Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014378.1 Corchorus capsularis cultivar CVL-1 contig14399, 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: 47545
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1836 original size:2 final size:2
Alignment explanation
Indices: 1829--1855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1819 TTTAACCTAG
1829 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1856 CGCTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2162 original size:8 final size:7
Alignment explanation
Indices: 2135--2160 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2125 ACAAAACTTC
2135 TTTTTAA
1 TTTTTAA
2142 TTTTTAA
1 TTTTTAA
2149 TTTTTAA
1 TTTTTAA
2156 TTTTT
1 TTTTT
2161 TATACATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:3042 original size:22 final size:23
Alignment explanation
Indices: 3017--3066 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
3007 ATCAATTAAC
3017 TAATTAAA-ACTAATAAACTAAA
1 TAATTAAATACTAATAAACTAAA
* *
3039 TAATTAAATACTAATTAATTAAA
1 TAATTAAATACTAATAAACTAAA
3062 -AATTA
1 TAATTA
3067 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (23 bp):
TAATTAAATACTAATAAACTAAA
Found at i:8993 original size:16 final size:16
Alignment explanation
Indices: 8972--9014 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
8962 CAATTGCTGG
8972 TTTAATATTTAATATA
1 TTTAATATTTAATATA
8988 TTTAATA-TT-ATATA
1 TTTAATATTTAATATA
9002 TATTATATATTTA
1 T-TTA-ATATTTA
9015 TCTTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.26
15 5 0.22
16 10 0.43
17 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATATTTAATATA
Found at i:9027 original size:23 final size:23
Alignment explanation
Indices: 8983--9027 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8973 TTAATATTTA
*
8983 ATATATTTAATATTATATATATT
1 ATATATTTAATATTATAAATATT
*
9006 ATATATTT-ATCTTATTAAATAT
1 ATATATTTAATATTA-TAAATAT
9028 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATTTAATATTATAAATATT
Found at i:10455 original size:24 final size:25
Alignment explanation
Indices: 10423--10470 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
10413 ATCTTTAAAT
*
10423 TTTTTTTGAAAAATAGTTA-TATAA
1 TTTTATTGAAAAATAGTTACTATAA
*
10447 TTTTATTGAAAATTAGTTACTATA
1 TTTTATTGAAAAATAGTTACTATA
10471 TGACTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (25 bp):
TTTTATTGAAAAATAGTTACTATAA
Found at i:10478 original size:27 final size:24
Alignment explanation
Indices: 10428--10479 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 24
10418 TAAATTTTTT
*
10428 TTGAAAAATAGTTATATAATTTTA
1 TTGAAAAATAGTTATATAACTTTA
*
10452 TTGAAAATTAGTTACTATATGACTTTA
1 TTGAAAAATAGTTA-TATA--ACTTTA
10479 T
1 T
10480 AAAAAGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.57
25 4 0.17
27 6 0.26
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (24 bp):
TTGAAAAATAGTTATATAACTTTA
Found at i:10606 original size:10 final size:10
Alignment explanation
Indices: 10591--10637 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
10581 TTTTCACCAA
10591 ATCTTCATAT
1 ATCTTCATAT
10601 ATCTTCTGCATAT
1 ATC-T-T-CATAT
*
10614 ATATTCATAT
1 ATCTTCATAT
10624 ATCTTCATAT
1 ATCTTCATAT
10634 ATCT
1 ATCT
10638 CACGACTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 21 0.66
11 2 0.06
12 2 0.06
13 7 0.22
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (10 bp):
ATCTTCATAT
Found at i:11361 original size:10 final size:10
Alignment explanation
Indices: 11348--11406 Score: 66
Period size: 10 Copynumber: 5.7 Consensus size: 10
11338 TTTTTACCAA
11348 ATCTTCATAT
1 ATCTTCATAT
11358 ATCTTCTTCATAT
1 A---TCTTCATAT
*
11371 ATATTCATAT
1 ATCTTCATAT
*
11381 ATATTCATAT
1 ATCTTCATAT
11391 ATCTTCATAT
1 ATCTTCATAT
11401 AT-TTCA
1 ATCTTCA
11407 CGACATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 4 0.09
10 30 0.68
13 10 0.23
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (10 bp):
ATCTTCATAT
Found at i:12126 original size:10 final size:10
Alignment explanation
Indices: 12111--12161 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
12101 TTTTCATCAA
12111 ATCTTCATAT
1 ATCTTCATAT
12121 ATCTTCTTCATAT
1 A---TCTTCATAT
*
12134 ATATTCATAT
1 ATCTTCATAT
*
12144 ATATTCATAT
1 ATCTTCATAT
12154 ATC-TCATA
1 ATCTTCATA
12162 ACTATGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 5 0.14
10 21 0.58
13 10 0.28
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (10 bp):
ATCTTCATAT
Found at i:12490 original size:746 final size:752
Alignment explanation
Indices: 10109--12682 Score: 3830
Period size: 761 Copynumber: 3.4 Consensus size: 752
10099 AAAAACTAAT
* * *
10109 CTCTATTTACGGAGTAACCATTTTTCTCTCCACCTCAGGAACGGAAAATAACATTATTGTCAATT
1 CTCTATTTACGGAGTAACCATTTTTCTCTCCAACTCAGGAACGGAAAATAACATCATTGCCAATT
* * * **
10174 TCGAAAGTGTTCATCTATAAGGTAAAGATAGAATATATAAGGAAGATTAAGATAGGAGAGATAAA
66 TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATATTTAAGGAAGATGGAGATAGGAGAGATAAA
* *
10239 CAAGCTAGTTACTGAACCTGTTAGGGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
131 CAAGCCAGTTACTGAACCTATTAGGGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
*
10304 AAAATATCATTGCCTTTGACACTGTGCTATCCTATTTATATCATTATTATATTTTTTTGGTAAGG
196 AAAATATCATTGCCTTTGACACTGTGCTATCATATTTATATCATTATTATATTTTTTTGGTAAGG
* *
10369 AATTACTTAATGAAAACAAGTGAAACTTTTAGCACATCACTACTATCTTTAAATTTTTTTTGAAA
261 AATTACTTAATGAAAACAAGTGAAACTTTTAGCACATCACGACTATCTTT-ATTTTTTTTTGAAA
* * *
10434 AATAGTTATATAATTTTATTGAAAATTAGTTACTATATGACTTTATAAAAAGACATACATAGTGT
325 AATAGTTATATAACTTTATTGAAAATTAGTTACTGTATGACTTTATAAAAAGACATATATAGTGT
*
10499 ATTATTAAAAAAACATATACAAAATAATAAAATGACATTATAAGCAGTGTCTTAATAAAAAGACA
390 CTTATTAAAAAAACATATACAAAATAATAAAATGACATTATAAGCAGTGTCTTAATAAAAAGACA
* *
10564 TACAATCTTTTTATTTTTTTTCACCAAATCTTCATATATCTTCTGCATATATATTCATATATCTT
455 TACAATCTTTTTA-TTTTTTTCACCAAATCTTCATATATCTTCTTCATATATATTCATATATATT
**
10629 CATATATCTCACGACTATCTTTATTGCATTATGTATCAGAGCCATGATAATGGATAGAAAA-AGA
519 CATATATCTCATAACTATCTTTATTGCATTATGTATCAGAGCCATGATAATGGATA-AAAAGAGA
*
10693 CCTCCACCGGAGAAACATAGGGAGAAAGAAATTTTAAGGGAAAAAAGAAATACAACCAAACCAGC
583 CCTCCACCGGAGAAACATAGGGAGAAAGAAACTTTAAGGG-AAAAA-AAATACAACCAAACCAGC
*
10758 CACTTCTTGGTTTGAATCAAACTATTTTGTTCACACTTTTATTAATAATTATAAAAATCACACTT
646 CACTTCTTGGTTTGAATCAAACTATTTTGTTCACACTTTTATTAGTAATTATAAAAATCACACTT
*
10823 ATACATACTTATTTAGCCCACCTCAAACTTCTCAAACTTATACATTA
711 ATACATATTTATTTAG--C-CCTC-AAC-TCTCAAACTTATACATTA
* *
10870 CTCTATTTACGGAGTAACCATTTTTCTCTCCAACTCAGGAACCGAAAATAACATTATTGCCAATT
1 CTCTATTTACGGAGTAACCATTTTTCTCTCCAACTCAGGAACGGAAAATAACATCATTGCCAATT
* * * * * * *
10935 CCAAAAGTGTTCATATATAAGGTAATGATAGAATATTTAAGGAAGATGGGGAAATGAGAGATAAA
66 TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATATTTAAGGAAGATGGAGATAGGAGAGATAAA
* * * *
11000 CAAGCCAGTTACTAAACCTGTTCGAGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
131 CAAGCCAGTTACTGAACCTATTAGGGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
* *
11065 AAAATGTCATTGCCTTTGACACTATGCTATCATATTTATATCATTATTATA-TTTTTTGGTAAGG
196 AAAATATCATTGCCTTTGACACTGTGCTATCATATTTATATCATTATTATATTTTTTTGGTAAGG
* * *
11129 AA-TAATATAATGAAAACAAGTGAAGCTTTTAGCACATCACTACTATCTTTATTTATTTTTTTGA
261 AATTACT-TAATGAAAACAAGTGAAACTTTTAGCACATCACGACTATCTTTA-TT-TTTTTTTGA
*
11193 AAAATAGTTATATAACTTTATTGAAAATTAGTTATTGTATGACTTTATAAAAAGACATATATAGT
323 AAAATAGTTATATAACTTTATTGAAAATTAGTTACTGTATGACTTTATAAAAAGACATATATAGT
*
11258 -TCTTCTTAAAAAAACATATACAAAATAATAAAATGACATTATAA--A-TGTCTTAATAAAAAGA
388 GTCTTATTAAAAAAACATATACAAAATAATAAAATGACATTATAAGCAGTGTCTTAATAAAAAGA
*
11319 CATACAATCTTTTTATTTTTTTTTACCAAATCTTCATATATCTTCTTCATATATATTCATATATA
453 CATACAATCTTTTTA-TTTTTTTCACCAAATCTTCATATATCTTCTTCATATATATTCATATATA
* * *
11384 TTCATATATCTTCATATATTTCACGACATTTTTTATTGCATTATGTATTAGAGCCATGATAATGG
517 TTCATATATC-TC--ATA----AC--TA-TCTTTATTGCATTATGTATCAGAGCCATGATAATGG
* * *
11449 GTAGAAAGAGACCTCCACCGGAGAAACATAGGGAGAAAGAAACTTT-AGGGAAAAAAAATCCAAC
572 ATAAAAAGAGACCTCCACCGGAGAAACATAGGGAGAAAGAAACTTTAAGGGAAAAAAAATACAAC
* * **
11513 AAAAGCAGCCACTTCTTGGTTTGAATCAAACTATTTTACTCACACTTTTATTAGTAATTATAAAA
637 CAAACCAGCCACTTCTTGGTTTGAATCAAACTATTTTGTTCACACTTTTATTAGTAATTATAAAA
*
11578 ATCACACTTATATATATTTATTTAGCCCACCTCAGACTTCTCAAACTTATACATTA
702 ATCACACTTATACATATTTATTTAG--C-CCTCA-AC-TCTCAAACTTATACATTA
* ** * ** * *
11634 CTTTATTTACGGAGTAATTATTTTTCTCTTCAACTCAAAAACGCAAAATAACATCATTGTCAATT
1 CTCTATTTACGGAGTAACCATTTTTCTCTCCAACTCAGGAACGGAAAATAACATCATTGCCAATT
* *
11699 TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATATTTAAGGAAGATGGAGATACGAGAGATAAT
66 TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATATTTAAGGAAGATGGAGATAGGAGAGATAAA
* * * * * * *
11764 TAAGCCAATTAATGAACCTATTATGGAGCATATGGTTTCAATGTCTTTTTAAAACAGGATTCCTG
131 CAAGCCAGTTACTGAACCTATTAGGGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
* * * * *
11829 AAAATATCATTGTCTTTGATACTGTGCTATCCTATTTATTTCATTATTATA-TTTTTT-CTAAGG
196 AAAATATCATTGCCTTTGACACTGTGCTATCATATTTATATCATTATTATATTTTTTTGGTAAGG
*
11892 AATTACTTAATGAAAACAAGTGAAACTTTTAGCACATCACGACTCTCTTTATTTTTTTTTGAAAA
261 AATTACTTAATGAAAACAAGTGAAACTTTTAGCACATCACGACTATCTTTATTTTTTTTTGAAAA
*
11957 ATAGTTATATAACTTTATTGAAAATTAGTTACCGTATGACTTTATAAAAAGACATATATAGTGTC
326 ATAGTTATATAACTTTATTGAAAATTAGTTACTGTATGACTTTATAAAAAGACATATATAGTGTC
*
12022 TTATTAAAAAAACATATACAAAATAATAAAATGACATTATAAGCAGTGTCTTAATGAAAAGACAT
391 TTATTAAAAAAACATATACAAAATAATAAAATGACATTATAAGCAGTGTCTTAATAAAAAGACAT
*
12087 ACAATCTTTTTA-TTTTTTCATCAAATCTTCATATATCTTCTTCATATATATTCATATATATTCA
456 ACAATCTTTTTATTTTTTTCACCAAATCTTCATATATCTTCTTCATATATATTCATATATATTCA
*
12151 TATATCTCATAACTATGTTTATTGCATTATGTATCAGAGCCATGATAATGGATAAAAAGAGACCT
521 TATATCTCATAACTATCTTTATTGCATTATGTATCAGAGCCATGATAATGGATAAAAAGAGACCT
* * *
12216 CCACCGGAGAAACATAGGGTGAAAGAAACTTTAAAGGGAAAAAAAATTCAACCAAACCAGTCACT
586 CCACCGGAGAAACATAGGGAGAAAGAAACTTT-AAGGGAAAAAAAATACAACCAAACCAGCCACT
* * *
12281 TCTTGGTTTGAATAAAACTATTTTGTTCATACTTTTATTAGTAATTATAAAAGTCACACTTATAC
650 TCTTGGTTTGAATCAAACTATTTTGTTCACACTTTTATTAGTAATTATAAAAATCACACTTATAC
12346 ATATTTATTTAG-CC-C-AC-CTCAAACTTATACATTA
715 ATATTTATTTAGCCCTCAACTCTCAAACTTATACATTA
* * *
12380 CTCTATTTACGGTGTAACCATTTTTCTCTCCAACTCAGGAATGGAAAATAACGTCATTGCCAATT
1 CTCTATTTACGGAGTAACCATTTTTCTCTCCAACTCAGGAACGGAAAATAACATCATTGCCAATT
* * *
12445 TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATTTTTAAGGAAGATGTAGATAGGAGAGATAAT
66 TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATATTTAAGGAAGATGGAGATAGGAGAGATAAA
* * **
12510 TAAGACAGTTACTGAACCTATTAGGGAGCATATGGTTACAATATCTTTGTAAAACAGGATTCCTG
131 CAAGCCAGTTACTGAACCTATTAGGGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
* * * *
12575 AAAATATCACTGCCTCTGATACTGTGCTATCATATTTATATCTTTATTATATTTTTTT-GTAAGG
196 AAAATATCATTGCCTTTGACACTGTGCTATCATATTTATATCATTATTATATTTTTTTGGTAAGG
*
12639 AATTACTTAATGAAAACAAGTGAAACTTTTAGCATATCACGACT
261 AATTACTTAATGAAAACAAGTGAAACTTTTAGCACATCACGACT
12683 GTAGACACCC
Statistics
Matches: 1651, Mismatches: 139, Indels: 60
0.89 0.08 0.03
Matches are distributed among these distances:
746 236 0.14
747 54 0.03
748 2 0.00
750 1 0.00
751 2 0.00
753 77 0.05
754 1 0.00
755 98 0.06
756 2 0.00
757 88 0.05
758 3 0.00
759 4 0.00
760 104 0.06
761 368 0.22
762 47 0.03
763 105 0.06
764 343 0.21
765 35 0.02
766 8 0.00
767 73 0.04
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (752 bp):
CTCTATTTACGGAGTAACCATTTTTCTCTCCAACTCAGGAACGGAAAATAACATCATTGCCAATT
TCGAAAGTGTTCATATAGAAGGTAAAGATAGAATATTTAAGGAAGATGGAGATAGGAGAGATAAA
CAAGCCAGTTACTGAACCTATTAGGGAGCATATGGTTACAATGCCTTTGTAAAACAGGATTCCTG
AAAATATCATTGCCTTTGACACTGTGCTATCATATTTATATCATTATTATATTTTTTTGGTAAGG
AATTACTTAATGAAAACAAGTGAAACTTTTAGCACATCACGACTATCTTTATTTTTTTTTGAAAA
ATAGTTATATAACTTTATTGAAAATTAGTTACTGTATGACTTTATAAAAAGACATATATAGTGTC
TTATTAAAAAAACATATACAAAATAATAAAATGACATTATAAGCAGTGTCTTAATAAAAAGACAT
ACAATCTTTTTATTTTTTTCACCAAATCTTCATATATCTTCTTCATATATATTCATATATATTCA
TATATCTCATAACTATCTTTATTGCATTATGTATCAGAGCCATGATAATGGATAAAAAGAGACCT
CCACCGGAGAAACATAGGGAGAAAGAAACTTTAAGGGAAAAAAAATACAACCAAACCAGCCACTT
CTTGGTTTGAATCAAACTATTTTGTTCACACTTTTATTAGTAATTATAAAAATCACACTTATACA
TATTTATTTAGCCCTCAACTCTCAAACTTATACATTA
Found at i:12790 original size:27 final size:27
Alignment explanation
Indices: 12760--12828 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
12750 CACCTGGGGA
12760 CATTTTGGTCATTTTCACATTCAAGGG
1 CATTTTGGTCATTTTCACATTCAAGGG
* ** *
12787 CATTTTGATCATTTTTGCATTCAGGGG
1 CATTTTGGTCATTTTCACATTCAAGGG
*
12814 AATTTTGGTCATTTT
1 CATTTTGGTCATTTT
12829 GAGTCCATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.46
Consensus pattern (27 bp):
CATTTTGGTCATTTTCACATTCAAGGG
Found at i:17020 original size:22 final size:21
Alignment explanation
Indices: 16979--17030 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
16969 GTCAAATTTC
16979 AAGGAAAATGCAAAAAAAAAGA
1 AAGGAAAATGCAAAAAAAAA-A
17001 AAGGAAAA-G-AAAAATGAAAAA
1 AAGGAAAATGCAAAAA--AAAAA
17022 AATGGAAAA
1 AA-GGAAAA
17031 ATTAGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 18 0.67
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (21 bp):
AAGGAAAATGCAAAAAAAAAA
Found at i:18156 original size:10 final size:10
Alignment explanation
Indices: 18124--18157 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18114 TTTTCACCAA
18124 ATCTTCATAT
1 ATCTTCATAT
*
18134 ATATTCATAT
1 ATCTTCATAT
*
18144 ATCTTTATAT
1 ATCTTCATAT
18154 ATCT
1 ATCT
18158 CACGACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (10 bp):
ATCTTCATAT
Found at i:22464 original size:13 final size:13
Alignment explanation
Indices: 22446--22470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22436 AGATTTAGCC
22446 ATGTTAATATTGA
1 ATGTTAATATTGA
22459 ATGTTAATATTG
1 ATGTTAATATTG
22471 TTTGCTTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTTAATATTGA
Found at i:23301 original size:30 final size:30
Alignment explanation
Indices: 23265--23339 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
23255 GAAGTAGTAG
* *
23265 TGGAAGACAACAATGGAAACCAGCAGCAAA
1 TGGAAGATAACAATGGAAACCAGCAACAAA
* *
23295 TGGAAGATAACAATGGAAACGAGCAACAAG
1 TGGAAGATAACAATGGAAACCAGCAACAAA
23325 TGGAAGATAACAATG
1 TGGAAGATAACAATG
23340 TTGGAGAGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (30 bp):
TGGAAGATAACAATGGAAACCAGCAACAAA
Found at i:23559 original size:3 final size:3
Alignment explanation
Indices: 23551--23591 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
23541 TGATTATCTT
23551 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
23592 GAATGAAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31047 original size:17 final size:18
Alignment explanation
Indices: 31019--31053 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
31009 TATGTGGATT
31019 TTTGTCTCAAATTGTTTG
1 TTTGTCTCAAATTGTTTG
31037 TTTGT-TCAAATTGTTTG
1 TTTGTCTCAAATTGTTTG
31054 CATTAGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (18 bp):
TTTGTCTCAAATTGTTTG
Found at i:34568 original size:15 final size:15
Alignment explanation
Indices: 34550--34584 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
34540 CTTGATAATT
34550 AGCAATTTATTACCC
1 AGCAATTTATTACCC
34565 AGCAATTTATTACCC
1 AGCAATTTATTACCC
34580 AGCAA
1 AGCAA
34585 AAAGCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (15 bp):
AGCAATTTATTACCC
Found at i:34864 original size:31 final size:30
Alignment explanation
Indices: 34827--34974 Score: 122
Period size: 31 Copynumber: 4.9 Consensus size: 30
34817 CACGTGTACA
* *
34827 AAAAAGTGACATGTGACATTCCACATGTGCC
1 AAAAAGTGACACGTGACATGCCACATGT-CC
* * * *
34858 AAAAAGTGACACAT-ATCACGCCATATGTAC
1 AAAAAGTGACACGTGA-CATGCCACATGTCC
* * *
34888 AAAAAGTGACACGT--CACGCCACATATACA
1 AAAAAGTGACACGTGACATGCCACATGT-CC
* *
34917 AAAAAATGACACGTGACATGCCACATGTTTC
1 AAAAAGTGACACGTGACATGCCACATG-TCC
* *
34948 AAAAAGTGACATGTGGCATGCCACATG
1 AAAAAGTGACACGTGACATGCCACATG
34975 CACTCACAAT
Statistics
Matches: 93, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
28 10 0.11
29 13 0.14
30 15 0.16
31 54 0.58
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (30 bp):
AAAAAGTGACACGTGACATGCCACATGTCC
Found at i:34893 original size:30 final size:28
Alignment explanation
Indices: 34857--34920 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
34847 CCACATGTGC
* *
34857 CAAAAAGTGACACATATCACGCCATATGTA
1 CAAAAAGTGACAC--ATCACGCCACATATA
*
34887 CAAAAAGTGACACGTCACGCCACATATA
1 CAAAAAGTGACACATCACGCCACATATA
34915 CAAAAA
1 CAAAAA
34921 AATGACACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 18 0.58
30 13 0.42
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.16
Consensus pattern (28 bp):
CAAAAAGTGACACATCACGCCACATATA
Found at i:34930 original size:29 final size:28
Alignment explanation
Indices: 34873--34930 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
34863 GTGACACATA
* * *
34873 TCACGCCATATGTACAAAAAGTGACACG
1 TCACGCCACATATACAAAAAATGACACG
34901 TCACGCCACATATACAAAAAAATGACACG
1 TCACGCCACATATAC-AAAAAATGACACG
34930 T
1 T
34931 GACATGCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (28 bp):
TCACGCCACATATACAAAAAATGACACG
Found at i:35474 original size:78 final size:79
Alignment explanation
Indices: 35392--35553 Score: 254
Period size: 78 Copynumber: 2.1 Consensus size: 79
35382 GTTATTATAG
* * *
35392 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAAC-TATTATATT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTTATTATATT
*
35456 TTACCATTTTACTA
66 TTAACATTTTACTA
* *
35470 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTTATTATATT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTTATTATATT
*
35535 TTAATATTTTACTA
66 TTAACATTTTACTA
35549 TTTTA
1 TTTTA
35554 ATTAAAAAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
78 50 0.66
79 26 0.34
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (79 bp):
TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTTATTATATT
TTAACATTTTACTA
Found at i:47122 original size:6 final size:6
Alignment explanation
Indices: 47111--47144 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
47101 GTGCCAATAA
*
47111 TTTTAT TTTTAT TTTTAT TTTTAT TATT-T TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
47145 AAAAAACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Done.