Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 103 of 199
Found at i:31270961 original size:14 final size:15
Alignment explanation
Indices: 31270939--31270972 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31270929 CTTAAACCAG
*
31270939 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
31270953 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
31270968 AATCT
1 AATCT
31270973 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:31271357 original size:114 final size:114
Alignment explanation
Indices: 31271226--31271774 Score: 608
Period size: 114 Copynumber: 4.8 Consensus size: 114
31271216 AGTGGCGCTT
* * *
31271226 CATAAAAACGCCACTAAATCCCCGAAAGCTAAAAAAATGGCGTCGTTGGGCTGAAGTATTTTTGC
1 CATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTTTTGC
*
31271291 GGCGCTTTCCCAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCACATA
66 GGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCACATA
* ** * *
31271340 CATAAAAACGCCACTAAATCCTTC-TCAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTATTA
1 CATAAAAACGCCACTAAATCC-CCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTTTTG
* * * * * * * * *
31271404 TGACGCTTTCACAAAAACGCCGCTAAA-TCACTGAGTATTAACGACGCTTTA
65 CGGCGCTTTCCCAAAAACGCCGCTAAAGAC-CTGAGCATTAGCGGCAC-ATA
* *
31271455 -ATAAAAACGCCACTAAATCCCCCGAAGGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTGTTG
1 CATAAAAACGCCACTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTTTTG
* * ** *
31271519 TGGCGCTTTCACAAAAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCATA
65 CGGCGCTTTC-CCAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCACATA
* ** * ** *
31271570 CATAAAAACGCCACTAAATCCTTC-TCAGCTCAGAAAACGGTGTCGTTGGGCTGAAGTACGTTTA
1 CATAAAAACGCCACTAAATCC-CCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTTTTG
* * *
31271634 CGGCGCTTTCCCAAAAATGCCGCTAAAGACCTGAGCATTAGCGGCGA-TTT
65 CGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATTAGCGGC-ACATA
* **
31271684 CATGAAAACGCCACTAAATCCCCCGAAAGCTCAG-AAACGGCGTCGTTGGGCTGAAGTACGTTTG
1 CATAAAAACGCCACTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTTTTG
* *
31271748 CGGCGC-ATCCCAAAAAACGCCACTAAA
65 CGGCGCTTTCCC-AAAAACGCCGCTAAA
31271775 TCCCCGAAAG
Statistics
Matches: 364, Mismatches: 58, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
113 5 0.01
114 207 0.57
115 103 0.28
116 48 0.13
117 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (114 bp):
CATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTTTTGC
GGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCACATA
Found at i:31271658 original size:230 final size:229
Alignment explanation
Indices: 31271227--31271778 Score: 781
Period size: 230 Copynumber: 2.4 Consensus size: 229
31271217 GTGGCGCTTC
* * * *
31271227 ATAAAAACGCCACTAAAT-CCCCGAAAGCTAAAAAAATGGCGTCGTTGGGCTGAAGTATTTTTGC
1 ATAAAAACGCCACTAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTGTTGC
* **
31271291 GGCGCTTTCCCAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCACATACATAAAAACGCCACTA
66 GGCGCTTTCCAAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACATACATAAAAACGCCACTA
* *
31271356 AATCCTTCTCAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTATTATGACGCTTTCACAAAAA
131 AATCCTTCTCAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTAGTATTACGACGCTTTCACAAAAA
* *
31271421 CGCCGCTAAATCA-CTGAGTATTAACGACGCTTTA
196 CGCCGCTAAA-CACCTGAGCATTAACGACGATTTA
* *
31271455 ATAAAAACGCCACTAAATCCCCCGAAGGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTGTTGT
1 ATAAAAACGCCACTAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTGTTGC
* *
31271520 GGCGCTTTCACAAAAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCATACATAAAAACGCCACT
66 GGCGCTTTC-CAAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACATACATAAAAACGCCACT
* * *
31271585 AAATCCTTCTCAGCTCAGAAAACGGTGTCGTTGGGCTGAAGTACGT-TTACGGCGCTTTCCCAAA
130 AAATCCTTCTCAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTA-GTATTACGACGCTTTCACAAA
* * * * *
31271649 AATGCCGCTAAAGACCTGAGCATTAGCGGCGATTTC
194 AACGCCGCTAAACACCTGAGCATTAACGACGATTTA
* *
31271685 ATGAAAACGCCACTAAATCCCCCGAAAGCTCAG-AAACGGCGTCGTTGGGCTGAAGTA-CGTTTG
1 ATAAAAACGCCACTAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTG-TTG
* * *
31271748 CGGCGCATCCCAAAAAACGCCACTAAATCCC
65 CGGCGCTTTCCAAAAAACGCCGCTAAATCCC
31271779 CGAAAGCTTA
Statistics
Matches: 289, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
228 39 0.13
229 84 0.29
230 165 0.57
231 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (229 bp):
ATAAAAACGCCACTAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTATTGTTGC
GGCGCTTTCCAAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCACATACATAAAAACGCCACTA
AATCCTTCTCAGCTCAGAAAACGGCGTCGTTGGGCTGAAGTAGTATTACGACGCTTTCACAAAAA
CGCCGCTAAACACCTGAGCATTAACGACGATTTA
Found at i:31272450 original size:18 final size:18
Alignment explanation
Indices: 31272427--31272471 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
31272417 AAACAATTTT
31272427 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
31272445 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
31272463 TAACTTATA
1 TAAATTATA
31272472 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:31272456 original size:9 final size:9
Alignment explanation
Indices: 31272431--31272471 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
31272421 AATTTTTAAA
31272431 TTATATAAC
1 TTATATAAC
* *
31272440 TTACATAAA
1 TTATATAAC
31272449 TTATATAAC
1 TTATATAAC
*
31272458 TTACATAAC
1 TTATATAAC
31272467 TTATA
1 TTATA
31272472 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:31272513 original size:17 final size:18
Alignment explanation
Indices: 31272493--31272526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31272483 ACATTTTTAA
31272493 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
31272510 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
31272527 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:31272955 original size:9 final size:9
Alignment explanation
Indices: 31272941--31273172 Score: 196
Period size: 9 Copynumber: 26.4 Consensus size: 9
31272931 NNNNNNNNNN
31272941 TAACTTACA
1 TAACTTACA
*
31272950 TAACTTAAA
1 TAACTTACA
31272959 TAACTTACA
1 TAACTTACA
31272968 TAA--TACA
1 TAACTTACA
*
31272975 TAACCTT-CC
1 TAA-CTTACA
*
31272984 TAACTTAAA
1 TAACTTACA
* *
31272993 TTATTTACA
1 TAACTTACA
31273002 TAA--TACA
1 TAACTTACA
31273009 TAACTTAGTACA
1 TAAC-T--TACA
31273021 TAACTTACA
1 TAACTTACA
**
31273030 TAA-TT-TT
1 TAACTTACA
** *
31273037 TTTC-TAAA
1 TAACTTACA
**
31273045 TTGCTTACA
1 TAACTTACA
* *
31273054 TAAATTATA
1 TAACTTACA
31273063 TAACTTACA
1 TAACTTACA
*
31273072 TATCTTACA
1 TAACTTACA
31273081 TAACTTACA
1 TAACTTACA
* *
31273090 TAAATTAAA
1 TAACTTACA
31273099 TAACTTACA
1 TAACTTACA
31273108 TAACTTACA
1 TAACTTACA
31273117 TAACTTACA
1 TAACTTACA
*
31273126 TAAATTACA
1 TAACTTACA
31273135 TAACTTACA
1 TAACTTACA
31273144 TAACTTACA
1 TAACTTACA
31273153 TAACTTACA
1 TAACTTACA
31273162 TAA--TACA
1 TAACTTACA
31273169 TAAC
1 TAAC
31273173 CTTCCTTACT
Statistics
Matches: 179, Mismatches: 31, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
7 23 0.13
8 8 0.04
9 138 0.77
10 1 0.01
11 1 0.01
12 8 0.04
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.37
Consensus pattern (9 bp):
TAACTTACA
Found at i:31278713 original size:21 final size:21
Alignment explanation
Indices: 31278689--31278733 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31278679 CAACTTAAAA
* *
31278689 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCAGCAACGAGAGAAG
*
31278710 CAGAGGCTGCAACGAGAGAAG
1 CAGAGGCAGCAACGAGAGAAG
31278731 CAG
1 CAG
31278734 CGAGAGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.42, T:0.02
Consensus pattern (21 bp):
CAGAGGCAGCAACGAGAGAAG
Found at i:31279216 original size:43 final size:43
Alignment explanation
Indices: 31279169--31279261 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
31279159 ATAATATAGT
*
31279169 GGCGTTTGTAAAAT-AAGCGCCGCGAAAGAACACTACTTTTAGC
1 GGCGTTTGT-AAATGAAGCGCAGCGAAAGAACACTACTTTTAGC
* * *
31279212 GGCGTTTGTAGATGAAGCGCAGCTAAAGAACATTACTTTTAGC
1 GGCGTTTGTAAATGAAGCGCAGCGAAAGAACACTACTTTTAGC
31279255 GGCGTTT
1 GGCGTTT
31279262 TTTACCAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.07
43 42 0.93
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTAAATGAAGCGCAGCGAAAGAACACTACTTTTAGC
Found at i:31279453 original size:42 final size:41
Alignment explanation
Indices: 31279182--31279454 Score: 232
Period size: 43 Copynumber: 6.5 Consensus size: 41
31279172 GTTTGTAAAA
* * ***
31279182 TAAGCGCCGCGAAAGAACACT-ACTTTTAGCGGCGTTTGTAGA
1 TAAGCGCCGCTAAAGAACA-TGA-TTTTAGCGGCGTTTTTTCC
* *
31279224 TGAAGCGCAGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
1 T-AAGCGCCGCTAAAGAACATGA-TTTTAGCGGCGTTTTTT-CC
* * * * *
31279268 -AAGCGTCGCTATAGAACATTACTTT---GGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATTTTAGCGGCGTTTTTTCC
* * * * *
31279305 TAAACGCTGCTAAAGATCATGTTTCTTTAGCGGCGTTTTCTCC
1 TAAGCGCCGCTAAAGAACATG-AT-TTTAGCGGCGTTTTTTCC
* *
31279348 CAAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGAT-TTTAGCGGCG-TTTTTTCC
31279391 TAAGCGCCGCTAAAGAACATGATTATTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATT-TTAGCGGCGTTTTTTCC
* *
31279433 TAAGTGACGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGA
31279455 CTGTAATGGC
Statistics
Matches: 188, Mismatches: 32, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
37 1 0.01
38 24 0.13
40 3 0.02
41 3 0.02
42 59 0.31
43 98 0.52
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATGATTTTAGCGGCGTTTTTTCC
Found at i:31280328 original size:29 final size:30
Alignment explanation
Indices: 31280269--31280326 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31280259 TCTGAGCCTT
*
31280269 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
31280299 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
31280327 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:31280558 original size:13 final size:13
Alignment explanation
Indices: 31280540--31280569 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31280530 TCCAGCAACT
31280540 ATGAATTTATTTC
1 ATGAATTTATTTC
*
31280553 ATGAATTTATTTG
1 ATGAATTTATTTC
31280566 ATGA
1 ATGA
31280570 TTATCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:31280775 original size:50 final size:50
Alignment explanation
Indices: 31280664--31280912 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
31280654 ATTTGGGTAA
*
31280664 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
*
31280720 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
31280770 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
31280820 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
31280870 AGAACATCCCATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31280913 TGTTATGATC
Statistics
Matches: 176, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
50 98 0.56
51 33 0.19
53 3 0.02
55 2 0.01
56 40 0.23
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:31282441 original size:22 final size:22
Alignment explanation
Indices: 31282413--31282455 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31282403 TAGCGGCGCT
*
31282413 AAAAAGCGCCACTAAAGGCCTA
1 AAAAAGCGCCACTAAAAGCCTA
*
31282435 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCACTAAAAGCCT
31282456 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCACTAAAAGCCTA
Found at i:31282451 original size:76 final size:76
Alignment explanation
Indices: 31282325--31282469 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 76
31282315 CGCAAATGCA
* * * *
31282325 TTTAGTGGCGTTAAAAAGCGTCGCTAAAGGCATAAAAAAACGCCGCTAAAAACCTATTCTGGTGT
1 TTTAGCGGCGCTAAAAAGCGCCACTAAAGGCATAAAAAAACGCCGCTAAAAACCTATTCTGGTGT
31282390 AGTGAAATACT
66 AGTGAAATACT
* * * * *
31282401 TTTAGCGGCGCTAAAAAGCGCCACTAAAGGCCTAAAAAAGCGCCGCTAAAAGCCTGTTTTGGTGT
1 TTTAGCGGCGCTAAAAAGCGCCACTAAAGGCATAAAAAAACGCCGCTAAAAACCTATTCTGGTGT
31282466 AGTG
66 AGTG
31282470 TTTTAATCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (76 bp):
TTTAGCGGCGCTAAAAAGCGCCACTAAAGGCATAAAAAAACGCCGCTAAAAACCTATTCTGGTGT
AGTGAAATACT
Found at i:31283128 original size:25 final size:26
Alignment explanation
Indices: 31283100--31283162 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
31283090 AAAGTGCTTG
31283100 GAAGTGAAAAAAA-ACTGAGTTAAGA
1 GAAGTGAAAAAAACACTGAGTTAAGA
*
31283125 GAA--GAAAGAAAACAGTGAGTTAAGA
1 GAAGTGAAA-AAAACACTGAGTTAAGA
31283150 G-AGTTGAAAAAAA
1 GAAG-TGAAAAAAA
31283163 TATATTTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
23 4 0.12
24 5 0.16
25 15 0.47
26 4 0.12
27 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.25, T:0.14
Consensus pattern (26 bp):
GAAGTGAAAAAAACACTGAGTTAAGA
Found at i:31284710 original size:30 final size:30
Alignment explanation
Indices: 31284676--31284740 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
31284666 ACTTATTTTA
31284676 TTGTTAATTTTGTTATTATTTTAAAAGCAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
* *
31284706 TTGTTAATTTTGTTATTATTTTATAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
31284736 TTGTT
1 TTGTT
31284741 TGTTAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAAGCAT
Found at i:31285388 original size:13 final size:11
Alignment explanation
Indices: 31285352--31285382 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31285342 CGGTCCGTAT
31285352 TAATTTTTATA
1 TAATTTTTATA
*
31285363 TTATTTTTATA
1 TAATTTTTATA
31285374 TAATTTTTA
1 TAATTTTTA
31285383 AATATATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:31285811 original size:5 final size:5
Alignment explanation
Indices: 31285803--31285828 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31285793 TTTCATCCGA
31285803 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
31285829 GCCAATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:31289050 original size:37 final size:37
Alignment explanation
Indices: 31289009--31289086 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
31288999 AAATATTTAT
* *
31289009 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
*
31289046 TAATCAATGTTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
31289083 TAAT
1 TAAT
31289087 TAATATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (37 bp):
TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
Found at i:31289170 original size:33 final size:33
Alignment explanation
Indices: 31289133--31289208 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
31289123 TTAAAACTTG
* *
31289133 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAAATAATTTTAGGTC
31289166 AATTATACATACACCAACAAATAATTTTAGGTC
1 AATTATACATACACCAACAAATAATTTTAGGTC
31289199 AATTATACAT
1 AATTATACAT
31289209 GTTTTATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (33 bp):
AATTATACATACACCAACAAATAATTTTAGGTC
Found at i:31292366 original size:91 final size:91
Alignment explanation
Indices: 31292241--31292448 Score: 258
Period size: 91 Copynumber: 2.3 Consensus size: 91
31292231 TTGATTTTAC
* * *
31292241 TAAATTGATATAAGAACATTTTATTATTAAGAATTTTATGAAATT-ATATATCACTATTAAATTA
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTCA-ATATCACTATTAAATTA
* * *
31292305 TATTTAAT-GTTAATTATTTTAAATTGTA
64 TATGTAATAATT-ATTATTTTAAATTATA
* * *
31292333 TAAATTTATATAAGAAAATTTATTATCAAGAATTTTATGAAATTCAATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTCAATATCACTATTAAATTATA
31292398 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
31292424 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
31292449 GTTATAATTA
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
91 83 0.82
92 18 0.18
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTCAATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:31292577 original size:66 final size:63
Alignment explanation
Indices: 31292502--31292832 Score: 220
Period size: 66 Copynumber: 5.4 Consensus size: 63
31292492 AAATATATTT
31292502 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
31292567 G
63 G
* * * * **
31292568 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
31292622 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
31292686 AG
62 AG
* * * * * **
31292688 AATATTAATTATTAAGAAATTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * *
31292742 AATAATAATTATGTT-AATTTATATTTTACAATATCTTATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
31292806 AG
62 AG
*
31292808 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
31292833 AAATTATATA
Statistics
Matches: 200, Mismatches: 32, Indels: 67
0.67 0.11 0.22
Matches are distributed among these distances:
53 9 0.05
54 26 0.13
55 10 0.05
56 8 0.04
57 6 0.03
58 2 0.01
59 19 0.09
60 16 0.08
61 20 0.10
62 2 0.01
63 6 0.03
64 8 0.04
65 14 0.07
66 45 0.22
67 9 0.05
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:31292588 original size:120 final size:120
Alignment explanation
Indices: 31292464--31292902 Score: 758
Period size: 120 Copynumber: 3.7 Consensus size: 120
31292454 AATTATTTTA
* * *
31292464 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
31292526 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
31292584 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
31292649 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
31292704 AAATTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
31292769 ACAATATCTTATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
31292824 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
31292889 AAAGTATCATATAT
66 ACAGTATCATATAT
31292903 AATAATAATT
Statistics
Matches: 305, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
119 6 0.02
120 297 0.97
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:31292624 original size:15 final size:15
Alignment explanation
Indices: 31292589--31292640 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31292579 TTAAGAATTT
*
31292589 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31292603 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31292617 TATTTAATAATAAT-
1 TATTTAATTATAATA
31292631 TATGTTAATT
1 TAT-TTAATT
31292641 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31292744 original size:15 final size:15
Alignment explanation
Indices: 31292709--31292760 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31292699 TTAAGAAATT
*
31292709 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31292723 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31292737 TATTTAATAATAAT-
1 TATTTAATTATAATA
31292751 TATGTTAATT
1 TAT-TTAATT
31292761 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31292864 original size:15 final size:15
Alignment explanation
Indices: 31292829--31292880 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31292819 TTAAGAATTT
*
31292829 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31292843 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31292857 TATTTAATAATAAT-
1 TATTTAATTATAATA
31292871 TATGTTAATT
1 TAT-TTAATT
31292881 TATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31292909 original size:41 final size:42
Alignment explanation
Indices: 31292834--31292917 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
31292824 AATTTTATTA
*
31292834 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTATATATTTTAAGTATAATATA-TTAATAATAATTATGTT
*
31292877 AATT-TATATTTTAAAGTATCATATA-TAATAATAATTATGTT
1 AATTATATATTTT-AAGTATAATATATTAATAATAATTATGTT
31292918 TAAATATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 16 0.42
42 8 0.21
43 14 0.37
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (42 bp):
AATTATATATTTTAAGTATAATATATTAATAATAATTATGTT
Found at i:31293208 original size:66 final size:66
Alignment explanation
Indices: 31293102--31293234 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
31293092 ACGCCTCTAT
31293102 TCCATTAGATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCGATACACCTCTAATCCA
1 TCCATTAGATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCGATACACCTCTAATCCA
31293167 A
66 A
31293168 TCCATTAGATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCGATACACCTCTAATCCA
1 TCCATTAGATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCGATACACCTCTAATCCA
31293233 A
66 A
31293234 T
1 T
31293235 AGACCTCTAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.31
Consensus pattern (66 bp):
TCCATTAGATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCGATACACCTCTAATCCA
A
Found at i:31293223 original size:16 final size:16
Alignment explanation
Indices: 31293202--31293251 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
31293192 GATTTGCTAT
*
31293202 TACACCTCTAATCCGA
1 TACACCTCTAATCCAA
31293218 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31293234 TAGACCTCTAATCCAA
1 TACACCTCTAATCCAA
31293250 TA
1 TA
31293252 GAGCGAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.36, C:0.34, G:0.04, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31293326 original size:30 final size:30
Alignment explanation
Indices: 31293292--31293353 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
31293282 CAACTTAACA
*
31293292 AACAAATGCCTCTAAAATAATAAGAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAAATT
* * *
31293322 AACAAATGCTTTTAAATTAATAAAAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAAATT
31293352 AA
1 AA
31293354 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAAAAAAATT
Found at i:31293361 original size:11 final size:12
Alignment explanation
Indices: 31293335--31293360 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31293325 AAATGCTTTT
31293335 AAATTAATAAAA
1 AAATTAATAAAA
31293347 AAATTAATAAAA
1 AAATTAATAAAA
31293359 AA
1 AA
31293361 TAAGTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATTAATAAAA
Found at i:31296950 original size:107 final size:100
Alignment explanation
Indices: 31296832--31297039 Score: 317
Period size: 100 Copynumber: 2.0 Consensus size: 100
31296822 ATCCCAACAA
**
31296832 AAAAATATATGAGATTTGTTTTCAAAACAGGAAGGTTAAATTATACAAAAAAATAAATAAATAAA
1 AAAAATATATGAGATTTGTTTTCAAAACAACAAGGTTAAATTAT----AAAAA-AAA-AAA-AAA
31296897 GTTACTAAATTATTAAAAACAACAAAGCTAAATTCTAAATAT
59 GTTACTAAATTATTAAAAACAACAAAGCTAAATTCTAAATAT
* *
31296939 AAAAATGTATGAGATTTGTTTTCAAAACAACAAGGTTAAATTGTAAAAAAAAAAAAAAGTTACTA
1 AAAAATATATGAGATTTGTTTTCAAAACAACAAGGTTAAATTATAAAAAAAAAAAAAAGTTACTA
31297004 AATTATTAAAAACAACAAAGCTAAATTCTAAATAT
66 AATTATTAAAAACAACAAAGCTAAATTCTAAATAT
31297039 A
1 A
31297040 TATACGGAGA
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
100 46 0.47
101 3 0.03
102 3 0.03
103 5 0.05
107 40 0.41
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (100 bp):
AAAAATATATGAGATTTGTTTTCAAAACAACAAGGTTAAATTATAAAAAAAAAAAAAAGTTACTA
AATTATTAAAAACAACAAAGCTAAATTCTAAATAT
Found at i:31296993 original size:50 final size:50
Alignment explanation
Indices: 31296830--31296993 Score: 132
Period size: 50 Copynumber: 3.1 Consensus size: 50
31296820 GTATCCCAAC
**
31296830 AAAAAAATATATGAGATTTGTTTTCAAAACAGGAAGGTTAAATTATACAAA
1 AAAAAAATATATGAGATTTGTTTTCAAAACAACAAGGTTAAATTATA-AAA
* * * * * * * *
31296881 AAAATAAATAAAT-AAAGTTACTAAATTATTAAAAACAACAAAGCTAAATTCTAAAT
1 AAAA-AAATATATGAGA-TT--T--GTT-TTCAAAACAACAAGGTTAAATTATAAAA
* * *
31296937 ATAAAAATGTATGAGATTTGTTTTCAAAACAACAAGGTTAAATTGTAAAA
1 AAAAAAATATATGAGATTTGTTTTCAAAACAACAAGGTTAAATTATAAAA
31296987 AAAAAAA
1 AAAAAAA
31296994 AAAGTTACTA
Statistics
Matches: 84, Mismatches: 21, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
50 29 0.35
51 8 0.10
52 9 0.11
53 1 0.01
54 1 0.01
55 8 0.10
56 9 0.11
57 19 0.23
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (50 bp):
AAAAAAATATATGAGATTTGTTTTCAAAACAACAAGGTTAAATTATAAAA
Found at i:31303319 original size:46 final size:46
Alignment explanation
Indices: 31303227--31303548 Score: 448
Period size: 46 Copynumber: 7.0 Consensus size: 46
31303217 GAACAACAGT
* * * *
31303227 AACAACATTCGGACATCATTGATTTG-TACAAAAATGGATAGCATTTA
1 AACAACATTCGGACAACA-TAATATGCTA-AAAAATGGACAGCATTTA
*
31303274 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAACATTTA
1 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
31303320 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
1 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
* ** * *
31303366 AACAACATTCAGACAGTATAATATCCTTAAAAATGGACAGCATTTA
1 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
* *
31303412 AACAACATTCGGACATCATAATATGCTAAAAAATGGACAACATTTA
1 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
* *
31303458 AACAACATTCGGACAACATAATATGTTCAAAAATGGACAGCATTTA
1 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
** * * *
31303504 AACAACATTTAGACAACATAATATACTAAAAAATAGACAACATTT
1 AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTT
31303549 TGTTATCACA
Statistics
Matches: 246, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
46 227 0.92
47 19 0.08
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.25
Consensus pattern (46 bp):
AACAACATTCGGACAACATAATATGCTAAAAAATGGACAGCATTTA
Found at i:31304224 original size:43 final size:43
Alignment explanation
Indices: 31304158--31304330 Score: 138
Period size: 43 Copynumber: 4.0 Consensus size: 43
31304148 ATCTTGTACA
**
31304158 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATATCCCAGACAG-GGTCTTACATGTAATCAAATATCG
* * * *
31304201 ATGCCACTATCCTAGACAGGGTCTTACATGAAATCATATA-CG
1 ATGCCAATATCCCAGACAGGGTCTTACATGTAATCAAATATCG
* * * *
31304243 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATATCCCAGACAGGGTCTTACATGT-AATC-AAATATCG
** * * * *
31304287 ATGCCAACGTCCCAAAC-GTGGTCTTACACGAAATCACATATCG
1 ATGCCAATATCCCAGACAG-GGTCTTACATGTAATCAAATATCG
31304330 A
1 A
31304331 AATCCTAGGT
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
42 28 0.27
43 46 0.44
44 30 0.29
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATATCCCAGACAGGGTCTTACATGTAATCAAATATCG
Found at i:31304322 original size:86 final size:85
Alignment explanation
Indices: 31304158--31304322 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
31304148 ATCTTGTACA
* * * *
31304158 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTATCCTAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAAACAGGGT
*
31304223 CTTACATGAAATCATATACG
66 CTTACACGAAATCATATACG
* * *
31304243 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAAAC-G
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTATCCCAAACAG
31304305 TGGTCTTACACGAAATCA
63 -GGTCTTACACGAAATCA
31304323 CATATCGAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 29 0.43
86 35 0.51
87 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAAACAGGGT
CTTACACGAAATCATATACG
Found at i:31311219 original size:25 final size:25
Alignment explanation
Indices: 31311191--31311269 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 25
31311181 CCTTAGCGCT
31311191 CTCTCTGATTATTAGCACATCAATG
1 CTCTCTGATTATTAGCACATCAATG
* * * *
31311216 CTCTCTAATTATTAGCACGTTAGTG
1 CTCTCTGATTATTAGCACATCAATG
* *
31311241 CTCTC-CA--ATTAGCACATCTATG
1 CTCTCTGATTATTAGCACATCAATG
31311263 CTCTCTG
1 CTCTCTG
31311270 TATAGCACTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 16 0.37
24 1 0.02
25 26 0.60
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACATCAATG
Found at i:31311299 original size:47 final size:48
Alignment explanation
Indices: 31311191--31311299 Score: 118
Period size: 47 Copynumber: 2.3 Consensus size: 48
31311181 CCTTAGCGCT
*
31311191 CTCTCTGATTATTAGCACATCAATGCTCTCTAATTATTAGCACGTTAGTG
1 CTCTCT-ATTATTAGCACATCAATGCTCTCT-AGTATTAGCACGTTAGTG
* * *
31311241 CTCTCCA--ATTAGCACATCTATGCTCTCT-GTA-TAGCACTTTAGTG
1 CTCTCTATTATTAGCACATCAATGCTCTCTAGTATTAGCACGTTAGTG
*
31311285 TTCTCTATTCATTAG
1 CTCTCTATT-ATTAG
31311300 TGCATAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
44 17 0.34
45 2 0.04
47 25 0.50
49 1 0.02
50 5 0.10
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (48 bp):
CTCTCTATTATTAGCACATCAATGCTCTCTAGTATTAGCACGTTAGTG
Found at i:31319898 original size:20 final size:20
Alignment explanation
Indices: 31319839--31319889 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
31319829 AAAACGCTAT
31319839 ATAGAGGCACCGTAGTGCACA
1 ATAGAGGCACCGTAGTGCA-A
*
31319860 A-AGAGGCACTGTAGTGCAA
1 ATAGAGGCACCGTAGTGCAA
31319879 ATAGAGGCACC
1 ATAGAGGCACC
31319890 AAAGTGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.35, C:0.22, G:0.29, T:0.14
Consensus pattern (20 bp):
ATAGAGGCACCGTAGTGCAA
Found at i:31323660 original size:16 final size:17
Alignment explanation
Indices: 31323636--31323684 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
31323626 CGAATATAAT
* *
31323636 AAATATTTTTATTTTTA
1 AAATATTTTAAATTTTA
31323653 AAAT-TTTTAAATTTTA
1 AAATATTTTAAATTTTA
31323669 AAATACTTTTAAATTT
1 AAATA-TTTTAAATTT
31323685 AAATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATATTTTAAATTTTA
Found at i:31323685 original size:17 final size:16
Alignment explanation
Indices: 31323635--31323720 Score: 61
Period size: 16 Copynumber: 5.1 Consensus size: 16
31323625 CCGAATATAA
*
31323635 TAAATATTTTT-ATTTT
1 TAAA-ATTTTTAAATTT
31323651 TAAAATTTTTAAATTT
1 TAAAATTTTTAAATTT
31323667 TAAAATACTTTTAAATTT
1 TAAAAT--TTTTAAATTT
*
31323685 AAATTAATTTTT--ATTT
1 TAA--AATTTTTAAATTT
31323701 TAAATAATTTTTAAAATTT
1 T-AA-AATTTTT-AAATTT
31323720 T
1 T
31323721 GTTTTAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.10
16 26 0.45
17 2 0.03
18 16 0.28
19 5 0.09
20 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAAATTTTTAAATTT
Found at i:31323712 original size:16 final size:16
Alignment explanation
Indices: 31323635--31323713 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 16
31323625 CCGAATATAA
31323635 TAAAT-ATTTTTATTT
1 TAAATAATTTTTATTT
*
31323650 TTAA-AATTTTTAAATTT
1 TAAATAATTTTT--ATTT
* * *
31323667 TAAAATACTTTTAAATT
1 T-AAATAATTTTTATTT
31323684 TAAATTAATTTTTATTT
1 TAAA-TAATTTTTATTT
31323701 TAAATAATTTTTA
1 TAAATAATTTTTA
31323714 AAATTTTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 9 0.18
16 12 0.24
17 22 0.44
18 2 0.04
19 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAATAATTTTTATTT
Found at i:31325719 original size:16 final size:16
Alignment explanation
Indices: 31325698--31325773 Score: 50
Period size: 16 Copynumber: 4.6 Consensus size: 16
31325688 TAACTAGAAT
31325698 GTTTAAGAGATTAAAG
1 GTTTAAGAGATTAAAG
*
31325714 GTTTAAG-GTTTAAGAG
1 GTTTAAGAGATTAA-AG
*
31325730 GTTTTAAGGGATTTGAAAG
1 G-TTTAAGAGA-TT-AAAG
*
31325749 AGTTT-TGAGGATTAAAG
1 -GTTTAAGA-GATTAAAG
31325766 G-TTAAGAG
1 GTTTAAGAG
31325774 GTGTTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
15 8 0.17
16 13 0.28
17 10 0.21
18 4 0.09
19 9 0.19
20 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (16 bp):
GTTTAAGAGATTAAAG
Found at i:31329795 original size:2 final size:2
Alignment explanation
Indices: 31329788--31329817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31329778 TAAAGTAATA
31329788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31329818 GTATTAAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31331541 original size:2 final size:2
Alignment explanation
Indices: 31331534--31331560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31331524 TCAGATTTTA
31331534 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31331561 AAAGAAAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31334532 original size:22 final size:22
Alignment explanation
Indices: 31334483--31334543 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
31334473 TTCTTTCTCT
*
31334483 TCAAATTTCTAATTTTAAGTTA
1 TCAAATTTCTAATTTTAAGTGA
* *
31334505 TAAAATTTCTAATTTTAGAG-GG
1 TCAAATTTCTAATTTTA-AGTGA
*
31334527 TCAAATTT-GAATTTTAA
1 TCAAATTTCTAATTTTAA
31334544 ATTTGAGGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 7 0.21
22 23 0.70
23 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
TCAAATTTCTAATTTTAAGTGA
Found at i:31335038 original size:20 final size:21
Alignment explanation
Indices: 31334992--31335039 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
31334982 CTATTAAAAG
*
31334992 TTAATTAGCATTTAGATTAGT
1 TTAATTAGCATTTAGATTACT
*
31335013 TAAATTAG-ATTT-GATTAACT
1 TTAATTAGCATTTAGATT-ACT
31335033 TTAATTA
1 TTAATTA
31335040 AACCAAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (21 bp):
TTAATTAGCATTTAGATTACT
Found at i:31335349 original size:21 final size:21
Alignment explanation
Indices: 31335323--31335385 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31335313 TTGGTATTTG
31335323 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
31335344 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31335365 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
31335386 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:31336574 original size:30 final size:30
Alignment explanation
Indices: 31336516--31336574 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
31336506 TTGAAAAGGT
* *
31336516 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
31336546 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
31336575 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:31338464 original size:21 final size:21
Alignment explanation
Indices: 31338438--31338493 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
31338428 AACAGCGGTG
*
31338438 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
31338459 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
31338480 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
31338494 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:31350618 original size:25 final size:25
Alignment explanation
Indices: 31350564--31350612 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
31350554 AGCTCTCTCT
31350564 TGAGCCAAGTAACAGGAAGCTCATG
1 TGAGCCAAGTAACAGGAAGCTCATG
*
31350589 TGAGCCAAGTAACAGGAAGGTCAT
1 TGAGCCAAGTAACAGGAAGCTCAT
31350613 TCGAGCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (25 bp):
TGAGCCAAGTAACAGGAAGCTCATG
Found at i:31350783 original size:25 final size:25
Alignment explanation
Indices: 31350701--31350791 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
31350691 TCATTTATCG
* *
31350701 GGAAGCTCATAAGAGCCA-ATTATCA
1 GGAAGCTTATAAGAGCCATA-TAACA
* ** *
31350726 AGAAGCTCGTAAGAACCATATAACA
1 GGAAGCTTATAAGAGCCATATAACA
* *
31350751 GGAAGCTT-TAGAGAGCCATATATCG
1 GGAAGCTTATA-AGAGCCATATAACA
*
31350776 GGACGCTTATAAGAGC
1 GGAAGCTTATAAGAGC
31350792 TGTGGTGTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.04
25 48 0.91
26 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (25 bp):
GGAAGCTTATAAGAGCCATATAACA
Found at i:31351222 original size:21 final size:21
Alignment explanation
Indices: 31351205--31351246 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31351195 AAGTTTAACA
*
31351205 TCAATTTAATACAATTTACAT
1 TCAATTCAATACAATTTACAT
* *
31351226 TCAATTCAATCCAATTCACAT
1 TCAATTCAATACAATTTACAT
31351247 CTTAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAATTCAATACAATTTACAT
Found at i:31355507 original size:16 final size:16
Alignment explanation
Indices: 31355486--31355516 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31355476 CTTGTTCTTT
*
31355486 GACTTGGATTTGATTC
1 GACTTGGATTCGATTC
31355502 GACTTGGATTCGATT
1 GACTTGGATTCGATT
31355517 TGAGTCCAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (16 bp):
GACTTGGATTCGATTC
Found at i:31370055 original size:21 final size:18
Alignment explanation
Indices: 31370008--31370056 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
31369998 TAAAAATATA
31370008 TTATATTATTAAGAAATC
1 TTATATTATTAAGAAATC
*
31370026 TTA-ATTATTAAGTAAATG
1 TTATATTATTAAG-AAATC
31370044 TATATATGTATTA
1 T-TATAT-TATTA
31370057 TATAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 2 0.08
20 2 0.08
21 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (18 bp):
TTATATTATTAAGAAATC
Found at i:31371885 original size:128 final size:128
Alignment explanation
Indices: 31371469--31371852 Score: 709
Period size: 128 Copynumber: 3.0 Consensus size: 128
31371459 ATGAAATATG
*
31371469 ATAGCATGTGTAAATTGAATGTAGTATT-AAATAATGTGCTAATATGTATGAATTCAAAAGGTTC
1 ATAGCATGTGTAAATTGAATGTAGT-TTGAAATAATGTGCTGATATGTATGAATTCAAAAGGTTC
*
31371533 GCATATGATAGTTGTGATATTAGTCATTAATATGT-TTTAATAATTAAATTGTGCATTTTTTATT
65 GCATATGATAGTTGTGATATTAGTCATTAATATGTGTTT-ATAATTAAATTGTGCATTTTGTATT
31371597 ATAGCATGTGTAAATTGAATGTAGTTTGAAATAATGTGCTGATATGTATGAATTCAAAAGGTTCG
1 ATAGCATGTGTAAATTGAATGTAGTTTGAAATAATGTGCTGATATGTATGAATTCAAAAGGTTCG
31371662 CATATGATAGTTGTGATATTAGTCATTAATATGTGTTTATAATTAAATTGTGCATTTTGTATT
66 CATATGATAGTTGTGATATTAGTCATTAATATGTGTTTATAATTAAATTGTGCATTTTGTATT
31371725 ATAGCATGTGTAAATTGAATGTAGTTTGAAATAATGTGCTGATATGTATGAATTCAAAAGGTTCG
1 ATAGCATGTGTAAATTGAATGTAGTTTGAAATAATGTGCTGATATGTATGAATTCAAAAGGTTCG
*
31371790 CATATGATAGTTGTGATATTAGTCATTAATATGTGTTTATAATTAAATTATGCATTTTGTATT
66 CATATGATAGTTGTGATATTAGTCATTAATATGTGTTTATAATTAAATTGTGCATTTTGTATT
31371853 CCCCTGTCTT
Statistics
Matches: 251, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
127 2 0.01
128 246 0.98
129 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (128 bp):
ATAGCATGTGTAAATTGAATGTAGTTTGAAATAATGTGCTGATATGTATGAATTCAAAAGGTTCG
CATATGATAGTTGTGATATTAGTCATTAATATGTGTTTATAATTAAATTGTGCATTTTGTATT
Found at i:31377648 original size:24 final size:25
Alignment explanation
Indices: 31377554--31377646 Score: 86
Period size: 24 Copynumber: 3.8 Consensus size: 25
31377544 GCACTCTCCC
31377554 GAGCCATATAACGGGAAGCTCAT-AA
1 GAGCCAT-TAACGGGAAGCTCATGAA
* *
31377579 GAGCCA-TAATCAGGAAGCTCATG-C
1 GAGCCATTAA-CGGGAAGCTCATGAA
* * *
31377603 GAGCCAATAATGGGCAGCTC-TGAA
1 GAGCCATTAACGGGAAGCTCATGAA
*
31377627 GAGCCATTAACGGAAAGCTC
1 GAGCCATTAACGGGAAGCTC
31377647 TGGATAACCA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 5 0.09
24 40 0.74
25 9 0.17
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (25 bp):
GAGCCATTAACGGGAAGCTCATGAA
Found at i:31384389 original size:16 final size:16
Alignment explanation
Indices: 31384368--31384399 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31384358 ACAAGAAGAT
31384368 AACTAAATCAATCAGC
1 AACTAAATCAATCAGC
31384384 AACTAAATCAATCAGC
1 AACTAAATCAATCAGC
31384400 CTTTCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (16 bp):
AACTAAATCAATCAGC
Found at i:31388641 original size:39 final size:39
Alignment explanation
Indices: 31388598--31388712 Score: 221
Period size: 39 Copynumber: 2.9 Consensus size: 39
31388588 ACCTAAGACT
31388598 AAGGGCACATCAATTGAATTATCATTAGGTCCCATGTGG
1 AAGGGCACATCAATTGAATTATCATTAGGTCCCATGTGG
*
31388637 AAGGGCACATCAATTGAATTATCATTAGGTCCCATTTGG
1 AAGGGCACATCAATTGAATTATCATTAGGTCCCATGTGG
31388676 AAGGGCACATCAATTGAATTATCATTAGGTCCCATGT
1 AAGGGCACATCAATTGAATTATCATTAGGTCCCATGT
31388713 CTAAAACATA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (39 bp):
AAGGGCACATCAATTGAATTATCATTAGGTCCCATGTGG
Found at i:31393634 original size:25 final size:25
Alignment explanation
Indices: 31393604--31393722 Score: 93
Period size: 25 Copynumber: 4.8 Consensus size: 25
31393594 GCACTCTCTC
31393604 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGT
* * * **
31393629 GAGCCATGTAACGAGAAGCTTATCC
1 GAGCCATATAACGGGAAGCTCATGT
* * **
31393654 GGGCTATATAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATGT
*
31393679 GAGCCATAATTAA---GAAGCTTATGT
1 GAGCCAT-A-TAACGGGAAGCTCATGT
*
31393703 GAGCCA-ATAACGGGTAGCTC
1 GAGCCATATAACGGGAAGCTC
31393723 CAAAGAGCCA
Statistics
Matches: 70, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
21 3 0.04
22 1 0.01
24 19 0.27
25 43 0.61
26 1 0.01
27 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:31393834 original size:27 final size:26
Alignment explanation
Indices: 31393787--31393856 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 26
31393777 AGCCATATCG
* *
31393787 GGAAGCTCACAAAGAGGCTTTAATCA
1 GGAAGCTCACAAAGAGCCTTTAAACA
* *
31393813 GGAAGCTCATGAAAGAGCCTTTAAACG
1 GGAAGCTCA-CAAAGAGCCTTTAAACA
31393840 GGAAGCTCACAAAGAGC
1 GGAAGCTCACAAAGAGC
31393857 TAAGGTGTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 16 0.42
27 22 0.58
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTTTAAACA
Found at i:31395185 original size:25 final size:26
Alignment explanation
Indices: 31395150--31395207 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 26
31395140 TATATATAAT
31395150 ATATATATTTGATTAAAAAT-AAAAA
1 ATATATATTTGATTAAAAATAAAAAA
*
31395175 ATATATGTTTGATTAAAAATAAAAAA
1 ATATATATTTGATTAAAAATAAAAAA
31395201 ATATATA
1 ATATATA
31395208 ATTAGGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (26 bp):
ATATATATTTGATTAAAAATAAAAAA
Found at i:31406289 original size:49 final size:49
Alignment explanation
Indices: 31406207--31406300 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
31406197 GATGAAATAC
* ** *
31406207 GATATGATATGTTATAAGATATGCTTCGATATGAAATTTGATATGATAT
1 GATATGATATGTAATAAGATATGCCCCGATATGAAATCTGATATGATAT
* *
31406256 GATATGATATGTAATAA-ATTATGCCCCGTTATGATATCTGATATG
1 GATATGATATGTAATAAGA-TATGCCCCGATATGAAATCTGATATG
31406301 CCACGATACT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.03
49 37 0.97
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.39
Consensus pattern (49 bp):
GATATGATATGTAATAAGATATGCCCCGATATGAAATCTGATATGATAT
Found at i:31409864 original size:22 final size:22
Alignment explanation
Indices: 31409815--31409870 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
31409805 AAGAAGATGA
* * *
31409815 GAAAAAGTAGAGAAAGAGAATG
1 GAAAAAGAAGAAAAAAAGAATG
31409837 G--AAAGAAGAAAAAAAGAATG
1 GAAAAAGAAGAAAAAAAGAATG
31409857 GAAAAAGAA-AAAAA
1 GAAAAAGAAGAAAAA
31409871 GAATATGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 17 0.59
21 5 0.17
22 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (22 bp):
GAAAAAGAAGAAAAAAAGAATG
Found at i:31409866 original size:19 final size:20
Alignment explanation
Indices: 31409831--31409874 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
31409821 GTAGAGAAAG
31409831 AGAATGGAAAGAAGAAAAAA
1 AGAATGGAAAGAAGAAAAAA
31409851 AGAATGGAAA-AAGAAAAAA
1 AGAATGGAAAGAAGAAAAAA
31409870 AGAAT
1 AGAAT
31409875 ATGGCAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (20 bp):
AGAATGGAAAGAAGAAAAAA
Found at i:31410385 original size:3 final size:3
Alignment explanation
Indices: 31410377--31410401 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31410367 TTTGATCCCT
31410377 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
31410402 CCCAAGCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:31414970 original size:22 final size:22
Alignment explanation
Indices: 31414944--31414988 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
31414934 TCTGGTAATG
31414944 AATAAAGGCCATAATTTTAAAT
1 AATAAAGGCCATAATTTTAAAT
*
31414966 AATAAAGGCCATAATTTTGAAT
1 AATAAAGGCCATAATTTTAAAT
31414988 A
1 A
31414989 TTCTTAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (22 bp):
AATAAAGGCCATAATTTTAAAT
Found at i:31420967 original size:22 final size:22
Alignment explanation
Indices: 31420926--31420969 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31420916 AGTACCTAGG
*
31420926 TTTGAATCTTGTTGGTATCAAT
1 TTTGAATCTTGTTGGAATCAAT
* *
31420948 TTTGAATCTTTTTTGAATCAAT
1 TTTGAATCTTGTTGGAATCAAT
31420970 AGCAATAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (22 bp):
TTTGAATCTTGTTGGAATCAAT
Found at i:31433086 original size:23 final size:23
Alignment explanation
Indices: 31433060--31433110 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
31433050 ACCTACTTTC
* * *
31433060 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
31433083 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
31433106 TTACA
1 TTACA
31433111 TTTTCAGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:31433638 original size:70 final size:70
Alignment explanation
Indices: 31433491--31433871 Score: 426
Period size: 70 Copynumber: 5.5 Consensus size: 70
31433481 TAAAGCTTGT
* * *
31433491 AGGTTTAATACCGCAGCCTCCAAACAATTAGTGAGTGTTAAAAGCT-CCAACTGTCACTCTAAGG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCACTCTAAGG
31433555 CTCGT-
66 CTC-TC
* * * *
31433560 AGGTTTAATATCGCAGCCCCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCAATCTAAGG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCACTCTAAGG
31433625 CTCTC
66 CTCTC
* ** * * * * *
31433630 AGGTTTAATACCGCAACCTTTAAACAATTAGTGAGAGTTAAAAGCTCCTAAGTATCACTCTAAGG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCACTCTAAGG
*
31433695 CTCGC
66 CTCTC
* * * * *
31433700 AGGTTTAATACCTCAGCCTCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTATCATTCTAAGG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCACTCTAAGG
*
31433765 CTCGC
66 CTCTC
* * * ** *
31433770 AGGTTTAATACCACAGCCTTCAAACAGTTAGCGAGAGTTAAAAGCTCCTAGTTGTCATTCTAAGG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCACTCTAAGG
31433835 CTCGT-
66 CTC-TC
* * * * *
31433840 AGGTTTGATATCACAGCCTCGAAATAGTTAGC
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGC
31433872 ACGAGCTCAA
Statistics
Matches: 266, Mismatches: 43, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
69 41 0.15
70 225 0.85
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (70 bp):
AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCACTCTAAGG
CTCTC
Found at i:31433734 original size:140 final size:140
Alignment explanation
Indices: 31433473--31433871 Score: 550
Period size: 140 Copynumber: 2.9 Consensus size: 140
31433463 TATTTGTATT
* * * * * *
31433473 TATCATTCTAAAGCTTGTAGGTTTAATACCGCAGCCTCCAAACAATTAGTGAGTGTTAAAAGCTC
1 TATCAATCTAAGGCTCGCAGGTTTAATACCGCAGCCTTCAAACAATTAGTGAGAGTTAAAAGCTC
* * *
31433538 C-AACTGTCACTCTAAGGCTCGTAGGTTTAATATCGCAGCCCCCAAATAGTTAGCGAGAGTTAAA
66 CTAAGTGTCACTCTAAGGCTCGTAGGTTTAATATCACAGCCTCCAAATAGTTAGCGAGAGTTAAA
31433602 AGCTCCCAAC
131 AGCTCCCAAC
* * * *
31433612 TGTCAATCTAAGGCTCTCAGGTTTAATACCGCAACCTTTAAACAATTAGTGAGAGTTAAAAGCTC
1 TATCAATCTAAGGCTCGCAGGTTTAATACCGCAGCCTTCAAACAATTAGTGAGAGTTAAAAGCTC
* * * *
31433677 CTAAGTATCACTCTAAGGCTCGCAGGTTTAATACCTCAGCCTCCAAATAGTTAGCGAGAGTTAAA
66 CTAAGTGTCACTCTAAGGCTCGTAGGTTTAATATCACAGCCTCCAAATAGTTAGCGAGAGTTAAA
*
31433742 AGCTCCCAGC
131 AGCTCCCAAC
* * * *
31433752 TATCATTCTAAGGCTCGCAGGTTTAATACCACAGCCTTCAAACAGTTAGCGAGAGTTAAAAGCTC
1 TATCAATCTAAGGCTCGCAGGTTTAATACCGCAGCCTTCAAACAATTAGTGAGAGTTAAAAGCTC
* * *
31433817 CT-AGTTGTCATTCTAAGGCTCGTAGGTTTGATATCACAGCCTCGAAATAGTTAGC
66 CTAAG-TGTCACTCTAAGGCTCGTAGGTTTAATATCACAGCCTCCAAATAGTTAGC
31433872 ACGAGCTCAA
Statistics
Matches: 226, Mismatches: 32, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
139 58 0.26
140 168 0.74
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (140 bp):
TATCAATCTAAGGCTCGCAGGTTTAATACCGCAGCCTTCAAACAATTAGTGAGAGTTAAAAGCTC
CTAAGTGTCACTCTAAGGCTCGTAGGTTTAATATCACAGCCTCCAAATAGTTAGCGAGAGTTAAA
AGCTCCCAAC
Found at i:31437372 original size:60 final size:60
Alignment explanation
Indices: 31437243--31437374 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
31437233 CAACTATGCC
* *
31437243 TTTTACCTTTTTTGGTCACCTAACTAGGAAAAGTTAGAAAATGGTCACCCAACCATTAGTA
1 TTTTATCTTTTTTAGTCACCTAACTAGGAAAAGTTAGAAAATGGTCACCCAACCATTAG-A
** * * * * * *
31437304 AATT-TCTTTTTTAGTCGCCTAACTATGAAATGTTAGAAAATGGTTACCCTACTATTCA-A
1 TTTTATCTTTTTTAGTCACCTAACTAGGAAAAGTTAGAAAATGGTCACCCAACCATT-AGA
31437363 TTTTATCTTTTT
1 TTTTATCTTTTT
31437375 GGTAATTAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
59 3 0.05
60 51 0.89
61 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (60 bp):
TTTTATCTTTTTTAGTCACCTAACTAGGAAAAGTTAGAAAATGGTCACCCAACCATTAGA
Found at i:31447431 original size:25 final size:25
Alignment explanation
Indices: 31447345--31447461 Score: 105
Period size: 25 Copynumber: 4.7 Consensus size: 25
31447335 ATGTAAACGA
* * *
31447345 GAAGCTCTTGTGAGCCAATT-ATCGA
1 GAAGCTCATGAGAGCC-ATTAATCGG
*
31447370 GAAGCTCATGAGAGCCA-TAAACGG
1 GAAGCTCATGAGAGCCATTAATCGG
* *
31447394 AAAGCTCAAGAGAGCCATTAATCGG
1 GAAGCTCATGAGAGCCATTAATCGG
* *
31447419 GAAGCTCATGAGAGCCA-CATATCAG
1 GAAGCTCATGAGAGCCATTA-ATCGG
* *
31447444 GAAACTCGTGAGAGCCAT
1 GAAGCTCATGAGAGCCAT
31447462 ATAAGGGGGT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
23 1 0.01
24 20 0.27
25 54 0.72
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCATTAATCGG
Found at i:31451092 original size:57 final size:57
Alignment explanation
Indices: 31451031--31451200 Score: 243
Period size: 57 Copynumber: 3.0 Consensus size: 57
31451021 GAGCAACTTT
* * *
31451031 ATACTTGAGAAAATTTGAAAGATAACCAACTTGGGATGTAGATCCGCGAGCTGTTTC
1 ATACTTAAGAAAATTTGAAAGATAACCAACTGGGGATGTAGATCCGCAAGCTGTTTC
* *
31451088 ATACTTAAAAAAATTTGAAAGATAACCAACTGGGGATATAGATCCGCAAGCTGTTTC
1 ATACTTAAGAAAATTTGAAAGATAACCAACTGGGGATGTAGATCCGCAAGCTGTTTC
* * * *
31451145 ATACTTAAGAAAATTTAAAAGATAAACAACTGGGGATGT-GAAACCGCAAGTTGTTT
1 ATACTTAAGAAAATTTGAAAGATAACCAACTGGGGATGTAG-ATCCGCAAGCTGTTT
31451201 TATCCTACGA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
56 1 0.01
57 100 0.99
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (57 bp):
ATACTTAAGAAAATTTGAAAGATAACCAACTGGGGATGTAGATCCGCAAGCTGTTTC
Found at i:31451309 original size:69 final size:69
Alignment explanation
Indices: 31451198--31451430 Score: 342
Period size: 69 Copynumber: 3.4 Consensus size: 69
31451188 CCGCAAGTTG
* * * *
31451198 TTTTATCCTACGAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTATGTTGGAGGTTG
1 TTTTATCCTGCGAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGGCTA
31451263 CAGT
66 CAGT
*
31451267 TTTTATCCTGCGAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTTACTAACTGTGTTGGAGGCTA
1 TTTTATCCTGCGAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGGCTA
*
31451332 CGGT
66 CAGT
* *
31451336 TTTAATCCTGCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGGCTA
1 TTTTATCCTGCGAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGGCTA
31451401 CAGCT
66 CAG-T
* * * *
31451406 CTTCA-CGTGCGAGCCTTAATATGAC
1 TTTTATCCTGCGAGCCTTAGTATGAC
31451431 GTAAATGTTG
Statistics
Matches: 150, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
69 146 0.97
70 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (69 bp):
TTTTATCCTGCGAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGGCTA
CAGT
Found at i:31458520 original size:15 final size:16
Alignment explanation
Indices: 31458500--31458529 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31458490 ATTTTTATAG
31458500 TTATTTTTA-TTTTAA
1 TTATTTTTACTTTTAA
31458515 TTATTTTTACTTTTA
1 TTATTTTTACTTTTA
31458530 TCATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTTACTTTTAA
Found at i:31461001 original size:15 final size:15
Alignment explanation
Indices: 31460981--31461011 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31460971 AAAACAACAT
31460981 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
31460996 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
31461011 A
1 A
31461012 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:31464387 original size:15 final size:15
Alignment explanation
Indices: 31464369--31464398 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31464359 TCCCTTCTTG
*
31464369 ACCACGACCTTTTCC
1 ACCACGACCATTTCC
31464384 ACCACGACCATTTCC
1 ACCACGACCATTTCC
31464399 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCATTTCC
Found at i:31465348 original size:15 final size:15
Alignment explanation
Indices: 31465328--31465358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31465318 AAAACAACAT
*
31465328 AACTCTTGACCTTTC
1 AACTCTTGACATTTC
31465343 AACTCTTGACATTTC
1 AACTCTTGACATTTC
31465358 A
1 A
31465359 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACATTTC
Found at i:31465908 original size:37 final size:38
Alignment explanation
Indices: 31465841--31465914 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
31465831 CTTTTTTGTG
* * *
31465841 TTCTTTTTACCCCAAAAAAGCTCATGGATATGTTGTTA
1 TTCTTTTTACCCCAAAAAACCGCATGGATATATTGTTA
* *
31465879 TTCTTTTTA-CCCAAAATACCGCATTGATATATTGTT
1 TTCTTTTTACCCCAAAAAACCGCATGGATATATTGTT
31465915 GGGACATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 22 0.71
38 9 0.29
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (38 bp):
TTCTTTTTACCCCAAAAAACCGCATGGATATATTGTTA
Found at i:31467176 original size:2 final size:2
Alignment explanation
Indices: 31467169--31467198 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31467159 TGAATCCGTA
31467169 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31467199 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31467203 original size:2 final size:2
Alignment explanation
Indices: 31467198--31467227 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31467188 TCTCTCTCTC
31467198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31467228 CACGCATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31475276 original size:3 final size:3
Alignment explanation
Indices: 31475268--31475293 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31475258 AGAACCGAGT
31475268 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
31475294 TTTTTAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:31478892 original size:30 final size:31
Alignment explanation
Indices: 31478857--31478922 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
31478847 GTAAGGGTTA
* *
31478857 ATTTCAATTTTTG-AATCTTATTTAATATTTT
1 ATTTCAATTTATGTAATCTTAATTAAT-TTTT
*
31478888 -TTTC-ATTTATGTAATTTTAATTAATTTTT
1 ATTTCAATTTATGTAATCTTAATTAATTTTT
31478917 ATTTCA
1 ATTTCA
31478923 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (31 bp):
ATTTCAATTTATGTAATCTTAATTAATTTTT
Found at i:31480452 original size:18 final size:18
Alignment explanation
Indices: 31480429--31480464 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31480419 TGTCAGGTGC
*
31480429 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
31480447 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
31480465 ATTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:31480471 original size:18 final size:18
Alignment explanation
Indices: 31480430--31480471 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31480420 GTCAGGTGCG
* *
31480430 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATA
31480448 TATCCTAACCCTTATATA
1 TATCCTAACCCTTATATA
*
31480466 TTTCCT
1 TATCCT
31480472 TTTCCCAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:31480907 original size:34 final size:34
Alignment explanation
Indices: 31480869--31480950 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
31480859 TTTCATTTAA
31480869 TAAAACCTAATTTAATTAATTTATTT-AAAACTCC
1 TAAAACCTAATTTAATTAATTTATTTAAAAACT-C
* * *
31480903 TAAAATCTAATTTAATTAATTTTTTTAAAAACTT
1 TAAAACCTAATTTAATTAATTTATTTAAAAACTC
*
31480937 TAAACCCTAATTTA
1 TAAAACCTAATTTA
31480951 TTTTTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 36 0.86
35 6 0.14
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAAACCTAATTTAATTAATTTATTTAAAAACTC
Found at i:31480953 original size:29 final size:28
Alignment explanation
Indices: 31480915--31480970 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
31480905 AAATCTAATT
31480915 TAATTAATTTTTTTAAAAACT-TTAAACCC
1 TAATTAA-TTTTTT-AAAACTCTTAAACCC
*
31480944 TAATTTATTTTTTAAAACTCTTAAACC
1 TAATTAATTTTTTAAAACTCTTAAACC
31480971 TTAAATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 13 0.52
29 6 0.24
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATTAATTTTTTAAAACTCTTAAACCC
Found at i:31499695 original size:13 final size:13
Alignment explanation
Indices: 31499677--31499704 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31499667 AGCACAAAAC
31499677 CTAGTTCCTTTAA
1 CTAGTTCCTTTAA
31499690 CTAGTTCCTTTAA
1 CTAGTTCCTTTAA
31499703 CT
1 CT
31499705 GGCAAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.46
Consensus pattern (13 bp):
CTAGTTCCTTTAA
Found at i:31505250 original size:13 final size:13
Alignment explanation
Indices: 31505232--31505256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31505222 GTTTACAAGA
31505232 TTACATAATCAAT
1 TTACATAATCAAT
31505245 TTACATAATCAA
1 TTACATAATCAA
31505257 ATTAAATCTC
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:31505295 original size:25 final size:25
Alignment explanation
Indices: 31505267--31505320 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
31505257 ATTAAATCTC
*
31505267 ATCTTATAAGA-TATGATTCCCTTTA
1 ATCTTATAAGATTA-GATTCCCCTTA
* *
31505292 ATCTTCTAAGATTAGTTTCCCCTTA
1 ATCTTATAAGATTAGATTCCCCTTA
31505317 ATCT
1 ATCT
31505321 GACAGGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.44
Consensus pattern (25 bp):
ATCTTATAAGATTAGATTCCCCTTA
Found at i:31507716 original size:27 final size:25
Alignment explanation
Indices: 31507681--31507741 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
31507671 AAAGGTTGTT
*
31507681 AAATGACCAAAATACCCTCGAAGGGTA
1 AAATAACCAAAATACCC-C-AAGGGTA
* *
31507708 AAATAACCATAATACCCCTAGGGTA
1 AAATAACCAAAATACCCCAAGGGTA
*
31507733 AAATTACCA
1 AAATAACCA
31507742 TTTTACCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 14 0.47
26 1 0.03
27 15 0.50
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (25 bp):
AAATAACCAAAATACCCCAAGGGTA
Found at i:31507736 original size:25 final size:25
Alignment explanation
Indices: 31507702--31507752 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
31507692 ATACCCTCGA
31507702 AGGGTAAAATAACCATAATACCCCT
1 AGGGTAAAATAACCATAATACCCCT
* **
31507727 AGGGTAAAATTACCATTTTACCCCT
1 AGGGTAAAATAACCATAATACCCCT
31507752 A
1 A
31507753 ACTGACGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (25 bp):
AGGGTAAAATAACCATAATACCCCT
Found at i:31510772 original size:22 final size:22
Alignment explanation
Indices: 31510745--31510824 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
31510735 TTACTTAATA
**
31510745 GTACTAAGCTCTCATGTTTAAC
1 GTACTAAGCTCTCATGGCTAAC
* * *
31510767 GAACTAAACCCTCATGGCTAAC
1 GTACTAAGCTCTCATGGCTAAC
31510789 GTACTAAGCTCTCATGGCTAAC
1 GTACTAAGCTCTCATGGCTAAC
31510811 GTACTAAGCTCTCA
1 GTACTAAGCTCTCA
31510825 CAAAGGGCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (22 bp):
GTACTAAGCTCTCATGGCTAAC
Found at i:31532575 original size:19 final size:17
Alignment explanation
Indices: 31532543--31532578 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
31532533 AATTCCAATT
31532543 CAATTTCATATTTTCAC
1 CAATTTCATATTTTCAC
31532560 CAATTTACACTATTTTCAC
1 CAATTT-CA-TATTTTCAC
31532579 TTTTGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (17 bp):
CAATTTCATATTTTCAC
Found at i:31533266 original size:19 final size:19
Alignment explanation
Indices: 31533238--31533277 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31533228 TTATACTTTA
31533238 ATTATAA-TTTTTATAACAT
1 ATTATAATTTTTTAT-ACAT
*
31533257 ATTATTATTTTTTATACAT
1 ATTATAATTTTTTATACAT
31533276 AT
1 AT
31533278 ATTTAACCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATAATTTTTTATACAT
Found at i:31541578 original size:17 final size:16
Alignment explanation
Indices: 31541539--31541589 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 16
31541529 ATGTACCTAT
31541539 ATAATTCAATTTAATCA
1 ATAATTCAATTT-ATCA
31541556 ATAATTCATATTTATGCA
1 ATAATTCA-ATTTAT-CA
31541574 A-AATTACAAATTTATC
1 ATAATT-C-AATTTATC
31541590 CTTTAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 15 0.50
18 14 0.47
19 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATTCAATTTATCA
Found at i:31541832 original size:21 final size:21
Alignment explanation
Indices: 31541808--31541850 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
31541798 TGTTTATTTT
31541808 TCAAC-AAGTATTCATAATCTA
1 TCAACAAAG-ATTCATAATCTA
31541829 TCAACAAAGATTCATAATCTA
1 TCAACAAAGATTCATAATCTA
31541850 T
1 T
31541851 AAAAAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TCAACAAAGATTCATAATCTA
Found at i:31550710 original size:15 final size:16
Alignment explanation
Indices: 31550690--31550719 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31550680 TGGTGCTTTA
31550690 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
31550705 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
31550720 AGTAGGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:31553988 original size:11 final size:11
Alignment explanation
Indices: 31553972--31553997 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31553962 ACTTACCCCC
31553972 ATAATTATTGT
1 ATAATTATTGT
31553983 ATAATTATTGT
1 ATAATTATTGT
31553994 ATAA
1 ATAA
31553998 AATCGATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (11 bp):
ATAATTATTGT
Found at i:31559449 original size:50 final size:50
Alignment explanation
Indices: 31559390--31559500 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
31559380 CACACCAAAA
* * * *
31559390 CTCGTATGAGCTTACCAATTTGTAGCTCCTGAGAGCTTACCAATTC-TCAG
1 CTCGTATGAGCTTACCAATTTGCAGCTCATAAGAGCATACCAATTCAT-AG
** *
31559440 CTCGTATGAGCTTACTGATTTGCAGCTCATAAGAGCATACCGATTCATAG
1 CTCGTATGAGCTTACCAATTTGCAGCTCATAAGAGCATACCAATTCATAG
31559490 CTCGTATGAGC
1 CTCGTATGAGC
31559501 ATACATGTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
50 52 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (50 bp):
CTCGTATGAGCTTACCAATTTGCAGCTCATAAGAGCATACCAATTCATAG
Found at i:31559504 original size:25 final size:25
Alignment explanation
Indices: 31559390--31559500 Score: 91
Period size: 25 Copynumber: 4.4 Consensus size: 25
31559380 CACACCAAAA
*
31559390 CTCGTATGAGCTTACCAATTTGTAG
1 CTCGTATGAGCTTACCAATTCGTAG
*
31559415 CTCCTGA-GAGCTTACCAATTC-TCAG
1 CTCGT-ATGAGCTTACCAATTCGT-AG
** * *
31559440 CTCGTATGAGCTTACTGATTTGCAG
1 CTCGTATGAGCTTACCAATTCGTAG
* * * * *
31559465 CTCATAAGAGCATACCGATTCATAG
1 CTCGTATGAGCTTACCAATTCGTAG
31559490 CTCGTATGAGC
1 CTCGTATGAGC
31559501 ATACATGTAC
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
24 2 0.03
25 63 0.95
26 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (25 bp):
CTCGTATGAGCTTACCAATTCGTAG
Found at i:31568704 original size:15 final size:15
Alignment explanation
Indices: 31568680--31568710 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31568670 CTTTTTCCAA
31568680 CATCAAGGGTTGATT
1 CATCAAGGGTTGATT
*
31568695 CATCATGGGTTGATT
1 CATCAAGGGTTGATT
31568710 C
1 C
31568711 TTACATATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (15 bp):
CATCAAGGGTTGATT
Found at i:31569795 original size:40 final size:40
Alignment explanation
Indices: 31569740--31569820 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
31569730 ATGGATAATG
31569740 TCTATGAATGGTATAAGGTCCTTTCCATCGGGATTTGAGC
1 TCTATGAATGGTATAAGGTCCTTTCCATCGGGATTTGAGC
31569780 TCTATGAATGGTATAAGGTCCTTTCCATCGGGATTTGAGC
1 TCTATGAATGGTATAAGGTCCTTTCCATCGGGATTTGAGC
31569820 T
1 T
31569821 TTCCCGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (40 bp):
TCTATGAATGGTATAAGGTCCTTTCCATCGGGATTTGAGC
Found at i:31594868 original size:16 final size:17
Alignment explanation
Indices: 31594847--31594880 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31594837 AAATATTATG
31594847 AAATAAA-AACAAACAA
1 AAATAAATAACAAACAA
*
31594863 AAATAAATATCAAACAA
1 AAATAAATAACAAACAA
31594880 A
1 A
31594881 TGTCATCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAATAACAAACAA
Found at i:31601309 original size:29 final size:29
Alignment explanation
Indices: 31601277--31601363 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
31601267 AAAATCTGCC
*
31601277 AAATAACGAATAAATGCGATAAAATCACA
1 AAATAACGAATAAATGAGATAAAATCACA
** *
31601306 AAATAACGAATAAATGAGATAAAATTGCC
1 AAATAACGAATAAATGAGATAAAATCACA
*
31601335 AAATAACGAATAATTGAGATAAAAATCAC
1 AAATAACGAATAAATGAGAT-AAAATCAC
31601364 CAGATTCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 44 0.88
30 6 0.12
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (29 bp):
AAATAACGAATAAATGAGATAAAATCACA
Found at i:31605817 original size:29 final size:29
Alignment explanation
Indices: 31605775--31605833 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
31605765 TCATGTAGGC
31605775 TGGGTAAAAATTAGGCATTACATCCTTAT
1 TGGGTAAAAATTAGGCATTACATCCTTAT
31605804 TGGGTAAAAATTAGGCATTACATCCTTAT
1 TGGGTAAAAATTAGGCATTACATCCTTAT
31605833 T
1 T
31605834 CTTGAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (29 bp):
TGGGTAAAAATTAGGCATTACATCCTTAT
Found at i:31610079 original size:11 final size:11
Alignment explanation
Indices: 31610059--31610156 Score: 61
Period size: 11 Copynumber: 9.4 Consensus size: 11
31610049 TAAAAATTAA
31610059 AAAAAGTATTTT
1 AAAAA-TATTTT
31610071 AAAAATATTTT
1 AAAAATATTTT
*
31610082 --AAA-A-TTA
1 AAAAATATTTT
31610089 AAAAAGTATTTT
1 AAAAA-TATTTT
*
31610101 AAAAAAATTTT
1 AAAAATATTTT
31610112 --AAA-A-TTT
1 AAAAATATTTT
31610119 AAAAA-ATTTAAT
1 AAAAATATTT--T
*
31610131 AAAAGTATTTT
1 AAAAATATTTT
*
31610142 AAAAGTATTTT
1 AAAAATATTTT
31610153 AAAA
1 AAAA
31610157 TTAAAAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 23
0.72 0.04 0.23
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 13 0.18
10 2 0.03
11 28 0.39
12 17 0.24
13 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:31610094 original size:30 final size:30
Alignment explanation
Indices: 31610051--31610145 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 30
31610041 AATTAAAATA
31610051 AAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATT-AAAAAAGTATTTTAAAAATATTTT
*
31610082 AAAATTAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAGTATTTTAAAAATATTTT
* *
31610112 AAAATTTAAAAAA-T-TTAATAAAAGTATTTT
1 AAAA-TTAAAAAAGTATT-TTAAAAATATTTT
31610142 AAAA
1 AAAA
31610146 GTATTTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
29 2 0.03
30 42 0.72
31 14 0.24
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTAAAAAAGTATTTTAAAAATATTTT
Found at i:31610135 original size:41 final size:40
Alignment explanation
Indices: 31610082--31610166 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 40
31610072 AAAATATTTT
*
31610082 AAAA-TTAAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
1 AAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAATTAAA
**
31610121 AAAATTTAATAAAAGTATTTTAAAAGTATTTTAAAATTAAA
1 AAAATTTAA-AAAAGTATTTTAAAAAAATTTTAAAATTAAA
31610162 AAAAT
1 AAAAT
31610167 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 4 0.10
40 4 0.10
41 33 0.80
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (40 bp):
AAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAATTAAA
Found at i:31615614 original size:3 final size:3
Alignment explanation
Indices: 31615606--31615652 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
31615596 CCTGACTTTC
* * * *
31615606 ATT ATT ATT ATT ATT ATT ATT AGT AGT AGT AGT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
31615653 CCAGTACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:31623142 original size:38 final size:38
Alignment explanation
Indices: 31623099--31623173 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
31623089 ACACACCAAA
*
31623099 CTAGCAC-CGAAGTGCATCCTGGCGAACA-AAACACATAT
1 CTAGCACACAAAGTGCATCCTGGCG--CATAAACACATAT
*
31623137 CTAGCACACAAAGTGCATCTTGGCGCATAAACACATA
1 CTAGCACACAAAGTGCATCCTGGCGCATAAACACATA
31623174 ACCCCATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 2 0.06
38 16 0.48
39 15 0.45
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (38 bp):
CTAGCACACAAAGTGCATCCTGGCGCATAAACACATAT
Found at i:31637519 original size:6 final size:6
Alignment explanation
Indices: 31637508--31637532 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31637498 AATAAACCAT
31637508 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
31637533 TCATAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:31638532 original size:99 final size:99
Alignment explanation
Indices: 31638359--31638554 Score: 338
Period size: 99 Copynumber: 2.0 Consensus size: 99
31638349 ATTGCTTCAC
*
31638359 TATTTCAGCCTCCCTCATCTTCAAGTTCTCAAAATCTCTTCTGAGATTAATAAGTTATTGGTACC
1 TATTTCAGCCTCCCTCATCTTCAAGTTCTCAAAATCTCTTCTGAGATTAATAAGTTATTGCTACC
* *
31638424 TGGTGTTGTCTGAACCTTGAAACTCTTCTTTTAG
66 TGGTCTTGTCTGAACCTTGAAACTCCTCTTTTAG
* * *
31638458 TATTTTAGCCTCCCTCATCTTCAAGTTCTTAAAATCTCTTCTGAGATTAATAAGTTGTTGCTACC
1 TATTTCAGCCTCCCTCATCTTCAAGTTCTCAAAATCTCTTCTGAGATTAATAAGTTATTGCTACC
31638523 TGGTCTTGTCTGAACCTTGAAACTCCTCTTTT
66 TGGTCTTGTCTGAACCTTGAAACTCCTCTTTT
31638555 GGTTTATCCC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (99 bp):
TATTTCAGCCTCCCTCATCTTCAAGTTCTCAAAATCTCTTCTGAGATTAATAAGTTATTGCTACC
TGGTCTTGTCTGAACCTTGAAACTCCTCTTTTAG
Found at i:31641828 original size:19 final size:22
Alignment explanation
Indices: 31641798--31641853 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 22
31641788 ATATTATTTT
*
31641798 TAATTTTTTTAA-AATATTT-A
1 TAATTATTTTAATAATATTTAA
31641818 T-ATTATTTTAATTTAATATTTAA
1 TAATTATTTTAA--TAATATTTAA
31641841 TAATTATTTTAAT
1 TAATTATTTTAAT
31641854 TTATTGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 9 0.30
20 1 0.03
22 8 0.27
23 2 0.07
24 10 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATTATTTTAATAATATTTAA
Found at i:31641832 original size:24 final size:25
Alignment explanation
Indices: 31641809--31641856 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
31641799 AATTTTTTTA
31641809 AAATATTT-AT-ATTATTTTAATTT
1 AAATATTTAATAATTATTTTAATTT
31641832 -AATATTTAATAATTATTTTAATTT
1 AAATATTTAATAATTATTTTAATTT
31641856 A
1 A
31641857 TTGAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
24 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AAATATTTAATAATTATTTTAATTT
Found at i:31643677 original size:32 final size:31
Alignment explanation
Indices: 31643633--31643700 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
31643623 TTTATTTAAA
* *
31643633 TATGTATA-AT-TAAATTAAAATTA-AACTTT
1 TATGTATACATATTAATTAAAA-TACAAATTT
*
31643662 TATGTATACATATTAATTACAATACAAATTT
1 TATGTATACATATTAATTAAAATACAAATTT
31643693 TATGTATA
1 TATGTATA
31643701 TAATTACACC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.24
30 4 0.12
31 21 0.64
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (31 bp):
TATGTATACATATTAATTAAAATACAAATTT
Found at i:31657945 original size:17 final size:17
Alignment explanation
Indices: 31657923--31657959 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
31657913 TTGGAGAGTG
31657923 TTAGCTATATGCTACAC
1 TTAGCTATATGCTACAC
31657940 TTAGCTATATGCTACAC
1 TTAGCTATATGCTACAC
31657957 TTA
1 TTA
31657960 TGGGACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (17 bp):
TTAGCTATATGCTACAC
Found at i:31660884 original size:14 final size:14
Alignment explanation
Indices: 31660865--31660896 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
31660855 GAGTTTAGGG
31660865 GAGAAATAAGGTTA
1 GAGAAATAAGGTTA
31660879 GAGAAATAAGGTTA
1 GAGAAATAAGGTTA
31660893 GAGA
1 GAGA
31660897 CATTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (14 bp):
GAGAAATAAGGTTA
Done.