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 112 of 199
Found at i:34006726 original size:17 final size:16
Alignment explanation
Indices: 34006683--34006752 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
34006673 TTTTTGGTAC
* * *
34006683 TTTAGGGTTTATGTTT
1 TTTAGAGTTTAAGGTT
*
34006699 TTTAGATTTTAAGGTT
1 TTTAGAGTTTAAGGTT
*
34006715 TTTACGAGTTTAGGGCTT
1 TTTA-GAGTTTAAGG-TT
34006733 TTATAG-GTTTAAGGTT
1 TT-TAGAGTTTAAGGTT
34006749 TTTA
1 TTTA
34006753 ACTGTTCTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.05
16 20 0.45
17 15 0.34
18 5 0.11
19 2 0.05
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTAGAGTTTAAGGTT
Found at i:34011411 original size:23 final size:23
Alignment explanation
Indices: 34011381--34011425 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
34011371 TTTCTTAGTG
*
34011381 TAGTAATTTTCGGGATATTACAA
1 TAGTAATTTTCAGGATATTACAA
34011404 TAGTAATTTTCAGGATATTACA
1 TAGTAATTTTCAGGATATTACA
34011426 GAGCAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCAGGATATTACAA
Found at i:34023311 original size:27 final size:25
Alignment explanation
Indices: 34023256--34023323 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
34023246 CTTCCCTAAA
* *
34023256 CCCCCAAAACTTTTTTCCTTTTGCTTT
1 CCCCCAAAAC--TTTTACTTTTCCTTT
34023283 CCCCCAAAACTTTTACTTTCTCCTGTT
1 CCCCCAAAACTTTTACTTT-TCCT-TT
*
34023310 CCCTCAAAACTTTT
1 CCCCCAAAACTTTT
34023324 TTTTCAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 8 0.22
26 3 0.08
27 25 0.69
ACGTcount: A:0.19, C:0.35, G:0.03, T:0.43
Consensus pattern (25 bp):
CCCCCAAAACTTTTACTTTTCCTTT
Found at i:34023700 original size:19 final size:19
Alignment explanation
Indices: 34023676--34023713 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
34023666 AAGTTAATAC
34023676 AAATTTGATTACGATGGGT
1 AAATTTGATTACGATGGGT
*
34023695 AAATTTGATTACGGTGGGT
1 AAATTTGATTACGATGGGT
34023714 GGCAGAGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (19 bp):
AAATTTGATTACGATGGGT
Found at i:34024985 original size:16 final size:16
Alignment explanation
Indices: 34024964--34024994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34024954 ACCATGAATG
*
34024964 TCACAAGTGAATTAAT
1 TCACAAATGAATTAAT
34024980 TCACAAATGAATTAA
1 TCACAAATGAATTAA
34024995 GAATTAATTC
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:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (16 bp):
TCACAAATGAATTAAT
Found at i:34026022 original size:24 final size:24
Alignment explanation
Indices: 34025990--34026038 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
34025980 CCTAAGAGTT
34025990 TGATTTTCTCCCTTTTACATAGTC
1 TGATTTTCTCCCTTTTACATAGTC
34026014 TGATTTTCTCCCTTTTACATAGTC
1 TGATTTTCTCCCTTTTACATAGTC
34026038 T
1 T
34026039 TCAATCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (24 bp):
TGATTTTCTCCCTTTTACATAGTC
Found at i:34026107 original size:25 final size:26
Alignment explanation
Indices: 34026073--34026131 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
34026063 ATAAAACAAC
*
34026073 AAAA-AGAAAATCTACTCTA-AAAAG
1 AAAAGAGAAAATCTAATCTACAAAAG
*
34026097 AAAAGAGAAAATCTAATCTACAAATG
1 AAAAGAGAAAATCTAATCTACAAAAG
34026123 AAAAG-GAAA
1 AAAAGAGAAA
34026132 GGAAAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 4 0.13
25 18 0.58
26 9 0.29
ACGTcount: A:0.63, C:0.10, G:0.12, T:0.15
Consensus pattern (26 bp):
AAAAGAGAAAATCTAATCTACAAAAG
Found at i:34032585 original size:21 final size:23
Alignment explanation
Indices: 34032543--34032588 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
34032533 TAATTAATCA
*
34032543 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
34032566 TAAA-AGAAG-AAATAT-TTTT-
1 TAAACAGAAGCAAATATCTTTTC
34032585 TAAA
1 TAAA
34032589 AAAATTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 5 0.23
22 5 0.23
23 4 0.18
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:34035865 original size:14 final size:15
Alignment explanation
Indices: 34035835--34035866 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34035825 TCTCCAAATT
34035835 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
34035850 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
34035864 TTT
1 TTT
34035867 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:34039174 original size:10 final size:12
Alignment explanation
Indices: 34039149--34039178 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
34039139 TTTGGAAGTT
34039149 ACACGGCCTAAC
1 ACACGGCCTAAC
34039161 ACACGGCCTAAC
1 ACACGGCCTAAC
34039173 ACACGG
1 ACACGG
34039179 GCGTGTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:34039368 original size:35 final size:35
Alignment explanation
Indices: 34039322--34039392 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
34039312 CACACGGCCA
*
34039322 TGTGACCCCTGCAGTATGAAATTTTCTATCTTTTT
1 TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
*
34039357 TGTGATCCCTGCAGTATAAAATTTTCTATCTTTTT
1 TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
34039392 T
1 T
34039393 CTTAATGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (35 bp):
TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
Found at i:34040594 original size:42 final size:43
Alignment explanation
Indices: 34040544--34040628 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 43
34040534 ATTCATATGT
34040544 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAA-AAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAGAAAA
*
34040586 TTGGTTTAGTGGAATAGAGACTGTAATAGCATAAGGAAGAAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAGAAAA
34040629 ATGCTCAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.25
Consensus pattern (43 bp):
TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAGAAAA
Found at i:34041669 original size:16 final size:16
Alignment explanation
Indices: 34041648--34041688 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
34041638 AATAACCTAT
34041648 ATTTAAAAGA-ATATA
1 ATTTAAAAGACATATA
34041663 CATTTAAAA-ACATATA
1 -ATTTAAAAGACATATA
*
34041679 ATTGAAAAGA
1 ATTTAAAAGA
34041689 TCTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (16 bp):
ATTTAAAAGACATATA
Found at i:34042255 original size:66 final size:65
Alignment explanation
Indices: 34042167--34042344 Score: 187
Period size: 66 Copynumber: 2.7 Consensus size: 65
34042157 CTAGTGAGCT
* * **
34042167 TACTGACTTGGGTCACATGGCCAAGCCACACGTCCATGTGCTAGGCTGTGTGAAAAAT-GATGGG
1 TACTGACTTGTGTCACA-GGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGGA-GGG
34042231 CA
64 CA
* ** * * *
34042233 TACTGACTTGTGACACACGGCCAAGCCACACACCCGTGAGCTAGGCCATGTGAAAACTGGAGGGT
1 TACTGACTTGTGTCACA-GGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGGAGGGC
34042298 A
65 A
* ** * *
34042299 TACTGACTTATGTCACAGGTTAAGTCACACGTCTGTGTGCTAGGCC
1 TACTGACTTGTGTCACAGGCCAAGCCACACGTCCGTGTGCTAGGCC
34042345 GTCTGAGACT
Statistics
Matches: 91, Mismatches: 20, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
65 22 0.24
66 67 0.74
67 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (65 bp):
TACTGACTTGTGTCACAGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGGAGGGCA
Found at i:34043667 original size:36 final size:35
Alignment explanation
Indices: 34043617--34043688 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
34043607 ACATTTAATA
34043617 CATATCTCGGAAGATCA-TCTTCCATATTTGCCAAG
1 CATATCTCGGAAGATCACT-TTCCATATTTGCCAAG
* *
34043652 CATATCTTTGGAAGATCACTTTCCTTATTTGCCAAG
1 CATATC-TCGGAAGATCACTTTCCATATTTGCCAAG
34043688 C
1 C
34043689 TCCAAAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 6 0.18
36 26 0.79
37 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (35 bp):
CATATCTCGGAAGATCACTTTCCATATTTGCCAAG
Found at i:34045201 original size:34 final size:34
Alignment explanation
Indices: 34045120--34045202 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 34
34045110 ATAATTTTGA
* *
34045120 GCCCAGCTCTAGTTGGATAAACCAACGGTAATTGC
1 GCCCAGCACTAGTCGGATAAACCAACGGT-ATTGC
* * * *
34045155 GCCCAACGCTAGTCGGATAAACCGACGGT-TGTGT
1 GCCCAGCACTAGTCGGATAAACCAACGGTAT-TGC
34045189 GCCCAGCACTAGTC
1 GCCCAGCACTAGTC
34045203 AAACAAGCTG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
33 1 0.03
34 14 0.35
35 25 0.62
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (34 bp):
GCCCAGCACTAGTCGGATAAACCAACGGTATTGC
Found at i:34046125 original size:14 final size:15
Alignment explanation
Indices: 34046093--34046125 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34046083 GAATGAACCC
34046093 TTTTCCCTTCTTCCT
1 TTTTCCCTTCTTCCT
*
34046108 TTTTCCTTTCTT-CT
1 TTTTCCCTTCTTCCT
34046122 TTTT
1 TTTT
34046126 GACAAGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCCCTTCTTCCT
Found at i:34046201 original size:3 final size:3
Alignment explanation
Indices: 34046193--34046240 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
34046183 ATGACTCACC
34046193 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34046240 T
1 T
34046241 CTTTAACTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:34048451 original size:31 final size:31
Alignment explanation
Indices: 34048416--34048478 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
34048406 AAAAAATCAA
34048416 CAATACATAACAAAACCAAAATTTGTATTTT
1 CAATACATAACAAAACCAAAATTTGTATTTT
*
34048447 CAATACATAACAAAACCTAAATTTGTATTTT
1 CAATACATAACAAAACCAAAATTTGTATTTT
34048478 C
1 C
34048479 CCTATATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.33
Consensus pattern (31 bp):
CAATACATAACAAAACCAAAATTTGTATTTT
Found at i:34048960 original size:41 final size:41
Alignment explanation
Indices: 34048898--34049035 Score: 204
Period size: 41 Copynumber: 3.4 Consensus size: 41
34048888 CCTTTCGGGG
*
34048898 CTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
34048939 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
* * * ** **
34048980 CTTTAGCGGCGATTCTAGAACAGCGCCGCTAATGCTTGGGG
1 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
34049021 CTTTAGCGGCGTTTT
1 CTTTAGCGGCGTTTT
34049036 CCAATAAGCG
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
Found at i:34049046 original size:41 final size:40
Alignment explanation
Indices: 34048892--34049090 Score: 191
Period size: 41 Copynumber: 4.8 Consensus size: 40
34048882 AGCCCACCTT
*
34048892 TCGGGGCTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCG-TTTTCGAAAAGCGCCGCTAATGC
* ** *
34048933 TCAGATCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCG-TTTTCGAAAAGCGCCGCTAATGC
* ** * * *
34048974 TCAGATCTTTAGCGGCGATTCTAGAACAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCG-TTTTCGAAAAGCGCCGCTAATGC
* * * *
34049015 TTGGGGCTTTAGCGGCGTTTTCCAATAAGCGCCTCTAATGG
1 TCGGGGCTTTAGCGGCGTTTTCGAA-AAGCGCCGCTAATGC
* * *
34049056 TCGGGGCTTTCGTGGCGTTTTTGAAAAAGCGCCGC
1 TCGGGGCTTTAGCGGCGTTTTCG-AAAAGCGCCGC
34049091 AAAAACATTT
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 5 0.04
41 126 0.95
42 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (40 bp):
TCGGGGCTTTAGCGGCGTTTTCGAAAAGCGCCGCTAATGC
Found at i:34049789 original size:22 final size:23
Alignment explanation
Indices: 34049764--34049814 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
34049754 TATTAAATAA
* *
34049764 GGTTTAGGG-GTTAGTGGTTTGG
1 GGTTTAGGGAGTTAGTGATTTAG
*
34049786 GGTTT-GGGAGTTGGTGATTTAG
1 GGTTTAGGGAGTTAGTGATTTAG
34049808 GGTTTAG
1 GGTTTAG
34049815 AGATTCGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 20 0.83
23 1 0.04
ACGTcount: A:0.12, C:0.00, G:0.47, T:0.41
Consensus pattern (23 bp):
GGTTTAGGGAGTTAGTGATTTAG
Found at i:34050877 original size:40 final size:40
Alignment explanation
Indices: 34050833--34050908 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
34050823 TTTTTTACGG
34050833 CAAAAGATAAGCAAAAACGGCATTTTTATAAAAAACATCA
1 CAAAAGATAAGCAAAAACGGCATTTTTATAAAAAACATCA
* *
34050873 CAAAAGATAAGCAAAAGCGGCGTTTTTATAAAAAAC
1 CAAAAGATAAGCAAAAACGGCATTTTTATAAAAAAC
34050909 GCCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.13, T:0.20
Consensus pattern (40 bp):
CAAAAGATAAGCAAAAACGGCATTTTTATAAAAAACATCA
Found at i:34055526 original size:43 final size:43
Alignment explanation
Indices: 34055474--34055783 Score: 404
Period size: 43 Copynumber: 7.2 Consensus size: 43
34055464 AGATTATGTT
* *
34055474 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * * *
34055517 TATGGCGGCGTTTGAGGGAAAAGTGTCACTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
** * * *
34055560 AATAGCAGCGTTTGTTGGAAAAGCGCCGCTAATGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * * *
34055603 TTTAGCGGCGTTTTTGGAAAAAGTGCTGCTAAATGTCATGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
34055646 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATAGTA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
34055689 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
34055732 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
34055775 TTTAGCGGC
1 TTTAGCGGC
34055784 ATTTTTTGTG
Statistics
Matches: 225, Mismatches: 42, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 225 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:34055831 original size:22 final size:22
Alignment explanation
Indices: 34055803--34055865 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
34055793 GGCGTTTCTC
34055803 AAAGCGCCGCTAAAGGCCTAAA
1 AAAGCGCCGCTAAAGGCCTAAA
34055825 AAAGCGCCGCTAAAGGCCTAAA
1 AAAGCGCCGCTAAAGGCCTAAA
* *
34055847 AAAGCACCGCTAAAAGCCT
1 AAAGCGCCGCTAAAGGCCT
34055866 GTTTTGGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.41, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAGCGCCGCTAAAGGCCTAAA
Found at i:34057793 original size:202 final size:202
Alignment explanation
Indices: 34057441--34057849 Score: 696
Period size: 202 Copynumber: 2.0 Consensus size: 202
34057431 AAATTTTATC
** * *
34057441 AAAATAATTTATGATTCGTGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTACTTA
1 AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
* *
34057506 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTCAATTGTGAAATATCTATTTGGTTGGAA
66 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCTATTTGGTTGGAA
*
34057571 TATTTATTTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
131 TATTTAATTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
34057636 ATGATGA
196 ATGATGA
*
34057643 AAAATAAAGTATGATTCATGAATGGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
1 AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
*
34057708 AATTAGATAATTATGAAAAGCTTAATGATTAAGGGCTAAATTGTGAAAAATCTAATTT-GTTGGA
66 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCT-ATTTGGTTGGA
*
34057772 ATATTTAATTATT-TGTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTATAGAA
130 ATATTTAATTATTAT-TTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAA
34057836 AGATGATGA
194 AGATGATGA
34057845 AAAAT
1 AAAAT
34057850 CATCCATGTC
Statistics
Matches: 195, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
201 1 0.01
202 190 0.97
203 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39
Consensus pattern (202 bp):
AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCTATTTGGTTGGAA
TATTTAATTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
ATGATGA
Found at i:34060004 original size:29 final size:30
Alignment explanation
Indices: 34059960--34060016 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
34059950 TCAAGTCGTG
34059960 CGTTGTTTGCAAGATACATT-AATGCCCTA
1 CGTTGTTTGCAAGATACATTAAATGCCCTA
*
34059989 CGTTGTTTGCAGGATACATTAAATGCCC
1 CGTTGTTTGCAAGATACATTAAATGCCC
34060017 CTATAAGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (30 bp):
CGTTGTTTGCAAGATACATTAAATGCCCTA
Found at i:34066676 original size:2 final size:2
Alignment explanation
Indices: 34066669--34066699 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34066659 GTCTGCTATT
*
34066669 TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34066700 TGAAGCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:34069195 original size:9 final size:9
Alignment explanation
Indices: 34069181--34069256 Score: 109
Period size: 9 Copynumber: 8.4 Consensus size: 9
34069171 AAGTAATTTC
34069181 AATTCGGTT
1 AATTCGGTT
*
34069190 AATTCGGGT
1 AATTCGGTT
34069199 AATTCGGTT
1 AATTCGGTT
34069208 AATTCGGTT
1 AATTCGGTT
*
34069217 AATTTAGG-T
1 AA-TTCGGTT
34069226 AATTCGGTT
1 AATTCGGTT
34069235 AATTCGGTT
1 AATTCGGTT
*
34069244 AATTCGGGT
1 AATTCGGTT
34069253 AATT
1 AATT
34069257 TTTAACCAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 4 0.07
9 52 0.87
10 4 0.07
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:34069213 original size:27 final size:27
Alignment explanation
Indices: 34069181--34069256 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
34069171 AAGTAATTTC
34069181 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTT
**
34069208 AATTCGGTTAATTTAGGTAATTCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTT
34069235 AATTCGGTTAATTCGGGTAATT
1 AATTCGGTTAATTCGGGTAATT
34069257 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTCGGTT
Found at i:34084671 original size:8 final size:9
Alignment explanation
Indices: 34084638--34084677 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
34084628 TGAGCTCCAC
*
34084638 TTTTGTTTA
1 TTTTATTTA
34084647 TTTTATTTTA
1 TTTTA-TTTA
34084657 TTTTATTTA
1 TTTTATTTA
34084666 -TTTATTTA
1 TTTTATTTA
34084674 TTTT
1 TTTT
34084678 CGGTTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.29
9 11 0.39
10 9 0.32
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTTATTTA
Found at i:34093859 original size:19 final size:19
Alignment explanation
Indices: 34093812--34093862 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
34093802 GTAATATATA
34093812 TAATTGATAT-TTTATGAT
1 TAATTGATATATTTATGAT
34093830 TGAATTG-TATATTTATG-T
1 T-AATTGATATATTTATGAT
34093848 TAATTGAATATATTT
1 TAATTG-ATATATTT
34093863 TGAATTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTGATATATTTATGAT
Found at i:34095943 original size:25 final size:23
Alignment explanation
Indices: 34095899--34095944 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
34095889 ATGTTAATTG
34095899 ATTTAATTTTAAATAAAATAATA
1 ATTTAATTTTAAATAAAATAATA
* *
34095922 ATTTACATATTTAGATAGAATAA
1 ATTTA-AT-TTTAAATAAAATAA
34095945 ATATGTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 2 0.11
25 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTTAATTTTAAATAAAATAATA
Found at i:34100867 original size:26 final size:25
Alignment explanation
Indices: 34100838--34100894 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
34100828 CTTGTTATCT
34100838 TTTTTTCAAATTTCAG-CTTCTCATAC
1 TTTTTTCAAATTTCAGCCTT-TC-TAC
** *
34100864 TTTTCCCAAATTTCGGCCTTTCTAC
1 TTTTTTCAAATTTCAGCCTTTCTAC
34100889 TTTTTT
1 TTTTTT
34100895 TTGACATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 7 0.28
26 15 0.60
27 3 0.12
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.53
Consensus pattern (25 bp):
TTTTTTCAAATTTCAGCCTTTCTAC
Found at i:34104615 original size:7 final size:7
Alignment explanation
Indices: 34104603--34104628 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34104593 AAAATCCCCC
34104603 AAGCCCT
1 AAGCCCT
34104610 AAGCCCT
1 AAGCCCT
34104617 AAGCCCT
1 AAGCCCT
34104624 AAGCC
1 AAGCC
34104629 TCAACCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.42, G:0.15, T:0.12
Consensus pattern (7 bp):
AAGCCCT
Found at i:34105339 original size:24 final size:24
Alignment explanation
Indices: 34105307--34105358 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
34105297 GAATTTCATA
*
34105307 TTTTACTATTGCTTTTGGA-TTGCT
1 TTTTACTATTGATTTTGGACTT-CT
*
34105331 TTTTTCTATTGATTTTGGACTTCT
1 TTTTACTATTGATTTTGGACTTCT
34105355 TTTT
1 TTTT
34105359 CTTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.12, C:0.12, G:0.13, T:0.63
Consensus pattern (24 bp):
TTTTACTATTGATTTTGGACTTCT
Found at i:34107261 original size:6 final size:6
Alignment explanation
Indices: 34107224--34107269 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
34107214 AGTACCTGAT
* * *
34107224 CAGTAA TCAGTAA CGGTAG CAGTAA CAATAA CAGTAA CAGTAA CAG
1 CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAG
34107270 AATTCAACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:34107327 original size:45 final size:45
Alignment explanation
Indices: 34107256--34107355 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
34107246 TAACAATAAC
* *
34107256 AGTAACAGTAACAGAATTCAACACACAAAGTG-CTGAATCTGTCAT
1 AGTAACAGTAACAGAATTCAACACACAAAGTGTC-GAATCGGTAAT
* * * *
34107301 AGTAACGGTAACAGTATTCGATACACAAAGTGTCGAATCGGTAAT
1 AGTAACAGTAACAGAATTCAACACACAAAGTGTCGAATCGGTAAT
34107346 AGTAACAGTA
1 AGTAACAGTA
34107356 GTCAGCATCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 46 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAACAGTAACAGAATTCAACACACAAAGTGTCGAATCGGTAAT
Found at i:34107635 original size:40 final size:40
Alignment explanation
Indices: 34107555--34107638 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
34107545 AATTCATTAC
* * *
34107555 TTCAGTAATTTCACAGTTCAATGCAATACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
* * * *
34107595 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAGAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
34107635 TTCA
1 TTCA
34107639 ATATTCCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:34108442 original size:5 final size:5
Alignment explanation
Indices: 34108432--34108468 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
34108422 TTACCTATTT
*
34108432 ATATA ATATA ATATA GTATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
34108469 CTTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:34108921 original size:16 final size:17
Alignment explanation
Indices: 34108890--34108921 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34108880 CCAGTTCCCA
34108890 TATGGCTTCTTCCACAC
1 TATGGCTTCTTCCACAC
34108907 TATGGCTTC-TCCACA
1 TATGGCTTCTTCCACA
34108922 GTACTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.34
Consensus pattern (17 bp):
TATGGCTTCTTCCACAC
Found at i:34110188 original size:34 final size:34
Alignment explanation
Indices: 34110150--34110220 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
34110140 GATTTCAAAA
34110150 TCTCAAACAATCATGATCATCAACACTAAAATTT
1 TCTCAAACAATCATGATCATCAACACTAAAATTT
34110184 TCTCAAACAATCATGATCATCAACACTAAAATTT
1 TCTCAAACAATCATGATCATCAACACTAAAATTT
34110218 TCT
1 TCT
34110221 ACTGGGCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (34 bp):
TCTCAAACAATCATGATCATCAACACTAAAATTT
Found at i:34114525 original size:45 final size:45
Alignment explanation
Indices: 34114456--34114555 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
34114446 TAACGGTAGT
* *
34114456 AGTAACAGTAACAGTATTCAACACAAAAAGTGTTGAATCTATAAC
1 AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
* * *
34114501 AGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCAATAAC
1 AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
34114546 AGTAACAGTA
1 AGTAACAGTA
34114556 GTTGGCATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
Found at i:34114824 original size:40 final size:40
Alignment explanation
Indices: 34114756--34114842 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
34114746 AATTCATTAC
* * * *
34114756 TTCAGTAATTTCACAGTTCAATGCAATACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGAAATACACAAAACAATA
* * **
34114796 TTCAGTAACTTCACAATTTAATTAAATACTGAAAACAATA
1 TTCAGTAACTTCACAATTCAATGAAATACACAAAACAATA
34114836 TTCAGTA
1 TTCAGTA
34114843 TTCCATAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGAAATACACAAAACAATA
Found at i:34115639 original size:5 final size:5
Alignment explanation
Indices: 34115629--34115759 Score: 253
Period size: 5 Copynumber: 26.2 Consensus size: 5
34115619 TTTCTTTACC
34115629 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
34115679 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*
34115729 TATAA TATAA TATAA TATAA TACAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
34115760 CTTATTTATT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 124 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:34117141 original size:33 final size:34
Alignment explanation
Indices: 34117104--34117167 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
34117094 TTTTTTGGCT
34117104 TCTATTTC-ATTAGTAGCAAATAAT-TCTTTGGTC
1 TCTATTTCTA-TAGTAGCAAATAATATCTTTGGTC
* *
34117137 TCTATTTCTATAGTATCATATAATATCTTTG
1 TCTATTTCTATAGTAGCAAATAATATCTTTG
34117168 ATAATGAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (34 bp):
TCTATTTCTATAGTAGCAAATAATATCTTTGGTC
Found at i:34118558 original size:20 final size:20
Alignment explanation
Indices: 34118535--34118589 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
34118525 GTGACAAGGC
*
34118535 ACACGCCCGTGTGACTGAGG
1 ACACGCCCATGTGACTGAGG
**
34118555 ACACTTCCATGTGACTGAAGG
1 ACACGCCCATGTGACTG-AGG
* *
34118576 TCACACCCATGTGA
1 ACACGCCCATGTGA
34118590 GTAGGCCGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (20 bp):
ACACGCCCATGTGACTGAGG
Found at i:34118587 original size:21 final size:20
Alignment explanation
Indices: 34118544--34118589 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
34118534 CACACGCCCG
**
34118544 TGTGACTGAGGACACTTCCA
1 TGTGACTGAGGACACACCCA
*
34118564 TGTGACTGAAGGTCACACCCA
1 TGTGACTG-AGGACACACCCA
34118585 TGTGA
1 TGTGA
34118590 GTAGGCCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (20 bp):
TGTGACTGAGGACACACCCA
Found at i:34119482 original size:15 final size:16
Alignment explanation
Indices: 34119462--34119491 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34119452 GAAATTTCCT
34119462 ACTAACTCG-ACAATC
1 ACTAACTCGCACAATC
34119477 ACTAACTCGCACAAT
1 ACTAACTCGCACAAT
34119492 TTGCTACCAC
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:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (16 bp):
ACTAACTCGCACAATC
Found at i:34125590 original size:12 final size:11
Alignment explanation
Indices: 34125550--34125582 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
34125540 TTTGTAAAGT
34125550 TTTA-TTTTTA
1 TTTATTTTTTA
34125560 TTTATTTATTTA
1 TTTATTT-TTTA
34125572 TTTATTTTTTA
1 TTTATTTTTTA
34125583 CTTAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:34134787 original size:24 final size:24
Alignment explanation
Indices: 34134758--34134803 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
34134748 TGAACGGAAT
34134758 TTCGGTAAGTACATATGTGTTGAA
1 TTCGGTAAGTACATATGTGTTGAA
*
34134782 TTCGGTAAGTACATATTTGTTG
1 TTCGGTAAGTACATATGTGTTG
34134804 TGGCACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (24 bp):
TTCGGTAAGTACATATGTGTTGAA
Found at i:34137730 original size:41 final size:41
Alignment explanation
Indices: 34137521--34137715 Score: 250
Period size: 41 Copynumber: 4.8 Consensus size: 41
34137511 AGAATATCCT
*
34137521 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * *
34137562 TGAATTGCATATATGTGCCTCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* *
34137603 TGAATTGCACATACGTG-CCCTTTTTCTTACTTTGGTA-CCC
1 TGAATTGCACATACGTGCCCCTGTTT-GTACTTTGGTACCCC
** *
34137643 TCGAATTGCACATATATGCCCCTATTTGTACTTTGGTACCCC
1 T-GAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* *
34137685 TGAATTGCACATACGTGCCACTTTTTGTACT
1 TGAATTGCACATACGTGCCCCTGTTTGTACT
34137716 ACAGTACCCT
Statistics
Matches: 131, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
40 10 0.08
41 110 0.84
42 11 0.08
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.37
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
Found at i:34143715 original size:31 final size:31
Alignment explanation
Indices: 34143666--34144179 Score: 664
Period size: 31 Copynumber: 16.7 Consensus size: 31
34143656 GTATATGTTT
* * *
34143666 TATACATTGTC-AAATTGATTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
34143696 TATACATTGCAGAATTTGATTTGTTTATAGG
1 TATACATTGCCGAATTTGATTTGTATATAGA
** * * *
34143727 TATACATTGCTAAAATTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
34143758 TATACATTGTC-AAATTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34143788 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34143819 TATACATTGCCGAATTTAATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
34143850 TATATATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
34143880 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34143911 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
34143942 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34143973 TATATATTCCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
34144003 TATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34144033 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34144064 TATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34144095 TATTCATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
34144125 TATACATTGCCGAATTTGATTCGTATATGAATA
1 TATACATTGCCGAATTTGATTTGTATAT--AGA
*
34144158 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
34144180 AGCATTGAAT
Statistics
Matches: 429, Mismatches: 47, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
29 2 0.00
30 143 0.33
31 262 0.61
32 7 0.02
33 15 0.03
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:34143735 original size:61 final size:61
Alignment explanation
Indices: 34143666--34144179 Score: 606
Period size: 61 Copynumber: 8.4 Consensus size: 61
34143656 GTATATGTTT
* * * *
34143666 TATACATTGTCAAATTGATTTGTATAAAGATATACATTGCAGAATTTGATTTGTTTATAGG
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCAGAATTTGATTTGTATATAGA
* * * *
34143727 TATACATTGCTAAAATTGAATTGTTTATAGATATACATTGTCA-AA-TTGATTTGTTTATAGA
1 TATACATTGC-CAAATTGATTTGTATATAGATATACATTG-CAGAATTTGATTTGTATATAGA
* * * * * *
34143788 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTAATTTGTATATGGA
1 TATACATTGCC-AAATTGATTTGTATATAGATATACATTGCAGAATTTGATTTGTATATAGA
* * *
34143850 TATATATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCAGAATTTGATTTGTATATAGA
* * * *
34143911 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCC-AAATTGATTTGTATATAGATATACATTGCAGAATTTGATTTGTATATAGA
* * *
34143973 TATATATTCCCGAATTGATTTGTATATAGATATACATTGCCA-AA-TTGATTTGTATATAGA
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTG-CAGAATTTGATTTGTATATAGA
* * * *
34144033 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCA-AATTTGATTTGTATATGGA
1 TATACATTGCC-AAATTGATTTGTATATAGATATACATTG-CAGAATTTGATTTGTATATAGA
* * * *
34144095 TATTCATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTCGTATATGAATA
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCAGAATTTGATTTGTATAT--AGA
* *
34144158 TATATATTGCCGAATTGATTTG
1 TATACATTGCCAAATTGATTTG
34144180 AGCATTGAAT
Statistics
Matches: 388, Mismatches: 53, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
60 27 0.07
61 208 0.54
62 131 0.34
63 22 0.06
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (61 bp):
TATACATTGCCAAATTGATTTGTATATAGATATACATTGCAGAATTTGATTTGTATATAGA
Found at i:34143823 original size:92 final size:92
Alignment explanation
Indices: 34143666--34144179 Score: 653
Period size: 92 Copynumber: 5.6 Consensus size: 92
34143656 GTATATGTTT
* * * *
34143666 TATACATTGTC-AAATTGATTTGTATAAAGATATACATTGCAGAATTTGATTTGTTTATAGG-TA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATAT-GGATA
* * *
34143729 TACATTGCTAAAATTGAATTGTTTATAGA
65 TACATTGC-CAAATTGATTTGTATATAGA
* * *
34143758 TATACATTGTC-AAATTGATTTGTTTATAGATATACATTGCCGAATTTGATTTGTATATGGTTAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATAT
* * *
34143822 ACATTGCCGAATTTAATTTGTATATGGA
66 ACATTGCC-AAATTGATTTGTATATAGA
* *
34143850 TATATATTGCCG-AATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATAT
* * *
34143914 ACATTGCCGAATTTGATTTGTATATGGT
66 ACATTGCC-AAATTGATTTGTATATAGA
* * * *
34143942 TATACATTGCCGAATTTGATTTGTATATAGATATATATTCCCGAA-TTGATTTGTATATAGATAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATAT
34144006 ACATTGCCAAATTGATTTGTATATAGA
66 ACATTGCCAAATTGATTTGTATATAGA
* * * *
34144033 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCAAATTTGATTTGTATATGGATAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATAT
*
34144098 TCATTGCCAAATTGATTTGTATATAGA
66 ACATTGCCAAATTGATTTGTATATAGA
* * * *
34144125 TATACATTGCCGAATTTGATTCGTATATGAATATATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAAATTGATTTGTATAT--AGATATACATTGCCGAATTTGATTTG
34144180 AGCATTGAAT
Statistics
Matches: 378, Mismatches: 37, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
91 58 0.15
92 271 0.72
93 37 0.10
94 12 0.03
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (92 bp):
TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATAT
ACATTGCCAAATTGATTTGTATATAGA
Found at i:34144369 original size:42 final size:42
Alignment explanation
Indices: 34144310--34144417 Score: 198
Period size: 42 Copynumber: 2.6 Consensus size: 42
34144300 TTCATATAAG
34144310 ACCATGTTTGGGACGTTGGCATCGAAGTGAGAAAACGTGTAA
1 ACCATGTTTGGGACGTTGGCATCGAAGTGAGAAAACGTGTAA
*
34144352 ACCATGTTTGGGACGTTGGCATCGAAGTGAGAAAATGTGTAA
1 ACCATGTTTGGGACGTTGGCATCGAAGTGAGAAAACGTGTAA
*
34144394 ACCATGTTTGGGACATTGGCATCG
1 ACCATGTTTGGGACGTTGGCATCG
34144418 TATATGATTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.26
Consensus pattern (42 bp):
ACCATGTTTGGGACGTTGGCATCGAAGTGAGAAAACGTGTAA
Found at i:34145963 original size:30 final size:31
Alignment explanation
Indices: 34145927--34146012 Score: 113
Period size: 30 Copynumber: 2.8 Consensus size: 31
34145917 ATAGTACGAG
**
34145927 GTATGAATATGTTAATATGAATG-TTACAAT
1 GTATGAATATGAAAATATGAATGATTACAAT
*
34145957 GTATGAATATGAAAATATGAATGATTAC-AG
1 GTATGAATATGAAAATATGAATGATTACAAT
* *
34145987 GTAAGAAAATGAAAATATGAATGATT
1 GTATGAATATGAAAATATGAATGATT
34146013 TATGCCCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (31 bp):
GTATGAATATGAAAATATGAATGATTACAAT
Found at i:34152622 original size:4 final size:4
Alignment explanation
Indices: 34152613--34152638 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
34152603 CACCAATAAC
34152613 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
34152639 AAAAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:34157922 original size:21 final size:22
Alignment explanation
Indices: 34157879--34157925 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
34157869 AAATTTAGTA
*
34157879 TATTTTAAATTTATTACCATAT
1 TATTTTAAATTTATTAACATAT
34157901 TATTTT-AATATTA-TAACATAT
1 TATTTTAAAT-TTATTAACATAT
34157922 TATT
1 TATT
34157926 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATTAACATAT
Found at i:34158147 original size:2 final size:2
Alignment explanation
Indices: 34158140--34158173 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
34158130 TTAAATTATT
*
34158140 TA TA TA TA TA TA TA TA TA TA TA TA CA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34158174 TATCGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34163103 original size:33 final size:33
Alignment explanation
Indices: 34163058--34163120 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
34163048 NNNNNNNNNN
34163058 CCAACAAGTAATTTTAGGTCAATTATACATACA
1 CCAACAAGTAATTTTAGGTCAATTATACATACA
*
34163091 CCAACAATTAATTTTAGGTCAATTATACAT
1 CCAACAAGTAATTTTAGGTCAATTATACAT
34163121 GCTTTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (33 bp):
CCAACAAGTAATTTTAGGTCAATTATACATACA
Found at i:34166408 original size:16 final size:16
Alignment explanation
Indices: 34166387--34166438 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
34166377 GATTTGCTAT
34166387 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34166403 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34166419 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34166435 TACA
1 TACA
34166439 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:34166976 original size:15 final size:16
Alignment explanation
Indices: 34166949--34166979 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34166939 ATTTTATTTT
34166949 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
34166965 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
34166980 TTATATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:34167040 original size:15 final size:15
Alignment explanation
Indices: 34167016--34167048 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34167006 ATTTGATATT
*
34167016 AATATTTTAATAATA
1 AATATATTAATAATA
34167031 AATATATTAATAATA
1 AATATATTAATAATA
34167046 AAT
1 AAT
34167049 GTTCTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:34189234 original size:30 final size:30
Alignment explanation
Indices: 34189198--34189265 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
34189188 CATTGCAGGG
*
34189198 TCACACGGCCATGTGGTCAGGTCATGTGAC
1 TCACACGGCCATGTGGTCAGGCCATGTGAC
34189228 TCACACGGCCATGTGGTCAGGCCATGTGAC
1 TCACACGGCCATGTGGTCAGGCCATGTGAC
34189258 TCACACGG
1 TCACACGG
34189266 TTTGGAGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (30 bp):
TCACACGGCCATGTGGTCAGGCCATGTGAC
Found at i:34189252 original size:13 final size:13
Alignment explanation
Indices: 34189204--34189255 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
34189194 AGGGTCACAC
34189204 GGCCATGTGGTCA
1 GGCCATGTGGTCA
* *
34189217 GGTCATGTGACTCACA
1 GGCCATGTG-GT--CA
34189233 CGGCCATGTGGTCA
1 -GGCCATGTGGTCA
34189247 GGCCATGTG
1 GGCCATGTG
34189256 ACTCACACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 17 0.55
14 3 0.10
16 3 0.10
17 8 0.26
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (13 bp):
GGCCATGTGGTCA
Found at i:34190595 original size:41 final size:41
Alignment explanation
Indices: 34190534--34190654 Score: 161
Period size: 41 Copynumber: 2.9 Consensus size: 41
34190524 AACCCATAAG
* * *
34190534 GGCTGAACGGAAACTCATAAGGGTTAAACTGAAGCTTAAAA
1 GGCTGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAA
* *
34190575 GGCTAAACAGAAACCCATAAGGATTAAACTGAAGCTCAAAA
1 GGCTGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAA
* * *
34190616 GAGCTGAACAAAAACCCATAAAGGTTAAACTGAAACTCA
1 G-GCTGAACAGAAACCCATAAGGGTTAAACTGAAGCTCA
34190655 TATGAGTTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
41 37 0.54
42 32 0.46
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (41 bp):
GGCTGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAA
Found at i:34190651 original size:21 final size:21
Alignment explanation
Indices: 34190514--34190656 Score: 76
Period size: 21 Copynumber: 6.9 Consensus size: 21
34190504 GCACATAAGT
** * *
34190514 GCTAAACAAAAACCCATAAGG
1 GCTAAACTGAAACTCATAAAG
* * *
34190535 GCTGAACGGAAACTCATAAGG
1 GCTAAACTGAAACTCATAAAG
* * *
34190556 GTTAAACTGAAGCTTA-AAAG
1 GCTAAACTGAAACTCATAAAG
* *
34190576 GCTAAACAGAAACCCAT-AAG
1 GCTAAACTGAAACTCATAAAG
* *
34190596 GATTAAACTGAAGCTCA-AAAG
1 G-CTAAACTGAAACTCATAAAG
* ** *
34190617 AGCTGAACAAAAACCCATAAAG
1 -GCTAAACTGAAACTCATAAAG
*
34190639 GTTAAACTGAAACTCATA
1 GCTAAACTGAAACTCATA
34190657 TGAGTTAATA
Statistics
Matches: 87, Mismatches: 30, Indels: 10
0.69 0.24 0.08
Matches are distributed among these distances:
20 18 0.21
21 64 0.74
22 5 0.06
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (21 bp):
GCTAAACTGAAACTCATAAAG
Found at i:34192548 original size:12 final size:12
Alignment explanation
Indices: 34192528--34192567 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
34192518 TTTTCATCTA
*
34192528 TCTTCTTTATTT
1 TCTTTTTTATTT
34192540 TCTTTTTTATTT
1 TCTTTTTTATTT
*
34192552 TCTTTTCTATTAT
1 TCTTTTTTATT-T
34192565 TCT
1 TCT
34192568 AGTATTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTTTTATTT
Found at i:34192587 original size:20 final size:17
Alignment explanation
Indices: 34192570--34192613 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
34192560 ATTATTCTAG
*
34192570 TATTTGATTTATTGTTC
1 TATTTGATTTATTATTC
*
34192587 TATTTGATTTATTTATTT
1 TATTTGATTTA-TTATTC
34192605 TATTT-ATTT
1 TATTTGATTT
34192614 TAATTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.70
Consensus pattern (17 bp):
TATTTGATTTATTATTC
Found at i:34193035 original size:17 final size:18
Alignment explanation
Indices: 34192998--34193036 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
34192988 TAAATCTAAA
34192998 TAAAACTATTAAGTATAC
1 TAAAACTATTAAGTATAC
* *
34193016 TAAAACT-TTAATTATCC
1 TAAAACTATTAAGTATAC
34193033 TAAA
1 TAAA
34193037 CAAAAAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAACTATTAAGTATAC
Found at i:34194612 original size:24 final size:26
Alignment explanation
Indices: 34194585--34194632 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34194575 TTTTCTTTAG
34194585 TTATAATC-TT-ATTATTTTTATTGA
1 TTATAATCTTTAATTATTTTTATTGA
* *
34194609 TTATATTCTTTAATTTTTTTTATT
1 TTATAATCTTTAATTATTTTTATT
34194633 TCTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 2 0.10
26 11 0.55
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATAATCTTTAATTATTTTTATTGA
Found at i:34194694 original size:23 final size:23
Alignment explanation
Indices: 34194618--34194694 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
34194608 ATTATATTCT
* * *
34194618 TTAATTTTTTTTATTTCTTATAAA
1 TTAA-TTTTTTAATTTTTTAAAAA
* *
34194642 TT-ATATTTTAATTTTTTTATAATA
1 TTAATTTTTTAA-TTTTTTA-AAAA
*
34194666 TAAATTTTTTAATTTTTTAAAAA
1 TTAATTTTTTAATTTTTTAAAAA
34194689 TTAATT
1 TTAATT
34194695 AATTATTGAC
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
22 6 0.15
23 15 0.37
24 12 0.29
25 8 0.20
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (23 bp):
TTAATTTTTTAATTTTTTAAAAA
Found at i:34206436 original size:2 final size:2
Alignment explanation
Indices: 34206431--34206479 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
34206421 TAAATATGCG
*
34206431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
34206472 CA TA TA TA
1 TA TA TA TA
34206480 CATAGATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:34214106 original size:50 final size:50
Alignment explanation
Indices: 34213990--34214182 Score: 287
Period size: 50 Copynumber: 3.8 Consensus size: 50
34213980 AATAATAACA
* ** * *
34213990 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
34214041 TTCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34214091 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
34214141 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34214183 TTACCCAAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 94 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34214178 original size:100 final size:101
Alignment explanation
Indices: 34213990--34214182 Score: 316
Period size: 100 Copynumber: 1.9 Consensus size: 101
34213980 AATAATAACA
* * * *
34213990 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCAGTTCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTTCTCATCTCAGTGCCAATGCCATGT
34214055 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
34214091 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CTTCTCATCTCGGTGCCAATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTTCTCATCTCAGTGCCAATGCCATGT
*
34214155 CCCAGACATGGTCTTACATGGGACCTCT
66 CCCAGACATGGTCTTACAGGGGACCTCT
34214183 TTACCCAAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 49 0.58
101 36 0.42
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTTCTCATCTCAGTGCCAATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:34214555 original size:30 final size:29
Alignment explanation
Indices: 34214520--34214576 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
34214510 CCTAGACTCT
34214520 AACTTTGT-CAAAATTACAATTTTGCCCCTA
1 AACTTT-TACAAAATTAC-ATTTTGCCCCTA
* *
34214550 AACTTTTACATAATTACATTTTTCCCC
1 AACTTTTACAAAATTACATTTTGCCCC
34214577 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTGCCCCTA
Found at i:34220116 original size:2 final size:2
Alignment explanation
Indices: 34220109--34220148 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
34220099 CAGCAGTAGA
34220109 AT AT AT AT AT 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 AT AT AT AT AT
34220149 GTACATAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34225838 original size:17 final size:18
Alignment explanation
Indices: 34225798--34225839 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
34225788 GATCTAAATT
* *
34225798 AATAATTTCATTCAATAT
1 AATAATTTCATACAATAA
*
34225816 ATTAATTT-ATACAATAA
1 AATAATTTCATACAATAA
34225833 AATAATT
1 AATAATT
34225840 CATTTCATGC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATTTCATACAATAA
Found at i:34243391 original size:39 final size:39
Alignment explanation
Indices: 34243351--34243527 Score: 237
Period size: 39 Copynumber: 4.5 Consensus size: 39
34243341 ATTCACTTTT
* * *
34243351 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
34243390 AAGCATATATCACAATACTCATATAATTACATAACGTTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * *
34243429 AAGCATATGTCGCAATACTCATATGATTACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
34243468 AAGCATATATCGCAATACTTATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
34243507 AAACATATGTCACAATACTCA
1 AAGCATATATCACAATACTCA
34243528 AAAACATGTT
Statistics
Matches: 121, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 121 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:34255860 original size:2 final size:2
Alignment explanation
Indices: 34255853--34255892 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
34255843 TGGTTACACC
34255853 AT AT AT AT AT 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 AT AT AT AT AT
34255893 TCTTTCTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34265691 original size:10 final size:10
Alignment explanation
Indices: 34265675--34265722 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
34265665 ATAGATATCT
34265675 TAAAAAATTA
1 TAAAAAATTA
*
34265685 TAGAAAATTA
1 TAAAAAATTA
* *
34265695 TTAAAAATCA
1 TAAAAAATTA
*
34265705 TAAAAAAGTA
1 TAAAAAATTA
34265715 TAAAAAAT
1 TAAAAAAT
34265723 AGTAAAATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:34265728 original size:20 final size:19
Alignment explanation
Indices: 34265675--34265729 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
34265665 ATAGATATCT
* *
34265675 TAAAAAATTATAGAAAATTA
1 TAAAAAA-TATAAAAAAGTA
*
34265695 TTAAAAATCATAAAAAAGTA
1 TAAAAAAT-ATAAAAAAGTA
34265715 TAAAAAATAGTAAAA
1 TAAAAAATA-TAAAA
34265730 TTGTTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAAATATAAAAAAGTA
Found at i:34273046 original size:60 final size:60
Alignment explanation
Indices: 34272884--34273070 Score: 241
Period size: 60 Copynumber: 3.1 Consensus size: 60
34272874 GTGTCTCTTC
* * * ** *
34272884 TTACACTTCGGTGCCTCTTCTTACACTTCGGTGTCTCTG-TTAAAACTTTGATGCCTTTAT
1 TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATT-TCACTTTGGTGCCTTTAT
* * * *
34272944 TTGCACTTCAGTGCATTTGCTTACACTTTGGTGTCTTTGATTTCACTTTGGTGCCTTTAT
1 TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
* *
34273004 TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTAT
1 TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
*
34273064 TTGCACT
1 TTACACT
34273071 AAGGTGCCTC
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 107 0.98
61 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (60 bp):
TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
Found at i:34273070 original size:20 final size:20
Alignment explanation
Indices: 34272861--34273080 Score: 124
Period size: 20 Copynumber: 11.0 Consensus size: 20
34272851 TACGATAGAT
* *
34272861 TATTTGCACTTCGGTGTCTC
1 TATTTACACTTCGGTGCCTC
34272881 T-TCTTACACTTCGGTGCCTC
1 TAT-TTACACTTCGGTGCCTC
*
34272901 T-TCTTACACTTCGGTGTCTC
1 TAT-TTACACTTCGGTGCCTC
* * * * * *
34272921 TGTTAAAACTTTGATGCCTT
1 TATTTACACTTCGGTGCCTC
* * * *
34272941 TATTTGCACTTCAGTGCATT
1 TATTTACACTTCGGTGCCTC
** * * *
34272961 TGCTTACACTTTGGTGTCTT
1 TATTTACACTTCGGTGCCTC
* *
34272981 TGATTT-CACTTTGGTGCCTT
1 T-ATTTACACTTCGGTGCCTC
*
34273001 TATTTACACTTCGGTGCATC
1 TATTTACACTTCGGTGCCTC
** * *
34273021 TGCTTACACTTTGGTGTCTC
1 TATTTACACTTCGGTGCCTC
34273041 TGATTT-CACTTCGGTGCCTC
1 T-ATTTACACTTCGGTGCCTC
* **
34273061 TATTTGCACTAAGGTGCCTC
1 TATTTACACTTCGGTGCCTC
34273081 CGTATAGCAT
Statistics
Matches: 153, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
19 9 0.06
20 139 0.91
21 5 0.03
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (20 bp):
TATTTACACTTCGGTGCCTC
Found at i:34273077 original size:60 final size:60
Alignment explanation
Indices: 34272862--34273077 Score: 213
Period size: 60 Copynumber: 3.6 Consensus size: 60
34272852 ACGATAGATT
* * * * *
34272862 ATTTGCACTTCGGTGTCTCT-TCTTACACTTCGGTGCCTCTTCTTACACTTCGGTGTCTCTG
1 ATTT-CACTTCGGTGCCTCTAT-TTACACTTAGGTGCATCTGCTTACACTTTGGTGTCTCTG
** * * * * * *
34272923 -TTAAAACTTTGATGCCTTTATTTGCACTTCA-GTGCATTTGCTTACACTTTGGTGTCTTTG
1 ATT-TCACTTCGGTGCCTCTATTTACACTT-AGGTGCATCTGCTTACACTTTGGTGTCTCTG
* * *
34272983 ATTTCACTTTGGTGCCTTTATTTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTG
1 ATTTCACTTCGGTGCCTCTATTTACACTTAGGTGCATCTGCTTACACTTTGGTGTCTCTG
* *
34273043 ATTTCACTTCGGTGCCTCTATTTGCACTAAGGTGC
1 ATTTCACTTCGGTGCCTCTATTTACACTTAGGTGC
34273078 CTCCGTATAG
Statistics
Matches: 125, Mismatches: 25, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
60 122 0.98
61 3 0.02
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (60 bp):
ATTTCACTTCGGTGCCTCTATTTACACTTAGGTGCATCTGCTTACACTTTGGTGTCTCTG
Found at i:34274649 original size:15 final size:15
Alignment explanation
Indices: 34274631--34274674 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
34274621 GTATGCTTAA
34274631 ACCCTAGGAGTAACG
1 ACCCTAGGAGTAACG
34274646 ACCCTAGGAGTAACG
1 ACCCTAGGAGTAACG
34274661 ACCCTAGGAAGTAA
1 ACCCTAGG-AGTAA
34274675 TTTGGGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 23 0.82
16 5 0.18
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.14
Consensus pattern (15 bp):
ACCCTAGGAGTAACG
Found at i:34276246 original size:11 final size:11
Alignment explanation
Indices: 34276232--34276273 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
34276222 TAAATATTAC
34276232 TTTATTAATAT
1 TTTATTAATAT
*
34276243 TTTAATGAGATAT
1 TTT-ATTA-ATAT
34276256 TTTATTAATAT
1 TTTATTAATAT
34276267 TTTATTA
1 TTTATTA
34276274 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:34276322 original size:15 final size:15
Alignment explanation
Indices: 34276298--34276327 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34276288 AAAAGGAGAG
*
34276298 AAAGATGAAGAAAGA
1 AAAGAAGAAGAAAGA
34276313 AAAGAAGAAGAAAGA
1 AAAGAAGAAGAAAGA
34276328 TGATTCTCCC
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:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (15 bp):
AAAGAAGAAGAAAGA
Found at i:34289422 original size:5 final size:5
Alignment explanation
Indices: 34289412--34289436 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34289402 ATTACACTTC
34289412 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
34289437 GAATAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:34295806 original size:12 final size:11
Alignment explanation
Indices: 34295777--34295805 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
34295767 AATATATTTT
34295777 TATTTTTAAAA
1 TATTTTTAAAA
34295788 TATTTTTAAAA
1 TATTTTTAAAA
34295799 TATTTTT
1 TATTTTT
34295806 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:34297109 original size:22 final size:20
Alignment explanation
Indices: 34297084--34297136 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
34297074 TTCTATTTCT
* *
34297084 TTATTTGTTTTTTTTTAATTA
1 TTATTTATTTTGTTTT-ATTA
34297105 CTTATTTATTTTGTTTTATTA
1 -TTATTTATTTTGTTTTATTA
34297126 TTATTTCATTT
1 TTATTT-ATTT
34297137 ACTTTGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 8 0.29
22 14 0.50
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (20 bp):
TTATTTATTTTGTTTTATTA
Found at i:34297116 original size:21 final size:21
Alignment explanation
Indices: 34297091--34297136 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
34297081 TCTTTATTTG
*
34297091 TTTTTTTTTAATTACTTATTT-A
1 TTTTGTTTT-ATTA-TTATTTCA
34297113 TTTTGTTTTATTATTATTTCA
1 TTTTGTTTTATTATTATTTCA
34297134 TTT
1 TTT
34297137 ACTTTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 8 0.36
22 8 0.36
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTGTTTTATTATTATTTCA
Found at i:34297121 original size:25 final size:25
Alignment explanation
Indices: 34297083--34297152 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
34297073 TTTCTATTTC
* *
34297083 TTTATTTGTTTTTTTTTAATTACTT-A
1 TTTATTT-TGTTTTATT-ATTACTTCA
*
34297109 TTTATTTTGTTTTATTATTATTTCA
1 TTTATTTTGTTTTATTATTACTTCA
*
34297134 TTTACTTTGTTATTATTAT
1 TTTATTTTGTT-TTATTAT
34297153 AACAATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 6 0.16
25 18 0.47
26 14 0.37
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTATTTTGTTTTATTATTACTTCA
Found at i:34297228 original size:19 final size:20
Alignment explanation
Indices: 34297176--34297235 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
34297166 CTATACTTAA
34297176 ATATTAATTA-ATACATAT-T
1 ATATT-ATTATATACATATGT
*
34297195 TTATTATTATATACATATGT
1 ATATTATTATATACATATGT
* *
34297215 ATATTATT-TTTACAAATGT
1 ATATTATTATATACATATGT
34297234 AT
1 AT
34297236 TCACCAACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 23 0.66
20 8 0.23
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (20 bp):
ATATTATTATATACATATGT
Found at i:34309377 original size:29 final size:29
Alignment explanation
Indices: 34309282--34309378 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
34309272 AAACTACACC
*
34309282 ACACCAGGTTGCTCA-TCCAAGCTAAAATT
1 ACACTAGGTTGCT-AGTCCAAGCTAAAATT
* * * *
34309311 TCA-TAAGGTTGCTAGTCTAGGCTAAAAGT
1 ACACT-AGGTTGCTAGTCCAAGCTAAAATT
* * *
34309340 ATACAAGGTTGCTTGTCCAAGCTAAAATT
1 ACACTAGGTTGCTAGTCCAAGCTAAAATT
34309369 ACACTAGGTT
1 ACACTAGGTT
34309379 AGGTTACTAA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 1 0.02
29 50 0.98
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (29 bp):
ACACTAGGTTGCTAGTCCAAGCTAAAATT
Found at i:34311492 original size:17 final size:17
Alignment explanation
Indices: 34311470--34311506 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34311460 GCAATGCTAC
*
34311470 CAAACTTAACCATCAAG
1 CAAACTTAACAATCAAG
*
34311487 CAAACTTGACAATCAAG
1 CAAACTTAACAATCAAG
34311504 CAA
1 CAA
34311507 GCATTTGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.27, G:0.08, T:0.16
Consensus pattern (17 bp):
CAAACTTAACAATCAAG
Found at i:34318297 original size:3 final size:3
Alignment explanation
Indices: 34318289--34318337 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
34318279 ATGAAAGACC
34318289 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34318337 T
1 T
34318338 GAAAATATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34319016 original size:12 final size:13
Alignment explanation
Indices: 34318990--34319023 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
34318980 AACTGATGCA
*
34318990 AAAACAGAGAAAG
1 AAAACAGAAAAAG
34319003 AAAA-AGAAAAAG
1 AAAACAGAAAAAG
34319015 AAAACAGAA
1 AAAACAGAA
34319024 CAAACAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAACAGAAAAAG
Found at i:34324783 original size:16 final size:15
Alignment explanation
Indices: 34324762--34324791 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
34324752 AAGATATTAG
34324762 AAGTTGAAAGCGAAAA
1 AAGTTGAAAG-GAAAA
34324778 AAGTTGAAAGGAAA
1 AAGTTGAAAGGAAA
34324792 GTGAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.03, G:0.27, T:0.13
Consensus pattern (15 bp):
AAGTTGAAAGGAAAA
Found at i:34325191 original size:20 final size:20
Alignment explanation
Indices: 34325166--34325205 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34325156 CGTAAAATGA
*
34325166 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
34325186 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
34325206 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:34325195 original size:34 final size:35
Alignment explanation
Indices: 34325151--34325217 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
34325141 CAGTAAAATA
*
34325151 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
34325185 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
34325218 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:34325221 original size:14 final size:15
Alignment explanation
Indices: 34325145--34325221 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
34325135 GATTGCCAGT
* *
34325145 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
34325159 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
34325173 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
34325193 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
34325208 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
34325222 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:34325936 original size:19 final size:19
Alignment explanation
Indices: 34325902--34325941 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
34325892 GTGGATAGAG
*
34325902 ATGAATTTATTTTTATATAA
1 ATGAATTTAGTTTTATA-AA
34325922 ATGAATTT-GTTTTATAAA
1 ATGAATTTAGTTTTATAAA
34325940 AT
1 AT
34325942 AACTCATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (19 bp):
ATGAATTTAGTTTTATAAA
Found at i:34326132 original size:9 final size:9
Alignment explanation
Indices: 34326115--34326150 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
34326105 TGAGTTTTCG
34326115 AATTCGAAT
1 AATTCGAAT
*
34326124 AACTCGAAT
1 AATTCGAAT
34326133 -ATTCGAAT
1 AATTCGAAT
34326141 AATTCGAAT
1 AATTCGAAT
34326150 A
1 A
34326151 TCAAACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34326138 original size:17 final size:17
Alignment explanation
Indices: 34326116--34326151 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
34326106 GAGTTTTCGA
34326116 ATTCGAATAACTCGAAT
1 ATTCGAATAACTCGAAT
*
34326133 ATTCGAATAATTCGAAT
1 ATTCGAATAACTCGAAT
34326150 AT
1 AT
34326152 CAAACTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (17 bp):
ATTCGAATAACTCGAAT
Found at i:34326397 original size:30 final size:31
Alignment explanation
Indices: 34326363--34326422 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
34326353 AAATCTTTTA
34326363 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCAC
* *
34326393 TTTTCCCCTAAAATTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCA
34326423 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTTACTCCCTTCCCAC
Found at i:34327396 original size:16 final size:16
Alignment explanation
Indices: 34327366--34327396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34327356 CACTGTAACA
*
34327366 GAATAGAGCTGTAATG
1 GAATAAAGCTGTAATG
34327382 GAATAAAGCTGTAAT
1 GAATAAAGCTGTAAT
34327397 TAGTAATTCA
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:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
GAATAAAGCTGTAATG
Found at i:34327654 original size:58 final size:60
Alignment explanation
Indices: 34327575--34327717 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 60
34327565 TTTTAATAAG
* ** *
34327575 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAA-CCATATT-TTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAAAATTCTTAACATA
** *
34327633 ATTATTATTAAATATAATTTAAT-AAAATAATTTATAATTTAATAAAAATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAAAATTCTTAACATA
*
34327692 ATTATTATT--ATATGAATTTACTAAAA
1 ATTATTATTAAATAT-AATTTAATAAAA
34327718 TCATAATGTA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
57 21 0.29
58 33 0.45
59 19 0.26
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (60 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAAAATTCTTAACATA
Found at i:34337300 original size:14 final size:14
Alignment explanation
Indices: 34337277--34337321 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
34337267 TAGAAAAAAT
34337277 ATATAAATATATAC
1 ATATAAATATATAC
*
34337291 ATATACATATATA-
1 ATATAAATATATAC
34337304 A-A-AAATTATATAC
1 ATATAAA-TATATAC
34337317 ATATA
1 ATATA
34337322 TATAGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
11 2 0.08
12 7 0.28
13 2 0.08
14 13 0.52
15 1 0.04
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAAATATATAC
Found at i:34337337 original size:30 final size:31
Alignment explanation
Indices: 34337298--34337355 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
34337288 TACATATACA
*
34337298 TATATAAAAA-ATTATATACATATATATAGAT
1 TATATAAAAAGATAAT-TACATATATATAGAT
34337329 TATA-AAAAAGATAATTACATATATATA
1 TATATAAAAAGATAATTACATATATATA
34337356 AAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (31 bp):
TATATAAAAAGATAATTACATATATATAGAT
Found at i:34337353 original size:21 final size:23
Alignment explanation
Indices: 34337329--34337376 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34337319 ATATATAGAT
*
34337329 TATAAAAAA-GATAATTACATATA
1 TATAAAAAATAATAATTACA-ATA
34337352 TATAAAAAATAATAATTAC-ATA
1 TATAAAAAATAATAATTACAATA
34337374 TAT
1 TAT
34337377 TGAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 9 0.39
24 8 0.35
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
TATAAAAAATAATAATTACAATA
Found at i:34337386 original size:22 final size:24
Alignment explanation
Indices: 34337297--34337376 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
34337287 ATACATATAC
*
34337297 ATATATAAAAAATTATATACATATATAT
1 ATATATAAAAAA-TA-ATA-AT-TACAT
* *
34337325 AGATTATAAAAAA-GATAATTACAT
1 ATA-TATAAAAAATAATAATTACAT
34337349 ATATATAAAAAATAATAATTACAT
1 ATATATAAAAAATAATAATTACAT
34337373 ATAT
1 ATAT
34337377 TGAAATTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
23 9 0.20
24 20 0.44
25 2 0.04
26 3 0.07
28 2 0.04
29 9 0.20
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (24 bp):
ATATATAAAAAATAATAATTACAT
Found at i:34337615 original size:2 final size:2
Alignment explanation
Indices: 34337608--34337636 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34337598 AAATAGAATA
34337608 AT 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 AT A
34337637 ATAGGTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34337734 original size:3 final size:3
Alignment explanation
Indices: 34337728--34337757 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34337718 ATAGTAGTAG
34337728 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34337758 CTTAATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34339408 original size:44 final size:42
Alignment explanation
Indices: 34339337--34339456 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 42
34339327 ACCCGATGTG
* * * **
34339337 ATCTACTCTACTACAACTTTAGAGAGATAAGATATGTGGTTTT
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATAT-TGACTTT
* * *
34339380 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGACTTT
1 -ATCTACTCCACTGCAACTTTAGGGAGATAAGA-TATTGACTTT
34339424 ATCTACTCCACTGCAACTTTAGGGAGATAAGAT
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGAT
34339457 TTGCCATATT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 29 0.45
44 31 0.48
45 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (42 bp):
ATCTACTCCACTGCAACTTTAGGGAGATAAGATATTGACTTT
Found at i:34339440 original size:43 final size:45
Alignment explanation
Indices: 34339337--34339457 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 45
34339327 ACCCGATGTG
* * * **
34339337 ATCTACTCTACTACAACTTTAGAGAGATAAGA-TATGTGGTTTTA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTATGTGACTTTA
* * *
34339381 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAT-TGACTTT-
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTATGTGACTTTA
34339424 ATCTACTCCACTGCAACTTTAGGGAGATAAGATT
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATT
34339458 TGCCATATTC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 31 0.48
44 31 0.48
45 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (45 bp):
ATCTACTCCACTGCAACTTTAGGGAGATAAGATTATGTGACTTTA
Found at i:34339604 original size:99 final size:100
Alignment explanation
Indices: 34339465--34339671 Score: 317
Period size: 99 Copynumber: 2.1 Consensus size: 100
34339455 ATTTGCCATA
*
34339465 TTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCAC
* *
34339530 TACATCGCCAAGGAAGTAAGATTCGCCGTTGCGGC
66 TACACCGCCAAGGAAGTAAGAATCGCCGTTGCGGC
* * *
34339565 TTCAATCTTTTTAATTGCAATG-TGGGGAAACGAGATTCACTGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCAC
* * *
34339629 TACACCGCCAGGGGAGTAAGAATCGCTGTTGCGGC
66 TACACCGCCAAGGAAGTAAGAATCGCCGTTGCGGC
*
34339664 TTTAATCT
1 TTCAATCT
34339672 GTTCCACTGT
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 77 0.79
100 20 0.21
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (100 bp):
TTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCAC
TACACCGCCAAGGAAGTAAGAATCGCCGTTGCGGC
Found at i:34339966 original size:44 final size:44
Alignment explanation
Indices: 34339874--34340121 Score: 360
Period size: 44 Copynumber: 5.7 Consensus size: 44
34339864 TGCTATTTTT
* * *
34339874 AACCTACTCCACTGCT-ACTCACGGAGATATGATT---AATCTTC
1 AACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTC
* *
34339915 AACCTATTCCACTGCTGACCAGAGAGATAGGACTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
34339959 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
34340003 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
* *
34340047 AACCTATTCCACTACTGACCAGGGAGATATGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
* * * *
34340091 AGCCTATTCCACTGTTGTCTAGGGAGATAGG
1 AACCTATTCCACTGCTGACCAGGGAGATAGG
34340122 GCTGGGGTCA
Statistics
Matches: 188, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
41 26 0.14
42 2 0.01
44 160 0.85
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (44 bp):
AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
Found at i:34342784 original size:34 final size:34
Alignment explanation
Indices: 34342741--34342808 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
34342731 CCTTTCATTT
34342741 GTGTCTTCCTATATGTCATTGATGTGAACACTTC
1 GTGTCTTCCTATATGTCATTGATGTGAACACTTC
34342775 GTGTCTTCCTATATGTCATTGATGTGAACACTTC
1 GTGTCTTCCTATATGTCATTGATGTGAACACTTC
34342809 CCAACATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (34 bp):
GTGTCTTCCTATATGTCATTGATGTGAACACTTC
Done.