Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014196.1 Corchorus capsularis cultivar CVL-1 contig14217, 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: 43322
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3217 original size:2 final size:2
Alignment explanation
Indices: 3210--3240 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3200 ACTTGTTTAT
3210 TA 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 TA T
3241 TGTTGTGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5837 original size:10 final size:10
Alignment explanation
Indices: 5822--5846 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5812 ATTCTAATGA
5822 AATTATTTAC
1 AATTATTTAC
5832 AATTATTTAC
1 AATTATTTAC
5842 AATTA
1 AATTA
5847 GCGAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
AATTATTTAC
Found at i:7083 original size:33 final size:32
Alignment explanation
Indices: 7046--7152 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
7036 CGCCAAGCGA
* *
7046 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGGCATATCCA-GTCGCG
*
7079 TGGCCGGTGTTGGCCGGGTATATCCGAGTCGCG
1 TGGCCGGTGTTGGCCGGGCATATCC-AGTCGCG
* * *
7112 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGGCATATCC-AGTCGCG
7145 TGGCCGGT
1 TGGCCGGT
7153 CACTCGCGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 62 0.97
34 2 0.03
ACGTcount: A:0.08, C:0.27, G:0.40, T:0.24
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGGCATATCCAGTCGCG
Found at i:10990 original size:19 final size:18
Alignment explanation
Indices: 10957--10993 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10947 TTGAAATAAT
10957 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
10975 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
10994 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:11284 original size:38 final size:38
Alignment explanation
Indices: 11231--11316 Score: 118
Period size: 38 Copynumber: 2.3 Consensus size: 38
11221 GGCTCGATCA
* * *
11231 GTCATCTTTCAGCAATTATTAAGATCGACTGGAAACAG
1 GTCATCTTTCAGCAATTATCAAAATCGACTAGAAACAG
* * *
11269 GTCATCTTTCGGCAATTATCAAAATCGATTAGAAACGG
1 GTCATCTTTCAGCAATTATCAAAATCGACTAGAAACAG
11307 GTCATCTTTC
1 GTCATCTTTC
11317 CGCAGTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (38 bp):
GTCATCTTTCAGCAATTATCAAAATCGACTAGAAACAG
Found at i:11446 original size:43 final size:42
Alignment explanation
Indices: 11331--11618 Score: 360
Period size: 43 Copynumber: 6.8 Consensus size: 42
11321 GTTTTAAGTT
*
11331 GCCCCCAAGGGGAGCATTCCAACAACTTTTCAGTTTTCAGCA
1 GCCCCCAAGGGGGGCATTCCAACAACTTTTCAGTTTTCAGCA
** * * *
11373 GCCCCCAAATGAGGCATCCCAACAAGTTTTCAGTTTTCAGCA
1 GCCCCCAAGGGGGGCATTCCAACAACTTTTCAGTTTTCAGCA
* *
11415 GCCCCCAAGGGTGGGCATTCCAACAACTTTTCCGTTTTCAGCT
1 GCCCCCAAGGG-GGGCATTCCAACAACTTTTCAGTTTTCAGCA
* * *
11458 GCTCCCAATGGGGGACATTCCAACAACTTTTCACTTTTCAGCA
1 GCCCCCAA-GGGGGGCATTCCAACAACTTTTCAGTTTTCAGCA
* * * *
11501 GCCACCAAGTGGGGCATTCCAACAACTTTCCCGTTTTCAGCA
1 GCCCCCAAGGGGGGCATTCCAACAACTTTTCAGTTTTCAGCA
* * * *
11543 GTCCCCAAGGGGGGGCATTCCAACAAATTTTCAGTTTTTAGCT
1 GCCCCCAA-GGGGGGCATTCCAACAACTTTTCAGTTTTCAGCA
*
11586 GCTCCCAAAGGGGGGCATTCCAACAACTTTTCA
1 GC-CCCCAAGGGGGGCATTCCAACAACTTTTCA
11619 ACTTTCAGTT
Statistics
Matches: 206, Mismatches: 36, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
42 80 0.39
43 118 0.57
44 8 0.04
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (42 bp):
GCCCCCAAGGGGGGCATTCCAACAACTTTTCAGTTTTCAGCA
Found at i:11465 original size:85 final size:84
Alignment explanation
Indices: 11331--11617 Score: 353
Period size: 85 Copynumber: 3.4 Consensus size: 84
11321 GTTTTAAGTT
* * * * *
11331 GCCCCCAAGGGGAGCATTCCAACAACTTTTCAGTTTTCAGCAGCCCCCAAATGAGGCATCCCAAC
1 GCCCCCAAGGGGGGCATTCCAACAACTTTTCCGTTTTCAGCAGCTCCCAAATGGGGCATTCCAAC
*
11396 AAGTTTTCAGTTTTCAGCA
66 AAATTTTCAGTTTTCAGCA
*
11415 GCCCCCAAGGGTGGGCATTCCAACAACTTTTCCGTTTTCAGCTGCTCCC-AATGGGGGACATTCC
1 GCCCCCAAGGG-GGGCATTCCAACAACTTTTCCGTTTTCAGCAGCTCCCAAAT-GGGG-CATTCC
* *
11479 AACAACTTTTCACTTTTCAGCA
63 AACAAATTTTCAGTTTTCAGCA
* * * **
11501 GCCACCAAGTGGGGCATTCCAACAACTTTCCCGTTTTCAGCAG-TCCCCAAGGGGGGGCATTCCA
1 GCCCCCAAGGGGGGCATTCCAACAACTTTTCCGTTTTCAGCAGCT-CCCAA-ATGGGGCATTCCA
* *
11565 ACAAATTTTCAGTTTTTAGCT
64 ACAAATTTTCAGTTTTCAGCA
*
11586 GCTCCCAAAGGGGGGCATTCCAACAACTTTTC
1 GC-CCCCAAGGGGGGCATTCCAACAACTTTTC
11618 AACTTTCAGT
Statistics
Matches: 174, Mismatches: 22, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
84 15 0.09
85 95 0.55
86 64 0.37
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (84 bp):
GCCCCCAAGGGGGGCATTCCAACAACTTTTCCGTTTTCAGCAGCTCCCAAATGGGGCATTCCAAC
AAATTTTCAGTTTTCAGCA
Found at i:11496 original size:128 final size:128
Alignment explanation
Indices: 11339--11623 Score: 417
Period size: 128 Copynumber: 2.2 Consensus size: 128
11329 TTGCCCCCAA
* * * *
11339 GGGGAGCATTCCAACAACTTTTCAGTTTTCAGCAGCCCCCAAATGAGGCATCCCAACAAGTTTTC
1 GGGGA-CATTCCAACAACTTTTCACTTTTCAGCAGCCACCAAATGAGGCATCCCAACAACTTTCC
* * * *
11404 AGTTTTCAGCAGCCCCCAAGGGTGGGCATTCCAACAACTTTTCCGTTTTCAGCTGCTCCCAATG
65 AGTTTTCAGCAGCCCCCAAGGGGGGGCATTCCAACAAATTTTCAGTTTTCAGCTGCTCCCAAAG
* * * *
11468 GGGGACATTCCAACAACTTTTCACTTTTCAGCAGCCACCAAGTGGGGCATTCCAACAACTTTCCC
1 GGGGACATTCCAACAACTTTTCACTTTTCAGCAGCCACCAAATGAGGCATCCCAACAACTTTCCA
* *
11533 GTTTTCAGCAGTCCCCAAGGGGGGGCATTCCAACAAATTTTCAGTTTTTAGCTGCTCCCAAAG
66 GTTTTCAGCAGCCCCCAAGGGGGGGCATTCCAACAAATTTTCAGTTTTCAGCTGCTCCCAAAG
*
11596 GGGGGCATTCCAACAACTTTTCAACTTT
1 GGGGACATTCCAACAACTTTTC-ACTTT
11624 CAGTTGCTCC
Statistics
Matches: 140, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
128 130 0.93
129 10 0.07
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (128 bp):
GGGGACATTCCAACAACTTTTCACTTTTCAGCAGCCACCAAATGAGGCATCCCAACAACTTTCCA
GTTTTCAGCAGCCCCCAAGGGGGGGCATTCCAACAAATTTTCAGTTTTCAGCTGCTCCCAAAG
Found at i:11641 original size:43 final size:42
Alignment explanation
Indices: 11334--11660 Score: 300
Period size: 43 Copynumber: 7.7 Consensus size: 42
11324 TTAAGTTGCC
* * * *
11334 CCCAAGGGGAGCATTCCAACAACTTTTCAGTTTTCAGCAGCC
1 CCCAAGGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
** * * * * * *
11376 CCCAAATGAGGCATCCCAACAAGTTTTCAGTTTTCAGCAGCC
1 CCCAAGGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
**
11418 CCCAAGGGTGGGCATTCCAACAACTTTTCCGTTTTCAGCTGCT
1 CCCAAGGG-GGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
* * *
11461 CCCAATGGGGGACATTCCAACAACTTTTCACTTTTCAGCAGC-
1 CCCAA-GGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
* * ** *
11503 CACCAAGTGGGGCATTCCAACAACTTTCCCGTTTTCAGCAG-T
1 C-CCAAGGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
* * *
11545 CCCCAAGGGGGGGCATTCCAACAAATTTTCAGTTTTTAGCTGCT
1 -CCCAA-GGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
* *
11589 CCCAAAGGGGGGCATTCCAACAACTTTTCAACTTTCAGTTGCT
1 CCC-AAGGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
* * * *
11632 -CCGAGAGGGGCATTCTAACAAGTTTTCAA
1 CCCAAGGGGGGCATTCCAACAACTTTTCAA
11661 GGGGGGCATT
Statistics
Matches: 239, Mismatches: 38, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
41 23 0.10
42 79 0.33
43 131 0.55
44 6 0.03
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (42 bp):
CCCAAGGGGGGCATTCCAACAACTTTTCAATTTTCAGCTGCT
Found at i:15064 original size:35 final size:35
Alignment explanation
Indices: 14945--15491 Score: 537
Period size: 35 Copynumber: 15.8 Consensus size: 35
14935 GTCAACAAGA
* *
14945 ACTTAATTCAGTGTAATTAAGTAAACA-CAGTTA-AGG
1 ACTTAATTCAGGGTAATTAAGTAAA-ATCAG-CACA-G
* * * ** *
14981 ACTTAATTCAGGGCAATTAAATAGAATCAATAAATG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACA-G
* *
15017 GCTTAATTCAGGGTAATTAAGTGAAATCAGCACAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
*
15052 ACTTAATTCAGGGTAATTAAATAAAATCAGCACAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* * *
15087 GCTTAATTCGGGGTAATTAAGTAAAACCAGCACAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* *
15122 ACTTAATTCAGAGTAATTAAGTAAAATCTGCACA-
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* *
15156 AGCTTAAATCAGGGTAATTAAGTAAAACCAGCACAG
1 A-CTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* * *
15192 GCTTGATTCAGGGTAATTAAGT-AAATCA-CAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* * * * *
15225 GCTTAGTTCATGGTAATTAAGTAAAATCAACACAT
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
*
15260 ACTTAATTCAGGGTAATTAAGTAAAACCAGCACAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* *
15295 ACTTGATTCA-GGTAATTAAGT-AAATCA-CAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* * *
15327 GCTTAATTCAGGGTAATTAGGTAAAATCAGCACAT
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* * *
15362 ACTTGATTCGGGGTAATTATGTAAAATCAGCACAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* *
15397 ACTTAATTCAGGATAATTAAGTAAAATCA--A-TG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
* *
15429 ACTTGATTCAAGG-AGATTAAGT-AAATCAGCA-AGG
1 ACTTAATTCAGGGTA-ATTAAGTAAAATCAGCACA-G
* ** *
15463 ACTTAGTTTCAAAGAAATTAAGTAAAATC
1 ACTTA-ATTCAGGGTAATTAAGTAAAATC
15492 CACAAAGGCT
Statistics
Matches: 424, Mismatches: 71, Indels: 32
0.80 0.13 0.06
Matches are distributed among these distances:
31 7 0.02
32 30 0.07
33 40 0.09
34 34 0.08
35 256 0.60
36 57 0.13
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (35 bp):
ACTTAATTCAGGGTAATTAAGTAAAATCAGCACAG
Found at i:15438 original size:102 final size:102
Alignment explanation
Indices: 14945--15459 Score: 551
Period size: 102 Copynumber: 5.0 Consensus size: 102
14935 GTCAACAAGA
* * * *
14945 ACTTAATTCAGTGTAATTAAGT-AAACACAGTTA-AGGACTTAATTCAGGGCAATTAAATAGAAT
1 ACTTAATTCAGGGTAATTAAGTAAAAC-CAG-CACA-GACTTAATTCAGGGTAATTAAGTA-AAT
* * *
15008 CAATAAATGGCTTAATTCAGGGTAATTAAGTGAAATCAGCACAG
62 --ACAAA-GGCTTAATTCAGGGTAATTAAGTAAAATCAGCACAT
* * * *
15052 ACTTAATTCAGGGTAATTAAATAAAATCAGCACAGGCTTAATTCGGGGTAATTAAGTAAA-ACCA
1 ACTTAATTCAGGGTAATTAAGTAAAACCAGCACAGACTTAATTCAGGGTAATTAAGTAAATA-CA
* * *
15116 GCACAGACTTAATTCAGAGTAATTAAGTAAAATCTGCACA-
65 --A-AGGCTTAATTCAGGGTAATTAAGTAAAATCAGCACAT
* * *
15156 AGCTTAAATCAGGGTAATTAAGTAAAACCAGCACAGGCTTGATTCAGGGTAATTAAGTAAATCAC
1 A-CTTAATTCAGGGTAATTAAGTAAAACCAGCACAGACTTAATTCAGGGTAATTAAGTAAAT-AC
* * *
15221 AAAGGCTTAGTTCATGGTAATTAAGTAAAATCAACACAT
64 AAAGGCTTAATTCAGGGTAATTAAGTAAAATCAGCACAT
*
15260 ACTTAATTCAGGGTAATTAAGTAAAACCAGCACAGACTTGATTCA-GGTAATTAAGTAAATCACA
1 ACTTAATTCAGGGTAATTAAGTAAAACCAGCACAGACTTAATTCAGGGTAATTAAGTAAAT-ACA
*
15324 AAGGCTTAATTCAGGGTAATTAGGTAAAATCAGCACAT
65 AAGGCTTAATTCAGGGTAATTAAGTAAAATCAGCACAT
* * * * *
15362 ACTTGATTCGGGGTAATTATGTAAAATCAGCACAGACTTAATTCAGGATAATTAAGTAAA-ATCA
1 ACTTAATTCAGGGTAATTAAGTAAAACCAGCACAGACTTAATTCAGGGTAATTAAGTAAATA-CA
* * * *
15426 ATGACTTGATTCAAGG-AGATTAAGT-AAATCAGCA
65 AAGGCTTAATTCAGGGTA-ATTAAGTAAAATCAGCA
15460 AGGACTTAGT
Statistics
Matches: 354, Mismatches: 41, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
101 11 0.03
102 114 0.32
103 86 0.24
104 3 0.01
105 88 0.25
106 24 0.07
107 25 0.07
108 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (102 bp):
ACTTAATTCAGGGTAATTAAGTAAAACCAGCACAGACTTAATTCAGGGTAATTAAGTAAATACAA
AGGCTTAATTCAGGGTAATTAAGTAAAATCAGCACAT
Found at i:15596 original size:36 final size:36
Alignment explanation
Indices: 15542--15683 Score: 212
Period size: 36 Copynumber: 3.9 Consensus size: 36
15532 AAGACTTAAT
*
15542 AGTGAAGTAAAGAACTTAATTCGGGGTAATTAAGTAA
1 AGTGAA-TAAAGAACTTAATTCAGGGTAATTAAGTAA
* * * *
15579 AGTCAATAAAGAACTTAATTAAGGGCAATTAAGTAG
1 AGTGAATAAAGAACTTAATTCAGGGTAATTAAGTAA
* *
15615 AGTGAATAAAGAACTTAATTCAGGGAAATTAAGTCA
1 AGTGAATAAAGAACTTAATTCAGGGTAATTAAGTAA
15651 AGTGAATAAAGAACTTAATTCAGGGTAATTAAG
1 AGTGAATAAAGAACTTAATTCAGGGTAATTAAG
15684 AGGGATATTA
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 89 0.95
37 5 0.05
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (36 bp):
AGTGAATAAAGAACTTAATTCAGGGTAATTAAGTAA
Found at i:24549 original size:19 final size:18
Alignment explanation
Indices: 24509--24554 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
24499 AGGATAAGTG
24509 GAAAAAATGAAAAAAAAAA
1 GAAAAAA-GAAAAAAAAAA
* *
24528 GAAGAAAGAAAGAAAAAGA
1 GAAAAAAGAAA-AAAAAAA
24547 GAAAAAAG
1 GAAAAAAG
24555 CAACGATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
GAAAAAAGAAAAAAAAAA
Found at i:24586 original size:19 final size:19
Alignment explanation
Indices: 24564--24622 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
24554 GCAACGATGA
24564 TTTTCAAAAAGAGTCATGG
1 TTTTCAAAAAGAGTCATGG
24583 TTTTCAAAAAG-G---T--
1 TTTTCAAAAAGAGTCATGG
24596 TTTT-AAAAAGAGTCATGG
1 TTTTCAAAAAGAGTCATGG
24614 TTTTCAAAA
1 TTTTCAAAA
24623 GGTTCTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
15 1 0.03
16 1 0.03
18 5 0.15
19 15 0.45
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (19 bp):
TTTTCAAAAAGAGTCATGG
Found at i:24605 original size:31 final size:30
Alignment explanation
Indices: 24564--24626 Score: 108
Period size: 31 Copynumber: 2.1 Consensus size: 30
24554 GCAACGATGA
24564 TTTTCAAAAAGAGTCATGGTTTTCAAAAAGG
1 TTTTCAAAAAGAGTCATGGTTTTC-AAAAGG
*
24595 TTTTTAAAAAGAGTCATGGTTTTCAAAAGG
1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGG
24625 TT
1 TT
24627 CTGATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (30 bp):
TTTTCAAAAAGAGTCATGGTTTTCAAAAGG
Found at i:24637 original size:44 final size:44
Alignment explanation
Indices: 24588--24693 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
24578 CATGGTTTTC
*
24588 AAAAAGGTTTTTAAAAAGAGTCAT-GGTTTTCAAAAGGTTCTGAT
1 AAAAAGGTTTTCAAAAAGAGTC-TCGGTTTTCAAAAGGTTCTGAT
*
24632 AAAAAGGTTTTCAAAAAGAGTCTCGGTTTTCAAAAGGTTTTGAT
1 AAAAAGGTTTTCAAAAAGAGTCTCGGTTTTCAAAAGGTTCTGAT
*
24676 AAAATGGTTTTCCAAAAA
1 AAAAAGGTTTT-CAAAAA
24694 TGATTTCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
43 1 0.02
44 50 0.88
45 6 0.11
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (44 bp):
AAAAAGGTTTTCAAAAAGAGTCTCGGTTTTCAAAAGGTTCTGAT
Found at i:25397 original size:17 final size:16
Alignment explanation
Indices: 25372--25428 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
25362 AAGTGCACTG
25372 AAAAA-AAAAAAGAAA
1 AAAAAGAAAAAAGAAA
25387 AGAAAAG--AAAAG-AA
1 A-AAAAGAAAAAAGAAA
25401 AAAAAGAAAGAAAGAAA
1 AAAAAGAAA-AAAGAAA
25418 AAAAAGAAAAA
1 AAAAAGAAAAA
25429 TGAATGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 7 0.19
16 10 0.28
17 11 0.31
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:25444 original size:26 final size:26
Alignment explanation
Indices: 25371--25428 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
25361 CAAGTGCACT
*
25371 GAAAAAAAAAAAGAAAAGAAAAGAAAA
1 GAAAAAAAGAAAG-AAAGAAAAGAAAA
25398 GAAAAAAAGAAAGAAAGAAAA-AAAA
1 GAAAAAAAGAAAGAAAGAAAAGAAAA
25423 GAAAAA
1 GAAAAA
25429 TGAATGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 10 0.33
26 8 0.27
27 12 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (26 bp):
GAAAAAAAGAAAGAAAGAAAAGAAAA
Found at i:25446 original size:5 final size:5
Alignment explanation
Indices: 25374--25427 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
25364 GTGCACTGAA
*
25374 AAAAA AAAAG AAAAG AAAAG AAAAG -AAA- AAAAG -AAAG -AAAG AAAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
25419 AAAAG AAAA
1 AAAAG AAAA
25428 ATGAATGATG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
4 18 0.41
5 26 0.59
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:26597 original size:36 final size:36
Alignment explanation
Indices: 26551--26654 Score: 113
Period size: 35 Copynumber: 2.9 Consensus size: 36
26541 TGACCCATGA
*
26551 TGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGG
1 TGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
** * *
26587 TGGTCTTTCTTTGGTTTATTTCGG-TTGACTC-AGGG
1 TGGTCTTTCTTCAGTTTATGTCGGAATGA-TCGAGGG
* * *
26622 CGGCCTTTCTTCAGTTTATGTCAGAATGATCGA
1 TGGTCTTTCTTCAGTTTATGTCGGAATGATCGA
26655 TTCAGTCGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
35 27 0.51
36 26 0.49
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (36 bp):
TGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
Found at i:26722 original size:72 final size:72
Alignment explanation
Indices: 26634--26830 Score: 274
Period size: 71 Copynumber: 2.8 Consensus size: 72
26624 GCCTTTCTTC
*
26634 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAAGGCGGTATTTCTTCAGTTAT-TTT-CAAGT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTATTTCTTCAGTT-TGTTTCCAAG-
*
26697 TTTATTCGA
64 TTTATTCCA
* *
26706 AGTTTATATCAGAATGATCGATTCAGTCGACCCAGGGC-GTCTTTCTTCAGTTTGTTTCCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTATTTCTTCAGTTTGTTTCCAAGTT
26770 TATTCCA
66 TATTCCA
* * * * *
26777 AGTTTANGTCAGAATGAACGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTATTTCTTCAGTTT
26831 ATGTCGGAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
70 1 0.01
71 57 0.51
72 54 0.48
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (72 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTATTTCTTCAGTTTGTTTCCAAGTT
TATTCCA
Found at i:26866 original size:36 final size:36
Alignment explanation
Indices: 26810--26917 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
26800 CAGTTGACCC
* *
26810 AGGGTGGTTTTTCTTCAGTTTATGTCGGAATGTTCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* * * * * *
26846 AGGGCGGTCTTTCTTTAGTTTATTTCGG-TTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* *
26881 AGGATGGTCTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
26917 A
1 A
26918 TTCAGTCGAC
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
35 26 0.47
36 29 0.53
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.42
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
Found at i:26901 original size:35 final size:35
Alignment explanation
Indices: 26802--26906 Score: 120
Period size: 36 Copynumber: 3.0 Consensus size: 35
26792 GAACGATTCA
*
26802 GTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTCG
1 GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
* ** * * * *
26837 GAATGTTCGAGGGCGGTCTTTCTTTAGTTTATTTCG
1 G-TTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
*
26873 GTTGACCCAGGATGGTCTTTCTTCAGTTTATGTC
1 GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTC
26907 AGAATGATCG
Statistics
Matches: 53, Mismatches: 16, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
35 26 0.49
36 27 0.51
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.43
Consensus pattern (35 bp):
GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
Found at i:27014 original size:189 final size:192
Alignment explanation
Indices: 26706--27409 Score: 1024
Period size: 189 Copynumber: 3.7 Consensus size: 192
26696 TTTTATTCGA
* * *
26706 AGTTTATATCAGAATGATCGATTCAGTCGACCCAGGG-CGTCTTTCTTCAGTTTGTTTCCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTTGTTTTCAAGTT
* * *
26770 TATTCCAAGTTTANGTCAGAATGAACGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTTATGT
66 TATTCCAAGTTTATGTCAGAATGATCGATTCACTTGACCCAGGGTGGTTTTTCTTCAGTTTATGT
* * **
26835 CGGAATGTTCGAGGGCGGTCTTTCTTTAGTTTATTTCGGTTGACCCAGGATGGTCTTTCTTC
131 CGGAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTC
26897 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAG-TTG-TTTCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTTGTTTTCAAGTT
*
26960 TA-TCCAAGTTTATGTCAGAATGATCGATTCACTTGACCAAGGGTGGTTTTTCTTCAGTTTATGT
66 TATTCCAAGTTTATGTCAGAATGATCGATTCACTTGACCCAGGGTGGTTTTTCTTCAGTTTATGT
* *
27024 CGGAATGATCGAGGGTGGCCTTTCTTTAGTTTATTTCGGTTGACCTAGGGCGGTCTTTCTTC
131 CGGAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTC
27086 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTGAAGTTTA
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCA---GTTT---GTTT-
* *
27151 TCGAAGTTTA-TCCAAGTTTTTGTCAGAATGATCGATTCACTTGACCCAGGTTGGTTTTTCCTTC
59 TC-AAGTTTATTCCAAGTTTATGTCAGAATGATCGATTCACTTGACCCAGGGTGGTTTTT-CTTC
* *
27215 AATTTATGTCGGAATGATAGAGGGTGGTCTTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCT
122 AGTTTATGTCGGAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCT
*
27280 TTCTTA
187 TTCTTC
* * * *
27286 AGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAG-TTGTTTTCAACTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTTGTTTTCAAGTT
* * * * * * *
27350 TATTCGAAGTTTATGTCAGAATGATTGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTT
66 TATTCCAAGTTTATGTCAGAATGATCGATTCACTTGACCCAGGGTGGTTTTTCTTCAGTT
27410 ATTTCCAAGT
Statistics
Matches: 465, Mismatches: 35, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
189 164 0.35
190 10 0.02
191 51 0.11
192 55 0.12
193 6 0.01
196 3 0.01
197 3 0.01
198 2 0.00
199 53 0.11
200 118 0.25
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (192 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTTGTTTTCAAGTT
TATTCCAAGTTTATGTCAGAATGATCGATTCACTTGACCCAGGGTGGTTTTTCTTCAGTTTATGT
CGGAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTC
Found at i:27048 original size:36 final size:36
Alignment explanation
Indices: 26999--27106 Score: 128
Period size: 36 Copynumber: 3.0 Consensus size: 36
26989 CACTTGACCA
*
26999 AGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* * * * * *
27035 AGGGTGGCCTTTCTTTAGTTTATTTCGG-TTGACCT
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* *
27070 AGGGCGGTCTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
27106 A
1 A
27107 TTCAGTCGAC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
35 27 0.48
36 29 0.52
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.41
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
Found at i:27469 original size:70 final size:70
Alignment explanation
Indices: 27285--27918 Score: 871
Period size: 70 Copynumber: 9.0 Consensus size: 70
27275 GGTCTTTCTT
* * * * *
27285 AAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAACTG
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
*
27350 TATTCG
66 TA-TCC
* *
27356 AAGTTTATGTCAGAATGATTGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
27421 TATCC
66 TATCC
* * * * * *
27426 AAGTTTCTGTCAGAATGATCGATTCGGTTGAACCAGGGTGGTCTTTCTTCAG-TAGTTTCCACGT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGT
27490 TTATCC
65 TTATCC
*
27496 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGCTTT-CAAGT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTT-ATTTCCAAGT
*
27560 TTATTCG
65 TTA-TCC
* *
27567 AAGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGCCGGTCTTTCTTCAGTTATTTCCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
27632 TATCC
66 TATCC
* * * *
27637 AAGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAG-TAGTTTCCACGT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGT
27701 TTATCC
65 TTATCC
*
27707 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTTCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
27772 TATTCC
66 TA-TCC
* * * * *
27778 AAGTTTACGTCAGAATGATCGATTCAGTCGACCTAGGGTGGTCTTTCTTCAG-TATTTTCTACGT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGT
27842 TTATCC
65 TTATCC
* * * * *
27848 AAGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCAGTTTTTCATCAGTTGTTTCCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
*
27913 GATCC
66 TATCC
27918 A
1 A
27919 GGGTGGTCTT
Statistics
Matches: 497, Mismatches: 56, Indels: 21
0.87 0.10 0.04
Matches are distributed among these distances:
69 4 0.01
70 303 0.61
71 190 0.38
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (70 bp):
AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTT
TATCC
Found at i:27531 original size:211 final size:211
Alignment explanation
Indices: 27285--27918 Score: 1009
Period size: 211 Copynumber: 3.0 Consensus size: 211
27275 GGTCTTTCTT
* * *
27285 AAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAACTG
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTT
*
27350 TATTCGAAGTTTATGTCAGAATGATTGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTC
66 TATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTC
* * *
27415 CAAGTTTATCCAAGTTTCTGTCAGAATGATCGATTCGGTTGAACCAGGGTGGTCTTTCTTCAGTA
131 CAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTA
27480 GTTTCCACGTTTATCC
196 GTTTCCACGTTTATCC
*
27496 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGCTTTCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTT
* * *
27561 TATTCGAAGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGCCGGTCTTTCTTCAGTTATTTC
66 TATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTC
*
27626 CAAGTTTATCCAAGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTA
131 CAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTA
27691 GTTTCCACGTTTATCC
196 GTTTCCACGTTTATCC
*
27707 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTTCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTT
* * *
27772 TATTCCAAGTTTACGTCAGAATGATCGATTCAGTCGACCTAGGGTGGTCTTTCTTCAG-TATTTT
66 TATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTA-TTT
* * * * ** * *
27836 CTACGTTTATCCAAGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCAGTTTTTCATCAGT
130 CCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGT
* * *
27901 TGTTTCCAAGTTGATCC
195 AGTTTCCACGTTTATCC
27918 A
1 A
27919 GGGTGGTCTT
Statistics
Matches: 391, Mismatches: 31, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
210 2 0.01
211 389 0.99
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (211 bp):
AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTT
TATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTC
CAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTA
GTTTCCACGTTTATCC
Found at i:27911 original size:141 final size:140
Alignment explanation
Indices: 27285--27918 Score: 878
Period size: 141 Copynumber: 4.5 Consensus size: 140
27275 GGTCTTTCTT
* * * *
27285 AAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAACTG
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
* * *
27350 TATTCGAAGTTTATGTCAGAATGATTGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTC
66 TA-TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTC
27415 CAAGTTTATCC
130 CAAGTTTATCC
* * * * * * *
27426 AAGTTTCTGTCAGAATGATCGATTCGGTTGAACCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
*
27491 TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGCTTT-
66 TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTT-ATTTC
*
27555 CAAGTTTATTCG
130 CAAGTTTA-TCC
* * *
27567 AAGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGCCGGTCTTTCTTCAGTTATTTCCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
* * *
27632 TATCCAAGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAG-TAGTTTC
66 TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTC
*
27696 CACGTTTATCC
130 CAAGTTTATCC
* *
27707 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTTCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
* * *
27772 TATTCCAAGTTTACGTCAGAATGATCGATTCAGTCGACCTAGGGTGGTCTTTCTTCAG-TATTTT
66 TA-TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTT
* *
27836 CTACGTTTATCC
129 CCAAGTTTATCC
* * * *
27848 AAGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCAGTTTTTCATCAGTTGTTTCCAAGTT
1 AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
*
27913 GATCCA
66 TATCCA
27919 GGGTGGTCTT
Statistics
Matches: 440, Mismatches: 48, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
140 136 0.31
141 304 0.69
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (140 bp):
AAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCC
AAGTTTATCC
Found at i:28921 original size:132 final size:132
Alignment explanation
Indices: 28785--29102 Score: 456
Period size: 132 Copynumber: 2.4 Consensus size: 132
28775 TAGTCGTTAT
* * * ***
28785 TTAATATATTTTACAAATTGGTTTTCGCAGCGACCTTAAAAGTCACTACAAAAAACATGGTTACT
1 TTAATATATTTTACAAATTGATTTTCGCAGCGACCTTGAAAGTCGCTACAAAAAACACAATTACT
* * *
28850 TTTGAAACGACAGATTAAGTCGCTGTGAAATCTTAAACTTTTCGCAACAACTTTTGTTAGTCATT
66 TTTGAAACCACAAATTAAGTCGCTGTGAAATCTTAAACTTTTCGCAACAACTATTGTTAGTCATT
28915 GC
131 GC
* *
28917 TTAATATATTTTACAAATTAATTTTCGCAGCGACTTTGAAAGTCGCTACAAAAAACACAATTACT
1 TTAATATATTTTACAAATTGATTTTCGCAGCGACCTTGAAAGTCGCTACAAAAAACACAATTACT
* * ** * *
28982 TTTGAAGCCACAAATTAAGTTGCTGTGAAATCTTACTCTTTTCGCAACGACTATTGTTAGTCGTT
66 TTTGAAACCACAAATTAAGTCGCTGTGAAATCTTAAACTTTTCGCAACAACTATTGTTAGTCATT
*
29047 GT
131 GC
* *
29049 TTAATATATTTTACAAATTGATTTTCGTAGCGACCTTGAAAGTTGCTACAAAAA
1 TTAATATATTTTACAAATTGATTTTCGCAGCGACCTTGAAAGTCGCTACAAAAA
29103 GTTTTTTTGA
Statistics
Matches: 164, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 164 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (132 bp):
TTAATATATTTTACAAATTGATTTTCGCAGCGACCTTGAAAGTCGCTACAAAAAACACAATTACT
TTTGAAACCACAAATTAAGTCGCTGTGAAATCTTAAACTTTTCGCAACAACTATTGTTAGTCATT
GC
Found at i:32457 original size:20 final size:20
Alignment explanation
Indices: 32432--32476 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
32422 ACAGCGGACA
32432 CTTAAGTCGTCGCGTTAGAT
1 CTTAAGTCGTCGCGTTAGAT
*
32452 CTTAAGTCGTTGCGTTAGAT
1 CTTAAGTCGTCGCGTTAGAT
*
32472 ATTAA
1 CTTAA
32477 ACAACGGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (20 bp):
CTTAAGTCGTCGCGTTAGAT
Found at i:32647 original size:19 final size:19
Alignment explanation
Indices: 32623--32661 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
32613 ATATCACTTT
*
32623 TAATTTTGCATTTAACATA
1 TAATTTCGCATTTAACATA
* *
32642 TAATTTCGCTTTTAATATA
1 TAATTTCGCATTTAACATA
32661 T
1 T
32662 CATGTTCCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATTTCGCATTTAACATA
Found at i:38008 original size:215 final size:207
Alignment explanation
Indices: 37577--37997 Score: 504
Period size: 215 Copynumber: 1.9 Consensus size: 207
37567 AATACAACAA
* *
37577 TATATAATAAGAGAAGTGTCAATTACCTTTTTATCCAACCGTATCTTGCATCACATTGATTTGGT
1 TATATAATAAGAGAAGTGTCAATTACCTTTTTATCCAACAGTATCTTGCATCACATTGATTTGGC
* *
37642 TACTATTTGCACGGTTTTTTTGTTATTTGTGAAAACAACTAAGGGCATTTCTAGAACTCTGTAAA
66 TACTATTTGCACGGTTTTTTTGTTATTTGAGAAAACAACTAAGGGCATTTCGAGAACTCTGTAAA
* *
37707 TAATTGGTCGGCCCCATTTTCCACCAACAAATATTTTCTTGGATTATTTATCAATTGACTCTCAT
131 TAATTGGTCGGCCCCATTCTCCACCAACAAATATTTTCTTGGATTATTTATCAAATGACTCTCA-
37772 ACTTCTCTACTTTTATTTTT
195 A-----CTAC--TTATTTTT
*
37792 TATATAATAAGAGAAGTGTCAATTACCTTTTTATCCAACAGTATCTTGCA-CAACATTGGTTTGG
1 TATATAATAAGAGAAGTGTCAATTACCTTTTTATCCAACAGTATCTTGCATC-ACATTGATTTGG
* *
37856 CTACTATTTGTACGGTTTTTTTTGTTATTTGAGAAAACAATTAAGGGCATTTCCGA-AACTCTGC
65 CTACTATTTGCACGG-TTTTTTTGTTATTTGAGAAAACAACTAAGGGCATTT-CGAGAACTCTG-
* * * * *
37920 AATTAATTTACCCTTGGTGGGTCCCATTCTCCACCAACAAAGATTTTCTTACTTGGATTATTTAT
127 ---TAA-ATA--ATTGGTCGGCCCCATTCTCCACCAAC-AA-ATATT-TT-CTTGGATTATTTAT
37985 CAAATGACTCTCA
182 CAAATGACTCTCA
37998 TACTTTTTTT
Statistics
Matches: 178, Mismatches: 14, Indels: 16
0.86 0.07 0.08
Matches are distributed among these distances:
214 1 0.01
215 73 0.41
216 41 0.23
217 2 0.01
220 3 0.02
221 2 0.01
223 22 0.12
224 2 0.01
225 4 0.02
226 2 0.01
227 26 0.15
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (207 bp):
TATATAATAAGAGAAGTGTCAATTACCTTTTTATCCAACAGTATCTTGCATCACATTGATTTGGC
TACTATTTGCACGGTTTTTTTGTTATTTGAGAAAACAACTAAGGGCATTTCGAGAACTCTGTAAA
TAATTGGTCGGCCCCATTCTCCACCAACAAATATTTTCTTGGATTATTTATCAAATGACTCTCAA
CTACTTATTTTT
Found at i:38378 original size:16 final size:16
Alignment explanation
Indices: 38359--38418 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
38349 ATTTTAAATC
38359 ATATTAATTTATTTTA
1 ATATTAATTTATTTTA
*
38375 ATA-TAAGTTATTTTA
1 ATATTAATTTATTTTA
* * *
38390 AAATCAACTTAATTTTA
1 ATATTAA-TTTATTTTA
*
38407 CATATTGATTTA
1 -ATATTAATTTA
38419 ACGCTTCACG
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
15 13 0.41
16 5 0.16
17 10 0.31
18 4 0.12
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (16 bp):
ATATTAATTTATTTTA
Found at i:38738 original size:38 final size:38
Alignment explanation
Indices: 38661--38738 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
38651 ATATTGCATG
* *
38661 ATCTACGACTTCATGAAGGGGCCCGAAAGCTCAATTTT
1 ATCTACGACTTCATGAAGGGGCCCAAAAGATCAATTTT
* *
38699 ATCTACGAGTTTCATGAA-GGGCTCAAAAGAT-AATCTTT
1 ATCTACGA-CTTCATGAAGGGGCCCAAAAGATCAAT-TTT
38737 AT
1 AT
38739 GTTTTAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 3 0.09
38 23 0.68
39 8 0.24
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (38 bp):
ATCTACGACTTCATGAAGGGGCCCAAAAGATCAATTTT
Found at i:39385 original size:66 final size:66
Alignment explanation
Indices: 39224--39733 Score: 501
Period size: 66 Copynumber: 7.6 Consensus size: 66
39214 ATGACGAGAT
* * * * *
39224 TGACCCTTCGACCAAAAGGGTAATCTTGGAAATGAAAAATACTAAACTTAAGTGCCAAAAGACAA
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATG-AAAATACTAAACTCAAATG-CAAAAGACAA
*
39289 TGC
64 TAC
* * * *
39292 TGAGCTTTTTACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAGAAGACAATA
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAAAAGACAATA
39357 C
66 C
* * ** *
39358 TGACCCTTTGACCGAAAGGGTACTCTTGGAAATGGAAATGAAAGACTTGACTTAAATGCAAAAGA
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAAT-G--A--AAATACTAAACTCAAATGCAAAAGA
*
39423 TAATAC
61 CAATAC
* * * * *
39429 TGACCCTTTGACCAAAAGGGTATTCTTGGAAAGGAATATACTAAGCTCAAATGCAAAAGATAATA
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAAAAGACAATA
39494 C
66 C
* *
39495 TGACCCTTTGACCGAAAGGGTATTCTTGGAAAAGAAAATACTAAACTCAAATACAAAAGACAATA
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAAAAGACAATA
39560 C
66 C
** * * *
39561 CAACCCTTTGACCGAAAGGGTATTCTTGGAAATG-AAAGACTAGACTTAAATGCAATAACCTGAT
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAA-AA---GA-
*
39625 GAA-AC
61 CAATAC
* * * * * *
39630 TGACCCTTCGACCGGAAGGGTATTTTTGGAAA-GTAAA-ACTTAAC-CTGAATGCAAAAAGACGA
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTC-AAATGC-AAAAGAC-A
39692 A-AC
63 ATAC
* * *
39695 TGACCCTTCGACCGAAAGGGTATTTTTGGAAATTAAAAT
1 TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAAT
39734 CAAACTTTAC
Statistics
Matches: 370, Mismatches: 56, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
65 54 0.15
66 161 0.44
67 18 0.05
68 42 0.11
69 37 0.10
70 3 0.01
71 55 0.15
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (66 bp):
TGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAAAAGACAATA
C
Found at i:39470 original size:137 final size:133
Alignment explanation
Indices: 39224--39727 Score: 495
Period size: 137 Copynumber: 3.8 Consensus size: 133
39214 ATGACGAGAT
* * *
39224 TGACCCTTCGACCAAAAGGGTAATCTTGGAAATG-AAAAATACTAAACTTAAGTGCCAAAAGACA
1 TGACCCTTTGACCGAAAGGGTAATCTTGGAAATGAAAAAATACTAAACTTAAATG-CAAAAGACA
* * * * *
39288 ATGCTGAGCTTTTTACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAGAAGAC
65 ATACTGACCCTTTGACCGAAAGGGTATTCTTGGAAATG-AAATACTAAACTCAAATGCAAAAGAC
39353 AATAC
129 AATAC
* * **
39358 TGACCCTTTGACCGAAAGGGTACTCTTGGAAATGGAAATGAAAGACTTGACTTAAATGCAAAAGA
1 TGACCCTTTGACCGAAAGGGTAATCTTGGAAAT-GAAA--AAATACTAAACTTAAATGCAAAAGA
* * * *
39423 TAATACTGACCCTTTGACCAAAAGGGTATTCTTGGAAAGGAATATACTAAGCTCAAATGCAAAAG
63 CAATACTGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAA-ATACTAAACTCAAATGCAAAAG
*
39488 ATAATAC
127 ACAATAC
* * * *
39495 TGACCCTTTGACCGAAAGGGTATTCTTGGAAA--AGAAAATACTAAACTCAAATACAAAAGACAA
1 TGACCCTTTGACCGAAAGGGTAATCTTGGAAATGAAAAAATACTAAACTTAAATGCAAAAGACAA
** * * *
39558 TACCAACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAGACTAGACTTAAATGCAATAACCTG
66 TACTGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAATACTAAACTCAAATGCAA-AA---G
*
39623 ATGAA-AC
127 A-CAATAC
* * * * * * * *
39630 TGACCCTTCGACCGGAAGGGTATTTTTGGAAA-G--TAAA-ACTTAACCTGAATGCAAAAAGACG
1 TGACCCTTTGACCGAAAGGGTAATCTTGGAAATGAAAAAATACTAAACTTAAATGC-AAAAGAC-
* *
39691 AA-ACTGACCCTTCGACCGAAAGGGTATTTTTGGAAAT
64 AATACTGACCCTTTGACCGAAAGGGTATTCTTGGAAAT
39728 TAAAATCAAA
Statistics
Matches: 310, Mismatches: 47, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
131 15 0.05
132 59 0.19
133 10 0.03
134 73 0.24
135 36 0.12
136 6 0.02
137 97 0.31
138 14 0.05
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (133 bp):
TGACCCTTTGACCGAAAGGGTAATCTTGGAAATGAAAAAATACTAAACTTAAATGCAAAAGACAA
TACTGACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAATACTAAACTCAAATGCAAAAGACAA
TAC
Found at i:39575 original size:203 final size:197
Alignment explanation
Indices: 39224--39726 Score: 584
Period size: 203 Copynumber: 2.5 Consensus size: 197
39214 ATGACGAGAT
* *
39224 TGACCCTTCGACCAAAAGGGTAATCTTGGAAATGAAAAATACTAAACTTAAGTGCCAAAAGACAA
1 TGACCCTTCGACCAAAAGGGTATTCTTGGAAA-G-AAAATACTAAAC-TAAATG-CAAAAGACAA
* * * * * * *
39289 TGCTGAGCTTTTTACCGAAAGGGTATTCTTGGAAATGAAAATACTAAACTCAAATGCAGAAGACA
62 TACTGACCCTTTGACCGAAAGGGTATTCTTGGAAAAGAAAATACTAAACTCAAATACAAAAGACA
** *
39354 ATACTGACCCTTTGACCGAAAGGGTACTCTTGGAAATGGAAATGAAAGACTTGACTTAAATGCAA
127 ATACCAACCCTTTGACCGAAAGGGTACTC-T-----TGGAAATGAAAGACTAGACTTAAATGCAA
39419 -AA-GAT-AATAC
186 TAACGATGAA-AC
* * * *
39429 TGACCCTTTGACCAAAAGGGTATTCTTGGAAAGGAATATACTAAGCTCAAATGCAAAAGATAATA
1 TGACCCTTCGACCAAAAGGGTATTCTTGGAAA-GAAAATACTAAACT-AAATGCAAAAGACAATA
39494 CTGACCCTTTGACCGAAAGGGTATTCTTGGAAAAGAAAATACTAAACTCAAATACAAAAGACAAT
64 CTGACCCTTTGACCGAAAGGGTATTCTTGGAAAAGAAAATACTAAACTCAAATACAAAAGACAAT
*
39559 ACCAACCCTTTGACCGAAAGGGTATTCTTGGAAATGAAAGACTAGACTTAAATGCAATAACCTGA
129 ACCAACCCTTTGACCGAAAGGGTACTCTTGGAAATGAAAGACTAGACTTAAATGCAATAA-C-GA
39624 TGAAAC
192 TGAAAC
** * * * *
39630 TGACCCTTCGACCGGAAGGGTATTTTTGGAAAGTAAA-ACTTAACCTGAATGCAAAAAGACGAA-
1 TGACCCTTCGACCAAAAGGGTATTCTTGGAAAGAAAATAC-TAAACTAAATGC-AAAAGAC-AAT
* *
39693 ACTGACCCTTCGACCGAAAGGGTATTTTTGGAAA
63 ACTGACCCTTTGACCGAAAGGGTATTCTTGGAAA
39727 TTAAAATCAA
Statistics
Matches: 260, Mismatches: 29, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
197 28 0.11
198 2 0.01
199 7 0.03
200 46 0.18
201 35 0.13
202 3 0.01
203 94 0.36
204 14 0.05
205 31 0.12
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (197 bp):
TGACCCTTCGACCAAAAGGGTATTCTTGGAAAGAAAATACTAAACTAAATGCAAAAGACAATACT
GACCCTTTGACCGAAAGGGTATTCTTGGAAAAGAAAATACTAAACTCAAATACAAAAGACAATAC
CAACCCTTTGACCGAAAGGGTACTCTTGGAAATGAAAGACTAGACTTAAATGCAATAACGATGAA
AC
Done.