Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold310
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: 899071
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.31
Warning! 72433 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:479520 original size:50 final size:50
Alignment explanation
Indices: 479465--479698 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
479455 GGGAATGAGA
* * *
479465 TCCCATGAAAGACCATGTCTGGGTCATGGCATTGACACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGG
* * *
479515 TCCCATGTAAGACCATGTTTGGGGCATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGG
* * *
479565 TCTCATGTAAGACCATGTTTGGGACATGGCAATGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGG
** * * * * * * **
479615 TCCCCCGTAAGAGCATGTCTGGGACGTTGCATGGACACCGATATGAGAAC
1 TCCCATGTAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGG
* *
479665 TCCCATGTAAGACCATATTTGGGATATGGCATTG
1 TCCCATGTAAGACCATGTTTGGGACATGGCATTG
479699 GCAGTACAAG
Statistics
Matches: 153, Mismatches: 31, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 153 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGG
Found at i:483136 original size:14 final size:15
Alignment explanation
Indices: 483106--483138 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
483096 TCCTATTTCT
*
483106 ATTGCTCCTTATAGA
1 ATTGCTCCGTATAGA
483121 ATTGCTCCGT-TAGA
1 ATTGCTCCGTATAGA
483135 ATTG
1 ATTG
483139 AAAGAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (15 bp):
ATTGCTCCGTATAGA
Found at i:486696 original size:50 final size:50
Alignment explanation
Indices: 486639--486809 Score: 224
Period size: 50 Copynumber: 3.5 Consensus size: 50
486629 GGGAATGAGA
* *
486639 TCCCATGTAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
486689 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT--GAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * **
486737 TCCCCA--TAAGAGCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 T-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
486786 TCCCATGTAAGACCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
486810 TATGACTTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
47 33 0.31
48 9 0.09
49 7 0.07
50 56 0.53
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:486821 original size:97 final size:97
Alignment explanation
Indices: 486646--486822 Score: 255
Period size: 97 Copynumber: 1.8 Consensus size: 97
486636 AGATCCCATG
* * ** *
486646 TAAGACCATGTTTGGGACATGGCATTGACACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
1 TAAGACCATGTCTGGGACATGGCATGGACACCGAGATGAGAACTCCCATGTAAGACCATATCTGG
*
486711 GACATGGCGTTGGCACCGAGATGAGGTCCCCA
66 GACATGACGTTGGCACCGAGATGAGGTCCCCA
* * *
486743 TAAGAGCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGG
1 TAAGACCATGTCTGGGACATGGCATGGACACCGAGATGAGAACTCCCATGTAAGACCATATCTGG
* *
486808 GATATGACTTTGGCA
66 GACATGACGTTGGCA
486823 TGTTATTATC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 69 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (97 bp):
TAAGACCATGTCTGGGACATGGCATGGACACCGAGATGAGAACTCCCATGTAAGACCATATCTGG
GACATGACGTTGGCACCGAGATGAGGTCCCCA
Found at i:495938 original size:40 final size:39
Alignment explanation
Indices: 495885--495964 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
495875 GTTTGGATAA
* *
495885 AAAACGCCCCTAAAGATCGAGCATTAGCGGCGCTTTCTGG
1 AAAACGCCCCTAAA-AACAAGCATTAGCGGCGCTTTCTGG
** * *
495925 AAAACGCTGCTAAAAACAAGCATTAGCGGCGTTTTTTGG
1 AAAACGCCCCTAAAAACAAGCATTAGCGGCGCTTTCTGG
495964 A
1 A
495965 GCCTGAGCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (39 bp):
AAAACGCCCCTAAAAACAAGCATTAGCGGCGCTTTCTGG
Found at i:496043 original size:41 final size:41
Alignment explanation
Indices: 495982--496148 Score: 178
Period size: 41 Copynumber: 4.1 Consensus size: 41
495972 CTTTCGGGGA
*
495982 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
*
496023 TTTAGCGGCGTTTTTTGGAAAGCGCCGCTAATGC-CTAGGGC
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTC-AGGGC
* * * * * *
496064 TGTAACGGCGTTTTTAAGAAAGCGCTGCTAATGCTTAGAGC
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
** * *
496105 TTTAGCGGCGCTTCCCTA--AAAACGCCGCTAATGCTCATGGC
1 TTTAGCGGCG-TT-TTTAGGAAAGCGCCGCTAATGCTCAGGGC
496146 TTT
1 TTT
496149 TAGGGGTAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 100 0.95
42 2 0.02
43 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
Found at i:496131 original size:82 final size:82
Alignment explanation
Indices: 495987--496138 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 82
495977 GGGGATTTAG
** * *** * *
495987 CGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTTGGAAAGCGCCGCT
1 CGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTCCCTGAAAAACGCCGCT
496052 AATGCCTAGGGCTGTAA
66 AATGCCTAGGGCTGTAA
* *
496069 CGGCGTTTTTAAGAAAGCGCTGCTAATGCTTAGAGCTTTAGCGGCGCTTCCCT-AAAAACGCCGC
1 CGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCG-TTCCCTGAAAAACGCCGC
496133 TAATGC
65 TAATGC
496139 TCATGGCTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 56 0.95
83 3 0.05
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (82 bp):
CGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTCCCTGAAAAACGCCGCT
AATGCCTAGGGCTGTAA
Found at i:496410 original size:7 final size:7
Alignment explanation
Indices: 496386--496538 Score: 96
Period size: 7 Copynumber: 21.7 Consensus size: 7
496376 TATCACTACA
*
496386 GTTTAGG
1 GTTTATG
* *
496393 GTTTTTA
1 GTTTATG
496400 GTTTATG
1 GTTTATG
*
496407 GTTTAGG
1 GTTTATG
*
496414 GGTTATG
1 GTTTATG
496421 GTTTATG
1 GTTTATG
*
496428 GTTTAGG
1 GTTTATG
*
496435 GGTTATG
1 GTTTATG
496442 GTTTATG
1 GTTTATG
496449 GTTTATG
1 GTTTATG
*
496456 GTTTAAAG
1 GTTT-ATG
* *
496464 G-CTAGG
1 GTTTATG
*
496470 GTTTAAG
1 GTTTATG
496477 GTTTA-G
1 GTTTATG
*
496483 AGGTTATG
1 -GTTTATG
* *
496491 TGTTAAGG
1 -GTTTATG
496499 GTTTATG
1 GTTTATG
*
496506 GTTTTAGG
1 G-TTTATG
*
496514 GTTTA-A
1 GTTTATG
496520 GTTTATG
1 GTTTATG
*
496527 GTTTAGG
1 GTTTATG
496534 GTTTA
1 GTTTA
496539 GATTAACTAG
Statistics
Matches: 111, Mismatches: 29, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
6 9 0.08
7 88 0.79
8 14 0.13
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (7 bp):
GTTTATG
Found at i:496412 original size:21 final size:21
Alignment explanation
Indices: 496386--496453 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
496376 TATCACTACA
* * *
496386 GTTTAGGGTTTTTAGTTTATG
1 GTTTAGGGGTTATGGTTTATG
496407 GTTTAGGGGTTATGGTTTATG
1 GTTTAGGGGTTATGGTTTATG
496428 GTTTAGGGGTTATGGTTTATG
1 GTTTAGGGGTTATGGTTTATG
496449 GTTTA
1 GTTTA
496454 TGGTTTAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (21 bp):
GTTTAGGGGTTATGGTTTATG
Found at i:496419 original size:14 final size:14
Alignment explanation
Indices: 496400--496539 Score: 106
Period size: 14 Copynumber: 9.9 Consensus size: 14
496390 AGGGTTTTTA
496400 GTTTATGGTTTAGG
1 GTTTATGGTTTAGG
* *
496414 GGTTATGGTTTATG
1 GTTTATGGTTTAGG
* * *
496428 GTTTAGGGGTTATG
1 GTTTATGGTTTAGG
*
496442 GTTTATGGTTTATG
1 GTTTATGGTTTAGG
* *
496456 GTTTAAAGG-CTAGG
1 GTTT-ATGGTTTAGG
*
496470 GTTTAAGGTTTAGAG
1 GTTTATGGTTTAG-G
*
496485 G-TTATGTGTTAAGG
1 GTTTATG-GTTTAGG
496499 GTTTATGGTTTTAGG
1 GTTTATGG-TTTAGG
* *
496514 GTTTA-AGTTTATG
1 GTTTATGGTTTAGG
*
496527 GTTTAGGGTTTAG
1 GTTTATGGTTTAG
496540 ATTAACTAGT
Statistics
Matches: 101, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
13 14 0.14
14 62 0.61
15 25 0.25
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (14 bp):
GTTTATGGTTTAGG
Found at i:496808 original size:14 final size:14
Alignment explanation
Indices: 496789--496815 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
496779 ATATATGGAT
496789 TTAGGGATTATAGA
1 TTAGGGATTATAGA
496803 TTAGGGATTATAG
1 TTAGGGATTATAG
496816 TTTAAGGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATAGA
Found at i:496869 original size:22 final size:21
Alignment explanation
Indices: 496816--496881 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
496806 GGGATTATAG
* * *
496816 TTTAAGGTTGGGATTTAAGG-
1 TTTAGGGTTAGGAGTTAAGGA
*
496836 TTTAAGGGTTAGGAGTTAGGGA
1 TTT-AGGGTTAGGAGTTAAGGA
*
496858 TTTAGGGTTTAGGATTTAAGGA
1 TTTAGGG-TTAGGAGTTAAGGA
496880 TT
1 TT
496882 CAAGGGTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 3 0.08
21 17 0.46
22 17 0.46
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (21 bp):
TTTAGGGTTAGGAGTTAAGGA
Found at i:501618 original size:43 final size:43
Alignment explanation
Indices: 501557--501668 Score: 197
Period size: 43 Copynumber: 2.6 Consensus size: 43
501547 GCTTTTGTCG
* *
501557 AAAGGTTGTGGTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCT
1 AAAGGTCGTGGTCTTTAGCGGCGTTTGCGACAAAAGCGCCGCT
501600 AAAGGTCGTGGTCTTTAGCGGCGTTTGCGACAAAAGCGCCGCT
1 AAAGGTCGTGGTCTTTAGCGGCGTTTGCGACAAAAGCGCCGCT
*
501643 AAAGGTCATGGTCTTTAGCGGCGTTT
1 AAAGGTCGTGGTCTTTAGCGGCGTTT
501669 ATGGAAATAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.28
Consensus pattern (43 bp):
AAAGGTCGTGGTCTTTAGCGGCGTTTGCGACAAAAGCGCCGCT
Found at i:502544 original size:2 final size:2
Alignment explanation
Indices: 502537--502572 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
502527 TAAATTGTTT
*
502537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
502573 AAGACAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:513528 original size:15 final size:16
Alignment explanation
Indices: 513508--513539 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
513498 TAATCTTTAG
513508 ATGTG-AAACTATAGA
1 ATGTGAAAACTATAGA
513523 ATGTGAAAACTATAGA
1 ATGTGAAAACTATAGA
513539 A
1 A
513540 AACTATAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTGAAAACTATAGA
Found at i:516802 original size:120 final size:120
Alignment explanation
Indices: 516590--516809 Score: 289
Period size: 120 Copynumber: 1.8 Consensus size: 120
516580 TGTTATAATG
* * * *
516590 GGAGACTCTGTGTACCTTCTAATTCTGAGTTGAGGAAGTCTATACTTCGGGAGGTGCATAGCAAC
1 GGAGACTCTGTCTACCTTCTAATTCTAAGTTGAGGAAGTCTATACTTCGGGAAGCGCATAGCAAC
* * * * *
516655 CCCTACGCTATGCATTTTGTTGGTAGTATGATGTAAGGAGTTCTGTGTTATCGTC
66 CCCTACGATATACATCTTGTAGGTAGTAAGATGTAAGGAGTTCTGTGTTATCGTC
* * * * *
516710 GGAGACTCTGTCTACCTTCTGATTTTAAGTTGAGGCAGTCTATACTTCGGGAAGCGCTTAGCAGC
1 GGAGACTCTGTCTACCTTCTAATTCTAAGTTGAGGAAGTCTATACTTCGGGAAGCGCATAGCAAC
*
516775 CCCTATGATATACATCTTG-AGGATAGTAAGATGTA
66 CCCTACGATATACATCTTGTAGG-TAGTAAGATGTA
516810 TCGCGATCTC
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 2 0.02
120 82 0.98
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (120 bp):
GGAGACTCTGTCTACCTTCTAATTCTAAGTTGAGGAAGTCTATACTTCGGGAAGCGCATAGCAAC
CCCTACGATATACATCTTGTAGGTAGTAAGATGTAAGGAGTTCTGTGTTATCGTC
Found at i:521537 original size:16 final size:16
Alignment explanation
Indices: 521472--521542 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
521462 ATTTGGTTCA
* *
521472 CTGTAATGCAATAGGG
1 CTGTAATGGAATAGAG
* *
521488 CTATAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
521504 CAT-TAATTGAATAAAG
1 C-TGTAATGGAATAGAG
521520 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
521536 CTGTAAT
1 CTGTAAT
521543 CAGTAATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
15 1 0.02
16 44 0.96
17 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:521616 original size:44 final size:46
Alignment explanation
Indices: 521524--521616 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
521514 ATAAAGCTGT
*
521524 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
* *
521570 AATGGAATAGAACTGTAAT-AGT-CTT-ATTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATCAGTAATTCAAT-TGTTTGGTTGAATGG
521614 AAT
1 AAT
521617 AGATTTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 20 0.47
45 3 0.07
46 18 0.42
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:524496 original size:22 final size:21
Alignment explanation
Indices: 524466--524516 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
524456 AAGGCATCAA
*
524466 TTCCCTTCTTTCTCTTCTCTTT
1 TTCCTTTCTTTCTCTT-TCTTT
* *
524488 TTCCTTTCTTTTTCTTTTTTT
1 TTCCTTTCTTTCTCTTTCTTT
*
524509 TTTCTTTC
1 TTCCTTTC
524517 CGAAAGCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCCTTTCTTTCTCTTTCTTT
Found at i:532732 original size:14 final size:14
Alignment explanation
Indices: 532713--532743 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
532703 ATCACCCAAA
532713 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
*
532727 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
532741 AAA
1 AAA
532744 AGAATGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:532745 original size:5 final size:5
Alignment explanation
Indices: 532712--532747 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
532702 AATCACCCAA
*
532712 AAAAG AAAAA AAAAG -AAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
532748 TGTGTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:533087 original size:36 final size:35
Alignment explanation
Indices: 533020--533086 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
533010 ATTAGTAAAA
*
533020 AGAAAAAAAATAATATGAATTTAATAATTTTTAAG
1 AGAAAAAAAATAATATGAATTGAATAATTTTTAAG
533055 AGAAAACAAAATAA-AT-AATTGAATATATTTTT
1 AGAAAA-AAAATAATATGAATTGAATA-ATTTTT
533087 TTATAACGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
35 14 0.48
36 7 0.24
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (35 bp):
AGAAAAAAAATAATATGAATTGAATAATTTTTAAG
Found at i:535257 original size:264 final size:262
Alignment explanation
Indices: 534783--535309 Score: 993
Period size: 264 Copynumber: 2.0 Consensus size: 262
534773 TATTGATGTT
534783 AAAGTGTATATAATTTCTATTACATCAATAAGAAATTAGATTGGATCTAGAAATTTAAAATATTT
1 AAAGTGTATATAATTTCTATTACATCAATAAGAAATTAGATTGGATCTAGAAATTTAAAATATTT
534848 TTACTTTAATATCAAAATCAAAGGGGTTTATGAGTAAAAATCATTTAACTACAAAAATAATTTGA
66 TTACTTTAATATCAAAATCAAAGGGGTTTATGAGTAAAAATCATTTAACTACAAAAATAATTTGA
534913 AGGTTTGTTTAAATAGAAGGTAAAATAGTTTAAGGATTTTTATAAGTACATTAGCCAAAATGAAT
131 AGGTTTGTTTAAATAGAAGGTAAAATAGTTTAAGGATTTTTATAAGTACATTAGCCAAAATGAAT
*
534978 CTGGATTTCGATTTTTCATATTTTTCTACATGCTAATGAGAAAAAGGCTTGCATAGATGGCTAGA
196 CTAGATTTCGATTTTTCATATTTTTCTACATGCTAATGAG--AAAGGCTTGCATAGATGGCTAGA
535043 CTAG
259 CTAG
535047 AAAGTGTATATAATTTCTATTACATCAATAAGAAATTAGATTGGGATCTAGAAA-TTAAAATATT
1 AAAGTGTATATAATTTCTATTACATCAATAAGAAATTAGATT-GGATCTAGAAATTTAAAATATT
535111 TTTACTTTAATATCAAAATCAAAGGGGTTTATGAGTAAAAATCATTTAACTACAAAAATAATTTG
65 TTTACTTTAATATCAAAATCAAAGGGGTTTATGAGTAAAAATCATTTAACTACAAAAATAATTTG
*
535176 AAGGTTTGTTTAAATAGAAGGTAAAATAGTTTAAGGATTTTTATAAGTACATTAGTCAAAATGAA
130 AAGGTTTGTTTAAATAGAAGGTAAAATAGTTTAAGGATTTTTATAAGTACATTAGCCAAAATGAA
*
535241 TCTAGATTTTGATTTTTCATATTTTTCTACATGCTAATGAGAAAGGCTTGCATAGATGGCTAGAC
195 TCTAGATTTCGATTTTTCATATTTTTCTACATGCTAATGAGAAAGGCTTGCATAGATGGCTAGAC
535306 TAG
260 TAG
535309 A
1 A
535310 GTGAGAAACA
Statistics
Matches: 259, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
262 28 0.11
264 220 0.85
265 11 0.04
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (262 bp):
AAAGTGTATATAATTTCTATTACATCAATAAGAAATTAGATTGGATCTAGAAATTTAAAATATTT
TTACTTTAATATCAAAATCAAAGGGGTTTATGAGTAAAAATCATTTAACTACAAAAATAATTTGA
AGGTTTGTTTAAATAGAAGGTAAAATAGTTTAAGGATTTTTATAAGTACATTAGCCAAAATGAAT
CTAGATTTCGATTTTTCATATTTTTCTACATGCTAATGAGAAAGGCTTGCATAGATGGCTAGACT
AG
Found at i:550146 original size:40 final size:41
Alignment explanation
Indices: 550096--550180 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
550086 CATGTTATCA
* ** *
550096 CATATCGATGCCTCTGTCCCAGACAGGGTCGTACACG-AAT
1 CATATAGATGCCAATGTCCCAAACAGGGTCGTACACGAAAT
* *
550136 CATATAGATGCCAATGTCCCAAACATGGTCTTACACGAAAT
1 CATATAGATGCCAATGTCCCAAACAGGGTCGTACACGAAAT
550177 CATA
1 CATA
550181 CCTCAGAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 31 0.82
41 7 0.18
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (41 bp):
CATATAGATGCCAATGTCCCAAACAGGGTCGTACACGAAAT
Found at i:560189 original size:26 final size:25
Alignment explanation
Indices: 560160--560229 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
560150 TTCTCGAACT
560160 TTTATTAGGGGTAAAATAGTAAAAAA
1 TTTATTAGGGGTAAAATA-TAAAAAA
** * *
560186 TTTACCAAGGGTAAAATTATTAAAAA
1 TTTATTAGGGGTAAAA-TATAAAAAA
*
560212 TTTATTGGGGGTAAAATA
1 TTTATTAGGGGTAAAATA
560230 AGGATAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 2 0.06
26 31 0.89
27 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.33
Consensus pattern (25 bp):
TTTATTAGGGGTAAAATATAAAAAA
Found at i:567391 original size:22 final size:21
Alignment explanation
Indices: 567365--567416 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
567355 GATGTCTAAG
*
567365 AAATAAAAATAAAAAAATAAA
1 AAATAAAAATAAAAAAACAAA
* * *
567386 ACAATAAAACTGAAAAAACAAT
1 A-AATAAAAATAAAAAAACAAA
567408 AAATAAAAA
1 AAATAAAAA
567417 AAATTAGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (21 bp):
AAATAAAAATAAAAAAACAAA
Found at i:567417 original size:16 final size:15
Alignment explanation
Indices: 567372--567419 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
567362 AAGAAATAAA
567372 AATAAAAAAATAAAAC
1 AATAAAAAAA-AAAAC
*
567388 AATAAAACTGAAAAAAC
1 AATAAAA--AAAAAAAC
567405 AATAAATAAAAAAAA
1 AATAAA-AAAAAAAA
567420 TTAGAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 13 0.48
17 11 0.41
18 3 0.11
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (15 bp):
AATAAAAAAAAAAAC
Found at i:567418 original size:17 final size:16
Alignment explanation
Indices: 567372--567419 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
567362 AAGAAATAAA
*
567372 AATAAAAAAATAAAAC
1 AATAAAAAAAAAAAAC
**
567388 AATAAAACTGAAAAAAC
1 AATAAAA-AAAAAAAAC
567405 AATAAATAAAAAAAA
1 AATAAA-AAAAAAAA
567420 TTAGAAATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 7 0.28
17 17 0.68
18 1 0.04
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (16 bp):
AATAAAAAAAAAAAAC
Found at i:571752 original size:18 final size:18
Alignment explanation
Indices: 571726--571765 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
571716 AAAAATAATG
*
571726 ATTATATTATGAAAAATA
1 ATTACATTATGAAAAATA
* *
571744 ATTACATTATTAAAATTA
1 ATTACATTATGAAAAATA
571762 ATTA
1 ATTA
571766 ATTCCTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTACATTATGAAAAATA
Found at i:573916 original size:34 final size:34
Alignment explanation
Indices: 573873--573940 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
573863 TAATGCCAAA
573873 GAGATAGGATTCGATGCCTACAGCTTCAATCTAC
1 GAGATAGGATTCGATGCCTACAGCTTCAATCTAC
573907 GAGATAGGATTCGATGCCTACAGCTTCAATCTAC
1 GAGATAGGATTCGATGCCTACAGCTTCAATCTAC
573941 TCCACTTCAG
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:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
GAGATAGGATTCGATGCCTACAGCTTCAATCTAC
Found at i:585118 original size:18 final size:18
Alignment explanation
Indices: 585092--585131 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
585082 AAAAATAATG
*
585092 ATTATATTATGAAAAATA
1 ATTACATTATGAAAAATA
* *
585110 ATTACATTATTAAAATTA
1 ATTACATTATGAAAAATA
585128 ATTA
1 ATTA
585132 ATTCCTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTACATTATGAAAAATA
Found at i:589271 original size:20 final size:20
Alignment explanation
Indices: 589246--589283 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
589236 CGAAAAATGA
589246 TTTCTGGAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
*
589266 TTTCTGGAAAATGATTTA
1 TTTCTGGAAAATAATTTA
589284 GTGAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:589420 original size:20 final size:21
Alignment explanation
Indices: 589378--589420 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
589368 ATGTTTCTTT
589378 TACATTATTAATAAATTTATA
1 TACATTATTAATAAATTTATA
* *
589399 TACA-TATTAATAATTTTTTA
1 TACATTATTAATAAATTTATA
589419 TA
1 TA
589421 TTTTAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TACATTATTAATAAATTTATA
Found at i:594493 original size:50 final size:50
Alignment explanation
Indices: 594429--594564 Score: 175
Period size: 50 Copynumber: 2.7 Consensus size: 50
594419 AGTAAGTGGC
* *
594429 AGTATATCTTCATATCAATGGTGGCTTATCCACAAAATGTTATCAATAG-
1 AGTATATCTGCATATCAATGGTGGCTTGTCCACAAAATGTTATCAATAGT
* * *
594478 AGGTATATCTGCATATCAATGGTGGCTTGTCCACAAAGTGTTATCAGTGGT
1 A-GTATATCTGCATATCAATGGTGGCTTGTCCACAAAATGTTATCAATAGT
* * * *
594529 AGTTTATATGCAAATCAGTGGTGGCTTGTCCACAAA
1 AGTATATCTGCATATCAATGGTGGCTTGTCCACAAA
594565 TGGTGTTTGG
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 74 0.97
51 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (50 bp):
AGTATATCTGCATATCAATGGTGGCTTGTCCACAAAATGTTATCAATAGT
Found at i:597397 original size:29 final size:29
Alignment explanation
Indices: 597313--597398 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
597303 ATATGAGCAT
** * *
597313 ATATGAAAAATGATGGTTACGACCATAGA
1 ATATGAAAAGGGATGGTTTCGACCATCGA
597342 ATATGAAAAGGGATGGTTTCGACCATCGA
1 ATATGAAAAGGGATGGTTTCGACCATCGA
597371 ATATGAAAAGGGATGGTTTCGACCATCG
1 ATATGAAAAGGGATGGTTTCGACCATCG
597399 TTTAGCACAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (29 bp):
ATATGAAAAGGGATGGTTTCGACCATCGA
Found at i:598199 original size:14 final size:14
Alignment explanation
Indices: 598180--598207 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
598170 TAAAGTTATA
598180 TTTAATAATTCATT
1 TTTAATAATTCATT
598194 TTTAATAATTCATT
1 TTTAATAATTCATT
598208 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:599254 original size:34 final size:34
Alignment explanation
Indices: 599211--599279 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
599201 TGTTATCTAC
599211 ATAGTTTTTAGATTTGTGTGATTAAATTGTTTCA
1 ATAGTTTTTAGATTTGTGTGATTAAATTGTTTCA
599245 ATAGTTTTTAGATTTGTGTGATTAAATTGTTTCA
1 ATAGTTTTTAGATTTGTGTGATTAAATTGTTTCA
599279 A
1 A
599280 ACCTAAGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (34 bp):
ATAGTTTTTAGATTTGTGTGATTAAATTGTTTCA
Found at i:607060 original size:496 final size:496
Alignment explanation
Indices: 606127--607118 Score: 1984
Period size: 496 Copynumber: 2.0 Consensus size: 496
606117 TGGTCAATAA
606127 ATATGCGACATTAATGAACTTATTCATTTGTGAGTTGATGATTATGGTTTGATAAGTCATGAGGC
1 ATATGCGACATTAATGAACTTATTCATTTGTGAGTTGATGATTATGGTTTGATAAGTCATGAGGC
606192 ATTGGTATAGGTTTATATTTAACTTATAAATTTCATTATTGAAATGAAATATTATGCTTAAATTT
66 ATTGGTATAGGTTTATATTTAACTTATAAATTTCATTATTGAAATGAAATATTATGCTTAAATTT
606257 TATACGAACTTACTAAGAATACATTTCTTACCTAGTTATTTTCCTTTAGTTTACAGATTATCGGA
131 TATACGAACTTACTAAGAATACATTTCTTACCTAGTTATTTTCCTTTAGTTTACAGATTATCGGA
606322 AGCTCGATCGATTTGGAAGCAAATCGGAGATTCATCCCACTATCCAACAATTTTATCGATGGATT
196 AGCTCGATCGATTTGGAAGCAAATCGGAGATTCATCCCACTATCCAACAATTTTATCGATGGATT
606387 TTGAGGCTTTGATCGTGGTTATAATGACATGTATAGGTGGACTATTTCTAATGTTTAGATAATGA
261 TTGAGGCTTTGATCGTGGTTATAATGACATGTATAGGTGGACTATTTCTAATGTTTAGATAATGA
606452 TATTGATGTATGGTTTTATGATTGTTGACATTTTGGCAGTTTTGGGCTTTATGGCTAATGTTGAA
326 TATTGATGTATGGTTTTATGATTGTTGACATTTTGGCAGTTTTGGGCTTTATGGCTAATGTTGAA
606517 ATGGTTAGTGATGATATGGTTGGAATGGCCAAATTTGTATTCTTCTGTGTGATATTGGCATGAAA
391 ATGGTTAGTGATGATATGGTTGGAATGGCCAAATTTGTATTCTTCTGTGTGATATTGGCATGAAA
606582 TGTTGCTTTGAATTTGTGAAACTTAAGTTATTTCGATGCCT
456 TGTTGCTTTGAATTTGTGAAACTTAAGTTATTTCGATGCCT
606623 ATATGCGACATTAATGAACTTATTCATTTGTGAGTTGATGATTATGGTTTGATAAGTCATGAGGC
1 ATATGCGACATTAATGAACTTATTCATTTGTGAGTTGATGATTATGGTTTGATAAGTCATGAGGC
606688 ATTGGTATAGGTTTATATTTAACTTATAAATTTCATTATTGAAATGAAATATTATGCTTAAATTT
66 ATTGGTATAGGTTTATATTTAACTTATAAATTTCATTATTGAAATGAAATATTATGCTTAAATTT
606753 TATACGAACTTACTAAGAATACATTTCTTACCTAGTTATTTTCCTTTAGTTTACAGATTATCGGA
131 TATACGAACTTACTAAGAATACATTTCTTACCTAGTTATTTTCCTTTAGTTTACAGATTATCGGA
606818 AGCTCGATCGATTTGGAAGCAAATCGGAGATTCATCCCACTATCCAACAATTTTATCGATGGATT
196 AGCTCGATCGATTTGGAAGCAAATCGGAGATTCATCCCACTATCCAACAATTTTATCGATGGATT
606883 TTGAGGCTTTGATCGTGGTTATAATGACATGTATAGGTGGACTATTTCTAATGTTTAGATAATGA
261 TTGAGGCTTTGATCGTGGTTATAATGACATGTATAGGTGGACTATTTCTAATGTTTAGATAATGA
606948 TATTGATGTATGGTTTTATGATTGTTGACATTTTGGCAGTTTTGGGCTTTATGGCTAATGTTGAA
326 TATTGATGTATGGTTTTATGATTGTTGACATTTTGGCAGTTTTGGGCTTTATGGCTAATGTTGAA
607013 ATGGTTAGTGATGATATGGTTGGAATGGCCAAATTTGTATTCTTCTGTGTGATATTGGCATGAAA
391 ATGGTTAGTGATGATATGGTTGGAATGGCCAAATTTGTATTCTTCTGTGTGATATTGGCATGAAA
607078 TGTTGCTTTGAATTTGTGAAACTTAAGTTATTTCGATGCCT
456 TGTTGCTTTGAATTTGTGAAACTTAAGTTATTTCGATGCCT
607119 TAATGGTTGG
Statistics
Matches: 496, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
496 496 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (496 bp):
ATATGCGACATTAATGAACTTATTCATTTGTGAGTTGATGATTATGGTTTGATAAGTCATGAGGC
ATTGGTATAGGTTTATATTTAACTTATAAATTTCATTATTGAAATGAAATATTATGCTTAAATTT
TATACGAACTTACTAAGAATACATTTCTTACCTAGTTATTTTCCTTTAGTTTACAGATTATCGGA
AGCTCGATCGATTTGGAAGCAAATCGGAGATTCATCCCACTATCCAACAATTTTATCGATGGATT
TTGAGGCTTTGATCGTGGTTATAATGACATGTATAGGTGGACTATTTCTAATGTTTAGATAATGA
TATTGATGTATGGTTTTATGATTGTTGACATTTTGGCAGTTTTGGGCTTTATGGCTAATGTTGAA
ATGGTTAGTGATGATATGGTTGGAATGGCCAAATTTGTATTCTTCTGTGTGATATTGGCATGAAA
TGTTGCTTTGAATTTGTGAAACTTAAGTTATTTCGATGCCT
Found at i:616020 original size:50 final size:50
Alignment explanation
Indices: 615910--616022 Score: 127
Period size: 50 Copynumber: 2.3 Consensus size: 50
615900 TTATGAGAGG
* * * * **
615910 TATGTAAGACCATGTCTGGGACATGGCGTTGGCACCTAGATGAGAGGTCC
1 TATGTAAGACCATGTCCGGGACATGGCATTGGCACCGAGATAAGAACTCC
*** * *
615960 CCCGTCAGACCATGTCCGGGACATGGCATTGGCACCGATATAAGAACTCC
1 TATGTAAGACCATGTCCGGGACATGGCATTGGCACCGAGATAAGAACTCC
616010 TATGTAAGACCAT
1 TATGTAAGACCAT
616023 ATCTTGGGTA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (50 bp):
TATGTAAGACCATGTCCGGGACATGGCATTGGCACCGAGATAAGAACTCC
Found at i:616309 original size:12 final size:12
Alignment explanation
Indices: 616292--616330 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
616282 GTGAGTTATT
616292 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
616304 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
616316 TAAGTGAGTAAG
1 TAAGTAAGCAAG
616328 TAA
1 TAA
616331 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:623592 original size:50 final size:50
Alignment explanation
Indices: 623411--623598 Score: 171
Period size: 50 Copynumber: 3.7 Consensus size: 50
623401 ATTTGGGGAA
* * * * **
623411 AGAGATCCAATGTAAGACCATGTCTGGGACATGACATTGGCTCATTAAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATAGG--CA--CCGA-TATG
* ** * *
623466 AGAGGTCCCATGTAAGACCATGTCCGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
*
623516 AGAGGTCCTC-CGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
1 AGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
** * *
623566 AGAACTCCCATGTAAGACCATATCTGGGGCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATG
623599 ACATTGGTAG
Statistics
Matches: 111, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 71 0.64
51 3 0.03
53 2 0.02
55 34 0.31
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
Found at i:623873 original size:12 final size:12
Alignment explanation
Indices: 623856--623894 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
623846 ATGAGTTATT
623856 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
623868 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
623880 TAAGTGAGTAAG
1 TAAGTAAGCAAG
623892 TAA
1 TAA
623895 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:641944 original size:36 final size:36
Alignment explanation
Indices: 641897--641986 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
641887 CAATACCTTC
641897 AAAAAGAACTAGCTCAAGGTTAGTCTCTTCACACCG
1 AAAAAGAACTAGCTCAAGGTTAGTCTCTTCACACCG
641933 AAAAAGAACTAGCTCAAGGTTAGTCTCTTCACACCG
1 AAAAAGAACTAGCTCAAGGTTAGTCTCTTCACACCG
641969 AAAAAGAACTAGCTCAAG
1 AAAAAGAACTAGCTCAAG
641987 ATTTTTTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (36 bp):
AAAAAGAACTAGCTCAAGGTTAGTCTCTTCACACCG
Found at i:644665 original size:50 final size:50
Alignment explanation
Indices: 644604--644775 Score: 272
Period size: 50 Copynumber: 3.4 Consensus size: 50
644594 GAGATCACAC
644604 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
* **
644654 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
* * **
644704 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
*
644754 GTAAGACCATATCTGGGACATG
1 GTAAGACCATGTCTGGGACATG
644776 AAATTGGTAG
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCAT
Found at i:651231 original size:10 final size:10
Alignment explanation
Indices: 651216--651250 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
651206 CTGTACTATC
651216 CACATATAAG
1 CACATATAAG
*
651226 CACATATAAT
1 CACATATAAG
*
651236 CACATATGAG
1 CACATATAAG
651246 CACAT
1 CACAT
651251 TTAGTCACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (10 bp):
CACATATAAG
Found at i:651241 original size:20 final size:20
Alignment explanation
Indices: 651216--651264 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
651206 CTGTACTATC
651216 CACATATAAGCACATATAAT
1 CACATATAAGCACATATAAT
* * *
651236 CACATATGAGCACATTTAGT
1 CACATATAAGCACATATAAT
651256 CACAATATA
1 CAC-ATATA
651265 TGATAATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (20 bp):
CACATATAAGCACATATAAT
Found at i:662014 original size:26 final size:28
Alignment explanation
Indices: 661985--662045 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
661975 TTCAAAGATA
* *
661985 TTTATTTGTACTTGTTTTTC-TC-CTTT
1 TTTATTAGTACTTCTTTTTCTTCTCTTT
**
662011 TTTATTAGTTTTTCTTTTTCTTCTCTTT
1 TTTATTAGTACTTCTTTTTCTTCTCTTT
662039 TTTATTA
1 TTTATTA
662046 TATTAGGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 16 0.55
27 2 0.07
28 11 0.38
ACGTcount: A:0.10, C:0.13, G:0.05, T:0.72
Consensus pattern (28 bp):
TTTATTAGTACTTCTTTTTCTTCTCTTT
Found at i:670368 original size:20 final size:20
Alignment explanation
Indices: 670351--670389 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
670341 AAAATGCAGA
670351 CAGAGGCA-CGAATGTGCAAT
1 CAGAGGCACCGAA-GTGCAAT
670371 CAGAGGCACCGAAGTGCAA
1 CAGAGGCACCGAAGTGCAA
670390 ACCCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.23, G:0.31, T:0.10
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAT
Found at i:670415 original size:22 final size:22
Alignment explanation
Indices: 670387--670437 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
670377 CACCGAAGTG
670387 CAAACCCATAAAAGTCCGCGTT
1 CAAACCCATAAAAGTCCGCGTT
*
670409 CAAACCCATACAAGTCCGCGTT
1 CAAACCCATAAAAGTCCGCGTT
670431 CAAACCC
1 CAAACCC
670438 TATTGGCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.37, G:0.12, T:0.16
Consensus pattern (22 bp):
CAAACCCATAAAAGTCCGCGTT
Found at i:677290 original size:17 final size:17
Alignment explanation
Indices: 677268--677316 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
677258 TAAGATTAAT
**
677268 AAAAAATAAAATAAATG
1 AAAAAATAAAATAAAAC
677285 AAAAAATTTAAAATAAAAC
1 AAAAAA--TAAAATAAAAC
*
677304 AAAAATTAAAATA
1 AAAAAATAAAATA
677317 GGAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAAATAAAATAAAAC
Found at i:677307 original size:19 final size:17
Alignment explanation
Indices: 677268--677316 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
677258 TAAGATTAAT
*
677268 AAAAAATAAAATAAATGA-
1 AAAAATTAAAATAAA--AC
677286 AAAAATTTAAAATAAAAC
1 AAAAA-TTAAAATAAAAC
677304 AAAAATTAAAATA
1 AAAAATTAAAATA
677317 GGAAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.32
18 10 0.36
19 9 0.32
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAATTAAAATAAAAC
Found at i:681520 original size:24 final size:24
Alignment explanation
Indices: 681488--681533 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
681478 AAAAACACAC
*
681488 GAACGTACATTGCCCTTAATTTTG
1 GAACATACATTGCCCTTAATTTTG
681512 GAACATACATTGCCCTTAATTT
1 GAACATACATTGCCCTTAATTT
681534 AAAATAATTA
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:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (24 bp):
GAACATACATTGCCCTTAATTTTG
Found at i:690427 original size:19 final size:19
Alignment explanation
Indices: 690391--690426 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
690381 TTAATTAATT
690391 TTTACTTAAATTATTTTTA
1 TTTACTTAAATTATTTTTA
*
690410 TTTATTTAAA-TATTTTT
1 TTTACTTAAATTATTTTT
690427 TGGTACCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTACTTAAATTATTTTTA
Found at i:703042 original size:17 final size:17
Alignment explanation
Indices: 703020--703054 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
703010 ACACACAACC
703020 GTGTCAC-CAGGCCATGT
1 GTGTCACAC-GGCCATGT
703037 GTGTCACACGGCCATGT
1 GTGTCACACGGCCATGT
703054 G
1 G
703055 ACAGCCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (17 bp):
GTGTCACACGGCCATGT
Found at i:709482 original size:6 final size:6
Alignment explanation
Indices: 709471--709498 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
709461 AGGGGGTTCT
709471 TCTTTC TCTTTC TCTTTC TCTTTC TCTT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTT
709499 CCTTAAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:709609 original size:134 final size:134
Alignment explanation
Indices: 709439--709713 Score: 496
Period size: 134 Copynumber: 2.1 Consensus size: 134
709429 GAAACATATT
709439 TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTTCTCTTCCTTA
1 TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTTCTCTTCCTTA
*
709504 AGTAGAATTTACTGATACTGTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGGT
66 AGTAGAATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGGT
709569 TTTC
131 TTTC
* *
709573 TGTATATGAGAGTGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTTCTCTTCCTTA
1 TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTTCTCTTCCTTA
* * *
709638 AGTGGAATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAGCTTGAAATTATATAGGGTT
66 AGTAGAATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGGT
709703 TTTC
131 TTTC
709707 TATATAT
1 TATATAT
709714 TTTTACCACC
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (134 bp):
TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTTCTCTTCCTTA
AGTAGAATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGGT
TTTC
Found at i:709616 original size:6 final size:6
Alignment explanation
Indices: 709605--709632 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
709595 AGGGGGTTCT
709605 TCTTTC TCTTTC TCTTTC TCTTTC TCTT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTT
709633 CCTTAAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:712115 original size:37 final size:37
Alignment explanation
Indices: 712074--712146 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
712064 ATAGCTAGTG
* *
712074 TGACTGAAAATGCAATGAGGTTAAAATTGTTTCCATT
1 TGACTGAAAATACAATCAGGTTAAAATTGTTTCCATT
* *
712111 TGACTGAAGATACACTCAGGTTAAAATTGTTTCCAT
1 TGACTGAAAATACAATCAGGTTAAAATTGTTTCCAT
712147 ACTCATTGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (37 bp):
TGACTGAAAATACAATCAGGTTAAAATTGTTTCCATT
Found at i:717395 original size:36 final size:37
Alignment explanation
Indices: 717315--717419 Score: 110
Period size: 36 Copynumber: 2.9 Consensus size: 37
717305 TTTTAATTCG
* * * *
717315 TTTTTATCTTT-TC-TTAGTTTTATTTTTA-TTTCTCA
1 TTTTAATCTTTATCTTTAATTTTAATTTTAGTTTC-AA
* *
717350 TTTTTATCTTTGTCTTTAATTTTAA-TTTAGTTTCAA
1 TTTTAATCTTTATCTTTAATTTTAATTTTAGTTTCAA
*
717386 TTTTAATCTTTATTTTTAATTTTAATTTTAGTTT
1 TTTTAATCTTTATCTTTAATTTTAATTTTAGTTT
717420 TATTTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
35 11 0.18
36 29 0.48
37 20 0.33
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.69
Consensus pattern (37 bp):
TTTTAATCTTTATCTTTAATTTTAATTTTAGTTTCAA
Found at i:717404 original size:13 final size:12
Alignment explanation
Indices: 717332--717426 Score: 61
Period size: 12 Copynumber: 7.8 Consensus size: 12
717322 CTTTTCTTAG
717332 TTTTATTTTT-A
1 TTTTATTTTTAA
717343 TTTCTCATTTTT-A
1 TTT-T-ATTTTTAA
* *
717356 TCTTTGTCTTTAA
1 T-TTTATTTTTAA
* *
717369 TTTTA-ATTTAG
1 TTTTATTTTTAA
* *
717380 TTTCAATTTTAA
1 TTTTATTTTTAA
717392 TCTTTATTTTTAA
1 T-TTTATTTTTAA
* *
717405 TTTTAATTTTAG
1 TTTTATTTTTAA
717417 TTTTATTTTT
1 TTTTATTTTT
717427 TTAATAAAGG
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
11 11 0.17
12 31 0.48
13 21 0.32
14 2 0.03
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:717427 original size:19 final size:18
Alignment explanation
Indices: 717364--717425 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 18
717354 TATCTTTGTC
717364 TTTAATTTTAA-TTTAGT
1 TTTAATTTTAATTTTAGT
* *
717381 TTCAATTTTAATCTTTATT
1 TTTAATTTTAAT-TTTAGT
717400 TTTAATTTTAATTTTAGT
1 TTTAATTTTAATTTTAGT
717418 TTT-ATTTT
1 TTTAATTTT
717426 TTTAATAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.38
18 8 0.21
19 16 0.41
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTAATTTTAATTTTAGT
Found at i:719709 original size:25 final size:25
Alignment explanation
Indices: 719675--719725 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
719665 TTAAAGGGGG
*
719675 ATAAAGGATTTTGCATGAATTTTTA
1 ATAAAGGATTTCGCATGAATTTTTA
*
719700 ATAAGGGATTTCGCATGAATTTTTA
1 ATAAAGGATTTCGCATGAATTTTTA
719725 A
1 A
719726 GTATGTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (25 bp):
ATAAAGGATTTCGCATGAATTTTTA
Found at i:723416 original size:50 final size:47
Alignment explanation
Indices: 723357--723482 Score: 155
Period size: 50 Copynumber: 2.6 Consensus size: 47
723347 ACATGCCAAA
**
723357 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGCCC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CC
** *
723405 ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCC
1 --GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC
* *
723454 -CCATATCCCAGATATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
723483 TCTCATTCCC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 25 0.37
49 2 0.03
50 40 0.60
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (47 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC
Found at i:736981 original size:29 final size:29
Alignment explanation
Indices: 736939--736999 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
736929 ACCTATGATG
736939 AATCTTATTATTTAATTTCTGCTTTACGC
1 AATCTTATTATTTAATTTCTGCTTTACGC
*
736968 AATCTTATTATTTAATTTTTGCTTTACGC
1 AATCTTATTATTTAATTTCTGCTTTACGC
736997 AAT
1 AAT
737000 AAATATTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (29 bp):
AATCTTATTATTTAATTTCTGCTTTACGC
Found at i:742606 original size:80 final size:80
Alignment explanation
Indices: 742469--742617 Score: 244
Period size: 80 Copynumber: 1.9 Consensus size: 80
742459 AAATTAGATC
* * *
742469 AATTAATCGACTGATTAACTAAATTAGATTGGTTTGATTGATTAATTTAGTTCTAATCGAAATTT
1 AATTAATCGACTGATTAACTAAATTAAATTGATTTGATTGATTAATTTAATTCTAATCGAAATTT
742534 AAACACTCTTACTAA
66 AAACACTCTTACTAA
* * *
742549 AATTAATCGATTGATTAACTAAATTAAATTGATTTGGTTGATTAATTTAATTTTAATCGAAATTT
1 AATTAATCGACTGATTAACTAAATTAAATTGATTTGATTGATTAATTTAATTCTAATCGAAATTT
742614 AAAC
66 AAAC
742618 CCTCATTGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (80 bp):
AATTAATCGACTGATTAACTAAATTAAATTGATTTGATTGATTAATTTAATTCTAATCGAAATTT
AAACACTCTTACTAA
Found at i:744858 original size:2 final size:2
Alignment explanation
Indices: 744853--744885 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
744843 CTCCCCCCCA
*
744853 TC TC TC TC TC TC TT TC 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 TC T
744886 AGTGCATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:749974 original size:24 final size:23
Alignment explanation
Indices: 749945--749991 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
749935 AAGTTTTTAT
749945 ATGTTTTTTAAATTTTAAATATTA
1 ATGTTTTTTAAATTTTAAA-ATTA
*
749969 ATGTTTTTTAATTTTTAAAATTA
1 ATGTTTTTTAAATTTTAAAATTA
749992 TTTATTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
ATGTTTTTTAAATTTTAAAATTA
Found at i:750680 original size:18 final size:18
Alignment explanation
Indices: 750631--750701 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
750621 TATTCTGTTT
*
750631 ATAAAAATATTAAAAATC
1 ATAAAAATATTAAAAATA
*
750649 ACAAAAAT-TATAAAAA-A
1 ATAAAAATAT-TAAAAATA
750666 ATAAAAATGATT--AAATA
1 ATAAAAAT-ATTAAAAATA
*
750683 TTAAAAATATTTAAAAATA
1 ATAAAAATA-TTAAAAATA
750702 TGAAAAGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
16 4 0.10
17 18 0.43
18 14 0.33
19 6 0.14
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (18 bp):
ATAAAAATATTAAAAATA
Found at i:750736 original size:9 final size:9
Alignment explanation
Indices: 750629--750798 Score: 81
Period size: 9 Copynumber: 19.1 Consensus size: 9
750619 AATATTCTGT
750629 TTATAAAAA
1 TTATAAAAA
750638 -TATTAAAAA
1 TTA-TAAAAA
* *
750647 TCACAAAAA
1 TTATAAAAA
750656 TTATAAAAA
1 TTATAAAAA
*
750665 -AATAAAAA
1 TTATAAAAA
* *
750673 TGATTAAATA
1 TTA-TAAAAA
750683 TTA-AAAATA
1 TTATAAAA-A
750692 TT-TAAAAA
1 TTATAAAAA
*
750700 -TATGAAAAG
1 TTAT-AAAAA
* * *
750709 TGATATGAAC
1 TTATA-AAAA
*
750719 TTATGAAAA
1 TTATAAAAA
750728 TTATAAAAA
1 TTATAAAAA
750737 -TATAAAATA
1 TTATAAAA-A
*
750746 TTATAAATA
1 TTATAAAAA
750755 TTATAAAAA
1 TTATAAAAA
*
750764 TCTA-ATAAA
1 T-TATAAAAA
*
750773 TCTA-ATAAA
1 T-TATAAAAA
750782 TTATAAAAA
1 TTATAAAAA
750791 --ATAAAAA
1 TTATAAAAA
750798 T
1 T
750799 AAAAAATAAA
Statistics
Matches: 124, Mismatches: 22, Indels: 31
0.70 0.12 0.18
Matches are distributed among these distances:
7 8 0.06
8 23 0.19
9 70 0.56
10 23 0.19
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TTATAAAAA
Found at i:750802 original size:13 final size:13
Alignment explanation
Indices: 750784--750809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
750774 CTAATAAATT
750784 ATAAAAAATAAAA
1 ATAAAAAATAAAA
750797 ATAAAAAATAAAA
1 ATAAAAAATAAAA
750810 CATATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:750832 original size:23 final size:23
Alignment explanation
Indices: 750806--750854 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
750796 AATAAAAAAT
750806 AAAA-CATATTTAAAATTTTATAA
1 AAAACCATA-TTAAAATTTTATAA
750829 AAAACCATATTAAAATTTTATAA
1 AAAACCATATTAAAATTTTATAA
750852 AAA
1 AAA
750855 TCATGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAACCATATTAAAATTTTATAA
Found at i:754627 original size:59 final size:59
Alignment explanation
Indices: 754564--754687 Score: 221
Period size: 59 Copynumber: 2.1 Consensus size: 59
754554 TTCACATAAA
* * *
754564 AAATTAACAAATATGAACCATTTTATATACCTGTGTACTTTCACATAACAAGTTAAAAC
1 AAATTAACAAATACGAACCATTTTATATACCTATGCACTTTCACATAACAAGTTAAAAC
754623 AAATTAACAAATACGAACCATTTTATATACCTATGCACTTTCACATAACAAGTTAAAAC
1 AAATTAACAAATACGAACCATTTTATATACCTATGCACTTTCACATAACAAGTTAAAAC
754682 AAATTA
1 AAATTA
754688 TATTATACCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.31
Consensus pattern (59 bp):
AAATTAACAAATACGAACCATTTTATATACCTATGCACTTTCACATAACAAGTTAAAAC
Found at i:756326 original size:42 final size:43
Alignment explanation
Indices: 756273--756358 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 43
756263 ATATGTTATA
*
756273 ATATATCGATGCCACTGTCCCAGACAGGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
*
756316 ATATAT-GATGCCAATGTCCCAGACATGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
756358 A
1 A
756359 CACCTCAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 35 0.85
43 6 0.15
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
Found at i:762542 original size:23 final size:22
Alignment explanation
Indices: 762499--762576 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
762489 CCACAGCTTA
* *
762499 TATGAGCTTACCATTTTAGCTC
1 TATGAGCTTACCGTTTCAGCTC
*
762521 TTATGAGCTTACTGTTTCAGCTC
1 -TATGAGCTTACCGTTTCAGCTC
*
762544 TACAGAGCTTACCG-TTCAGCTC
1 TA-TGAGCTTACCGTTTCAGCTC
*
762566 GATAGAGCTTA
1 TAT-GAGCTTA
762577 TTATTTACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 18 0.39
23 28 0.61
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (22 bp):
TATGAGCTTACCGTTTCAGCTC
Found at i:762564 original size:22 final size:23
Alignment explanation
Indices: 762525--762576 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
762515 TAGCTCTTAT
* *
762525 GAGCTTACTGTTTCAGCTCTACA
1 GAGCTTACCGTTTCAGCTCGACA
*
762548 GAGCTTACCG-TTCAGCTCGATA
1 GAGCTTACCGTTTCAGCTCGACA
762570 GAGCTTA
1 GAGCTTA
762577 TTATTTACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGACA
Found at i:769488 original size:23 final size:22
Alignment explanation
Indices: 769452--769518 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
769442 GACTCACCAT
769452 AGCTCATATGAGCTTACCGTTTC
1 AGCTC-TATGAGCTTACCGTTTC
* ** *
769475 AGTTCTTATGAGCTTACTATTTT
1 AGCTC-TATGAGCTTACCGTTTC
769498 AGCTCTATGGAGCTTACCGTT
1 AGCTCTAT-GAGCTTACCGTT
769519 CAACTTGATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (22 bp):
AGCTCTATGAGCTTACCGTTTC
Found at i:776039 original size:16 final size:15
Alignment explanation
Indices: 776009--776049 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
775999 ATCGAGTTGA
*
776009 GAAAATTATTTAATT
1 GAAAATTAATTAATT
776024 GAAAAGTTAATTAATT
1 GAAAA-TTAATTAATT
776040 -AAAATTAATT
1 GAAAATTAATT
776050 TATAACGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
16 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
GAAAATTAATTAATT
Found at i:779639 original size:15 final size:14
Alignment explanation
Indices: 779598--779633 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
779588 AAAGAAGAAT
779598 AAAAAAAACGAAACC
1 AAAAAAAA-GAAACC
779613 AAAAAAAAGAAACC
1 AAAAAAAAGAAACC
779627 AAAAAAA
1 AAAAAAA
779634 TGGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.81, C:0.14, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAACC
Found at i:780111 original size:42 final size:42
Alignment explanation
Indices: 780052--780188 Score: 222
Period size: 42 Copynumber: 3.3 Consensus size: 42
780042 AAGGAAAGCA
*
780052 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACCT
*
780094 TTCATTGCATTTAGAGGCCTAGATGTGGAGGTCCATTTACCT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACCT
* *
780136 TTCATTGCATTTAGAGGCCCAGGTG-GAGAGGTCCATTTACGT
1 TTCATTGCATTTAGAGGCCTAGGTGTG-GAGGTCCATTTACCT
780178 TTCATTGCATT
1 TTCATTGCATT
780189 GTATATGAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 1 0.01
42 88 0.99
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACCT
Found at i:780639 original size:3 final size:3
Alignment explanation
Indices: 780633--780676 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
780623 TTATTATCAT
*
780633 TAC TAC TAC TAC TAC TAC TAC TAC TAC TGC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
780677 AATATTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:780805 original size:3 final size:3
Alignment explanation
Indices: 780799--780827 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
780789 AAGAGTAAAA
780799 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
780828 GTATTCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:781338 original size:21 final size:21
Alignment explanation
Indices: 781314--781353 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
781304 AGAAAAATAA
* *
781314 TGATTTTTTAAAAGAAAATTT
1 TGATTTTTCAAAACAAAATTT
781335 TGATTTTTCAAAACAAAAT
1 TGATTTTTCAAAACAAAAT
781354 ATTTTTAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
TGATTTTTCAAAACAAAATTT
Found at i:800952 original size:21 final size:21
Alignment explanation
Indices: 800885--800953 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
800875 GCATTGAAGA
* * *
800885 GTGTTGTGGCTACATCTGATT
1 GTGTTGTGGATGCATCTGAGT
* *
800906 CTGGTGTGGATGCATCTG-GCT
1 GTGTTGTGGATGCATCTGAG-T
*
800927 TTGTTGTGGATGCATCTGAGT
1 GTGTTGTGGATGCATCTGAGT
800948 GTGTTG
1 GTGTTG
800954 ATTATAGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.12, C:0.13, G:0.35, T:0.41
Consensus pattern (21 bp):
GTGTTGTGGATGCATCTGAGT
Found at i:806820 original size:50 final size:50
Alignment explanation
Indices: 806682--806820 Score: 170
Period size: 50 Copynumber: 2.8 Consensus size: 50
806672 GACAAGAACA
* ** *
806682 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTATCATATCGG
* * ** *
806733 TACCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTATCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATATCGG
* *
806783 TGCCAATGGCATGTCCCAGAAATGGTCTTACATGGGAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAC
806821 ATCTTTACCC
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 41 0.56
51 32 0.44
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATATCGG
Found at i:811457 original size:149 final size:150
Alignment explanation
Indices: 811188--811487 Score: 593
Period size: 149 Copynumber: 2.0 Consensus size: 150
811178 AGTTAAAAAG
811188 AAAACAAATACATTTTACCATCAGTGGACAATTTTTACAAACTTTATCCACCACCACAAACTGGC
1 AAAACAAATACATTTTACCATCAGTGGACAATTTTTACAAACTTTATCCACCACCACAAACTGGC
811253 CCAGGGGGTTCGAGACTTTAACCATAAATTCAGTAGGTTCAACAGACAAATTTTTAACAAATACT
66 CCAGGGGGTTCGAGACTTTAACCATAAATTCAGTAGGTTCAACAGACAAATTTTTAACAAATACT
811318 AATTTTGTGCATATGTATGA
131 AATTTTGTGCATATGTATGA
811338 AAAACAAATA-ATTTTACCATCAGTGGACAATTTTTACAAACTTTATCCACCACCACAAACTGGC
1 AAAACAAATACATTTTACCATCAGTGGACAATTTTTACAAACTTTATCCACCACCACAAACTGGC
811402 CCAGGGGGTTCGAGACTTTAACCATAAATTCAGTAGGTTCAACAGACAAATTTTTAACAAATACT
66 CCAGGGGGTTCGAGACTTTAACCATAAATTCAGTAGGTTCAACAGACAAATTTTTAACAAATACT
811467 AATTTTGTGCATATGTATGA
131 AATTTTGTGCATATGTATGA
811487 A
1 A
811488 TGTGTAGAGC
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 140 0.93
150 10 0.07
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (150 bp):
AAAACAAATACATTTTACCATCAGTGGACAATTTTTACAAACTTTATCCACCACCACAAACTGGC
CCAGGGGGTTCGAGACTTTAACCATAAATTCAGTAGGTTCAACAGACAAATTTTTAACAAATACT
AATTTTGTGCATATGTATGA
Found at i:816049 original size:26 final size:26
Alignment explanation
Indices: 816018--816483 Score: 447
Period size: 26 Copynumber: 17.7 Consensus size: 26
816008 GTAATGGGCC
816018 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
816044 TAAATTACCGAAATACCCTCGTTGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
816070 TAAATTACCGAAATACCCTTGATAGG
1 TAAATTACCGAAATACCCTCGATGGG
* * *
816096 TAAATTACTGAAATACCTTTGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
816122 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
816148 TAAATTACTGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
816174 TAAATTATCGAAATACCCACGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
816200 TAAATT-CTTGAAATACCCTCGATGGG
1 TAAATTAC-CGAAATACCCTCGATGGG
816226 TAAATT-CTCGAAATACCCTCGATGGG
1 TAAATTAC-CGAAATACCCTCGATGGG
*
816252 TAAATTACTGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* * * *
816278 TAAAATTACCAAAATACCCT-AAAGAG
1 T-AAATTACCGAAATACCCTCGATGGG
* *
816304 TAAAATTATCGAAATACCCCCGA-GGTG
1 T-AAATTACCGAAATACCCTCGATGG-G
** *
816331 TAAAATT-TTGAAATACCCTCGATGTG
1 T-AAATTACCGAAATACCCTCGATGGG
* * ** *
816357 TAAAATGACAGAAATACCCTTAAAGGG
1 T-AAATTACCGAAATACCCTCGATGGG
* * * **
816384 TAAAATGACCCAAATATCCTCGAAAGG
1 T-AAATTACCGAAATACCCTCGATGGG
* * *
816411 TAAAATGATCGAAATACCCTCGAAGGG
1 T-AAATTACCGAAATACCCTCGATGGG
* * * *
816438 TAAAATGACCGACATACCCCCGAAGGG
1 T-AAATTACCGAAATACCCTCGATGGG
* *
816465 TAAAATAACCAAAATACCC
1 T-AAATTACCGAAATACCC
816484 CCATAGGGTA
Statistics
Matches: 378, Mismatches: 55, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
26 254 0.67
27 124 0.33
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (26 bp):
TAAATTACCGAAATACCCTCGATGGG
Found at i:816415 original size:54 final size:55
Alignment explanation
Indices: 816356--816500 Score: 170
Period size: 54 Copynumber: 2.7 Consensus size: 55
816346 CCCTCGATGT
* * *
816356 GTAAAATGA-CAGAAATACCCTTAAAGGGTAAAATGACCCAAATATCCTCGAAAG
1 GTAAAATGACCAGAAATACCCTCAAAGGGTAAAATGACCCAAATACCCCCGAAAG
* * * * *
816410 GTAAAATGATC-GAAATACCCTCGAAGGGTAAAATGACCGACATACCCCCGAAGG
1 GTAAAATGACCAGAAATACCCTCAAAGGGTAAAATGACCCAAATACCCCCGAAAG
* * *
816464 GTAAAATAACCA-AAATACCCCCATAGGGTAAAATGAC
1 GTAAAATGACCAGAAATACCCTCAAAGGGTAAAATGAC
816501 TATTATACCC
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 76 0.99
55 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (55 bp):
GTAAAATGACCAGAAATACCCTCAAAGGGTAAAATGACCCAAATACCCCCGAAAG
Found at i:816494 original size:81 final size:80
Alignment explanation
Indices: 816261--816499 Score: 248
Period size: 81 Copynumber: 3.0 Consensus size: 80
816251 GTAAATTACT
* * * * * *
816261 GAAATACCCTCGATGGGTAAAATTACCAAAATA-CCCTAAAGAGTAAAATTATCGAAATACCCCC
1 GAAATACCCTCGATGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAATAACCAAAATACCCCC
* * *
816325 GAGGTGTAAAAT-TTT
66 AAGG-GTAAAATGATC
* * * * * *
816340 GAAATACCCTCGATGTGTAAAATGACAGAAATACCCTTAAAGGGTAAAATGACCCAAATATCCTC
1 GAAATACCCTCGATGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAATAACCAAAATA-CCCC
* *
816405 GAAAGGTAAAATGATC
65 CAAGGGTAAAATGATC
* * **
816421 GAAATACCCTCGAAGGGTAAAATGACCGACATACCCCCGAAGGGTAAAATAACCAAAATACCCCC
1 GAAATACCCTCGATGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAATAACCAAAATACCCCC
816486 ATAGGGTAAAATGA
66 A-AGGGTAAAATGA
816500 CTATTATACC
Statistics
Matches: 129, Mismatches: 27, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
79 29 0.22
80 32 0.25
81 68 0.53
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.20
Consensus pattern (80 bp):
GAAATACCCTCGATGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAATAACCAAAATACCCCC
AAGGGTAAAATGATC
Found at i:816511 original size:27 final size:26
Alignment explanation
Indices: 816236--816500 Score: 142
Period size: 27 Copynumber: 10.0 Consensus size: 26
816226 TAAATTCTCG
* * * *
816236 AAATACCCTCGATGGGT-AAATTACTG
1 AAATACCCCCGAAGGGTAAAATGAC-C
* * *
816262 AAATACCCTCGATGGGTAAAATTACC
1 AAATACCCCCGAAGGGTAAAATGACC
** * * *
816288 AAAATA-CCCTAAAGAGTAAAATTATCG
1 -AAATACCCCCGAAGGGTAAAATGA-CC
****
816315 AAATACCCCCG-AGGTGTAAAATTTTG
1 AAATACCCCCGAAGG-GTAAAATGACC
* * * *
816341 AAATACCCTCGATGTGTAAAATGACAG
1 AAATACCCCCGAAGGGTAAAATGAC-C
***
816368 AAATACCCTTAAAGGGTAAAATGACCC
1 AAATACCCCCGAAGGGTAAAATGA-CC
* * * *
816395 AAATATCCTCGAAAGGTAAAATGATCG
1 AAATACCCCCGAAGGGTAAAATGA-CC
*
816422 AAATACCCTCGAAGGGTAAAATGACC
1 AAATACCCCCGAAGGGTAAAATGACC
* *
816448 GACATACCCCCGAAGGGTAAAATAACC
1 -AAATACCCCCGAAGGGTAAAATGACC
816475 AAAATACCCCC-ATAGGGTAAAATGAC
1 -AAATACCCCCGA-AGGGTAAAATGAC
816501 TATTATACCC
Statistics
Matches: 191, Mismatches: 38, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
26 57 0.30
27 133 0.70
28 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (26 bp):
AAATACCCCCGAAGGGTAAAATGACC
Found at i:816682 original size:27 final size:27
Alignment explanation
Indices: 816644--816717 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
816634 ATGGAGGAAG
*
816644 TACTATTACTGGTGGCTCTGCCACA-A
1 TACTGTTACTGGTGGCTCTGCCACATA
*
816670 TTACTGTTACTGGTGGCTTTGCCACATA
1 -TACTGTTACTGGTGGCTCTGCCACATA
**
816698 TACTG-TACTGGCAGCTCTGC
1 TACTGTTACTGGTGGCTCTGC
816718 TGCGATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.29
27 28 0.68
28 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTCTGCCACATA
Found at i:816751 original size:26 final size:26
Alignment explanation
Indices: 816703--816752 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
816693 ACATATACTG
* *
816703 TACTGGCAGCTCTGCTGCGATATTAT
1 TACTGGCAGCTATGCTGCAATATTAT
*
816729 TACTGGCAGCTATGTTGCAATATT
1 TACTGGCAGCTATGCTGCAATATT
816753 GGTGTATGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCAATATTAT
Found at i:832530 original size:13 final size:13
Alignment explanation
Indices: 832499--832536 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
832489 AAGAAAGAAA
*
832499 GAGGATTTTGGAT
1 GAGGATTTTGGAG
832512 GAGGATTTTGGAG
1 GAGGATTTTGGAG
*
832525 GGGGA-TTTGGAG
1 GAGGATTTTGGAG
832537 AATAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (13 bp):
GAGGATTTTGGAG
Found at i:834241 original size:27 final size:27
Alignment explanation
Indices: 834203--834255 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
834193 CTGTGGTTCA
834203 CAATGATGACAACGAACTCATTCCAAG
1 CAATGATGACAACGAACTCATTCCAAG
834230 CAATGATGACAACGAACTCATTCCAA
1 CAATGATGACAACGAACTCATTCCAA
834256 CTCGTACTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (27 bp):
CAATGATGACAACGAACTCATTCCAAG
Found at i:840258 original size:13 final size:13
Alignment explanation
Indices: 840227--840264 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
840217 AAAGAAAACA
*
840227 GAGGATTTTGGAT
1 GAGGATTTTGGAG
840240 GAGGATTTTGGAG
1 GAGGATTTTGGAG
*
840253 GGGGA-TTTGGAG
1 GAGGATTTTGGAG
840265 AGCAGTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (13 bp):
GAGGATTTTGGAG
Found at i:842754 original size:50 final size:50
Alignment explanation
Indices: 842603--842897 Score: 256
Period size: 50 Copynumber: 5.8 Consensus size: 50
842593 GACAATAACA
* * ** * *
842603 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCT-CGG
* ** * * * * * ** *
842652 TACCAATTCCATATCCCAAATATGATCTTA-ATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
842701 TGCCCATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
842751 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
842801 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGAACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
842855 ATGCCAATGCCATGTCTCAGACATGGTCTTACAGGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
842898 TTACCCAAAT
Statistics
Matches: 202, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
47 1 0.00
48 12 0.06
49 55 0.27
50 91 0.45
52 5 0.02
54 2 0.01
55 30 0.15
56 6 0.03
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:850286 original size:50 final size:50
Alignment explanation
Indices: 850162--850509 Score: 272
Period size: 50 Copynumber: 6.8 Consensus size: 50
850152 GATAATAACA
* * ** * *
850162 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTTCATGAAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATCGG
* ** * * **
850211 TACCAGTGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
850261 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * *
850311 TGTCAACGCTATGTCCTAGACATGGTCTTACATGGGACCTCTCGA-CTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-ATATCGG
* * * *
850361 TGCCAACGCCATGTCCCAGACATTGGTCTTACATAGGACCTCTCGTCTCCG
1 TGCCAACGCCATGTCCCAGACA-TGGTCTTACATGGGACCTCTCATATCGG
* * * *
850412 TGCCAACGCCATGTCTCAAACATGATCTTACCTGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
* * *
850467 ATGCCAATGCCATGTCTCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
850510 TTACCCAAAT
Statistics
Matches: 239, Mismatches: 47, Indels: 19
0.78 0.15 0.06
Matches are distributed among these distances:
48 2 0.01
49 37 0.15
50 113 0.47
51 47 0.20
53 2 0.01
55 1 0.00
56 37 0.15
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:850403 original size:51 final size:51
Alignment explanation
Indices: 850218--850509 Score: 279
Period size: 50 Copynumber: 5.7 Consensus size: 51
850208 AACTACCAGT
* * ** * * *
850218 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTC-ATATCGGTGTCC-AT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGTG-CCAAC
** ** *
850268 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTC-ATCTTGGTGTCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGTGCCAAC
* *
850318 GCTATGTCCTAGACATGGTCTTACATGGGACCTCTCGA-CTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGTGCCAAC
* *
850368 GCCATGTCCCAGACATTGGTCTTACATAGGACCTCTCG-TCTCCGTGCCAAC
1 GCCATGTCCCAGACA-TGGTCTTACATGGGACCTCTCGATCTCAGTGCCAAC
* * * * *
850419 GCCATGTCTCAAACATGATCTTACCTGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--GATCTC-A-G-TGCCAAC
* *
850475 GCCATGTCTCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
850510 TTACCCAAAT
Statistics
Matches: 200, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.00
50 110 0.55
51 46 0.23
52 1 0.00
53 4 0.02
55 1 0.00
56 37 0.19
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (51 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGTGCCAAC
Found at i:850435 original size:101 final size:105
Alignment explanation
Indices: 850268--850509 Score: 289
Period size: 101 Copynumber: 2.3 Consensus size: 105
850258 CGGTGTCCAT
** ** * * *
850268 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGTCAACGCTATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGTGCCAACGCCATGTCCTAAACA
*
850333 TGGTCTTACATGGGACCTCTC-GA-CTC-A-G-TGCCAAC
66 TGATCTTACATGGGACCTCTCAGATCTCAAGGATGCCAAC
* *
850368 GCCATGTCCCAGACATTGGTCTTACATAGGACCTCTCGTCTCCGTGCCAACGCCATGT-CTCAAA
1 GCCATGTCCCAGACA-TGGTCTTACATGGGACCTCTCATCTCCGTGCCAACGCCATGTCCT-AAA
* *
850432 CATGATCTTACCTGGGACCTCTCATGATCTCAAGGATGCCAAT
64 CATGATCTTACATGGGACCTCTCA-GATCTCAAGGATGCCAAC
* *
850475 GCCATGTCTCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
850510 TTACCCAAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
100 17 0.14
101 57 0.48
103 2 0.02
104 3 0.03
105 1 0.01
106 19 0.16
107 20 0.17
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (105 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGTGCCAACGCCATGTCCTAAACA
TGATCTTACATGGGACCTCTCAGATCTCAAGGATGCCAAC
Found at i:858413 original size:21 final size:21
Alignment explanation
Indices: 858389--858434 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
858379 ATAAATTAGT
858389 TTAGAGTTTTTAAGTTAAGGG
1 TTAGAGTTTTTAAGTTAAGGG
*
858410 TTAGATTTTTTAAGTTAAGGG
1 TTAGAGTTTTTAAGTTAAGGG
858431 TTAG
1 TTAG
858435 GGTTAGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
TTAGAGTTTTTAAGTTAAGGG
Found at i:858438 original size:6 final size:6
Alignment explanation
Indices: 858427--858482 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
858417 TTTTAAGTTA
*** *
858427 AGGGTT AGGGTT AGGGTT AGGGTT TTTGTT AGGGTTT AAGGTTT AGGGTT
1 AGGGTT AGGGTT AGGGTT AGGGTT AGGGTT AGGG-TT -AGGGTT AGGGTT
858477 AGGGTT
1 AGGGTT
858483 TTTGTTAGGG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 33 0.82
7 4 0.10
8 3 0.08
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (6 bp):
AGGGTT
Found at i:870024 original size:3 final size:3
Alignment explanation
Indices: 870016--870054 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
870006 ATCTTAGTCC
870016 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
870055 AAATGTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:872570 original size:17 final size:17
Alignment explanation
Indices: 872548--872587 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
872538 GATACAGGGG
872548 ACACACAACCGTGTGTC
1 ACACACAACCGTGTGTC
** *
872565 ACACACAGTCGTGTGTG
1 ACACACAACCGTGTGTC
872582 ACACAC
1 ACACAC
872588 GGCTGAGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (17 bp):
ACACACAACCGTGTGTC
Found at i:881968 original size:29 final size:28
Alignment explanation
Indices: 881922--881976 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
881912 AAAAATCCAG
*
881922 AAAATTAACATCACAAAAAAACCCATAA
1 AAAATTAACATAACAAAAAAACCCATAA
*
881950 AAAAGTTAACATAATAAAAAAACCCAT
1 AAAA-TTAACATAACAAAAAAACCCAT
881977 CAATCTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.64, C:0.18, G:0.02, T:0.16
Consensus pattern (28 bp):
AAAATTAACATAACAAAAAAACCCATAA
Found at i:886912 original size:43 final size:43
Alignment explanation
Indices: 886878--886960 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
886868 CTTACATGTT
* *
886878 ATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACACATA
1 ATCACATATCGATGCCAATGTCCAAGACAGGGTCTTACACATA
* *
886921 ATCTCATATCGATGCCAATGTCCAAGACATGGTCTTACAC
1 ATCACATATCGATGCCAATGTCCAAGACAGGGTCTTACAC
886961 GAAATCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
ATCACATATCGATGCCAATGTCCAAGACAGGGTCTTACACATA
Found at i:889191 original size:76 final size:76
Alignment explanation
Indices: 889104--889308 Score: 383
Period size: 76 Copynumber: 2.7 Consensus size: 76
889094 TACGATGGAA
889104 TCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGAAACCCCTTTCACATTTAAGA
1 TCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGAAACCCCTTTCACATTTAAGA
889169 GACGGTGGGGG
66 GACGGTGGGGG
889180 TCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGAAACCCCTTTCACATTTAAGA
1 TCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGAAACCCCTTTCACATTTAAGA
889245 GACGGTGGGGG
66 GACGGTGGGGG
* * *
889256 TCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
1 TCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGAAACCCCTT
889309 GGGGGAATCA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 126 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (76 bp):
TCAGCACTTAGCAACCACCAATGAATCAGGGAATTAGCACTTAGAAACCCCTTTCACATTTAAGA
GACGGTGGGGG
Found at i:891969 original size:16 final size:17
Alignment explanation
Indices: 891945--891977 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
891935 AGAATAAAAG
891945 AAAAGGAAAAAG-GAAA
1 AAAAGGAAAAAGTGAAA
*
891961 AAAATGAAAAAGTGAAA
1 AAAAGGAAAAAGTGAAA
891978 TAGAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
AAAAGGAAAAAGTGAAA
Found at i:895258 original size:43 final size:43
Alignment explanation
Indices: 895196--895459 Score: 321
Period size: 43 Copynumber: 6.1 Consensus size: 43
895186 TTTTAGAAAT
* *
895196 AAACGCCGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
* *
895239 AAACGCCGCTATAGGCCATGACCTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
** * * * *
895282 AAACGTTGCTATAGAACATGATCTTTAGCGACGCTTCTCCCGC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
* * * *
895325 AAACGCAGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
* * * * *
895368 AAACGCCGCTATAGGCCATAACCTTTAGCAGCACTTTTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
* * **
895411 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
895454 AAACGC
1 AAACGC
895460 AAAAGTTACG
Statistics
Matches: 187, Mismatches: 34, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 187 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTCTCCCAC
Found at i:895431 original size:129 final size:129
Alignment explanation
Indices: 895196--895460 Score: 386
Period size: 129 Copynumber: 2.1 Consensus size: 129
895186 TTTTAGAAAT
* *
895196 AAACGCCGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGGCCATGAC
1 AAACGCAGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGGCCATAAC
** * ** * * *
895261 CTTTAGTGGCGCTTCTCCCACAAACGTTGCTATAGAACATGATCTTTAGCGACGCTTCTCCCGC
66 CTTTAGCAGCACTTCTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTCTCCCAC
*
895325 AAACGCAGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCATAAACGCCGCTATAGGCCATAAC
1 AAACGCAGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGGCCATAAC
* * ** *
895390 CTTTAGCAGCACTTTTCCCACAAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTCTCCCAC
66 CTTTAGCAGCACTTCTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTCTCCCAC
895454 AAACGCA
1 AAACGCA
895461 AAAGTTACGA
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (129 bp):
AAACGCAGCTATAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGGCCATAAC
CTTTAGCAGCACTTCTCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGCTTCTCCCAC
Found at i:895675 original size:43 final size:43
Alignment explanation
Indices: 895604--895712 Score: 148
Period size: 43 Copynumber: 2.5 Consensus size: 43
895594 CTGGAGTTCT
**
895604 GGCCATGACCTTTAGCGGTACTTCTCCCACAAACG-CTACTATA
1 GGCCATGACCTTTAGCGGCGCTTCTCCCACAAACGTC-ACTATA
* *
895647 GGCCATGACCTTTAGCGGCGCTTTTCCCACAAACGTCACTGTA
1 GGCCATGACCTTTAGCGGCGCTTCTCCCACAAACGTCACTATA
* *
895690 GGCCATAACTTTTAGCGGCGCTT
1 GGCCATGACCTTTAGCGGCGCTT
895713 GGTTTAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (43 bp):
GGCCATGACCTTTAGCGGCGCTTCTCCCACAAACGTCACTATA
Found at i:896131 original size:87 final size:87
Alignment explanation
Indices: 896037--896209 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 87
896027 TCTGCTCTGC
* * * **
896037 TCTGCTTCCCTTGTTGCAGCCTCTGCTTTTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
1 TCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
*
896102 TTCTTCATATTTCTTTTGAACA
66 TTCTTCATATTTCCTTTGAACA
* * *
896124 TCTGCTTCTCTCGCTGCAGCCTCTACTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAG
1 TCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
896189 TTCTTCATATTTCCTTTGAAC
66 TTCTTCATATTTCCTTTGAAC
896210 CTCAACTGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (87 bp):
TCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
TTCTTCATATTTCCTTTGAACA
Found at i:896152 original size:21 final size:21
Alignment explanation
Indices: 896128--896168 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
896118 TGAACATCTG
*
896128 CTTCTCTCGCTGCAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTA
*
896149 CTTCCCTCGCTGCCGCCTCT
1 CTTCCCTCGCTGCAGCCTCT
896169 GCTTTAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.49, G:0.15, T:0.32
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTA
Found at i:896337 original size:21 final size:21
Alignment explanation
Indices: 896313--896356 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
896303 AGTTTATATA
*
896313 TAAGTT-TCTATATAAGTTATG
1 TAAGTTAT-TATATAAGTGATG
*
896334 TAAGTTATTATGTAAGTGATG
1 TAAGTTATTATATAAGTGATG
896355 TA
1 TA
896357 TTATGTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (21 bp):
TAAGTTATTATATAAGTGATG
Found at i:897461 original size:14 final size:14
Alignment explanation
Indices: 897442--897468 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
897432 ACAGAAACCT
897442 GAATAACAAAATCC
1 GAATAACAAAATCC
897456 GAATAACAAAATC
1 GAATAACAAAATC
897469 TGAAATATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.15
Consensus pattern (14 bp):
GAATAACAAAATCC
Found at i:897740 original size:21 final size:21
Alignment explanation
Indices: 897716--897759 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
897706 GATGAGACAG
897716 CGATGGTGATGAAGCAGGCGA
1 CGATGGTGATGAAGCAGGCGA
897737 CGATGGTGATGAAGCAGGCGA
1 CGATGGTGATGAAGCAGGCGA
897758 CG
1 CG
897760 GTGACGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.43, T:0.14
Consensus pattern (21 bp):
CGATGGTGATGAAGCAGGCGA
Found at i:898153 original size:147 final size:147
Alignment explanation
Indices: 898002--898614 Score: 469
Period size: 147 Copynumber: 4.2 Consensus size: 147
897992 GACTTAATCT
*
898002 TGGCGTTTTGGCATAAAACGCCACTCATAACATTGG-AAAACGACGACGTTTTCCATGACTAAAC
1 TGGCGTTTTGGCATAAAACGCCACTCATAACA-TGGAAAAACGACGACGTATTCCATGACTAAAC
* *
898066 TAACAAATTTGCGGCATTTCTACATAAGCGCCACTAAA-TAACCCTGGAAACGATGTTGTTT-CC
65 TAACAAATTTGCGGCATTTATACATAAGCGCCACTAAACTAACCCTGGAAACGATGTCGTTTCCC
*
898129 AAACACTTACGAAAAATTTC
130 AAACAATTA-GAAAAA-TTC
* * * * * *
898149 TGGCGTTTTGGTATAAAACGCCACT-ACTAAC-TAGAAAAATGACAACGTATTCC-TGACTGAAT
1 TGGCGTTTTGGCATAAAACGCCACTCA-TAACATGGAAAAACGACGACGTATTCCATGACTAAAC
* ** * * * *** * * * ** **
898211 TTACCTATTTGCGGCGTGTATACACAAGCGCCAC-AAACTAAAAGTAGAAACGCTATATTTTAAC
65 TAACAAATTTGCGGCATTTATACATAAGCGCCACTAAACTAACCCTGGAAACGATGTCGTTTCCC
** * *
898275 AGCCAATTAGTCAAAATTG
130 AAACAATTAG-AAAAATTC
* * * * *
898294 TGGCGTTTAGGCATAAAACGCCAGTCACAACATGGAAAAACGACGACGTTTTCCATGACTAAACG
1 TGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGACTAAACT
* * * * * * * * * *
898359 AAGAACTTTGCAGCGTTTACACGTAAGCGCCACTAAATTAACCGTGGAAACAAAGTCGTTTCCCA
66 AACAAATTTGCGGCATTTATACATAAGCGCCACTAAACTAACCCTGGAAACGATGTCGTTTCCCA
*
898424 AACAATTAGGACAACATTC
131 AACAATTA-GA-AAAATTC
* * * * *
898443 TGGCGTTTTGGTATAAAATGCCACTAAGAACATGGAAAAACGACGACATATT-CATGACTAAA-T
1 TGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGACTAAACT
** * * ** * *
898506 GAACCCATTCGCGGCATTGATA-ATCTTGTGCCACTAAA-TAA--CTGCAGAAACGACGTCGTTT
66 -AACAAATTTGCGGCATTTATACAT-AAGCGCCACTAAACTAACCCTG--GAAACGATGTCGTTT
* *
898567 CCCACACAATTATGTAAATATTC
127 CCCAAACAATTA-G-AAAAATTC
898590 TGGCGTTTTGGCATAAAACGCCACT
1 TGGCGTTTTGGCATAAAACGCCACT
898615 AAGAACATAG
Statistics
Matches: 354, Mismatches: 96, Indels: 32
0.73 0.20 0.07
Matches are distributed among these distances:
144 3 0.01
145 81 0.23
146 46 0.13
147 116 0.33
148 58 0.16
149 50 0.14
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (147 bp):
TGGCGTTTTGGCATAAAACGCCACTCATAACATGGAAAAACGACGACGTATTCCATGACTAAACT
AACAAATTTGCGGCATTTATACATAAGCGCCACTAAACTAACCCTGGAAACGATGTCGTTTCCCA
AACAATTAGAAAAATTC
Found at i:898703 original size:147 final size:146
Alignment explanation
Indices: 898002--898774 Score: 462
Period size: 147 Copynumber: 5.3 Consensus size: 146
897992 GACTTAATCT
* * * * * * *
898002 TGGCGTTTTGGCATAAAACGCCACTCATAACATTGGAAAACGACGACGTTTTCCATGACTAAACT
1 TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAAACGACGACATATT-CATGACTAAA-T
** * * * * * * *
898067 -AACAAATTTGCGGCATTTCTACATAAGCGCCACTAAATAACCCTGGAAACGATGTTGTTT-CCA
64 GAACCCATTTGCGGCGTTTATACGTATGCGCCACTAAATAACCGT-GAAACGACGTCGTTTCCCA
* * * *
898130 AACACTTACGA-AAAATTTC
128 CACAATTAGGACAATA-TTC
* * ** * * * * * **
898149 TGGCGTTTTGGTATAAAACGCCACTACTAAC-TAGAAAAATGACAACGTATTCCTGACTGAATTT
1 TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAAACGACGACATATTCATGACTAAATGA
* * ** * ** * ** **
898213 ACCTATTTGCGGCGTGTATACACAAGCGCCAC-AAACTAAAAGTAGAAACG-CTATATTTTAACA
66 ACCCATTTGCGGCGTTTATACGTATGCGCCACTAAA-TAACCGT-GAAACGAC-GTCGTTTCCCA
* * *
898276 GC-CAATTA-GTCAAAATTG
128 -CACAATTAGGACAATATTC
* * * * * * * * *
898294 TGGCGTTTAGGCATAAAACGCCAGTCACAACATGGAAAAACGACGACGTTTTCCATGACTAAACG
1 TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAAACGACGACATATT-CATGACTAAATG
** * * * * *
898359 AA-GAACTTTGCAGCGTTTACACGTAAGCGCCACTAAATTAACCGTGGAAACAAAGTCGTTTCCC
65 AACCCA-TTTGCGGCGTTTATACGTATGCGCCACTAAA-TAACCGT-GAAACGACGTCGTTTCCC
* *
898423 AAACAATTAGGACAACATTC
127 ACACAATTAGGACAATATTC
* *
898443 TGGCGTTTTGGTATAAAATGCCACTAAGAACATGGAAAAACGACGACATATTCATGACTAAATGA
1 TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAAACGACGACATATTCATGACTAAATGA
* * * * * *
898508 ACCCATTCGCGGCATTGATAATC-T-TGTGCCACTAAATAACTGCAGAAACGACGTCGTTTCCCA
66 ACCCATTTGCGGCGTTTAT-A-CGTATGCGCCACTAAATAACCG-TGAAACGACGTCGTTTCCCA
*
898571 CACAATTATGTA-AATATTC
128 CACAATTA-GGACAATATTC
* * * * * ** *
898590 TGGCGTTTTGGCATAAAACGCCACTAAGAACATAGTAATACGATGCCAT-TTTTTGGGATTAAAT
1 TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAAACGACGACATATTCAT--GACTAAAT
* * *
898654 TAACCCGTTTGCGGCGTTTATACGTATGCACCACTAAATAACCGTGAAACG-CTGTCGTTTCCC-
64 GAACCCATTTGCGGCGTTTATACGTATGCGCCACTAAATAACCGTGAAACGAC-GTCGTTTCCCA
* * *
898717 CGATAATTAGGACAATTTTG
128 C-ACAATTAGGACAATATTC
*
898737 TGGCGTTTTTGCATAAAATGCCACTAAGAACAT-GAAAA
1 TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAA
898775 TTTTGAAAAA
Statistics
Matches: 482, Mismatches: 119, Indels: 51
0.74 0.18 0.08
Matches are distributed among these distances:
144 4 0.01
145 76 0.16
146 54 0.11
147 196 0.41
148 97 0.20
149 54 0.11
150 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (146 bp):
TGGCGTTTTGGCATAAAATGCCACTAAGAACATAGAAAAACGACGACATATTCATGACTAAATGA
ACCCATTTGCGGCGTTTATACGTATGCGCCACTAAATAACCGTGAAACGACGTCGTTTCCCACAC
AATTAGGACAATATTC
Done.