAATAAATTTTTACAAGCATCCGA-ATTATGTTTCGAT
* * * * * *
6416 TTAAATCGAAA--AAATAGGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGACG
130 TTAATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCG
* * * *
6479 TTGAGTTACATATTTTTTATGAGTATTGTGGCTAAAAAATTAGCAAAAAATTTTCGGGATAGTTT
195 TTGAGTTATATATTTTTTATGAGTATTGTGGC-AAAAAATTAGGAAAAATTTTTCGGGACAGTTT
* * ** * ** * *
6544 TTGAAAAAATTTGGCCGAAATCGTACACTAACTATCATTGTTTATTGCAAAAAAACGCGCGTTCT
259 TTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTT-TTGGATAAAAA--CGCGTTCT
* * * *
6609 GGGGCCC-CGACTTAGTTTTGTATGATTTTTGGCAG-CAATACTCCTTAAAATATTTATATTCAT
321 TGGGCCCGC-AC--AGTTTTGCATGA-TTTTGGC-GCCAAT-CTCATTAAAATATCTATATTCAT
* * * *
6672 CTATCCAAATCTCAGCCACAATGGATTTAAGGATAAT-TTTTTACGAGCATCTGAATTATGTTTC
380 CTA-ACAATTCTCAGCCACATTGGATTTAAGGAT-TTGTTTTTACGAGCATCTGAATTATGTTTC
* * * ** *
6736 GATTTAATTAGAAATTAATTCGG-AAAAAT-GATAT---TAA--AAGCCTGAAAAGCCCTTAAAG
443 GATTTAATTAGAAATTAATTTGGAAAAAATGGAAATCGATAATGAAGCATCTAAAGCCCTT-CAG
* * * *
6794 T-TTATTGG-TGTTGAGTTATATATTTTTTATGAGTATTGTTGCAAAAAATTGAGGAAAAATTTT
507 TCTTTTTGGAT-TTAAG-TATATAATTTTTATGAGTATTG-TGCCAAAAATTGAGGAAAAATTTT
6857 TCGGGACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTAC-TAACCATCACAGTTTTTGGTTAAA
569 TCGGGACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACGT----ATCACAGTTTTTGGTTAAA
*
6921 AACGCGTTCTTGGGCCCCGGCACAATTTTGCATGATTTTTGGCAGCAATACTCCTTAAAATATCT
630 AACGCGTTCTTGGGCCCCGGCACAATTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCT
* *
6986 ATTTTCTTCTAACCAAATCTCAGATGCAATGGATTTAAGTATAAGGTTTTACGAGCATCTAAATT
695 ATTTTCTTCTAACCAAACCTCAGATGCAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATT
7051 ATGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGC
760 ATGTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGC
7116 CCTAAAATTTTACTGCCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAA
825 CCTAAAATTTTACTGCCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAA
*
7181 AATTTTTCGGGATAGTTTTTTGCAAAATTTTGGCTGAAATCGTGTACTAACCATCACTGTTTTTT
890 AATTTTTCGGGATAGTTTTTTGCAAAATTTTGGCTGAAATCGTGCACTAACCATCACTGTTTTTT
* *
7246 GCTAAAAACGCGTGTTCTG
955 GCTAAAAACGCGCGTTCTA
* * * *
7265 GGGTCTCGACTTAGTTCTGCATGATTTTTGTCAGCAAGACTCCTTAAAATTTATATATTCATCTA
1 GGGCCCCGACTTAGTTCTGCATAATTTTTGGCAGCAAGACTCCTTAAAATTTATATATTCATCTA
** * *
7330 ACCAAATCTCAGCCACAATGGATTTAAGAATAAATTTTTATGAGCATCTGAATTATTTTTCGATT
66 ACCAAATCTCAGCCACAATGGATTTAAGAATAAATTTTTACAAGCATCCGAATTATGTTTCGATT
* * * *
7395 TAATTAGAAATTATTTCGAAAAAATGATACTAGAAGCCTGAAAAACCCTTAAATTTTATTGGCGT
131 TAATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGT
* * * ** * *
7460 TGAGTTATATATTTTATATGAGTATTATAGCCTAAAATTAAGGAAAAATTTTTTGGGACAATTTT
196 TGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATT-AGGAAAAATTTTTCGGGACAGTTTT
*
7525 TGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCTTGGG
260 TGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGATAAAAACGCGTTCTTGGG
* *
7590 CTCCGACACAGTTTTGCATGATTTATGGCGCCAAATTTCATTGAAATATCTATATTCATCTAACC
325 C-CCG-CACAGTTTTGCATGATTT-TGGCGCC-AATCTCATTAAAATATCTATATTCATCTAA-C
* * * *
7655 ACTTCTCAGCGACATTGGATTGAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAA
385 AATTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAA
*
7720 TTAGAAATTAATTTGGAAAAAAATCGGAAATACGAAAATTGAAGCATCTAAAGCCCTTCAGTCTT
450 TTAGAAATTAATTTGG-AAAAAAT-GGAAAT-CGATAA-TGAAGCATCTAAAGCCCTTCAGTCTT
* * * * *
7785 TCTGGATTTGAATTATAT-ATCTTTTATGAGTGTTGTGGCCAAAAATTGAGAAAAAAATTTTCGG
511 TTTGGATTT-AAGTATATAAT-TTTTATGAGTATTGT-GCCAAAAATTGAGGAAAAATTTTTCGG
* *
7849 GACAGTTTTTGCAAAATTTTGCCCGAAATCGTGTACGT-T-ACAGTTTTTGGTTAAAAACGCGTT
573 GACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACGTATCACAGTTTTTGGTTAAAAACGCGTT
*
7912 CTTGGGCCCCGGCACAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTCTT
638 CTTGGGCCCCGGCACAATTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTCTT
*
7977 CTAACCAAACCTCAGATGCAATGGATTTAAGGATAAGGTTTTACGAGTATCTAAATTATGTTTCG
703 CTAACCAAACCTCAGATGCAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATGTTTCG
* *
8042 ATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAATTATATTAGAAGCCTGATAAGCCCTAAAA
768 ATTTAATTAGAAATTAATTCGAAAAAATA-GAAAAATCATATTAGAAGCCTGAAAAGCCCTAAAA
8107 TTTTACTGCCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTT
832 TTTTACTGCCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTT
* *
8172 CGGGATAG-TTTTTGCAAAATTTTGG-TCGAAATCGTGCAGTAACCATCATTGTTTTTTGCTAAA
897 CGGGATAGTTTTTTGCAAAATTTTGGCT-GAAATCGTGCACTAACCATCACTGTTTTTTGCTAAA
8235 AACGCGCGTTCTA
961 AACGCGCGTTCTA
* *
8248 GGGCCCCGACTTAGTTTTGCATAATTTTTGGCAGTAAGACTCCTTAAAATATT-TATATTCATCT
1 GGGCCCCGACTTAGTTCTGCATAATTTTTGGCAGCAAGACTCCTTAAAAT-TTATATATTCATCT
* * ***
8312 ATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACAATTTTGCCCGAATTATGTTTCG
65 AACCAAATCTCAGCCACAATGGATTTAAGAATAAATTTTTACAAGCAT--CCGAATTATGTTTCG
*
8377 ATTTAATTAGAAATTAATTCGGAAAAATGATATTAGAAGGCTGAAAAGCCCTTAAATTTTATTGG
128 ATTTAATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGG
*
8442 TGTTGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTCGGGACAGT
193 CGTTGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATT-AGGAAAAATTTTTCGGGACAGT
*
8507 TTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGTTAAAAACGCGTTCTT
257 TTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGATAAAAACGCGTTCTT
* * *
8572 CGGCCCATGCACAGTTTTGCATGATCTTTGGCGCCAAGTGTCATTTAAATATCTATATTCATCTA
322 GGGCCC--GCACAGTTTTGCATGAT-TTTGGCGCCAA-TCTCATTAAAATATCTATATTCATCTA
* * * * * *
8637 ACTGATTCTCAGCCACATTGGATTTAATGATTTGTTTTTATGAGCATTTGAATTTTGTTTCAATT
383 AC-AATTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATT
* * *
8702 TAATTAGAAAGTAATTTGGAAAAAATAGGAAATGCGATAATCGAAGCGTCTAATGCCCTTCAGTC
447 TAATTAGAAATTAATTTGGAAAAAAT-GGAAAT-CGATAAT-GAAGCATCTAAAGCCCTTCAGTC
* * * *
8767 TTTTTGGATTTCAAGTATATAATTTTTATGA-TTTTGTGACCAAAATTTTAGGAAAAGTTTTTCG
509 TTTTTGGATTT-AAGTATATAATTTTTATGAGTATTGTG-CCAAAAATTGAGGAAAAATTTTTCG
* *
8831 GGACAATTTTTGCAAAATTTTGGCTGAAATGGTGTACGT
572 GGACAGTTTTTGCAAAATTTTGGCTGAAATCGTGTACGT
8870 CAACGAACAT
Statistics
Matches: 1400, Mismatches: 158, Indels: 84
0.85 0.10 0.05
Matches are distributed among these distances:
973 99 0.07
974 1 0.00
975 1 0.00
976 5 0.00
977 122 0.09
978 15 0.01
979 22 0.02
980 128 0.09
981 4 0.00
982 2 0.00
983 396 0.28
984 178 0.13
985 319 0.23
986 3 0.00
987 5 0.00
988 97 0.07
989 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (973 bp):
GGGCCCCGACTTAGTTCTGCATAATTTTTGGCAGCAAGACTCCTTAAAATTTATATATTCATCTA
ACCAAATCTCAGCCACAATGGATTTAAGAATAAATTTTTACAAGCATCCGAATTATGTTTCGATT
TAATTAGAAATTAATTCGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGT
TGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTAGGAAAAATTTTTCGGGACAGTTTTT
GCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGATAAAAACGCGTTCTTGGGC
CCGCACAGTTTTGCATGATTTTGGCGCCAATCTCATTAAAATATCTATATTCATCTAACAATTCT
CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAA
ATTAATTTGGAAAAAATGGAAATCGATAATGAAGCATCTAAAGCCCTTCAGTCTTTTTGGATTTA
AGTATATAATTTTTATGAGTATTGTGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCA
AAATTTTGGCTGAAATCGTGTACGTATCACAGTTTTTGGTTAAAAACGCGTTCTTGGGCCCCGGC
ACAATTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTCTTCTAACCAAACCTC
AGATGCAATGGATTTAAGGATAAGGTTTTACGAGCATCTAAATTATGTTTCGATTTAATTAGAAA
TTAATTCGAAAAAATAGAAAAATCATATTAGAAGCCTGAAAAGCCCTAAAATTTTACTGCCGTTG
AGTTACATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAGTTTTTT
GCAAAATTTTGGCTGAAATCGTGCACTAACCATCACTGTTTTTTGCTAAAAACGCGCGTTCTA
Found at i:9898 original size:20 final size:20
Alignment explanation
Indices: 9839--9883 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
9829 ATTGAGCTAT
9839 ATCATATGTAATGCAGAAAA
1 ATCATATGTAATGCAGAAAA
9859 ATCATATGTAATGCAGAAAA
1 ATCATATGTAATGCAGAAAA
9879 ATCAT
1 ATCAT
9884 GTGATATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (20 bp):
ATCATATGTAATGCAGAAAA
Found at i:10728 original size:72 final size:70
Alignment explanation
Indices: 10626--10836 Score: 312
Period size: 72 Copynumber: 3.1 Consensus size: 70
10616 AGGTACACGA
10626 GAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAA
1 GAAGA-AGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAA
10691 GCCAGAG
65 G-CAGAG
10698 GAAGGAAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC--G-A
1 GAA-GAAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAA
10760 G-A-A-
65 GCAGAG
* *
10763 G-A-CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAG
1 GAAGAAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAG
10826 ACAGAG
66 -CAGAG
10832 GAAGA
1 GAAGA
10837 CAGGCACGAA
Statistics
Matches: 126, Mismatches: 3, Indels: 21
0.84 0.02 0.14
Matches are distributed among these distances:
62 53 0.42
64 2 0.02
65 3 0.02
66 1 0.01
67 2 0.02
68 1 0.01
69 3 0.02
70 2 0.02
72 57 0.45
73 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.40, T:0.03
Consensus pattern (70 bp):
GAAGAAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAG
CAGAG
Found at i:10749 original size:62 final size:62
Alignment explanation
Indices: 10608--10835 Score: 199
Period size: 62 Copynumber: 3.5 Consensus size: 62
10598 GACAGACACG
* *
10608 AGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGC
1 AGGCACGAAAGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAAC
* * ***** ** *
10670 AGGCACGAAGGTACACGAGAAGCCAGAGGAAGGAAGAGGAAGGAAG-AGGCCTCCGCAGGAGGCG
1 AGGCACGAAAGTACACGAGAAGACAGAGGAAGGAAGAGG-CCTCCGCAGG---AGGC--GAGGCC
*
10734 AGGCC
60 A--AC
*
10739 A-GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAA
1 AGGCACG-A--AA-GTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAA
10803 C
62 C
*
10804 AGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 AGGCACGAAAGTACACGAGAAGACAGAGGAAG
10836 ACAGGCACGA
Statistics
Matches: 128, Mismatches: 24, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
62 63 0.49
63 2 0.02
65 5 0.04
66 4 0.03
67 12 0.09
68 4 0.03
69 5 0.04
71 2 0.02
72 31 0.24
ACGTcount: A:0.36, C:0.21, G:0.40, T:0.03
Consensus pattern (62 bp):
AGGCACGAAAGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAAC
Found at i:10844 original size:24 final size:23
Alignment explanation
Indices: 10817--10913 Score: 62
Period size: 24 Copynumber: 4.2 Consensus size: 23
10807 CACGAAGGTA
10817 CACGAGAAGACAGAGGAAGACAGG
1 CACGAGAAGACAGA-GAAGACAGG
*
10841 CACGA-AGGTACACGAGAAGACA--
1 CACGAGAAG-ACA-GAGAAGACAGG
* *
10863 CA-G-GAAGACAGACACGA-AGG
1 CACGAGAAGACAGAGAAGACAGG
*
10883 TACACGAGAAGACAGAGGAAGACAGA
1 --CACGAGAAGACAGA-GAAGACAGG
10909 CACGA
1 CACGA
10914 AGGTAAACGA
Statistics
Matches: 55, Mismatches: 7, Indels: 22
0.65 0.08 0.26
Matches are distributed among these distances:
18 1 0.02
19 5 0.09
20 3 0.05
21 3 0.05
22 4 0.07
23 3 0.05
24 29 0.53
25 5 0.09
26 2 0.04
ACGTcount: A:0.46, C:0.20, G:0.32, T:0.02
Consensus pattern (23 bp):
CACGAGAAGACAGAGAAGACAGG
Found at i:10845 original size:34 final size:34
Alignment explanation
Indices: 10802--10930 Score: 222
Period size: 34 Copynumber: 3.8 Consensus size: 34
10792 GGCGAGGCCA
*
10802 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
* *
10836 ACAGGCACGAAGGTACACGAGAAGACACAGGAAG
1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
10870 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
*
10904 ACAGACACGAAGGTAAACGAGAAGACA
1 ACAGACACGAAGGTACACGAGAAGACA
10931 CAGTGGTGCT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 91 1.00
ACGTcount: A:0.47, C:0.19, G:0.32, T:0.03
Consensus pattern (34 bp):
ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
Found at i:11855 original size:45 final size:45
Alignment explanation
Indices: 11796--11894 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
11786 GTTAGAATCT
*
11796 ATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCC
1 ATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCC
*
11841 ATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCTCC
1 ATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCC
11886 ATGATTGCC
1 ATGATTGCC
11895 GAGTGGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (45 bp):
ATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCC
Found at i:16040 original size:22 final size:22
Alignment explanation
Indices: 15996--16041 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
15986 GAGAGAAGCC
*
15996 AAAGAGAAAAAGGAAGAGAGAG
1 AAAGAGAAAAAGGAAGAAAGAG
*
16018 AAAGTGAAAAA-GAAGAAATGAG
1 AAAGAGAAAAAGGAAGAAA-GAG
16040 AA
1 AA
16042 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.04
Consensus pattern (22 bp):
AAAGAGAAAAAGGAAGAAAGAG
Found at i:25900 original size:12 final size:12
Alignment explanation
Indices: 25883--25907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25873 GAAAAACTCA
25883 AGGCTTTGATTG
1 AGGCTTTGATTG
25895 AGGCTTTGATTG
1 AGGCTTTGATTG
25907 A
1 A
25908 TATCCCCATG
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:0.20, C:0.08, G:0.32, T:0.40
Consensus pattern (12 bp):
AGGCTTTGATTG
Found at i:29792 original size:13 final size:13
Alignment explanation
Indices: 29774--29817 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
29764 AAACTTTAAT
29774 GGCTTTGGCTCAA
1 GGCTTTGGCTCAA
29787 GGCTTTGGCTCAA
1 GGCTTTGGCTCAA
**
29800 GGCTCAAGGCTCAA
1 GGCT-TTGGCTCAA
29814 GGCT
1 GGCT
29818 CAAGTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (13 bp):
GGCTTTGGCTCAA
Found at i:29803 original size:7 final size:7
Alignment explanation
Indices: 29780--29821 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
29770 TAATGGCTTT
29780 GGCTCAA
1 GGCTCAA
**
29787 GGCT-TT
1 GGCTCAA
29793 GGCTCAA
1 GGCTCAA
29800 GGCTCAA
1 GGCTCAA
29807 GGCTCAA
1 GGCTCAA
29814 GGCTCAA
1 GGCTCAA
29821 G
1 G
29822 TTGTTTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (7 bp):
GGCTCAA
Found at i:35920 original size:16 final size:17
Alignment explanation
Indices: 35887--35920 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35877 TACCACACAT
*
35887 GATCACCACAAGTCAAA
1 GATCACCACAAATCAAA
35904 GATCACC-CAAATCAAA
1 GATCACCACAAATCAAA
35920 G
1 G
35921 GGCCCCGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.29, G:0.12, T:0.12
Consensus pattern (17 bp):
GATCACCACAAATCAAA
Found at i:49717 original size:20 final size:19
Alignment explanation
Indices: 49679--49717 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
49669 CTTTCACATG
*
49679 CAACTAAAAAAAGGATCAT
1 CAACTAAAAAAAGCATCAT
*
49698 CAACTAATAAAAAGCTTCAT
1 CAACTAA-AAAAAGCATCAT
49718 AATCTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.21
Consensus pattern (19 bp):
CAACTAAAAAAAGCATCAT
Found at i:50563 original size:19 final size:20
Alignment explanation
Indices: 50518--50575 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
50508 GCTGCTCTAA
*
50518 TAATCTCATCTGTACAGTACT
1 TAATCTCATCTGTACAGTA-G
*
50539 TAATCTAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAG
50558 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
50576 TACTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAG
Found at i:56179 original size:26 final size:21
Alignment explanation
Indices: 56122--56181 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
56112 ATGAAATTAC
56122 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATTAGATTAGGT
56143 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATTAGATTAGGT
*
56164 ACTGTACAGATAAGATTA
1 ACTGTACAGATTAGATTA
56182 TTAGAGCAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTGTACAGATTAGATTAGGT
Found at i:79851 original size:104 final size:104
Alignment explanation
Indices: 79667--79865 Score: 346
Period size: 104 Copynumber: 1.9 Consensus size: 104
79657 CATGCCCACC
* *
79667 CTCAATTTATGAAACTTTTCCATTTTATGTGTAATTTTGGACAGTGCCCATCCCAATTTGACCAA
1 CTCAATTTATGAAACTCTTCCATTTTATGCGTAATTTTGGACAGTGCCCATCCCAATTTGACCAA
* *
79732 GTGTATCTACTCTTAATTGATTAATTTATCGTGTTCACT
66 ATGTATCTACCCTTAATTGATTAATTTATCGTGTTCACT
79771 CTCAATTTATGAAACTCTTCCATTTTATGCGTAATTTTGGACAGTGCCCA-CTCCAATTTGACCA
1 CTCAATTTATGAAACTCTTCCATTTTATGCGTAATTTTGGACAGTGCCCATC-CCAATTTGACCA
79835 AATGTATCTACCCTTAATTGATTAATTTATC
65 AATGTATCTACCCTTAATTGATTAATTTATC
79866 ATTGTGCCCT
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 1 0.01
104 89 0.99
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (104 bp):
CTCAATTTATGAAACTCTTCCATTTTATGCGTAATTTTGGACAGTGCCCATCCCAATTTGACCAA
ATGTATCTACCCTTAATTGATTAATTTATCGTGTTCACT
Done.