Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020812.1 Corchorus olitorius cultivar O-4 contig20845, 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: 50545
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3498 original size:101 final size:101
Alignment explanation
Indices: 3348--3590 Score: 293
Period size: 101 Copynumber: 2.4 Consensus size: 101
3338 CTCCCGGGTA
* *
3348 TTTTGGCTCTGTTTTTTGTTCACTTATTGAAGGCCACCAGCATCTATATGGAGTTGA-AGACCAT
1 TTTTTGCTCTGTTTTTTGTTCACTTATTGAAGGCCACCAGCATCCATATGGAGTTGACA-A-C-T
3412 T-TGGAATGATGAATGAAGATTTT-GGAAGCTACAC-G-AAT
63 TCTGGAATGATGAATGAAGATTTTAGG-AGCT-C-CTGAAAT
* * *
3450 TTTTTGCTCTG-TTTTTGTTCATTTATTGATGGCCATCAGCATCCATATGGAGTTGACAACTTGC
1 TTTTTGCTCTGTTTTTTGTTCACTTATTGAAGGCCACCAGCATCCATATGGAGTTGACAACTT-C
* *
3514 TGGAATGATGAATGACGGTTTTAGGAGCTCCTGAAAT
65 TGGAATGATGAATGAAGATTTTAGGAGCTCCTGAAAT
*
3551 TTTTTGCTCTGTTTTTTGTTC-CTTTTGTGAAGGCCACCAG
1 TTTTTGCTCTGTTTTTTGTTCACTTAT-TGAAGGCCACCAG
3591 AATTTATAGC
Statistics
Matches: 122, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
99 3 0.02
100 3 0.02
101 83 0.68
102 33 0.27
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (101 bp):
TTTTTGCTCTGTTTTTTGTTCACTTATTGAAGGCCACCAGCATCCATATGGAGTTGACAACTTCT
GGAATGATGAATGAAGATTTTAGGAGCTCCTGAAAT
Found at i:4433 original size:23 final size:23
Alignment explanation
Indices: 4389--4435 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
4379 CCTTCAAATG
*
4389 GCTTTAGATCAATATCTGTTCAT
1 GCTTTAGATCAATATCAGTTCAT
4412 GCTTTAGATCAATAT-AGATTCAT
1 GCTTTAGATCAATATCAG-TTCAT
4435 G
1 G
4436 TTTTGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (23 bp):
GCTTTAGATCAATATCAGTTCAT
Found at i:9477 original size:21 final size:21
Alignment explanation
Indices: 9453--9497 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
9443 TAGTACCCCT
*
9453 AATAATTAAGGTAAGAAATTA
1 AATAATCAAGGTAAGAAATTA
9474 AATAATCAAGGTAAGAAATTA
1 AATAATCAAGGTAAGAAATTA
9495 AAT
1 AAT
9498 CCAGCTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (21 bp):
AATAATCAAGGTAAGAAATTA
Found at i:12489 original size:16 final size:16
Alignment explanation
Indices: 12464--12497 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12454 TGGTTTGTTT
12464 TTGCAACTTGATGTGC
1 TTGCAACTTGATGTGC
* *
12480 TTGCACCTTGCTGTGC
1 TTGCAACTTGATGTGC
12496 TT
1 TT
12498 ATCTATCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (16 bp):
TTGCAACTTGATGTGC
Found at i:28613 original size:6 final size:6
Alignment explanation
Indices: 28602--28646 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
28592 GATGCCGGTT
* * * *
28602 CCGATC CCGATC CCGATC CCGAAC CCGAAC CCGAAC CTGATC CCG
1 CCGATC CCGATC CCGATC CCGATC CCGATC CCGATC CCGATC CCG
28647 TCGGAGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.49, G:0.18, T:0.11
Consensus pattern (6 bp):
CCGATC
Found at i:28619 original size:12 final size:12
Alignment explanation
Indices: 28602--28646 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
28592 GATGCCGGTT
*
28602 CCGATCCCGATC
1 CCGATCCCGAAC
28614 CCGATCCCGAAC
1 CCGATCCCGAAC
*
28626 CCGAACCCGAAC
1 CCGATCCCGAAC
*
28638 CTGATCCCG
1 CCGATCCCG
28647 TCGGAGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.22, C:0.49, G:0.18, T:0.11
Consensus pattern (12 bp):
CCGATCCCGAAC
Found at i:29651 original size:3 final size:3
Alignment explanation
Indices: 29643--29674 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
29633 TAATGTTTTT
29643 AGA AGA AGA AGA AGA AGA AGA AGA ATGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA A
29675 ATTGGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:33714 original size:28 final size:29
Alignment explanation
Indices: 33655--33723 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
33645 CAATCTGTAT
* * *
33655 AAATTAATTAATTAATTAATTCGGTACCA
1 AAATAAATTAATTAATTAATTCCGTACAA
*
33684 AAA-AAATTAATTAATTAATTCCCTTA-AA
1 AAATAAATTAATTAATTAATT-CCGTACAA
*
33712 AAATTAATTAAT
1 AAATAAATTAAT
33724 CATAAATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 20 0.61
29 13 0.39
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (29 bp):
AAATAAATTAATTAATTAATTCCGTACAA
Found at i:46971 original size:331 final size:331
Alignment explanation
Indices: 46369--48018 Score: 2243
Period size: 331 Copynumber: 5.0 Consensus size: 331
46359 TGAATTATAT
* * *
46369 TCAAAAAATTGAGAAAAAAATTTTCAGCTCAATTTTTGCAAAATGTTAGCTGAAATCGTGTACT-
1 TCAAAAAATTGAG-AAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
** * *
46433 ACCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCAACTCTGTTTTGCATGATTTTTGGC
65 ACCATCACGGTTTTTGGCTAAAAACATGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
* * * *
46498 GCCAAGAATCCTTGAAATATCTATATTCATCATACCAAATCTCAGCCACAATTGATTTATAGACT
130 GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTTGATTTAAAGACT
* * *
46563 TGTTTTTACGAGGATCAGAATCTTGTTTCGATTTCTATTAGAAATTATTTCAAAAAAATAGGAAA
195 TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAAAAAATAGGAAA
46628 AACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGTATTGAATTATATAATTTTTACGAC
260 AACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGTATTGAATTATATAATTTTTACGAC
46693 TATTGTG
325 TATTGTG
*
46700 TCAAAAAATTGAGAAAAAATGTTTCGGCTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
1 TCAAAAAATTGAGAAAAAAT-TTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* * * * *
46765 ACCATCACAGTTTTTGGCAAAAAACACGCTCC-GGGCCCTGACAT-AGTTTTGCATGATTTTTGG
65 ACCATCACGGTTTTTGGCTAAAAACATGTTCCGGGGCCCCGAC-TCAGTTTTGCATGATTTTTGG
* * * * * * *
46828 CACCAAGACTCGTTGAAATATATATATTCATCTAACCAAATCTCAGTCACATTTGATTTAAGGAT
129 CGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTTGATTTAAAGAC
* *
46893 TTGATTTTACGAGCATCAGAATCTTGTTTCGTTTTTTATTAGAAATTAATTCAAAAAAATAGGAA
194 TTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAAAAAATAGGAA
* * * * * *
46958 AAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATACACTTTTTACAA
259 AAACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGTATTGAATTATATAATTTTTACGA
*
47023 CCATTGTG
324 CTATTGTG
* * *
47031 TCAAAAAATTGAGGAAAAAGTTTTCGGCTCAGTTTTTGTAAAATTTTAGCTTAAATCGTGTACTA
1 TCAAAAAATTGA-GAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* * * *
47096 TCCATCACGGTTTTTGGCTAAAAATATGTTCCGGGGCCCCGACTCAATTTTAG-ATGATTTTTGA
65 ACCATCACGGTTTTTGGCTAAAAACATGTTCCGGGGCCCCGACTCAGTTTT-GCATGATTTTTGG
* * *
47160 CGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAATTCTTAGCCATAATTAT-ATTTAAAG
129 CGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCA-CATT-TGATTTAAAG
*
47224 ACTTGTTTTTACGAGCATCAAAATCTTGTTTCGATTTCTT-TTAGAAATTAATTCAAAAAAAATA
192 ACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTT-TTATTAGAAATTAATTC-AAAAAAATA
* **
47288 GGAAAAACGATATTAAAAGCGTGAAAAGCCTTTTAATGTTTTTGGTAATTGAATTATATAATTTT
255 GGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGT-ATTGAATTATATAATTTT
* *
47353 TACAACTATTGCG
319 TACGACTATTGTG
** * * *
47366 TCAAATGATTAAGGAAAAAATTTTCGGCTCAATTTTTGCAAAATTTTAGTTGAAATCGTGTACTA
1 TCAAAAAATTGA-GAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* * * * * * * *
47431 ACCATCACAGTTTTTGGCTAAAAACATGTTCC-GGACCCAGGCACAATTTTGCATAATTTTTGGT
65 ACCATCACGGTTTTTGGCTAAAAACATGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
* * * * * *
47495 GCCAAGACTCGTTGAAATATATATATTCAT-ATAACCAAATCTCAGTCACATTGGATTTAAGGAT
130 GCCAAGACTCCTTGAAATATCTATATTCATCA-AACCAAATCTCAGCCACATTTGATTTAAAGAC
* *
47559 TTGTTTTTACGAGCATTAGAATCTTGTTTCGATTTTTATTATAAATTAATTC-AAAAAATAGGAA
194 TTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAAAAAATAGGAA
* * *
47623 AAACAATATTAGAAGCGTGAAAAGCCTTTTAATC-TTTT--TTTTGAATTATATACTTTTTACGA
259 AAACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGTATTGAATTATATAATTTTTACGA
47685 CTATTGTG
324 CTATTGTG
* *
47693 TCAAAAAATTGAGGAAAAATTTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATTGTGTACTA
1 TCAAAAAATTGA-GAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* ** * *
47758 TCCATCACGGTTTTTGGCTAAAAAGGTCTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGT
65 ACCATCACGGTTTTTGGCTAAAAACATGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
*
47823 GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTAAAGAC-
130 GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTTGATTTAAAGACT
* * * *
47887 -ATTTTTACGAGCATCAGAATCTTGTCTCGATTTCTATTAGAAATTAATTTAAAAAAATAGGAAA
195 TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAAAAAATAGGAAA
* * *
47951 AACGATATTAGAAGCGTGCAAAGCCTTTTAAT-AGTTTTGGCATTGAATTATAT-ATTTTTCCGA
260 AACGATATTAGAAGCGTGAAAAGCCTTTTAATCA-TTTTGGTATTGAATTATATAATTTTTACGA
48014 CTATT
324 CTATT
48019 TTAGCCGAAA
Statistics
Matches: 1152, Mismatches: 144, Indels: 48
0.86 0.11 0.04
Matches are distributed among these distances:
326 44 0.04
327 155 0.13
328 86 0.07
329 14 0.01
330 22 0.02
331 381 0.33
332 102 0.09
333 117 0.10
334 118 0.10
335 113 0.10
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (331 bp):
TCAAAAAATTGAGAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAA
CCATCACGGTTTTTGGCTAAAAACATGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCG
CCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTTGATTTAAAGACTT
GTTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAAAAAATAGGAAAA
ACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGTATTGAATTATATAATTTTTACGACT
ATTGTG
Found at i:47520 original size:666 final size:658
Alignment explanation
Indices: 46369--48018 Score: 2565
Period size: 662 Copynumber: 2.5 Consensus size: 658
46359 TGAATTATAT
* * * *
46369 TCAAAAAATTGAGAAAAAAATTTTCAGCTCAATTTTTGCAAAATGTTAGCTGAAATCGTGTACTA
1 TCAAAAAATTGAGGAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* *
46434 -CCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCAACTCTGTTTTGCATGATTTTTGGC
66 TCCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
* * *
46498 GCCAAGAATCCTTGAAATATCTATATTCATCATACCAAATCTCAGCCACAATTGATTTATAGACT
131 GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTAAAGACT
* *
46563 TGTTTTTACGAGGATCAGAATCTTGTTTCGATTTCTATTAGAAATTATTTCAAAAAAATAGGAAA
196 TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTCAAAAAAATAGGAAA
*
46628 AACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGTATTGAATTATATAATTTTTACGAC
261 AACGATATTAGAAGCGTGAAAAGCCTTTTAAT-GTTTTGGTATTGAATTATATAATTTTTACGAC
* * *
46693 TATTGTGTCAAAAAATTGAGAAAAAATGTTTCGGCTCAGTTTTTGCAAAATTTTAGCCGAAATCG
325 TATTGCGTCAAAAAATTAAGAAAAAATGTTTCGGCTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * * * *
46758 TGTACTAACCATCACAGTTTTTGGCAAAAAACACGCTCCGGGCCCTGACATAGTTTTGCATGATT
390 TGTACTAACCATCACAGTTTTTGGCAAAAAACACGCTCCGGACCCAGACACAATTTTGCATAATT
* *
46823 TTTGGCACCAAGACTCGTTGAAATATATATATTCATCTAACCAAATCTCAGTCACATTTGATTTA
455 TTTGGCACCAAGACTCGTTGAAATATATATATTCATATAACCAAATCTCAGTCACATTGGATTTA
*
46888 AGGATTTGATTTTACGAGCATCAGAATCTTGTTTCGTTTTTTATTAGAAATTAATTCAAAAAAAT
520 AGGATTTGATTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTC-AAAAAAT
46953 AGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATACACTTTT
584 AGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTT---ATTGAATTATACACTTTT
47018 TACAACCATTGTG
646 TACAACCATTGTG
* * *
47031 TCAAAAAATTGAGGAAAAAGTTTTCGGCTCAGTTTTTGTAAAATTTTAGCTTAAATCGTGTACTA
1 TCAAAAAATTGAGGAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
** * *
47096 TCCATCACGGTTTTTGGCTAAAAATATGTTCCGGGGCCCCGACTCAATTTTAG-ATGATTTTTGA
66 TCCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGACTCAGTTTT-GCATGATTTTTGG
* * * *
47160 CGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAATTCTTAGCCATAATTATATTTAAAGA
130 CGCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATT-GATTTAAAGA
* *
47225 CTTGTTTTTACGAGCATCAAAATCTTGTTTCGATTTCTTTTAGAAATTAATTCAAAAAAAATAGG
194 CTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTC-AAAAAAATAGG
*
47290 AAAAACGATATTAAAAGCGTGAAAAGCCTTTTAATGTTTTTGGTAATTGAATTATATAATTTTTA
258 AAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATG-TTTTGGT-ATTGAATTATATAATTTTTA
* ** **
47355 CAACTATTGCGTCAAATGATTAAGGAAAAAAT-TTTCGGCTCAATTTTTGCAAAATTTTAGTTGA
321 CGACTATTGCGTCAAAAAATTAA-GAAAAAATGTTTCGGCTCAATTTTTGCAAAATTTTAGCCGA
* * * *
47419 AATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACATGTTCCGGACCCAGGCACAATTTTGCA
385 AATCGTGTACTAACCATCACAGTTTTTGGCAAAAAACACGCTCCGGACCCAGACACAATTTTGCA
**
47484 TAATTTTTGGTGCCAAGACTCGTTGAAATATATATATTCATATAACCAAATCTCAGTCACATTGG
450 TAATTTTTGGCACCAAGACTCGTTGAAATATATATATTCATATAACCAAATCTCAGTCACATTGG
* * *
47549 ATTTAAGGATTTGTTTTTACGAGCATTAGAATCTTGTTTCGATTTTTATTATAAATTAATTCAAA
515 ATTTAAGGATTTGATTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAA
* *
47614 AAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTTTTGAATTATATACTTT
580 AAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTATTGAATTATACACTTT
* *
47679 TTACGACTATTGTG
645 TTACAACCATTGTG
* *
47693 TCAAAAAATTGAGGAAAAATTTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATTGTGTACTA
1 TCAAAAAATTGAGGAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* *
47758 TCCATCACGGTTTTTGGCTAAAAAGGTCTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGT
66 TCCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
47823 GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTAAAGAC-
131 GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTAAAGACT
* * *
47887 -ATTTTTACGAGCATCAGAATCTTGTCTCGATTTCTATTAGAAATTAATTTAAAAAAATAGGAAA
196 TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTCAAAAAAATAGGAAA
* * *
47951 AACGATATTAGAAGCGTGCAAAGCCTTTTAATAGTTTTGGCATTGAATTATAT-ATTTTTCCGAC
261 AACGATATTAGAAGCGTGAAAAGCCTTTTAAT-GTTTTGGTATTGAATTATATAATTTTTACGAC
48015 TATT
325 TATT
48019 TTAGCCGAAA
Statistics
Matches: 900, Mismatches: 79, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
656 13 0.01
657 12 0.01
658 50 0.06
659 46 0.05
661 11 0.01
662 253 0.28
663 104 0.12
664 58 0.06
665 103 0.11
666 242 0.27
667 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (658 bp):
TCAAAAAATTGAGGAAAAAATTTTCGGCTCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
TCCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
GCCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTAAAGACT
TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTCAAAAAAATAGGAAA
AACGATATTAGAAGCGTGAAAAGCCTTTTAATGTTTTGGTATTGAATTATATAATTTTTACGACT
ATTGCGTCAAAAAATTAAGAAAAAATGTTTCGGCTCAATTTTTGCAAAATTTTAGCCGAAATCGT
GTACTAACCATCACAGTTTTTGGCAAAAAACACGCTCCGGACCCAGACACAATTTTGCATAATTT
TTGGCACCAAGACTCGTTGAAATATATATATTCATATAACCAAATCTCAGTCACATTGGATTTAA
GGATTTGATTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAGAAATTAATTCAAAAAATAG
GAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTATTGAATTATACACTTTTTACAA
CCATTGTG
Found at i:49476 original size:328 final size:329
Alignment explanation
Indices: 48016--50545 Score: 3173
Period size: 328 Copynumber: 7.7 Consensus size: 329
48006 TTTTCCGACT
* * *
48016 ATTTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCTAAAAAGGTGTTTCGGGGCCTCGG
1 ATTTTAGCCGAAATCGTGAAC--T-CATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGG
* * *
48081 CTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCCTTGAAATATCTATATTCATCA-AACAAATTC
63 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAA-TC
*
48145 TTAGCCAC-ATTCGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTA
127 TCAGCCACAATT-GATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTA
48209 GAAATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGG
191 GAAATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGG
* * *
48274 CATAGAATTATATACTTTTTACAACCATTGTGTCAAAAAATTGAGGAAAATTTTTTCGGCTCAGT
256 CATTGAATTATATACTTTTTACAACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAGT
48339 TTTTGCAAA
321 TTTTGCAAA
** * * ** *
48348 ATTTTAGCTTAAATCATGTAC-CATCACGGTTTTTGGCTAAAAATATGTTACGGGGCCCCGGCTC
1 ATTTTAGCCGAAATCGTGAACTCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTC
* *
48412 AGTTTTAG-ATGATTTTTGGCGCCATGACTCCTTGAAATATCTATATTCATCATACCAATTCTCA
66 AGTTTT-GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAATCTCA
*
48476 GCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTT-GATTTCTGTTAGAAA
130 GCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAA
* * * *
48540 TTAATTC-AAAAAATAGGAAAAATGATATTAAAAGCATGCAAAGCCTTTTAATCTTTTTGGCATT
195 TTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATT
* * * * * * *
48604 GAATTATATA-TTATTTCCGACTATTGTGTGAAAAAATTGAGGAAAAATCTTACAGCTCAATTTT
260 GAATTATATACTT-TTTACAACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAGTTTT
48668 TGCAAA
324 TGCAAA
* * * *
48674 ATTTTAGCCGAAATCGTG---T-A-CACAGTTTTTGGTTAAAAAGGTGTTCCGGGGCTCCGACTC
1 ATTTTAGCCGAAATCGTGAACTCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTC
* * *
48734 AGTTTTGCATGATTTTTGGCACCAAGAATCCCTGAAATATCTATATTCATCATACCAAATCTCAG
66 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAATCTCAG
* * * * *
48799 CCACAATTGATTTAAAGACGTATTTTTACGAGCATCGGAATCTTGTTTCGATTTATATAAGAAAT
131 CCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAAT
* * * *
48864 TAATT-AAAAAAA-AGGAAAAATGATATTAGAATCGTGAAAAGCCTATTCATCTTTTTGGCATTG
196 TAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTG
* * * * *
48927 AATTATATATTTTTTACGACTATTGCGTCAAAAAATTGAGGAAAACTATTTCGGCTC-GATTTTT
261 AATTATATACTTTTTACAACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAG-TTTTT
48991 GCAAA
325 GCAAA
**
48996 ATTTTA-CCGAAATCGTGTATTA-TCCATCACTGG-TTTTGGCTAAAAAGGTGTTTGGGGGCCCC
1 ATTTTAGCCGAAATCGTG-A--ACT-CATCAC-GGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCC
*
49058 GGCTCAGTTTTGCATGATTTTTGGCGCCAAGATTCCTTGAAATATCTATATTCATCATACCAAAT
61 GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAAT
* *
49123 CTCAGCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGTTTTTTATTA
126 CTCAGCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTA
* * * *
49188 GAAATTAATTCAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTCTTCATATTTTTGG
191 GAAATTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGG
*
49253 CATTGAATTATATATTTTTTACGAA-TATTGTGTCAAAAAATTGAGGAAAAACTTTTT-GGCTCA
256 CATTGAATTATATACTTTTTAC-AACTATTGTGTCAAAAAATTGAGGAAAAA-TTTTTCGGCTCA
49316 GTTTTTGCAAA
319 GTTTTTGCAAA
* * *
49327 ATTTTAGCTGAAATCGTGAACTCATCACGGTTTTT-GTTAAAAAGGTGTTCCGGGGCTCCGGCTC
1 ATTTTAGCCGAAATCGTGAACTCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTC
* *
49391 AGTTTTGCAAGATTTTTGGCGCCAAGACTCCCTGAAATATCTATATTCATCATACCAAATCTCAG
66 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAATCTCAG
* *
49456 CCACAATTGATTTTAAGACTTGTTTTAACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAAT
131 CCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAAT
* * * *
49521 TAATT-AAAAAAATAGGGAAAACGATAATAAAAGCGTGAAAAGCCTTTCAATCTTTTTGGCATTG
196 TAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTG
* * *
49585 AATTATTTACTTTTTACAACCATTGTGTAAAAAAAATTGAGGAAAAATTTTTCGGCTCAGTTTTT
261 AATTATATACTTTTTACAACTATTGTGT-CAAAAAATTGAGGAAAAATTTTTCGGCTCAGTTTTT
49650 GCAAA
325 GCAAA
* * *
49655 GTTTTAG-C----T--T-AA---ATCACGGTTTTTGGCTAAAAATGTGTTCCGGGGCCCCAGCTC
1 ATTTTAGCCGAAATCGTGAACTCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTC
* * * *
49709 AGTTTTAG-ATGATTTTTGGCGCCAGGACTCCTTGAAATATCTATATTCATCAAACCAATTCTTA
66 AGTTTT-GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAATCTCA
* * *
49773 GCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGTATCTTGTTTCGATTTCCATTAGAAT
130 GCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAA
* * * *
49838 TTAATTC-AAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGCCTTTTATTCTTTTTGGAATT
195 TTAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATT
* *
49902 GAATTATATAATTTTTACAACTATTGTGTCAAAAAATTAAAGGAAAAATTTTTCGGCTCAGTTTT
260 GAATTATATACTTTTTACAACTATTGTGTCAAAAAATT-GAGGAAAAATTTTTCGGCTCAGTTTT
49967 TGCAAA
324 TGCAAA
* * * *** ***
49973 GTTTTAGCAGAAATCGTGTTTAAC-CATCACAGTTTTTGGCTAAAAACACGTTCC-GGGCCCAAA
1 ATTTTAGCCGAAATCGTG---AACTCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGG
* * ** * *
50036 CACAGTTTTGCATAATTTTTGGCGCCAAGACTTGTTGAATTATATATATATATATATATATATAT
63 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG--------A-A-ATATCTATAT-T-CAT
* * * * * *
50101 ATATGACCAAATCTCAGTCAC-ATTGGATTTAAGGA-TTCGTTTTTACGAGCATCATAATCATAT
116 -CAT-ACCAAATCTCAGCCACAATT-GATTTAAAGACTT-GTTTTTACGAGCATCAGAATCTTGT
* * * * * *
50164 TTCGATTTTTATTATAAATTAATTAAAAAAAAATAGGAAAAACAACATTAGAAGCGTG-AGAGCC
177 TTCGATTTCTATTAGAAATTAATT-CAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCC
50228 TTTTAATCTTTTTGGCATTGAATTATATACTTTTTACAACTATTGTGTCAAAAAATTGAGGAAAA
241 TTTTAATCTTTTTGGCATTGAATTATATACTTTTTACAACTATTGTGTCAAAAAATTGAGGAAAA
50293 ATTTTTCGGCTCAGTTTTTGCAAA
306 ATTTTTCGGCTCAGTTTTTGCAAA
* * * * * * *
50317 ATTTTAGCTGAAATCATGCACTATCCATCACTGTTTTTGGCTAAAAAGGTCTTCCGGGGCACCGA
1 ATTTTAGCCGAAATCGTGAAC--T-CATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGG
* * * *
50382 CTTAGTTTTGCATGATTTTTGTCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAAATC
63 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACC-AAATC
* *
50447 TCAGCCACAATTGATTTAAAGAC--ATTTTTACGAGCATCAGAATCTTGTTTCGATTTTTATTAG
127 TCAGCCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAG
* * *
50510 AGATTAATTTAAAAAAATAGGAAAAACAATATTAGA
192 AAATTAATTCAAAAAAATAGGAAAAACGATATTAGA
Statistics
Matches: 1914, Mismatches: 210, Indels: 150
0.84 0.09 0.07
Matches are distributed among these distances:
317 20 0.01
318 262 0.14
319 1 0.00
320 2 0.00
321 13 0.01
322 244 0.13
323 29 0.02
325 3 0.00
326 128 0.07
327 99 0.05
328 331 0.17
329 180 0.09
330 71 0.04
331 177 0.09
332 37 0.02
333 22 0.01
334 5 0.00
335 1 0.00
336 9 0.00
337 1 0.00
338 2 0.00
339 1 0.00
340 9 0.00
341 3 0.00
342 2 0.00
343 6 0.00
344 109 0.06
345 84 0.04
346 63 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (329 bp):
ATTTTAGCCGAAATCGTGAACTCATCACGGTTTTTGGCTAAAAAGGTGTTCCGGGGCCCCGGCTC
AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCATACCAAATCTCAG
CCACAATTGATTTAAAGACTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAAT
TAATTCAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTG
AATTATATACTTTTTACAACTATTGTGTCAAAAAATTGAGGAAAAATTTTTCGGCTCAGTTTTTG
CAAA
Found at i:50083 original size:2 final size:2
Alignment explanation
Indices: 50076--50104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
50066 CTTGTTGAAT
50076 TA 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 TA T
50105 GACCAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.