Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019080.1 Corchorus olitorius cultivar O-4 contig19113, 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: 25400
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:920 original size:31 final size:31
Alignment explanation
Indices: 856--920 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
846 TTATTACCCA
* *
856 CTTCAAGTAAAAAAGAAAGACCTTTTTCTTT
1 CTTCAAGTAAAAAAGAAAGACCTTTTCCCTT
*
887 CTTCAAGTAAAAAAGTAAG-CCATTTTCCCTT
1 CTTCAAGTAAAAAAGAAAGACC-TTTTCCCTT
918 CTT
1 CTT
921 TCTCAATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (31 bp):
CTTCAAGTAAAAAAGAAAGACCTTTTCCCTT
Found at i:1793 original size:93 final size:101
Alignment explanation
Indices: 1681--1881 Score: 258
Period size: 93 Copynumber: 2.0 Consensus size: 101
1671 AATTAATCTC
* *
1681 CATTTGAAACAATTTGAAACTTAATGTTCAAGTTAACTTGC-A-TTA-ATTTGG-T-A-T-A-AG
1 CATTTAAAACAATTTGAAACTTAATGTTCAAGTTAACAT-CAAGTTACATTTGGATGAGTAAGAG
*
1738 TTGTTGATT-AATTTCAAATTTGGGTTGTCAAATTTG
65 TTGTTGATTAAATTTAAAATTTGGGTTGTCAAATTTG
* *
1774 CATTTAAAACTATTTGAAACTTAATGTTTAAGTTAACATCAAGTTTACATTTGGTATGAGTAATG
1 CATTTAAAACAATTTGAAACTTAATGTTCAAGTTAACATCAAG-TTACATTTGG-ATGAGTAA-G
1839 AGTTGTTGATTAAATTTAAAATTTGGGTTGTCAAATTTG
63 AGTTGTTGATTAAATTTAAAATTTGGGTTGTCAAATTTG
1878 CATT
1 CATT
1882 CAAATGCTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
92 1 0.01
93 36 0.40
95 3 0.03
96 6 0.07
98 1 0.01
99 1 0.01
100 1 0.01
101 1 0.01
103 11 0.12
104 30 0.33
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (101 bp):
CATTTAAAACAATTTGAAACTTAATGTTCAAGTTAACATCAAGTTACATTTGGATGAGTAAGAGT
TGTTGATTAAATTTAAAATTTGGGTTGTCAAATTTG
Found at i:9694 original size:10 final size:10
Alignment explanation
Indices: 9679--9711 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
9669 ATTCCACAAC
9679 TTGCCCTAAA
1 TTGCCCTAAA
*
9689 TTGCCCTAAC
1 TTGCCCTAAA
9699 TTGCCCTAAA
1 TTGCCCTAAA
9709 TTG
1 TTG
9712 TCATGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (10 bp):
TTGCCCTAAA
Found at i:11256 original size:28 final size:31
Alignment explanation
Indices: 11206--11273 Score: 106
Period size: 29 Copynumber: 2.3 Consensus size: 31
11196 TTAGGGGGTT
*
11206 AAATGTCTTGAATTTGGAAATTC-AGGGGCA
1 AAATGTCCTGAATTTGGAAATTCAAGGGGCA
11236 AAATGTCCTG-ATTT-GAAATTCAAGGGGCA
1 AAATGTCCTGAATTTGGAAATTCAAGGGGCA
11265 AAATGTCCT
1 AAATGTCCT
11274 TGACACAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 7 0.19
29 20 0.56
30 9 0.25
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (31 bp):
AAATGTCCTGAATTTGGAAATTCAAGGGGCA
Found at i:16584 original size:56 final size:55
Alignment explanation
Indices: 16473--16580 Score: 121
Period size: 56 Copynumber: 2.0 Consensus size: 55
16463 ATAAGTCAAA
* * *
16473 TCCTCTTCTAGGGGCAAAGTCGTAATTGTACCAATTCTAGGGTAAAATGGTAATT
1 TCCTCTTATAGGGGCAAAATCGTAATTGTACCAATTCTAGGGTAAAATAGTAATT
* * * *
16528 TCCTCATTATAGGGGTAAAATCGTAATTTTATCAA-TC-AGGGGTAATATAGTAA
1 TCCTC-TTATAGGGGCAAAATCGTAATTGTACCAATTCTA-GGGTAAAATAGTAA
16581 ATTTGTCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
54 1 0.02
55 19 0.43
56 24 0.55
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (55 bp):
TCCTCTTATAGGGGCAAAATCGTAATTGTACCAATTCTAGGGTAAAATAGTAATT
Found at i:18344 original size:17 final size:16
Alignment explanation
Indices: 18324--18373 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
18314 TTTACTTCTA
18324 ATAATTATTTTTAGATT
1 ATAATTATTTTTA-ATT
*
18341 ATAA-TATATTTAATT
1 ATAATTATTTTTAATT
* *
18356 AT-ATTATTATTATTT
1 ATAATTATTTTTAATT
18371 ATA
1 ATA
18374 GTCATGAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 1 0.04
15 15 0.56
16 7 0.26
17 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATAATTATTTTTAATT
Found at i:19689 original size:335 final size:329
Alignment explanation
Indices: 18741--20474 Score: 1566
Period size: 335 Copynumber: 5.2 Consensus size: 329
18731 GGAAACATTG
** * *
18741 GATTTAAAAATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGA
1 GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
* * *
18806 AAAAA-ATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGCA-TTCAATTA
66 AAAAATATAAAAAAAAC--TATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGG-AGTTGAATTA
* *
18869 TATATTTTAATGAGTATTTTAGCCAAAAATTGAGGAGAA-ATCTTTCGAGTCAATTTTTGCAAAA
128 TATATTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AATATCTTTCGGGTCAA-TTTTGCAAAA
* * * * * *
18933 TGTTAGCCAAAATCATATACTAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGACC
191 TTTTAGCCGAAATC--AT-GTAA-TAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCC
* * * * * * *
18998 CGCCTCAATATTGCATGATTTTTTACTCCGAGACTACTTGAAATATCTATATTCATCTAATCAAA
252 CGACTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
19063 TCTCAGCCACATTA
317 TCTCAGCCACA-TA
* * * *
19077 GATTTAAGGATTTATTTTTATGAGCAATCTGAATCCTGTTTCGATTTAATTAGAAATTAATTCGG
1 GATTTAAGGATTTGTTTTTACGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG
** ** * * * *
19142 AAAAAATAGGGAAAACGA-TATTAGAAA-CGTCAAAAATCCTTCAATCTTTTCAATCTTTTTGGC
65 AAAAAATA-TAAAAAAAACTATTA-AAAGCGT-GAAAAGCC--C--TC----CAATATTTTTGGA
* * *
19205 GTTGAATTATATATTTTTTATGAGTATTTTAACCAAAAATTGATGAAATATCTTTCGGATCAATT
119 GTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAA-T
* * **
19270 TTTACAAAACTTTAGCCGAAATCATGTAATAACCATCACAGTTTTT-GCCTAAAAGA-GCG-TTC
182 TTTGCAAAATTTTAGCCGAAATCATGTAATAACCATCATGGTTTTTAG-CTAAAA-ACGCGTTTC
* * * * * * *
19332 TAGGGCTCCAACTCAGTTTTGCATGATTTTTGACACCAAGTCTCCTTGAGATATCCATATACATC
245 -GGGGCCCCGACTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATC
19397 TAATCAAATCTCAGCCACATA
309 TAATCAAATCTCAGCCACATA
** * * *
19418 GGATTTAAAAATTTGTTTTTACGAGCATCCGAATATTGTTTTGATTTAATTAGAAATTAATTCAG
1 -GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG
* * *
19483 AAAAAATATTAAAAAAAACTATTAAAACCGTGAAAAGTCCTCCAATATTTTTGGAGTTAAATTAT
65 AAAAAATA-TAAAAAAAACTATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGAGTTGAA-T-T
* * * *
19548 ATATATATTTTATGAGTGTTTTATCCAAAAATTGAGGAAACATTTTTCGGGTCATATTTTGCAAA
127 ATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCA-ATTTTGCAAA
* * * *
19613 ATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGG
190 ATTTTAGCCGAAATCATGTAATAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGA
* * * *
19678 CTCATTTTTGCATGATTTTTGACGCCAAGACTCCTTGAAAAATCTATATTCATCTAATAAAATCT
255 CTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* * *
19743 TAGCCATATT
320 CAGCCACATA
* * * *
19753 GCATTTTAGGACTT-TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTATTTCAG
1 G-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG
** * * * * ***
19817 AAAAAAT-TATGAAAAACGATATTAAAAGCGCGAGAAGCCCTTCAATCTTTTTTTTCGTTGAATT
65 AAAAAATATAAAAAAAAC--TATTAAAAGCGTGAAAAGCCCTCCAAT-ATTTTTGGAGTTGAATT
* * * * * **
19881 ATAT-TTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATCTTTCGGTTCATTTTTTAAAAAA
127 ATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCA-ATTTTGCAAAA
* ** * * *
19945 TTTTAGCCGAAATCATGTAATAATCATCACTCTTTTTTGGCTAAAAACGCGTTCCGTGG-CCCGA
191 TTTTAGCCGAAATCATGTAATAACCATCA-TGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGA
* * * * * * *
20009 TTTAGTTTTGCATGGTTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAGCAAATCT
255 CTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
20074 CAG-C-C---
320 CAGCCACATA
* ** *
20079 ---------A-TTGTTTTTACAAATATCTGAATCATGTTTCGATTTAATTAGAAATTAATTC-GA
1 GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
** * * * * * * *
20133 AAAAA-ATAGGAAAAACGATATTAGAAGCATAAAAAGCCCTTCAATCTTTTTGGTGCTGAATTAT
66 AAAAATATAAAAAAAAC--TATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGAGTTGAATTAT
* * * * *
20197 ATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCAAATTTTGCAAAAT
129 ATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTC-AATTTTGCAAAAT
* * * * * * *
20262 ATTAGACGAAATCGTGTAATAATCATCACTGTTTTTTATTTTTGTTAAAAACGCGTTTCAGGGCC
192 TTTAGCCGAAATCATGTAATAACCATCA-TGGTTTTTA-----GCTAAAAACGCGTTTCGGGGCC
* * **
20327 CCGAATCAGTTTTGCATGATTTTGGGTACCAAGACTCCTTGAAATATCTATATTCATCTAATCAA
251 CCGACTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAA
*
20392 ATCTTC-GCAACATTA
316 ATC-TCAGCCACA-TA
* * *
20407 GATTTAAGGATTTGTTTTTACTAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGA
1 GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
20472 AAA
66 AAA
20475 GGGATAGGCT
Statistics
Matches: 1146, Mismatches: 189, Indels: 123
0.79 0.13 0.08
Matches are distributed among these distances:
314 16 0.01
315 43 0.04
316 128 0.11
317 1 0.00
321 16 0.01
322 62 0.05
323 2 0.00
324 1 0.00
330 1 0.00
331 135 0.12
332 33 0.03
333 21 0.02
334 79 0.07
335 184 0.16
336 35 0.03
337 54 0.05
338 47 0.04
339 11 0.01
341 63 0.05
342 122 0.11
343 4 0.00
344 2 0.00
345 24 0.02
346 62 0.05
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (329 bp):
GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
AAAAATATAAAAAAAACTATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGAGTTGAATTATAT
ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTGCAAAATTTTA
GCCGAAATCATGTAATAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGT
TTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCA
CATA
Found at i:20077 original size:666 final size:665
Alignment explanation
Indices: 18739--20474 Score: 1961
Period size: 666 Copynumber: 2.6 Consensus size: 665
18729 TTGGAAACAT
* * *
18739 TGGATTTAAAAATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTA
1 TGGATTTAAAAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCA
* *
18804 GAAAAAAATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGCA-TTCAATT
66 GAAAAAAATAAGAAAAAC-ATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGG-AGTTAAATT
* * *
18868 ATATAT-TTTAATGAGTATTTTAGCCAAAAATTGAGGAGAAATCTTTCGAGTCAATTTTTGCAAA
129 ATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAATATTTCGGGTCAA-TTTTGCAAA
* * * * * *
18932 ATGTTAGCCAAAATCATATACTAACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGAC
192 ATATTAGCCAAAATC--GT-GT-ACTAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCC
* * * * * *
18997 CCGCCTCAATATTGCATGATTTTTTACTCCGAGACTACTTGAAATATCTATATTCATCTAATCAA
253 CCGACTCAATTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAA
* * * *
19062 ATCTCAGCCACATTAGATTTAAGGATTTATTTTTATGAGCAATCTGAATCCTGTTTCGATTTAAT
318 ATCTTAGCCACATTAGATTTAAGGATTTATTTTTACGAGC-ATCTAAATCTTGTTTCGATTTAAT
* *
19127 TAGAAATTAATTCGGAAAAAATAGGGAAAACGATATTAGAAACGTCAAAAATCCTTCAATCTTTT
382 TAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAACCCTTCAATC-TTT
* *
19192 CAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAACCAAAAATTGATGAAATATC
446 --ATCTTTTT-GCGTTGAATTATATATTTTTTATGAGTATTGTAACCAAAAATTGAGGAAATATC
*
19257 TTTCGGATCAATTTTTACAAAACTTTAGCCGAAATCATGTAATAACCATCACAGTTTTTGCCTAA
508 TTTCGGATCAATTTTTAAAAAACTTTAGCCGAAATCATGTAATAACCATCACAGTTTTTGCCTAA
* *
19322 AAGAGCGTTCTAGGGCTCCAACTCAGTTTTGCATGATTTTTGACACCAAGTCTCCTTGAGATATC
573 AAGAGCGTTCTAGGGCTCCAACTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATC
*
19387 CATATACATCTAATCAAATCTCAGCCACA
638 CATATACATCTAAGCAAATCTCAG-CACA
* *
19416 TAGGATTTAAAAATTTGTTTTTACGAGCATCCGAATATTGTTTTGATTTAATTAGAAATTAATTC
1 T-GGATTTAAAAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTC
* * *
19481 AGAAAAAATATTAAAAAAAAC-TATTAAAACCGTGAAAAGTCCTCCAATATTTTTGGAGTTAAAT
65 AGAAAAAA-A-TAAGAAAAACATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGAGTTAAA-
* * *
19545 TATATATATATTTTATGAGTGTTTTATCCAAAAATTGAGGAAACATTTTTCGGGTCATATTTTGC
127 T-TATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-ATATTTCGGGTCA-ATTTTGC
*
19610 AAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCC
189 AAAATATTAGCCAAAATCGTGTACTAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCC
* * * * *
19675 CGGCTCATTTTTGCATGATTTTTGACGCCAAGACTCCTTGAAAAATCTATATTCATCTAATAAAA
254 CGACTCAATTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
* * *
19740 TCTTAGCCATATT-GCATTTTAGGACTT-TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
319 TCTTAGCCACATTAG-ATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
* * * * *
19803 AGAAATTATTTCAGAAAAAATTATGAAAAACGATATTA-AAAGCG-CGAGAAGCCCTTCAATC-T
383 AGAAATTAATTCGGAAAAAA-TAGGAAAAACGATATTAGAAA-CGTC-AAAAACCCTTCAATCTT
** *
19865 T-T-TTTTT-CGTTGAA-T-TATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATCTT
445 TATCTTTTTGCGTTGAATTATATATTTTTTATGAGTATTGTAACCAAAAATTGAGGAAATATCTT
* * * * ** *
19925 TCGGTTCATTTTTTAAAAAATTTTAGCCGAAATCATGTAATAATCATCACTCTTTTTTGGCTAAA
510 TCGGATCAATTTTTAAAAAACTTTAGCCGAAATCATGTAATAACCATCAC-AGTTTTTGCCTAAA
* * * * * * * *
19990 A-ACGCGTTC-CGTGGC-CCGATTTAGTTTTGCATGGTTTTTGGCGCCGAGACTCCTTGAAATAT
574 AGA-GCGTTCTAG-GGCTCCAACTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATAT
* *
20052 CTATATTCATCTAAGCAAATCTCAGC-C-
637 CCATATACATCTAAGCAAATCTCAGCACA
* **
20079 -----------A-TTGTTTTTACAAATATCTGAATCA-TGTTTCGATTTAATTAGAAATTAATTC
1 TGGATTTAAAAATTTGTTTTTACGAGCATCTGAAT-ATTGTTTCGATTTAATTAGAAATTAATTC
* * * * * * * * *
20131 -GAAAAAAATAGGAAAAACGATATTAGAAGCATAAAAAGCCCTTCAATCTTTTTGGTGCTGAATT
65 AGAAAAAAATAAGAAAAAC-ATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGAGTTAAATT
* * *
20195 ATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCAAATTTTGCAAA
129 ATATATATTTTATGAGTATTTTAGCCAAAAATTGAGG-AAAATATTTCGGGTC-AATTTTGCAAA
* * * * * * *
20260 ATATTAGACGAAATCGTGTAATAATCATCACTGTTTTTTATTTTTGTTAAAAACGCGTTTCAGGG
192 ATATTAGCCAAAATCGTGTACTAACCATCA-TGGTTTTTA-----GCTAAAAACGCGTTTCGGGG
* * * **
20325 CCCCGAATCAGTTTTGCATGATTTTGGGTACCAAGACTCCTTGAAATATCTATATTCATCTAATC
251 CCCCGACTCAATTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATC
* * * *
20390 AAATCTTCGCAACATTAGATTTAAGGATTTGTTTTTACTAGCATCTAAATCTTGTTTCGATTTAA
316 AAATCTTAGCCACATTAGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
20455 TTAGAAATTAATTCGGAAAA
381 TTAGAAATTAATTCGGAAAA
20475 GGGATAGGCT
Statistics
Matches: 912, Mismatches: 118, Indels: 81
0.82 0.11 0.07
Matches are distributed among these distances:
647 87 0.10
648 14 0.02
649 39 0.04
650 44 0.05
651 2 0.00
653 97 0.11
654 52 0.06
664 1 0.00
665 1 0.00
666 147 0.16
667 22 0.02
668 7 0.01
670 5 0.01
671 1 0.00
674 2 0.00
675 45 0.05
676 40 0.04
677 119 0.13
678 104 0.11
679 3 0.00
680 17 0.02
681 62 0.07
682 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (665 bp):
TGGATTTAAAAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCA
GAAAAAAATAAGAAAAACATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGGAGTTAAATTAT
ATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATATTTCGGGTCAATTTTGCAAAATAT
TAGCCAAAATCGTGTACTAACCATCATGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCA
ATTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGC
CACATTAGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTA
ATTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAACCCTTCAATCTTTATCTTTTTGC
GTTGAATTATATATTTTTTATGAGTATTGTAACCAAAAATTGAGGAAATATCTTTCGGATCAATT
TTTAAAAAACTTTAGCCGAAATCATGTAATAACCATCACAGTTTTTGCCTAAAAGAGCGTTCTAG
GGCTCCAACTCAGTTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCCATATACATCTAA
GCAAATCTCAGCACA
Found at i:21711 original size:331 final size:330
Alignment explanation
Indices: 20569--21910 Score: 1330
Period size: 334 Copynumber: 4.0 Consensus size: 330
20559 AGCTTTCCCT
* * * **
20569 TTCGGA-AAAAGTAGGAAAAACGATATTAGAAGAG-TAAAAAACCTTCAATATTTTTGGCGTTGA
1 TTCGGATAAAA-TAGGAAAAACGATATTAGAAGCGTTAAAAATCCTTCAATCTTTTTAACGTTGA
* * *
20632 ATTATATATTTTTTGTGGGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGC
65 ATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGC
***** * *
20697 AAAATTTTAGACGAAATCGTGTACTAATCACAATTTTTTTTTTTGGCTAGAAACGCGTTTCGGGA
130 AAAATTTTAGACGAAATCGTGTACTAA-C-C-ATCACAGTTTTTGGCTAAAAACGCGTTCCGGG-
* * * * * *
20762 CCCTCACTCAGTTTTGCATGATTTTTGGCATCGACACTCCTTGAAATATTTATATTCATCTAATT
191 CCC-GACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATC
* * * *
20827 AAATCTCAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTATTTTGATTTAA
255 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
*
20892 TTAAAAATTAA
320 TTAGAAATTAA
* * * * * * * *
20903 TTCAGA-AAAATATGAAAAACTATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGA-GTTGA
1 TTCGGATAAAATAGGAAAAACGATATTAGAAGCGTTAAAAATCCTTCAATCTTTTT-AACGTTGA
* ** * * *
20966 ATTATATATATTTTATGAGTATTTTAGGAAAAAAATTGAGGAAAAATATTTCTGGTTAATTTTTG
65 ATTATATATTTTTTATGAGTATTTTA-GCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTG
** * *** ** *
21031 CAAAACATTAGACGAAATTGTGTACATTAGTTGAAAACACGATTTTTGGCTAAAAACGCGTTTCA
129 CAAAATTTTAGACGAAATCGTGTAC--TA-ACCATCACA-G-TTTTTGGCTAAAAACGCG-TTCC
** ** * * * * * * *
21096 GATCCCCGGGTCAGTTTTGCAAGATTTTTGGCGCTAAGACTCCTTAAAATATATTTATATTAAAC
188 G-GGCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTT-GAA-ATATCTATATTCATC
* * * *
21161 TAATCAAATTTCAGCCACATTGTATATAAGGATTTGTTTTTACGAGTATCTAAATCTTGTTTCGA
250 TAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGA
* *
21226 TTTAATCAGCAATTAA
315 TTTAATTAGAAATTAA
* * * * * * *** * *
21242 TTTTGAAATAAAATATGAAAAATGCTATTAGAAGCGTGAAAAAAGATTTGAAT-TTTTTAGCGTT
1 -TTCG-GATAAAATAGGAAAAACGATATTAGAAGCGT-TAAAAATCCTTCAATCTTTTTAACGTT
* * * * * *
21306 GAATTATATATTTTTTACGAGTATTGTCGCTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTC
63 GAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTT
* * * * * *
21371 GCAAAATTTTAGCCAAAATAGTGTACTAACCATCACAGTTTTCGGCTAAAAATGTGTTCCGGGCC
128 GCAAAATTTTAGACGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCC
* ** * *
21436 CGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATGTCTATATTCGTCTCAA-CAA
193 CGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCT-AATCAA
* * * *
21500 ATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTTTTTCGATTTAATT
257 ATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
21565 AGAAATTAA
322 AGAAATTAA
* * *
21574 TTCGGATAACAATAGGAAAAACAATATTAGAAGCGTTAAAAATCCTTCAATCTTTTTAATGTCGA
1 TTCGGATAA-AATAGGAAAAACGATATTAGAAGCGTTAAAAATCCTTCAATCTTTTTAACGTTGA
* * *
21639 ATTATATATTTTTTATGAGTAGTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTATGC
65 ATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGC
** * *
21704 AAAATTTTAGTTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAACCA
130 AAAATTTTAGACGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGG-GCC-
* ** * *
21769 CGACTCTGTTTTGCATGATTTTTGGCACCGCGGCTCCTTGAAAATATCTTTATTCATCTAATCAA
193 CGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTG-AAATATCTATATTCATCTAATCAA
* * * * * *
21834 ATCTCAGCTATATTAGATTTAATGATTTGTTTTTAC-ATGCATCTGAATCTTGTATCGATTTAAT
257 ATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA-GCATCTAAATCTTGTTTCGATTTAAT
21898 TAGAAATTAA
321 TAGAAATTAA
21908 TTC
1 TTC
21911 ATAAAAAATA
Statistics
Matches: 810, Mismatches: 173, Indels: 50
0.78 0.17 0.05
Matches are distributed among these distances:
330 14 0.02
331 143 0.18
332 80 0.10
333 59 0.07
334 175 0.22
335 60 0.07
336 15 0.02
337 49 0.06
338 12 0.01
339 85 0.10
340 2 0.00
341 52 0.06
342 56 0.07
343 8 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (330 bp):
TTCGGATAAAATAGGAAAAACGATATTAGAAGCGTTAAAAATCCTTCAATCTTTTTAACGTTGAA
TTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCA
AAATTTTAGACGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCCCGA
CTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
ATTAA
Found at i:21987 original size:671 final size:669
Alignment explanation
Indices: 20612--21979 Score: 1523
Period size: 671 Copynumber: 2.0 Consensus size: 669
20602 GTAAAAAACC
* ** * * * * * *
20612 TTCAATATTTTTGGCGTTGAATTATATATTTTTTGTGGGTATTTTAGCCAAAAATTGAGGAAATA
1 TTCAAT-TTTTTAGCGTTGAATTATATATTTTTTACGAGTATTGTCGCTAGAAATTGAGGAAAAA
* * * ***** *
20677 TCTTTCGGGTCAATTTTTGCAAAATTTTAGACGAAATCGTGTACTAATCACAATTTTTTTTTTTG
65 TCTTTCGGGTCAATTTTCGCAAAATTTTAGACAAAATAGTGTACTAATCACAATCACAGTTTTCG
* * * *
20742 GCTAGAAACGCGTTTCGGGACCCTCACTCAGTTTTGCATGATTTTTGGCATCGACACTCCTTGAA
130 GCTAAAAACGCGTTCCGGGACCCTCACTCAGTTTTGCATGATTTTTGGCACCAACACTCCTTGAA
* * * *
20807 ATATTTATATTCATCTAATTAAATCTCAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATC
195 ATATCTATATTCATCTAATCAAATCTCACCCACATTGCATTTAAGGATTTATTTTTACGAGCATA
* *
20872 TAAATCTTATTTTGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACTATATTAAAAGCGT
260 TAAATCTTATTTTGATTTAATTAAAAATTAATTCAGAAAAATAGGAAAAACAATATTAAAAGCGT
* * * *
20937 GAAAAGTCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGTATTTTAGGAAAAAAAT
325 GAAAAATCCTCCAATCTTTTTGAAGTCGAATTATATATATTTTATGAGTAGTTTAGGAAAAAAAT
* * * *
21002 TGAGGAAAAATATTTCTGGTTAATTTTTGCAAAACATTAGACGAAATTGTGTACATTAGTTGAAA
390 TGAGGAAAAATATTTCGGGTCAATTTATGCAAAACATTAGACGAAATCGTGTACA-TA---GAAA
* * * ** * *
21067 ACACGATTTTTGGCTAAAAACGCGTTTCAGATCCCCGGGTCAGTTTTGCAAGATTTTTGGCGCTA
451 ACACGATTTTTGGCTAAAAACGCGTTCCAGAACCACGACTCAGTTTTGCAAGATTTTTGGCACCA
* *
21132 AGACTCCTTAAAATATATTTATATTAAACTAATCAAATTTCAGCCACATTGTATATAAGGATTTG
516 AGACTCCTTAAAATATACTTATATTAAACTAATCAAATCTCAGCCACATTGTATATAAGGATTTG
* * * *
21197 TTTTTACGAGTATCTAAATCTTGTTTCGATTTAATCAGCAATTAATTTTGAAATAAAATATGAAA
581 TTTTTACGAGCATCTAAATCTTGTATCGATTTAATCAGAAATTAATTAT-AAATAAAATATGAAA
** * *
21262 AATGCTATTAGAAGCGTGAAAAAAGAT
645 AATGAAATTAAAAGCATG--AAAAGAT
*
21289 TTGAATTTTTTAGCGTTGAATTATATATTTTTTACGAGTATTGTCGCTAGAAATTGAGGAAAAAT
1 TTCAATTTTTTAGCGTTGAATTATATATTTTTTACGAGTATTGTCGCTAGAAATTGAGGAAAAAT
*
21354 CTTTCGGGTCAATTTTCGCAAAATTTTAGCCAAAATAGTGTACTAA-C-C-ATCACAGTTTTCGG
66 CTTTCGGGTCAATTTTCGCAAAATTTTAGACAAAATAGTGTACTAATCACAATCACAGTTTTCGG
* * ** ** *
21416 CTAAAAATGTGTTCCGGG-CCC-GGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAA
131 CTAAAAACGCGTTCCGGGACCCTCACTCAGTTTTGCATGATTTTTGGCACCAACACTCCTTGAAA
* * * *
21479 TGTCTATATTCGTCTCAA-CAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATA
196 TATCTATATTCATCT-AATCAAATCTCACCCACATTGCATTTAAGGATTTATTTTTACGAGCATA
* * * *
21543 TGAATCTT-TTTTCGATTTAATTAGAAATTAATTCGGATAACAATAGGAAAAACAATATTAGAAG
260 TAAATCTTATTTT-GATTTAATTAAAAATTAATTCAGA-AA-AATAGGAAAAACAATATTAAAAG
* * * **
21607 CGTTAAAAATCCTTCAATCTTTTT-AATGTCGAATTATATATTTTTTATGAGTAGTTTA-GCCAA
322 CGTGAAAAATCCTCCAATCTTTTTGAA-GTCGAATTATATATATTTTATGAGTAGTTTAGGAAAA
* * ** ** *
21670 AAATTGAGGAAATATCTTTCGGGTCAATTTATGCAAAATTTTAGTTGAAATCGTGTAC-TA-ACC
386 AAATTGAGGAAAAATATTTCGGGTCAATTTATGCAAAACATTAGACGAAATCGTGTACATAGA-A
* * * * *
21733 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAACCACGACTCTGTTTTGCATGATTTTTGGCACC
450 AACACGATTTTTGGCTAAAAACGCGTTCCAGAACCACGACTCAGTTTTGCAAGATTTTTGGCACC
** * * * * * * *
21798 GCGGCTCCTTGAAAATAT-CTT-TATTCATCTAATCAAATCTCAGCTATATTAG-ATTTAATGAT
515 AAGACTCCTT-AAAATATACTTATATTAAACTAATCAAATCTCAGCCACATT-GTATATAAGGAT
* *
21860 TTGTTTTTAC-ATGCATCTGAATCTTGTATCGATTTAATTAGAAATTAATTCAT-AA-AAAATAT
578 TTGTTTTTACGA-GCATCTAAATCTTGTATCGATTTAATCAGAAATTAATT-ATAAATAAAATAT
21922 GAAAAATGAAATTAAAAGCATG-AAAG-T
641 GAAAAATGAAATTAAAAGCATGAAAAGAT
*
21949 CTTCCAATTTTTTTGGCGTTGAATTATATAT
1 -TT-CAA-TTTTTTAGCGTTGAATTATATAT
21980 ATATATATAT
Statistics
Matches: 578, Mismatches: 100, Indels: 40
0.81 0.14 0.06
Matches are distributed among these distances:
660 1 0.00
661 6 0.01
662 2 0.00
663 22 0.04
664 25 0.04
665 3 0.01
666 76 0.13
667 64 0.11
668 7 0.01
670 6 0.01
671 117 0.20
672 59 0.10
673 91 0.16
674 1 0.00
675 1 0.00
676 92 0.16
677 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (669 bp):
TTCAATTTTTTAGCGTTGAATTATATATTTTTTACGAGTATTGTCGCTAGAAATTGAGGAAAAAT
CTTTCGGGTCAATTTTCGCAAAATTTTAGACAAAATAGTGTACTAATCACAATCACAGTTTTCGG
CTAAAAACGCGTTCCGGGACCCTCACTCAGTTTTGCATGATTTTTGGCACCAACACTCCTTGAAA
TATCTATATTCATCTAATCAAATCTCACCCACATTGCATTTAAGGATTTATTTTTACGAGCATAT
AAATCTTATTTTGATTTAATTAAAAATTAATTCAGAAAAATAGGAAAAACAATATTAAAAGCGTG
AAAAATCCTCCAATCTTTTTGAAGTCGAATTATATATATTTTATGAGTAGTTTAGGAAAAAAATT
GAGGAAAAATATTTCGGGTCAATTTATGCAAAACATTAGACGAAATCGTGTACATAGAAAACACG
ATTTTTGGCTAAAAACGCGTTCCAGAACCACGACTCAGTTTTGCAAGATTTTTGGCACCAAGACT
CCTTAAAATATACTTATATTAAACTAATCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTT
ACGAGCATCTAAATCTTGTATCGATTTAATCAGAAATTAATTATAAATAAAATATGAAAAATGAA
ATTAAAAGCATGAAAAGAT
Found at i:23599 original size:63 final size:63
Alignment explanation
Indices: 23494--23615 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
23484 AATTGTGACG
* * * *
23494 GATTCATGATATTGCTACCACCATTTTCATGATTCTGCTTCTGATCCACTGCAATTTGAAGTT
1 GATTCATAATATTGCTACCACCATTTTCATGATGCTGATTCTGATCAACTGCAATTTGAAGTT
* * * * *
23557 GATTCATAAT-TTCGCTACCGCCATTTTGATGCTGCTGATTCTGGTTAACTGCAATTTGA
1 GATTCATAATATT-GCTACCACCATTTTCATGATGCTGATTCTGATCAACTGCAATTTGA
23616 GGTAAAGCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 2 0.04
63 47 0.96
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (63 bp):
GATTCATAATATTGCTACCACCATTTTCATGATGCTGATTCTGATCAACTGCAATTTGAAGTT
Done.