Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 145 of 187
Found at i:43364473 original size:42 final size:42
Alignment explanation
Indices: 43364427--43364694 Score: 387
Period size: 42 Copynumber: 6.4 Consensus size: 42
43364417 AAAAATGCCA
* *
43364427 CTAAAGACCATGTTCTTTAGCGGCGTTTTTATCCAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTATCCAAGCGCCG
*
43364469 CTAAAGAACATGGTCTTTAGCGGCGTTTTAATCCAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTATCCAAGCGCCG
*
43364511 CTAAAGAACATGGTCTTTAGCGGCGTTTTAATCCAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTATCCAAGCGCCG
* * * *
43364553 CTAAAGAACATGGTCTTTAGTGGCATTTGTATCAAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTATCCAAGCGCCG
* * *
43364595 CTAAAGAACATGGTCTTTAGAGGCGTTTTT-TACTAAGCGCCA
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTAT-CCAAGCGCCG
* *
43364637 CTAAAGAACATGGTCTTTAGAGGCGTTTTT-TACTAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTAT-CCAAGCGCCG
43364679 CTAAAGAACATGGTCT
1 CTAAAGAACATGGTCT
43364695 GGCGTTTTTA
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
41 1 0.00
42 210 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (42 bp):
CTAAAGAACATGGTCTTTAGCGGCGTTTTTATCCAAGCGCCG
Found at i:43364486 original size:84 final size:82
Alignment explanation
Indices: 43364381--43364694 Score: 348
Period size: 84 Copynumber: 3.7 Consensus size: 82
43364371 CAAAAAAAAT
* * ** * * *
43364381 GCCGCTAAAGACCATGTTCTTTAGCGGTGCTTTGGTAAAAATGCCACTAAAGACCATGTTCTTTA
1 GCCGCTAAAGAACATGGTCTTTAGCGG-GCTTT-GTAAAAGCGCCGCTAAAGAACATGGTCTTTA
43364446 GCGGCGTTTTTATCCAAGC
64 GCGGCGTTTTTATCCAAGC
43364465 GCCGCTAAAGAACATGGTCTTTAGC-GGCGTTT-TAATCCAAGCGCCGCTAAAGAACATGGTCTT
1 GCCGCTAAAGAACATGGTCTTTAGCGGGC-TTTGTAA---AAGCGCCGCTAAAGAACATGGTCTT
*
43364528 TAGCGGCGTTTTAATCCAAGC
62 TAGCGGCGTTTTTATCCAAGC
*
43364549 GCCGCTAAAGAACATGGTCTTTAG-TGGCATTTGTATCAAAGCGCCGCTAAAGAACATGGTCTTT
1 GCCGCTAAAGAACATGGTCTTTAGCGGGC-TTTGTA--AAAGCGCCGCTAAAGAACATGGTCTTT
* *
43364613 AGAGGCGTTTTT-TACTAAGC
63 AGCGGCGTTTTTAT-CCAAGC
* * * * *
43364633 GCCACTAAAGAACATGGTCTTTAGAGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGGTCT
1 GCCGCTAAAGAACATGGTCTTTAGCGG-GCTTTGTA-AAAGCGCCGCTAAAGAACATGGTCT
43364695 GGCGTTTTTA
Statistics
Matches: 202, Mismatches: 17, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
81 3 0.01
82 2 0.01
83 5 0.02
84 182 0.90
85 8 0.04
86 1 0.00
87 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (82 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGGCTTTGTAAAAGCGCCGCTAAAGAACATGGTCTTTAGC
GGCGTTTTTATCCAAGC
Found at i:43365086 original size:21 final size:21
Alignment explanation
Indices: 43365021--43365088 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
43365011 TGGTCTGCTT
* *
43365021 TGCTTCTCTCGCTGTAGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
** *
43365042 CACTTCCCTCGCTGCAGCCGC
1 TGCTTCCCTCGCTGCAGCCTC
*
43365063 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
43365084 TGCTT
1 TGCTT
43365089 TAAGTTGTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.04, C:0.46, G:0.19, T:0.31
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:43370582 original size:9 final size:9
Alignment explanation
Indices: 43370565--43370849 Score: 208
Period size: 9 Copynumber: 32.8 Consensus size: 9
43370555 TATGTATTAA
*
43370565 GTAAATTAT
1 GTAAGTTAT
43370574 GTAAGTTAT
1 GTAAGTTAT
*
43370583 GTACGTGTA-
1 GTAAGT-TAT
43370592 -TAAGTTAT
1 GTAAGTTAT
43370600 GTAAGTTAT
1 GTAAGTTAT
*
43370609 GT-A-TTAA
1 GTAAGTTAT
43370616 GTAAGCTTA-
1 GTAAG-TTAT
** *
43370625 ACAAGTTGT
1 GTAAGTTAT
43370634 GT-A-TTAT
1 GTAAGTTAT
43370641 GTAAGTTAT
1 GTAAGTTAT
43370650 GTAAGTTAT
1 GTAAGTTAT
** *
43370659 CAAAGTAAT
1 GTAAGTTAT
*
43370668 GTATGTTAT
1 GTAAGTTAT
43370677 GTAAG-T-T
1 GTAAGTTAT
43370684 GTAAGTTAT
1 GTAAGTTAT
*
43370693 -TATGTATTAT
1 GTAAG--TTAT
43370703 GTAAGTTAT
1 GTAAGTTAT
43370712 GTAAGTTAT
1 GTAAGTTAT
43370721 GT-A-TTAT
1 GTAAGTTAT
*
43370728 GTACGTTAT
1 GTAAGTTAT
*
43370737 GTAAGTTGT
1 GTAAGTTAT
*
43370746 GTAAGATAT
1 GTAAGTTAT
*
43370755 TTAAGTTAT
1 GTAAGTTAT
*
43370764 GTAAGTTTT
1 GTAAGTTAT
43370773 GT-A-TTAT
1 GTAAGTTAT
43370780 GTAAGTTAT
1 GTAAGTTAT
43370789 GTAAGTTAT
1 GTAAGTTAT
* *
43370798 GTATGCTAT
1 GTAAGTTAT
43370807 GT-A-TTAT
1 GTAAGTTAT
43370814 GTAAGTTGTTAT
1 GTAA---GTTAT
*
43370826 GTTA-TTAT
1 GTAAGTTAT
43370834 GTAAGTTAT
1 GTAAGTTAT
*
43370843 GCAAGTT
1 GTAAGTT
43370850 TAACCACAAG
Statistics
Matches: 215, Mismatches: 37, Indels: 48
0.72 0.12 0.16
Matches are distributed among these distances:
7 34 0.16
8 26 0.12
9 136 0.63
10 9 0.04
11 3 0.01
12 7 0.03
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:43370585 original size:25 final size:25
Alignment explanation
Indices: 43370554--43370658 Score: 108
Period size: 25 Copynumber: 4.2 Consensus size: 25
43370544 TGATATATAT
*
43370554 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
43370579 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
**
43370605 TTATGTATTAAGTAAGCTTA-ACAAG
1 TTATGTATTAAGTAAG-TTATGTAAG
* *
43370630 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
43370655 TTAT
1 TTAT
43370659 CAAAGTAATG
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.02
24 5 0.08
25 34 0.52
26 22 0.34
27 2 0.03
28 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:43370671 original size:34 final size:35
Alignment explanation
Indices: 43370570--43370843 Score: 198
Period size: 34 Copynumber: 7.9 Consensus size: 35
43370560 ATTAAGTAAA
*
43370570 TTATGTAAGTTATGTACGTGTA--TAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGT-TATGTAAGTTATGT-AG
* ** *
43370605 TTATGT-A-TTAAGTAAGCTTA-ACAAGTTGTGTA-
1 TTATGTAAGTTATGTAAG-TTATGTAAGTTATGTAG
** *
43370637 TTATGTAAGTTATGTAAGTTATCAAAGTAATGTATG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA-G
*
43370673 TTATGTAAG-T-TGTAAGTTAT-TATGTATTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG--TTATGT-AG
*
43370708 TTATGTAAGTTATGT-A-TTATGTACGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGT-AG
* * * *
43370742 TTGTGTAAGATATTTAAGTTATGTAAGTTTTGTA-
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAG
* *
43370776 TTATGTAAGTTATGTAAGTTATGTATGCTATGTA-
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAG
*
43370810 TTATGTAAGTTGTTATGTTA-TTATGTAAGTTATG
1 TTATGTAA---GTTATGTAAGTTATGTAAGTTATG
43370844 CAAGTTTAAC
Statistics
Matches: 194, Mismatches: 27, Indels: 35
0.76 0.11 0.14
Matches are distributed among these distances:
32 6 0.03
33 16 0.08
34 93 0.48
35 28 0.14
36 40 0.21
37 11 0.06
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (35 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAG
Found at i:43370697 original size:19 final size:19
Alignment explanation
Indices: 43370673--43370711 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43370663 GTAATGTATG
43370673 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
43370692 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
43370711 T
1 T
43370712 GTAAGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:43370726 original size:25 final size:27
Alignment explanation
Indices: 43370565--43370849 Score: 208
Period size: 25 Copynumber: 10.9 Consensus size: 27
43370555 TATGTATTAA
* *
43370565 GTAAATTATGTAAGTTATGTACGTGTA-
1 GTAAGTTATGTAAGTTATGTAAGT-TAT
*
43370592 -TAAGTTATGTAAGTTATGT-A-TTAA
1 GTAAGTTATGTAAGTTATGTAAGTTAT
** *
43370616 GTAAGCTTA-ACAAGTTGTGT-A-TTAT
1 GTAAG-TTATGTAAGTTATGTAAGTTAT
** *
43370641 GTAAGTTATGTAAGTTATCAAAGTAAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
*
43370668 GTATGTTATGTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
*
43370693 -TATGTATTATGTAAGTTATGTAAGTTAT
1 GTAAG--TTATGTAAGTTATGTAAGTTAT
* *
43370721 GT-A-TTATGTACGTTATGTAAGTTGT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
* * *
43370746 GTAAGATATTTAAGTTATGTAAGTTTT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
43370773 GT-A-TTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT
* *
43370798 GTATGCTATGT-A-TTATGTAAGTTGTTAT
1 GTAAGTTATGTAAGTTATGTAA---GTTAT
* *
43370826 GTTA-TTATGTAAGTTATGCAAGTT
1 GTAAGTTATGTAAGTTATGTAAGTT
43370850 TAACCACAAG
Statistics
Matches: 206, Mismatches: 32, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
23 2 0.01
24 8 0.04
25 85 0.41
26 38 0.18
27 47 0.23
28 18 0.09
29 8 0.04
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (27 bp):
GTAAGTTATGTAAGTTATGTAAGTTAT
Found at i:43373716 original size:2 final size:2
Alignment explanation
Indices: 43373709--43373733 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43373699 ACTTCATTTC
43373709 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43373734 TTCCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43375202 original size:40 final size:41
Alignment explanation
Indices: 43375156--43375253 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
43375146 CGGCGCATAA
*
43375156 ACAAAAAACGCCGCTAAAACACCTAG-ATTAGCGGCGATTT
1 ACAAAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTT
* ** * * *
43375196 TCAAAAAACGCCACTAAAAGTCTTAGCCTTAGCGGCGCTTT
1 ACAAAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTT
43375237 ACAAAAAACGCCACTAA
1 ACAAAAAACGCCACTAA
43375254 TTCCCCCGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 21 0.43
41 28 0.57
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (41 bp):
ACAAAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTT
Found at i:43375343 original size:40 final size:40
Alignment explanation
Indices: 43375313--43375404 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
43375303 CGTTTTTTTA
43375313 TAAACGCCGCTAATGCTCACTCTCTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTCTAGCGGCGCTTTTCCT
* * *
43375353 TAAACGCCGCTAATGCTCACTCTTTAGTGGCTCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTCTAGCGGCGCTTTTCCT
* *
43375393 AAAACGCTGCTA
1 TAAACGCCGCTA
43375405 TTTCTCGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.32
Consensus pattern (40 bp):
TAAACGCCGCTAATGCTCACTCTCTAGCGGCGCTTTTCCT
Found at i:43376180 original size:27 final size:27
Alignment explanation
Indices: 43376126--43376183 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
43376116 AAAAAAACTA
* *
43376126 AAAATAATTTGTTTAGCAATACGAGAG
1 AAAATAATTGGTTTAGAAATACGAGAG
*
43376153 AAAATAATTGGTTTAAGAAAT-CGGGAG
1 AAAATAATTGGTTT-AGAAATACGAGAG
43376180 AAAA
1 AAAA
43376184 AATGAGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (27 bp):
AAAATAATTGGTTTAGAAATACGAGAG
Found at i:43383656 original size:28 final size:28
Alignment explanation
Indices: 43383602--43383657 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
43383592 TTTAAAATAA
* * *
43383602 TTTTGTATAAATAGAAGATAACTAATTT
1 TTTTATATAAATAGAAAATAACAAATTT
43383630 TTTTATATAAAATAGAAAATAA-AAATTT
1 TTTTATAT-AAATAGAAAATAACAAATTT
43383658 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (28 bp):
TTTTATATAAATAGAAAATAACAAATTT
Found at i:43391664 original size:26 final size:27
Alignment explanation
Indices: 43391577--43391665 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 27
43391567 AAAGGTACAC
* * *
43391577 ATATATATTATAAAAAATG-CATGTAT
1 ATATGTATTATAAAATATGAAATGTAT
* * *
43391603 ATGCATGGATTATAAAATATGGAATATAT
1 AT--ATGTATTATAAAATATGAAATGTAT
*
43391632 ATATGTATTATAAAATGT-AAATGTAT
1 ATATGTATTATAAAATATGAAATGTAT
43391658 ATATGTAT
1 ATATGTAT
43391666 ACATGTATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 16 0.31
27 14 0.27
28 14 0.27
29 7 0.14
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (27 bp):
ATATGTATTATAAAATATGAAATGTAT
Found at i:43391851 original size:3 final size:3
Alignment explanation
Indices: 43391843--43391893 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
43391833 TAACAACGAC
*
43391843 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43391891 AAT
1 AAT
43391894 GCAATATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43392662 original size:8 final size:8
Alignment explanation
Indices: 43392649--43392675 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43392639 AGAGAAGAAT
43392649 AAAAAATA
1 AAAAAATA
43392657 AAAAAATA
1 AAAAAATA
43392665 AAAAAATA
1 AAAAAATA
43392673 AAA
1 AAA
43392676 TCTAACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:43393525 original size:83 final size:83
Alignment explanation
Indices: 43393379--43393538 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
43393369 TGTTAGAGGC
* * * * *
43393379 TGCGACTCTTCACGTACGAGCCTTAATATGATAGCTAAGAGCTTTGCTCTCGCTAACTGTGTTGG
1 TGCGACTCTTCACCTACGAGCCATAATATAATAGCTAAGAGCTTTGCTCTCCCTAACTATGTTGG
43393444 AGGCTGCGGCTCACAGGT
66 AGGCTGCGGCTCACAGGT
* ** *
43393462 TGCGGCTCTTCACCTACGAGCCATAATATAATAGCTGGGAG-TTCTGCTTTCCCTAACTATGTTG
1 TGCGACTCTTCACCTACGAGCCATAATATAATAGCTAAGAGCTT-TGCTCTCCCTAACTATGTTG
43393526 GAGGCTGCGGCTC
65 GAGGCTGCGGCTC
43393539 TTCACCTGCG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
82 2 0.03
83 65 0.97
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (83 bp):
TGCGACTCTTCACCTACGAGCCATAATATAATAGCTAAGAGCTTTGCTCTCCCTAACTATGTTGG
AGGCTGCGGCTCACAGGT
Found at i:43393587 original size:69 final size:69
Alignment explanation
Indices: 43393462--43393828 Score: 373
Period size: 69 Copynumber: 5.3 Consensus size: 69
43393452 GCTCACAGGT
* * * * *
43393462 TGCGGCTCTTCACCTACGAGCCATAATATAATAGCTGGGAG-TTCTGCTT-TCCCTAACTATGTT
1 TGCGGCTCTTCACCTACGAGCCTTAATATGACAGCTGGGAGCTT-TG-TTCTCGCTAACTGTGTT
43393525 GGAGGC
64 GGAGGC
* * * *
43393531 TGCGGCTCTTCACCTGCGAGCCTTAATATGACAGATGAGAGCTTTGTTCTCGCTAACTATGTTGG
1 TGCGGCTCTTCACCTACGAGCCTTAATATGACAGCTGGGAGCTTTGTTCTCGCTAACTGTGTTGG
43393596 AGGC
66 AGGC
* * * * **
43393600 TACGACTCTTCACCTATGAGCCTTAATATGACTGCTGGGAGCTTTACTCTCGCTAACTGTGTTGG
1 TGCGGCTCTTCACCTACGAGCCTTAATATGACAGCTGGGAGCTTTGTTCTCGCTAACTGTGTTGG
43393665 AGGC
66 AGGC
* * ** * * *
43393669 TGCGACTCTTCACTTGTGAACCTTAATATGACAGCTGAGAGC-TTGTAACTCTCGCTAACTGCGT
1 TGCGGCTCTTCACCTACGAGCCTTAATATGACAGCTGGGAGCTTTGT---TCTCGCTAACTGTGT
43393733 TGGAGGC
63 TGGAGGC
** * * * *
43393740 TATGGCTCTTTACCTTCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCT-ACTTGTGTTG
1 TGCGGCTCTTCACCTACGAGCCTTAATATGACAGCTGGGAGCTTTGTTCTCGCTAAC-TGTGTTG
43393804 GAGGC
65 GAGGC
* * *
43393809 TGTGGTTATTCACCTACGAG
1 TGCGGCTCTTCACCTACGAG
43393829 TTTTATGTTC
Statistics
Matches: 248, Mismatches: 43, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
68 6 0.02
69 184 0.74
70 2 0.01
71 53 0.21
72 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (69 bp):
TGCGGCTCTTCACCTACGAGCCTTAATATGACAGCTGGGAGCTTTGTTCTCGCTAACTGTGTTGG
AGGC
Found at i:43393783 original size:140 final size:138
Alignment explanation
Indices: 43393464--43393810 Score: 432
Period size: 138 Copynumber: 2.5 Consensus size: 138
43393454 TCACAGGTTG
* * * * * * *
43393464 CGGCTCTTCACCTACGAGCCATAATATAATAGCTGGGAG-TTCTGCTTTCCCTAACTATGTTGGA
1 CGGCTCTTCACCTTCGAGCCTTAATATGACAGCTGGGAGCTT-TGCTCTCGCTAACTGTGTTGGA
* * *
43393528 GGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGATGAGAGCTTTGTTCTCGCTAACTATGT
65 GGCTGCGACTCTTCACCTGCGAACCTTAATATGACAGATGAGAGCTTTGTTCTCGCTAACTACGT
43393593 TGGAGGCTA
130 TGGAGGCTA
* * *
43393602 CGACTCTTCACCTAT-GAGCCTTAATATGACTGCTGGGAGCTTTACTCTCGCTAACTGTGTTGGA
1 CGGCTCTTCACCT-TCGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGA
* * * *
43393666 GGCTGCGACTCTTCACTTGTGAACCTTAATATGACAGCTGAGAGC-TTGTAACTCTCGCTAACTG
65 GGCTGCGACTCTTCACCTGCGAACCTTAATATGACAGATGAGAGCTTTGT---TCTCGCTAACTA
43393730 CGTTGGAGGCTA
127 CGTTGGAGGCTA
* * *
43393742 TGGCTCTTTACCTTCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCT-ACTTGTGTTGGA
1 CGGCTCTTCACCTTCGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAAC-TGTGTTGGA
43393806 GGCTG
65 GGCTG
43393811 TGGTTATTCA
Statistics
Matches: 179, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
137 4 0.02
138 90 0.50
139 5 0.03
140 80 0.45
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (138 bp):
CGGCTCTTCACCTTCGAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAG
GCTGCGACTCTTCACCTGCGAACCTTAATATGACAGATGAGAGCTTTGTTCTCGCTAACTACGTT
GGAGGCTA
Found at i:43394587 original size:85 final size:85
Alignment explanation
Indices: 43394444--43394612 Score: 338
Period size: 85 Copynumber: 2.0 Consensus size: 85
43394434 ACTTTTTCAT
43394444 ATGAAAAAGTAATAAGAATGAAAAATGAAAAGGTCGTCTTATTAAAAACCCCAATTATGAAATCC
1 ATGAAAAAGTAATAAGAATGAAAAATGAAAAGGTCGTCTTATTAAAAACCCCAATTATGAAATCC
43394509 CCTCTCTCCCACTTCACACA
66 CCTCTCTCCCACTTCACACA
43394529 ATGAAAAAGTAATAAGAATGAAAAATGAAAAGGTCGTCTTATTAAAAACCCCAATTATGAAATCC
1 ATGAAAAAGTAATAAGAATGAAAAATGAAAAGGTCGTCTTATTAAAAACCCCAATTATGAAATCC
43394594 CCTCTCTCCCACTTCACAC
66 CCTCTCTCCCACTTCACAC
43394613 CTCGAAATGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (85 bp):
ATGAAAAAGTAATAAGAATGAAAAATGAAAAGGTCGTCTTATTAAAAACCCCAATTATGAAATCC
CCTCTCTCCCACTTCACACA
Found at i:43397618 original size:2 final size:2
Alignment explanation
Indices: 43397611--43397651 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
43397601 AAATTACATA
*
43397611 AT AT AT AT AC AT 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 AT AT AT AT AT AT A
43397652 ACATAATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:43397626 original size:8 final size:8
Alignment explanation
Indices: 43397613--43397661 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
43397603 ATTACATAAT
43397613 ATATATAC
1 ATATATAC
*
43397621 ATATATAT
1 ATATATAC
*
43397629 ATATATAT
1 ATATATAC
*
43397637 ATATATAT
1 ATATATAC
43397645 ATATATAAC
1 ATATAT-AC
43397654 ATA-ATAC
1 ATATATAC
43397661 A
1 A
43397662 AAACATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 3 0.08
8 31 0.82
9 4 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATATAC
Found at i:43400023 original size:14 final size:15
Alignment explanation
Indices: 43399999--43400031 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
43399989 AAGTCTAAGT
*
43399999 TTTATTATGTTATTC
1 TTTATTATGTTATTA
43400014 TTTA-TATGTTATTA
1 TTTATTATGTTATTA
43400028 TTTA
1 TTTA
43400032 AAATCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTATTATGTTATTA
Found at i:43417714 original size:152 final size:152
Alignment explanation
Indices: 43417446--43417733 Score: 366
Period size: 152 Copynumber: 1.9 Consensus size: 152
43417436 AACAAAAAAT
* * *
43417446 CATGCATTCAACCTAACAAAACAGGGACACAGATATATCATAAACACTTTTCATTGTCAATTCTA
1 CATGCATTCAACCTAACAAAACAGGGACACAGATATATCATAAACACTTTTCAATGTCAACTCCA
* *
43417511 AAATATTAAAATCTAATTTGGGTTCTGATTTTATTGGTCTTAGTCTGGTACGAGTATGAGAACTA
66 AAATATTAAAATCTAATTTGGGTCCTGATTTTATTGGTCTCAGTCTGGTACGAGTATGAGAACTA
43417576 GAAGCCCATAAAAGAACAACAC
131 GAAGCCCATAAAAGAACAACAC
* * * * * * * *
43417598 CATGCATTCAACCTAATACAAC-TGGATCATAGGTATATCGTAAGCACTTTTTTAATGTCAACTC
1 CATGCATTCAACCTAACAAAACAGGGA-CACAGATATATCATAAACAC-TTTTCAATGTCAACTC
* * * * *
43417662 CAAATTATTTAAATCTAATTTGGAGTCCTGA-TTT-TTGTTCTCATTTTGGTACGAGTATGAGAA
64 CAAAATATTAAAATCTAATTTGG-GTCCTGATTTTATTGGTCTCAGTCTGGTACGAGTATGAGAA
43417725 CTAGAAGCC
128 CTAGAAGCC
43417734 AAAAAAGGAT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
151 3 0.03
152 70 0.61
153 36 0.31
154 6 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (152 bp):
CATGCATTCAACCTAACAAAACAGGGACACAGATATATCATAAACACTTTTCAATGTCAACTCCA
AAATATTAAAATCTAATTTGGGTCCTGATTTTATTGGTCTCAGTCTGGTACGAGTATGAGAACTA
GAAGCCCATAAAAGAACAACAC
Found at i:43417954 original size:83 final size:82
Alignment explanation
Indices: 43417816--43418014 Score: 312
Period size: 83 Copynumber: 2.4 Consensus size: 82
43417806 TTGAGATGGT
* * * *
43417816 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTATTGCTA-T
1 TAACATATTTTGTTTGTTTTTTTAAATGATTTGTTAAAATGGTTAGTTAACATCTTACTGCTATT
43417880 AGGATCATTTTGTTAGCA
66 A-GATCATTTTGTTAGCA
43417898 TAACATATTTTGTTTGTTTTTTTTAAATGATTTGTTAAAATGGTTAGTTAACATCTTACTGCTAT
1 TAACATATTTTGTTTG-TTTTTTTAAATGATTTGTTAAAATGGTTAGTTAACATCTTACTGCTAT
*
43417963 TAGATCATTTTGTTAGTA
65 TAGATCATTTTGTTAGCA
*
43417981 TAACATATTTTGTTTG-TTTTTTAAATGATCTGTT
1 TAACATATTTTGTTTGTTTTTTTAAATGATTTGTT
43418015 GAAAGATGTG
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
81 17 0.16
82 16 0.15
83 74 0.68
84 2 0.02
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (82 bp):
TAACATATTTTGTTTGTTTTTTTAAATGATTTGTTAAAATGGTTAGTTAACATCTTACTGCTATT
AGATCATTTTGTTAGCA
Found at i:43420058 original size:19 final size:19
Alignment explanation
Indices: 43420024--43420063 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
43420014 GTTTTAAATG
*
43420024 TTTTTTAATTTTAATT-AT
1 TTTTTTAATTTAAATTCAT
43420042 TTTTTTAAGTTTAAATTCAT
1 TTTTTTAA-TTTAAATTCAT
43420062 TT
1 TT
43420064 GCTGACGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTTAATTTAAATTCAT
Found at i:43421128 original size:3 final size:3
Alignment explanation
Indices: 43421110--43421174 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
43421100 AAATTTAAAA
* * * * *
43421110 AAT AAA AAT AAAT AAT AAT GAAA AAT AAAT AAT AAC AAT AAT AAT GAG
1 AAT AAT AAT -AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT
43421158 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
43421175 GAACAAAATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
3 41 0.84
4 8 0.16
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:43423014 original size:51 final size:51
Alignment explanation
Indices: 43422959--43423262 Score: 218
Period size: 51 Copynumber: 6.3 Consensus size: 51
43422949 GCACCATTGT
43422959 AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
1 AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
* * * *
43423010 AACTTTTAGGGAAATAAGA----T---TTGTAGCTTTAATCTGCTCAACTGC
1 AAC-TTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
* * * * *
43423055 AACTTTAGGGAGATAAGATTCGTAATTTATAGCTTTAATTTGTTCCACTGC
1 AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
* ** ** **
43423106 AACTTCAGGGAAATGTGATTTGTAAC-T-T--C---AATCTAATCCACTAT
1 AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
* * * * **
43423150 AACTTCAGAGAGATAAGATTTG-----T-TATCTTCAATCTGCTCCACTTT
1 AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
* * *
43423195 AACTTCAAGGATATAAGATTTG-AAGCTTGTAGCTTTAATCTATTCCACTGC
1 AACTTCAGGGAGATAAGATTTGTAA-CTTGTAGCTTTAATCTGTTCCACTGC
43423246 AACTTCAGGGAGATAAG
1 AACTTCAGGGAGATAAG
43423263 GCTTGCTATA
Statistics
Matches: 196, Mismatches: 38, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
40 2 0.01
42 1 0.01
44 42 0.21
45 57 0.29
47 1 0.01
48 2 0.01
49 1 0.01
50 2 0.01
51 75 0.38
52 13 0.07
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (51 bp):
AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGC
Found at i:43423065 original size:96 final size:95
Alignment explanation
Indices: 43422959--43423172 Score: 275
Period size: 95 Copynumber: 2.2 Consensus size: 95
43422949 GCACCATTGT
* *
43422959 AACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTTTAGGGAAA
1 AACTTCAGGGAGATAAGATTTGTAACTTATAGCTTTAATCTGTTCCACTGCAAC-TTCAGGGAAA
* * ** *
43423024 TAAGATTTGTAGCTTTAATCTGCTCAACTGC
65 TAAGATTTGTAACTTCAATCTAATCAACTAC
* * * *
43423055 AACTTTAGGGAGATAAGATTCGTAATTTATAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAAT
1 AACTTCAGGGAGATAAGATTTGTAACTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAAT
** * *
43423120 GTGATTTGTAACTTCAATCTAATCCACTAT
66 AAGATTTGTAACTTCAATCTAATCAACTAC
*
43423150 AACTTCAGAGAGATAAGATTTGT
1 AACTTCAGGGAGATAAGATTTGT
43423173 TATCTTCAAT
Statistics
Matches: 100, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
95 51 0.51
96 49 0.49
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (95 bp):
AACTTCAGGGAGATAAGATTTGTAACTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAAT
AAGATTTGTAACTTCAATCTAATCAACTAC
Found at i:43423139 original size:140 final size:140
Alignment explanation
Indices: 43423002--43423256 Score: 316
Period size: 140 Copynumber: 1.8 Consensus size: 140
43422992 TTTAATCTGT
* * * * * *
43423002 TCCACTGCAACTTTTAGGGAAATAAGATTTG-TAGCTTTAATCTGCTCAACTGCAACTTTAGGGA
1 TCCACTACAAC-TTCAGAGAAATAAGATTTGTTAGCTTCAATCTGCTCAACTGCAACTTCAAGGA
* * *
43423066 GATAAGATTCGTAA-TTTATAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATGTGATTTGTA
65 GATAAGATTCG-AAGCTTATAGCTTTAATCTATTCCACTGCAACTTCAGGGAAATGTGATTTGTA
43423130 ACTTCAATCTAA
129 ACTTCAATCTAA
* * * * ** *
43423142 TCCACTATAACTTCAGAGAGATAAGATTTGTTATCTTCAATCTGCTCCACTTTAACTTCAAGGAT
1 TCCACTACAACTTCAGAGAAATAAGATTTGTTAGCTTCAATCTGCTCAACTGCAACTTCAAGGAG
* *
43423207 ATAAGATTTGAAGCTTGTAGCTTTAATCTATTCCACTGCAACTTCAGGGA
66 ATAAGATTCGAAGCTTATAGCTTTAATCTATTCCACTGCAACTTCAGGGA
43423257 GATAAGGCTT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
139 18 0.19
140 77 0.81
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (140 bp):
TCCACTACAACTTCAGAGAAATAAGATTTGTTAGCTTCAATCTGCTCAACTGCAACTTCAAGGAG
ATAAGATTCGAAGCTTATAGCTTTAATCTATTCCACTGCAACTTCAGGGAAATGTGATTTGTAAC
TTCAATCTAA
Found at i:43423426 original size:44 final size:44
Alignment explanation
Indices: 43422985--43423903 Score: 477
Period size: 44 Copynumber: 19.9 Consensus size: 44
43422975 GATTTGTAAC
* * *
43422985 TTGTAGCTTTAATCTGTTCCACTGCAACTTTTAGGGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAAC-TTCAGGGAGATAAGAT
* *
43423030 TTGTAGCTTTAATCTGCTCAACTGCAACTTTAGGGAGATAAGATTCGTAAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT-A-A---G--AT
* * * * **
43423081 TTATAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATGTGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * ** ** *
43423125 TTGTAACTTCAATCTAATCCACTATAACTTCAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * ** * *
43423169 TTGTTATCTTCAATCTGCTCCACTTTAACTTCAAGGATATAAGATTT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T
** *
43423216 GAAGCTTGTAGCTTTAATCTATTCCACTGCAACTTCAGGGAGATAAGGCTT
1 -----TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA-G-AT
* * * *
43423267 GCTATAGTAGATTTAATCTGAC-CTACTGCAACTTCAGAGG-CAT-AGAA
1 --T-T-GTAGCTTTAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGAT
* * * ***
43423314 GT-TATCGTTTCAATTTGCTCCACTGCAAACTTCAAAAAGATAAGAT
1 TTGTAGC-TTT-AATCTGCTCCACTGC-AACTTCAGGGAGATAAGAT
** * * * * *
43423360 TTGCTATTTTTAA-CTTGGTCCACTACAATTTTAGGGAGATAAGGT
1 TTG-TAGCTTTAATC-TGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
43423405 TTGCAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
43423449 TTGTAGCCTGTCTTCAATTTGCTCCACTGCAATTTTTAGGTAGATAAGAT
1 TTGTAG-C--T-TT-AATCTGCTCCACTGCAA-CTTCAGGGAGATAAGAT
** * * * * *
43423499 TTGTTTATTTTTAACCTACTCTACTACAACTTCAAGGAGATAA-AGT
1 TTG--TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T
* * *
43423545 TTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
43423589 TTGTTATCTCTGATCTACTCCACTGCAACTTCAGTGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
43423634 CTATAACTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT-A-A-----GAT
* * **
43423685 TTGTAGCTTTAATCTGCTCTACTGCAACTTTATAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
** *** ** * *
43423729 TTGCTATATCCGATCTATTCCACTGTAACTTCAGAGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * *
43423774 TTGTAGCTTCAATATACTCTACTGCAACTTTAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
43423818 TCAT-TATAC-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAAAT
1 T--TGTA-GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
43423863 TTGTGGCTTTAATCTACTCCACTGCAACTTCAAGGAGATAA
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
43423904 AATTCGTCAT
Statistics
Matches: 664, Mismatches: 155, Indels: 111
0.71 0.17 0.12
Matches are distributed among these distances:
42 2 0.00
43 6 0.01
44 228 0.34
45 192 0.29
46 33 0.05
47 17 0.03
48 11 0.02
49 21 0.03
50 45 0.07
51 103 0.16
52 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
Found at i:43423494 original size:139 final size:140
Alignment explanation
Indices: 43423322--43423592 Score: 357
Period size: 140 Copynumber: 1.9 Consensus size: 140
43423312 AAGTTATCGT
* **
43423322 TTCAATTTGCTCCACTGCAAACTTCAAAAAGATAAGATTTG-CTATTTTTAACTTGGTCCACTAC
1 TTCAATTTGCTCCACTGCAAACTTCAAAAAGATAAGATTTGTCTATTTTTAACCTACTCCACTAC
* * * * *
43423386 AATTTTAGGGAGATAAGGTTTGCAGCTTTAATCTGCTCCACTGCAACTTCA-AGGAGATAAGATT
66 AACTTCAAGGAGATAAAGTTTACAGCTTTAATCTGCTCCACTGCAACTTCAGA-GAGATAAGATT
43423450 TGTAGCCTGTC
130 TGTAGCCTGTC
** * *** * *
43423461 TTCAATTTGCTCCACTGCAATTTTTAGGTAGATAAGATTTGTTTATTTTTAACCTACTCTACTAC
1 TTCAATTTGCTCCACTGCAAACTTCAAAAAGATAAGATTTGTCTATTTTTAACCTACTCCACTAC
* *
43423526 AACTTCAAGGAGATAAAGTTTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTT
66 AACTTCAAGGAGATAAAGTTTACAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTT
43423591 GT
131 GT
43423593 TATCTCTGAT
Statistics
Matches: 112, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
139 35 0.31
140 76 0.68
141 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (140 bp):
TTCAATTTGCTCCACTGCAAACTTCAAAAAGATAAGATTTGTCTATTTTTAACCTACTCCACTAC
AACTTCAAGGAGATAAAGTTTACAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTT
GTAGCCTGTC
Found at i:43423621 original size:89 final size:89
Alignment explanation
Indices: 43422988--43423903 Score: 382
Period size: 89 Copynumber: 9.9 Consensus size: 89
43422978 TTGTAACTTG
* * * * * * * *
43422988 TAGCTTTAATCTGTTCCACTGCAACTTTTAGGGAAATAAGATTTG-TAGCTTTAATCTGCTCAAC
1 TAGCTTTAATCTGCTCCACTGCAAC-TTCAGAGAGATAAGATTTGTTATCTCTAATCTACTCCAC
* *
43423052 TGCAACTTTAGGGAGATAAGATTCGTAATTTA
65 TGCAACTTCAAGGAGAT-A-A---G--ATTTA
* * * * ** * *
43423084 TAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATGTGATTTG-TAACT-TCAATCTAATCCAC
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTTATCTCT-AATCTACTCCAC
** *
43423147 TATAACTTC-AGAGAGATAAGATTTGT
65 TGCAACTTCAAG-GAGATAAGATTT-A
* * ** * * *
43423173 TATCTTCAATCTGCTCCACTTTAACTTCA-AGGATATAAGATTTGAAGCTTGTAGCTTTAATCTA
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGA-GAGATAAGATTT---G--T-TATCTCTAATCTA
* * *
43423237 TTCCACTGCAACTTCAGGGAGATAAGGCTTGCTATA
59 CTCCACTGCAACTTCAAGGAGATAA-G-AT--T-TA
* * * * * *
43423273 GTAGATTTAATCTGAC-CTACTGCAACTTCAGAG-GCAT-AGA--AGTTATCGTTTCAATTTGCT
1 -TAGCTTTAATCTG-CTCCACTGCAACTTCAGAGAG-ATAAGATTTGTTATC-TCT-AATCTACT
** *
43423333 CCACTGCAAACTTCAAAAAGATAAGATTTGC
61 CCACTGC-AACTTCAAGGAGATAAGATTT-A
** * * * * * * * * * *
43423364 TATTTTTAA-CTTGGTCCACTACAATTTTAGGGAGATAAGGTTTG-CAGCTTTAATCTGCTCCAC
1 TAGCTTTAATC-TGCTCCACTGCAACTTCAGAGAGATAAGATTTGTTATCTCTAATCTACTCCAC
*
43423427 TGCAACTTCAAGGAGATAAGATTTG
65 TGCAACTTCAAGGAGATAAGATTTA
* * * * * *
43423452 TAGCCTGTCTTCAATTTGCTCCACTGCAATTTTTAG-GTAGATAAGATTTGTTTATTTTTAACCT
1 TAG-C--T-TT-AATCTGCTCCACTGCAA-CTTCAGAG-AGATAAGATTTG-TTATCTCTAATCT
* *
43423516 ACTCTACTACAACTTCAAGGAGATAA-AGTTTA
58 ACTCCACTGCAACTTCAAGGAGATAAGA-TTTA
* *
43423548 TAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTATCTCTGATCTACTCCACT
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTTATCTCTAATCTACTCCACT
*
43423613 GCAACTTC-AGTGAGATAAGATCTA
66 GCAACTTCAAG-GAGATAAGATTTA
* * * * *
43423637 TAACTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGATTTGTAGCTTTAATCTGC
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TT-TG---T-TATCTCTAATCTAC
* * *
43423702 TCTACTGCAACTTTATA-GAGATAAGATTTGC
60 TCCACTGCAACTTCA-AGGAGATAAGATTT-A
** *** ** * * * *
43423733 TATATCCGATCTATTCCACTGTAACTTCAGAGAGATAAGATTTG-TAGCT-TCAATATACTCTAC
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTTATCTCT-AATCTACTCCAC
*
43423796 TGCAACTT-TAGAGAGATAAGATTCATTA
65 TGCAACTTCAAG-GAGATAAGA-T--TTA
* * * ** *
43423824 TA-C-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAAATTTG-TGGCTTTAATCTACTCCACT
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTTATCTCTAATCTACTCCACT
43423886 GCAACTTCAAGGAGATAA
66 GCAACTTCAAGGAGATAA
43423904 AATTCGTCAT
Statistics
Matches: 635, Mismatches: 122, Indels: 133
0.71 0.14 0.15
Matches are distributed among these distances:
87 1 0.00
88 9 0.01
89 215 0.34
90 62 0.10
91 28 0.04
92 12 0.02
93 22 0.03
94 36 0.06
95 91 0.14
96 123 0.19
97 4 0.01
98 1 0.00
100 4 0.01
101 25 0.04
102 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (89 bp):
TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTTATCTCTAATCTACTCCACT
GCAACTTCAAGGAGATAAGATTTA
Found at i:43423650 original size:229 final size:228
Alignment explanation
Indices: 43423415--43423903 Score: 551
Period size: 229 Copynumber: 2.1 Consensus size: 228
43423405 TTGCAGCTTT
*
43423415 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGT-AGCCTGT-CTTCAATTTGCTCCACTG
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTGA-CCTGTACTTCAATCTGCTCCACTG
* * * ** *
43423478 CAA-TTTTTAGGTAGATAAGATTTGTTTATTTTTAACCTACTCTACTACAACTTCA-AGGAGATA
65 CAACTTTATA-G-AGATAAGATTTG-CTATATCCAACCTACTCCACTACAACTTCAGA-GAGATA
* * * ** *
43423541 A-AGTTTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTAT-CTCTGATC
126 AGA-TTTATAGCTTCAATATACTCTACTGCAACTTCAGAGAGATAAGATTCATTATACTC-AATC
* *
43423604 TACTCCACTGCAACTTCAGTGAGATAAGATCTATAACTTC
189 TACTCCACTGCAACTTCAGGGAGATAAAATCTATAACTTC
** * *
43423644 AATCTGCTCCACTGCAACTTC-AGAGAGATAAGATTTGTGATTTGTAGCTTTAATCTGCTCTACT
1 AATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGTGACCTGTA-CTTCAATCTGCTCCACT
* * * **
43423708 GCAACTTTATAGAGATAAGATTTGCTATATCCGATCTATTCCACTGTAACTTCAGAGAGATAAGA
64 GCAACTTTATAGAGATAAGATTTGCTATATCCAACCTACTCCACTACAACTTCAGAGAGATAAGA
* * *
43423773 TTTGTAGCTTCAATATACTCTACTGCAACTTTAGAGAGATAAGATTCATTATACTCAATCTGCTC
129 TTTATAGCTTCAATATACTCTACTGCAACTTCAGAGAGATAAGATTCATTATACTCAATCTACTC
* * ** *
43423838 CACTGCAACTTCAGGGAGATAAAATTTGTGGCTTT
194 CACTGCAACTTCAGGGAGATAAAATCTATAACTTC
*
43423873 AATCTACTCCACTGCAACTTCAAGGAGATAA
1 AATCTGCTCCACTGCAACTTCAAGGAGATAA
43423904 AATTCGTCAT
Statistics
Matches: 218, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
228 2 0.01
229 172 0.79
230 20 0.09
231 19 0.09
232 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (228 bp):
AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTGACCTGTACTTCAATCTGCTCCACTGC
AACTTTATAGAGATAAGATTTGCTATATCCAACCTACTCCACTACAACTTCAGAGAGATAAGATT
TATAGCTTCAATATACTCTACTGCAACTTCAGAGAGATAAGATTCATTATACTCAATCTACTCCA
CTGCAACTTCAGGGAGATAAAATCTATAACTTC
Found at i:43423692 original size:140 final size:134
Alignment explanation
Indices: 43423545--43423903 Score: 416
Period size: 140 Copynumber: 2.6 Consensus size: 134
43423535 GAGATAAAGT
43423545 TTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTATCTCTGATCTACTCC
1 TTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTG-TATCTCTGATCTACTCC
* *
43423610 ACTGCAACTTCAGTGAGATAAGATCTATAACTTCAATCTGCTCCACTGCAACTTCAGAGAGATAA
65 ACTGCAACTTCAG-GAGATAAGATCTATAACTTCAATATACTCCACTGCAACTTCAGAGAGATAA
*
43423675 GATTTGTGA
129 GA--T-TCA
* * * * * *
43423684 TTTGTAGCTTTAATCTGCTCTACTGCAACTTTATAGAGATAAGATTTGCTATATCCGATCTATTC
1 -TTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTG-TATCTCTGATCTACTC
* * * * * *
43423749 CACTGTAACTTCAGAGAGATAAGATTTGTAGCTTCAATATACTCTACTGCAACTTTAGAGAGATA
64 CACTGCAACTTCAG-GAGATAAGATCTATAACTTCAATATACTCCACTGCAACTTCAGAGAGATA
43423814 AGATTCA
128 AGATTCA
* * * * ** * *
43423821 TTATA-C-TCAATCTGCTCCACTGCAACTTCAGGGAGATAAAATTTGTGGCTTTAATCTACTCCA
1 TTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTATCTCTGATCTACTCCA
43423884 CTGCAACTTCAAGGAGATAA
66 CTGCAACTTC-AGGAGATAA
43423904 AATTCGTCAT
Statistics
Matches: 186, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
133 27 0.15
134 35 0.19
135 1 0.01
136 4 0.02
137 2 0.01
138 1 0.01
140 116 0.62
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (134 bp):
TTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTATCTCTGATCTACTCCA
CTGCAACTTCAGGAGATAAGATCTATAACTTCAATATACTCCACTGCAACTTCAGAGAGATAAGA
TTCA
Found at i:43430726 original size:4 final size:4
Alignment explanation
Indices: 43430701--43430766 Score: 96
Period size: 4 Copynumber: 16.5 Consensus size: 4
43430691 ATACAAAAAG
* * * *
43430701 AATA AATG AATC AATG AATA AATA AATA CATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
43430749 AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AA
43430767 AGCTTTCATG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:43434360 original size:21 final size:21
Alignment explanation
Indices: 43434336--43434389 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
43434326 AAAAATATAC
43434336 AAATGAAACAGGAAAAGAAAA
1 AAATGAAACAGGAAAAGAAAA
* *** **
43434357 AAATAAAACCTCAAAAGGGAA
1 AAATGAAACAGGAAAAGAAAA
43434378 AAATGAAACAGG
1 AAATGAAACAGG
43434390 GATAAAAAAT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.09, G:0.19, T:0.07
Consensus pattern (21 bp):
AAATGAAACAGGAAAAGAAAA
Found at i:43434874 original size:17 final size:17
Alignment explanation
Indices: 43434854--43434900 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 17
43434844 GTATTTTTTA
*
43434854 TTATATTATATTAATGT
1 TTATATTATAATAATGT
43434871 TTATATTATAAAATAATGT
1 TTATATTAT--AATAATGT
43434890 TTA-ATTATAAT
1 TTATATTATAAT
43434901 TTGTTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 5 0.19
19 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TTATATTATAATAATGT
Found at i:43435128 original size:3 final size:3
Alignment explanation
Indices: 43435120--43435156 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
43435110 GTATGTTTTG
43435120 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43435157 ATCAATGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43439959 original size:14 final size:14
Alignment explanation
Indices: 43439940--43439966 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43439930 CATTGTATGA
43439940 CATATCTCAGTATC
1 CATATCTCAGTATC
43439954 CATATCTCAGTAT
1 CATATCTCAGTAT
43439967 TTCTTGACCA
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:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (14 bp):
CATATCTCAGTATC
Found at i:43446976 original size:15 final size:16
Alignment explanation
Indices: 43446956--43446990 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43446946 TTCTGTTCCT
*
43446956 TTTTTTTTCTTTTT-A
1 TTTTTTTCCTTTTTCA
43446971 TTTTTTTCCTTTTTCA
1 TTTTTTTCCTTTTTCA
43446987 TTTT
1 TTTT
43446991 CTATCTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTCCTTTTTCA
Found at i:43447568 original size:3 final size:3
Alignment explanation
Indices: 43447551--43447616 Score: 64
Period size: 3 Copynumber: 21.3 Consensus size: 3
43447541 TAGTCCTTTT
* *
43447551 TTA TTA -TA TTA -TA TTA TTTG TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
43447595 TTGCA TTA TATA TTA TTA TTA T
1 TT--A TTA T-TA TTA TTA TTA T
43447617 ACTTATGTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 4 0.08
3 41 0.77
4 5 0.09
5 3 0.06
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:43447832 original size:33 final size:34
Alignment explanation
Indices: 43447766--43447833 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
43447756 CGTATATCCA
* *
43447766 TTTATATTTTATAATATTCATACATTTTTTATAT
1 TTTACATTTTATAATATTCATACATTTTATATAT
*
43447800 TTTACATTTTATACATA-T-ATATATTTTATATAT
1 TTTACATTTTATA-ATATTCATACATTTTATATAT
43447833 T
1 T
43447834 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 14 0.47
34 13 0.43
35 3 0.10
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTACATTTTATAATATTCATACATTTTATATAT
Found at i:43452342 original size:18 final size:18
Alignment explanation
Indices: 43452304--43452339 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43452294 TTATTATTTT
*
43452304 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
43452322 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
43452340 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:43452415 original size:21 final size:22
Alignment explanation
Indices: 43452389--43452432 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
43452379 ATGTTTAATA
43452389 ATATTAAAAATTT-AATATTTT
1 ATATTAAAAATTTAAATATTTT
* *
43452410 ATATTAATATTTTAAATATTTT
1 ATATTAAAAATTTAAATATTTT
43452432 A
1 A
43452433 AATATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTAAAAATTTAAATATTTT
Found at i:43452417 original size:30 final size:31
Alignment explanation
Indices: 43452383--43452440 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
43452373 AAACGTATGT
43452383 TTAATAATATTAAA-AATTT-AATATTTTATA
1 TTAAT-ATATTAAATAATTTAAATATTTTATA
* *
43452413 TTAATATTTTAAATATTTTAAATATTTT
1 TTAATATATTAAATAATTTAAATATTTT
43452441 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TTAATATATTAAATAATTTAAATATTTTATA
Found at i:43452444 original size:10 final size:9
Alignment explanation
Indices: 43452415--43452440 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
43452405 ATTTTATATT
43452415 AATATTTTA
1 AATATTTTA
43452424 AATATTTTA
1 AATATTTTA
43452433 AATATTTT
1 AATATTTT
43452441 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:43454393 original size:31 final size:30
Alignment explanation
Indices: 43454358--43454417 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
43454348 GGAGGTGGGA
*
43454358 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
43454389 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
43454418 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:43454644 original size:9 final size:9
Alignment explanation
Indices: 43454630--43454666 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43454620 TATAGTTTGA
43454630 TATTCGAAT
1 TATTCGAAT
43454639 TATTCGAAT
1 TATTCGAAT
*
43454648 TATTCGAGT
1 TATTCGAAT
43454657 TATTCGAAT
1 TATTCGAAT
43454666 T
1 T
43454667 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43454737 original size:9 final size:9
Alignment explanation
Indices: 43454720--43454750 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43454710 TCGAGTTGAT
43454720 TCGAATAAC
1 TCGAATAAC
*
43454729 TCGATTAAC
1 TCGAATAAC
43454738 TCGAATAAC
1 TCGAATAAC
43454747 TCGA
1 TCGA
43454751 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:43457183 original size:16 final size:16
Alignment explanation
Indices: 43457162--43457201 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
43457152 TTTGGTTCGC
43457162 TGTAATAGAATAGAGG
1 TGTAATAGAATAGAGG
*
43457178 TGTAATGGAATAGAGG
1 TGTAATAGAATAGAGG
43457194 TGTAATAG
1 TGTAATAG
43457202 GTAATCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.28
Consensus pattern (16 bp):
TGTAATAGAATAGAGG
Found at i:43457274 original size:44 final size:46
Alignment explanation
Indices: 43457181--43457274 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
43457171 ATAGAGGTGT
** *
43457181 AATGGAATAGAGGTGTAATAGGTAATCCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGGTAATCCTTGTGTTTGGTTGAATGG
*
43457227 AATGGAATAGAACTGTAATA-GT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGGTAATCCTTGTGTTTGGTTGAATGG
43457271 AATG
1 AATG
43457275 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.55
45 2 0.05
46 18 0.41
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATAGGTAATCCTTGTGTTTGGTTGAATGG
Found at i:43457283 original size:39 final size:41
Alignment explanation
Indices: 43457181--43457286 Score: 101
Period size: 44 Copynumber: 2.5 Consensus size: 41
43457171 ATAGAGGTGT
* *
43457181 AATGGAATAGA-GGTGTAATAGGTAATCCTTTTGTTTGGTTG
1 AATGGAATAGATGCTGTAATA-GTAATCCTTGTGTTTGGTTG
* *
43457222 AATGGAATGGAATAGAACTGTAATAGT-ATTCTTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATCCTTGTGTTTGGTTG
*
43457266 AATGGAAT-GATGTTGTAATAG
1 AATGGAATAGATGCTGTAATAG
43457287 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
39 8 0.15
41 10 0.18
42 3 0.05
43 1 0.02
44 24 0.44
45 2 0.04
46 7 0.13
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATCCTTGTGTTTGGTTG
Found at i:43457441 original size:26 final size:26
Alignment explanation
Indices: 43457412--43457526 Score: 95
Period size: 26 Copynumber: 4.3 Consensus size: 26
43457402 TTAATCATAT
43457412 TTTAACATAATTATTATTAAATATAA
1 TTTAACATAATTATTATTAAATATAA
* * * * * *
43457438 TTTAATAAAATATATGAATTTACTAAAA
1 TTTAACATAAT-TAT-TATTAAATATAA
* * * *
43457466 TCATAATATATAATATTATAAAATATAA
1 T-TTAACATA-ATTATTATTAAATATAA
*
43457494 TTTAAAATAATTATTATTAAATATAA
1 TTTAACATAATTATTATTAAATATAA
43457520 TTTAACA
1 TTTAACA
43457527 AAAATATATA
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
26 30 0.45
27 9 0.14
28 17 0.26
29 9 0.14
30 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (26 bp):
TTTAACATAATTATTATTAAATATAA
Found at i:43457459 original size:18 final size:17
Alignment explanation
Indices: 43457432--43457548 Score: 59
Period size: 18 Copynumber: 7.0 Consensus size: 17
43457422 TTATTATTAA
43457432 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
43457449 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
43457467 -CATAATAT-ATAATATT
1 ATATAATTTAATAA-AAT
* *
43457483 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
43457502 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
*
43457514 ATATAATTTAACAAAAAT
1 ATATAATTTAA-TAAAAT
43457532 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43457549 TCTTAGTATT
Statistics
Matches: 72, Mismatches: 16, Indels: 24
0.64 0.14 0.21
Matches are distributed among these distances:
12 1 0.01
13 5 0.07
14 3 0.04
15 4 0.06
16 7 0.10
17 20 0.28
18 26 0.36
19 3 0.04
20 3 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43468682 original size:23 final size:23
Alignment explanation
Indices: 43468623--43468683 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
43468613 TTGTTCAACT
**
43468623 CAGGAACATGGCCACAATAAAAA
1 CAGGAACATGGCCTTAATAAAAA
43468646 CAGGAACATGGCCTTAATAAAAA
1 CAGGAACATGGCCTTAATAAAAA
43468669 CAGGAACATGGCCTT
1 CAGGAACATGGCCTT
43468684 CATTTGTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.15
Consensus pattern (23 bp):
CAGGAACATGGCCTTAATAAAAA
Found at i:43470360 original size:18 final size:17
Alignment explanation
Indices: 43470332--43470366 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43470322 ATTATTAAGG
*
43470332 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43470349 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43470367 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43470566 original size:120 final size:120
Alignment explanation
Indices: 43470211--43470625 Score: 672
Period size: 120 Copynumber: 3.5 Consensus size: 120
43470201 AATTATTTTA
* * *
43470211 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTACATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* *
43470275 TATAGCATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
43470331 GATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT-TGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
43470395 ATAGTAACATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* * * *
43470450 AATTTTATAAAATTATATATTTTAATTATAATATATTTAATAATAATTATGCTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
43470515 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
43470570 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAAA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
43470626 ATATGATTAA
Statistics
Matches: 272, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
119 107 0.39
120 165 0.61
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:43470605 original size:16 final size:16
Alignment explanation
Indices: 43470584--43470622 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
43470574 TTATTAAATT
*
43470584 ATATATTTTAATTATA
1 ATATATTTTAATAATA
43470600 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
43470615 ATTATATT
1 A-TATATT
43470623 AAAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 9 0.45
17 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:43472280 original size:51 final size:50
Alignment explanation
Indices: 43472204--43472308 Score: 165
Period size: 51 Copynumber: 2.1 Consensus size: 50
43472194 GTAGCTATAA
* * *
43472204 ATCATTTGTTTATATTAAGTGTCCATGTGTTGTATGTATCAAGATAGGGT
1 ATCATTTGTTTAAATTAAGTGTCCATGTGTTGCACGTATCAAGATAGGGT
*
43472254 ATCATTTGTTTAAATTTAAGTGTCCATTTGTTGCACGTATCAAGATAGGGT
1 ATCATTTGTTTAAA-TTAAGTGTCCATGTGTTGCACGTATCAAGATAGGGT
43472305 ATCA
1 ATCA
43472309 AAACCAGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 13 0.26
51 37 0.74
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (50 bp):
ATCATTTGTTTAAATTAAGTGTCCATGTGTTGCACGTATCAAGATAGGGT
Found at i:43477999 original size:20 final size:21
Alignment explanation
Indices: 43477966--43478005 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
43477956 CCAAGTGCAA
* *
43477966 AATGAAGCTTAATTTTAGCTC
1 AATGAAGCTCAATTCTAGCTC
43477987 AATG-AGCTCAATTCTAGCT
1 AATGAAGCTCAATTCTAGCT
43478006 TTTTCAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
AATGAAGCTCAATTCTAGCTC
Found at i:43478129 original size:19 final size:19
Alignment explanation
Indices: 43478105--43478160 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
43478095 TAAATTACTC
*
43478105 ATCTTAGTTAATTGAGTTT
1 ATCTTAGTTAATTAAGTTT
*
43478124 ATCTTAGTTAATTAAGTTG
1 ATCTTAGTTAATTAAGTTT
* **
43478143 CTGGTAGTTAATTAAGTT
1 ATCTTAGTTAATTAAGTT
43478161 GCTGGAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (19 bp):
ATCTTAGTTAATTAAGTTT
Found at i:43478161 original size:19 final size:19
Alignment explanation
Indices: 43478128--43478165 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43478118 GAGTTTATCT
43478128 TAGTTAATTAAGTTGCTGG
1 TAGTTAATTAAGTTGCTGG
43478147 TAGTTAATTAAGTTGCTGG
1 TAGTTAATTAAGTTGCTGG
43478166 AATAAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
TAGTTAATTAAGTTGCTGG
Found at i:43478340 original size:9 final size:10
Alignment explanation
Indices: 43478317--43478353 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
43478307 TAAGTCTAAT
43478317 ATGTGTTTAA
1 ATGTGTTTAA
43478327 ATGTGTTT-A
1 ATGTGTTTAA
43478336 ATGTGTTTAA
1 ATGTGTTTAA
43478346 ATGTGTTT
1 ATGTGTTT
43478354 GTTAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (10 bp):
ATGTGTTTAA
Found at i:43478341 original size:19 final size:19
Alignment explanation
Indices: 43478317--43478353 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
43478307 TAAGTCTAAT
43478317 ATGTGTTTAAATGTGTTTA
1 ATGTGTTTAAATGTGTTTA
43478336 ATGTGTTTAAATGTGTTT
1 ATGTGTTTAAATGTGTTT
43478354 GTTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (19 bp):
ATGTGTTTAAATGTGTTTA
Found at i:43478405 original size:64 final size:64
Alignment explanation
Indices: 43478331--43478450 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
43478321 GTTTAAATGT
43478331 GTTTAATGTGTTTAAATGTGTTTGTTAATAAATGCTTACAGGTGACTATTTAGTTGCTTATTAA
1 GTTTAATGTGTTTAAATGTGTTTGTTAATAAATGCTTACAGGTGACTATTTAGTTGCTTATTAA
* * **
43478395 GTTTAGTGTGTTTAAATGTGTTTGTTAATAAATGTTTGGAGGTGACTATTTAGTTG
1 GTTTAATGTGTTTAAATGTGTTTGTTAATAAATGCTTACAGGTGACTATTTAGTTG
43478451 GAATCAGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (64 bp):
GTTTAATGTGTTTAAATGTGTTTGTTAATAAATGCTTACAGGTGACTATTTAGTTGCTTATTAA
Found at i:43484936 original size:38 final size:38
Alignment explanation
Indices: 43484876--43484949 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
43484866 ATACCTAAAA
*
43484876 TTTTCTGGAGTGATCATTAATAAAAGCTAGAAGATAAC
1 TTTTCTGGAGTGATCATCAATAAAAGCTAGAAGATAAC
*
43484914 TTTTTTGGAGTGATCATCAATAAAAGCTAGAAGATA
1 TTTTCTGGAGTGATCATCAATAAAAGCTAGAAGATA
43484950 TCTGCTACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (38 bp):
TTTTCTGGAGTGATCATCAATAAAAGCTAGAAGATAAC
Found at i:43488552 original size:18 final size:18
Alignment explanation
Indices: 43488529--43488569 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
43488519 AAGTCCTAAG
43488529 AATAATATGATTATTTTT
1 AATAATATGATTATTTTT
43488547 AATAATATGATTATTTTT
1 AATAATATGATTATTTTT
43488565 AATAA
1 AATAA
43488570 GGTCATTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
AATAATATGATTATTTTT
Found at i:43491837 original size:19 final size:18
Alignment explanation
Indices: 43491785--43491837 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
43491775 AAATAGATAT
43491785 AATTATTTTGGTCAAAGTTA
1 AATTATTTTGG--AAAGTTA
*
43491805 AAATATTTAT-GAAAGTTA
1 AATTATTT-TGGAAAGTTA
43491823 ATATTATTTTGGAAA
1 A-ATTATTTTGGAAA
43491838 AAAATATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 9 0.32
19 10 0.36
20 8 0.29
21 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (18 bp):
AATTATTTTGGAAAGTTA
Found at i:43493985 original size:14 final size:14
Alignment explanation
Indices: 43493946--43493997 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
43493936 CAGAAGCAAA
*
43493946 TAAAAGAAAAAAAT
1 TAAAATAAAAAAAT
* **
43493960 TAGAATGTAAAAAT
1 TAAAATAAAAAAAT
*
43493974 TAAAATAAAAAAAA
1 TAAAATAAAAAAAT
*
43493988 TATAATAAAA
1 TAAAATAAAA
43493998 TAAAAAATGG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
TAAAATAAAAAAAT
Found at i:43495327 original size:31 final size:31
Alignment explanation
Indices: 43495289--43495350 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
43495279 TGGGATTAAA
43495289 ATATGTTAGTTTTATCATTTATCAAATATCC
1 ATATGTTAGTTTTATCATTTATCAAATATCC
43495320 ATATGTTAGTTTTATCATTTATCAAATATCC
1 ATATGTTAGTTTTATCATTTATCAAATATCC
43495351 CCAAACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (31 bp):
ATATGTTAGTTTTATCATTTATCAAATATCC
Found at i:43497630 original size:30 final size:30
Alignment explanation
Indices: 43497594--43497657 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
43497584 CTTAACTTAT
* *
43497594 ATAGCCAC-AGAGGTGTCCATACATCATTAG
1 ATAGCCACAAG-GGTGTCCACAAATCATTAG
43497624 ATAGCCACAAGGGTGTCCACAAATCATTAG
1 ATAGCCACAAGGGTGTCCACAAATCATTAG
43497654 ATAG
1 ATAG
43497658 TAATAAAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (30 bp):
ATAGCCACAAGGGTGTCCACAAATCATTAG
Found at i:43498111 original size:54 final size:54
Alignment explanation
Indices: 43498030--43498246 Score: 251
Period size: 53 Copynumber: 4.1 Consensus size: 54
43498020 GCCATTTTTA
* * * * * *
43498030 TCTTCTT-TCCTCACATGATACCATAGTCCCAGATTAGGTCTTACACTATGTGG
1 TCTTCTTATCTTCATATGATGCCATAGTCCTAGACTAGGTCTTACACTATATGG
* ** * * *
43498083 TCTTCGTATCCCCATATGATGCCATAGTCTTAGATTAGGTCTTACATTATATGG
1 TCTTCTTATCTTCATATGATGCCATAGTCCTAGACTAGGTCTTACACTATATGG
** *
43498137 TCTTCTTATCTTCATATGATG-TTTAGTCTTAGACTAGGTCTTACACTATATGG
1 TCTTCTTATCTTCATATGATGCCATAGTCCTAGACTAGGTCTTACACTATATGG
* * *
43498190 TCTTCTTATCTTCATATGATGTC-TAATCCTAGACTAGGTCTTACACTATATGA
1 TCTTCTTATCTTCATATGATGCCATAGTCCTAGACTAGGTCTTACACTATATGG
43498243 TCTT
1 TCTT
43498247 TTTGCCATGG
Statistics
Matches: 143, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
53 86 0.60
54 57 0.40
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (54 bp):
TCTTCTTATCTTCATATGATGCCATAGTCCTAGACTAGGTCTTACACTATATGG
Found at i:43499297 original size:27 final size:27
Alignment explanation
Indices: 43499259--43499536 Score: 282
Period size: 27 Copynumber: 10.3 Consensus size: 27
43499249 ACCCTACGAG
*
43499259 GTCATTTTACCCTTCGGGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCA
*
43499286 GTCATTTTACCCTT-TAGGGGTATTTC-
1 GTCATTTTACCCTTCGA-GGGTATTTCA
*
43499312 GATCATTTTACCCATT-GGGGGTATTTC-
1 G-TCATTTTACCC-TTCGAGGGTATTTCA
* * *
43499339 GATCATTTTACCCTACGGGGGTATTTTA
1 G-TCATTTTACCCTTCGAGGGTATTTCA
* *
43499367 GTCATTTTACCCTAC-AGAGGTATTTTA
1 GTCATTTTACCCTTCGAG-GGTATTTCA
*
43499394 GTCATTTTACCCCTCGAGGGTATTTC-
1 GTCATTTTACCCTTCGAGGGTATTTCA
* *
43499420 GATTATTTTACCCTTCGAGGGTATTTTA
1 G-TCATTTTACCCTTCGAGGGTATTTCA
* * *
43499448 GTCATTTTACCCCTCAAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCA
43499475 GTCATTTTACCCCTT-GAGGGTATTTCA
1 GTCATTTTA-CCCTTCGAGGGTATTTCA
* * * *
43499502 ATCATTTTATCCTTCAAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCA
43499529 GTCATTTT
1 GTCATTTT
43499537 CCCACAAATC
Statistics
Matches: 216, Mismatches: 24, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
26 8 0.04
27 198 0.92
28 10 0.05
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCA
Found at i:43499399 original size:81 final size:80
Alignment explanation
Indices: 43499260--43499536 Score: 369
Period size: 81 Copynumber: 3.4 Consensus size: 80
43499250 CCCTACGAGG
* * * * *
43499260 TCATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCCTTTAGGGGTA-TTTCGATCATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTTAGTCATTTTACCC-TCAGAGGTATTTTAG-TCATTTTACC
* *
43499324 CATTGGGGGTATTTCGA
64 CCTTGAGGGTATTTCGA
* *
43499341 TCATTTTACCCTACGGGGGTATTTTAGTCATTTTACCCTACAGAGGTATTTTAGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTTAGTCATTTTACCCT-CAGAGGTATTTTAGTCATTTTACCC
*
43499406 CTCGAGGGTATTTCGA
65 CTTGAGGGTATTTCGA
*
43499422 TTATTTTACCCTTCGAGGGTATTTTAGTCATTTTACCCCTCA-AGGGTATTTTAGTCATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTTAGTCATTTTA-CCCTCAGA-GGTATTTTAGTCATTTTACC
*
43499486 CCTTGAGGGTATTTCAA
64 CCTTGAGGGTATTTCGA
* *
43499503 TCATTTTATCCTTCAAGGGTATTTTAGTCATTTT
1 TCATTTTACCCTTCGAGGGTATTTTAGTCATTTT
43499537 CCCACAAATC
Statistics
Matches: 176, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
80 2 0.01
81 166 0.94
82 8 0.05
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (80 bp):
TCATTTTACCCTTCGAGGGTATTTTAGTCATTTTACCCTCAGAGGTATTTTAGTCATTTTACCCC
TTGAGGGTATTTCGA
Found at i:43502984 original size:54 final size:55
Alignment explanation
Indices: 43502812--43502989 Score: 161
Period size: 54 Copynumber: 3.3 Consensus size: 55
43502802 TACAAAGTGT
* * * * *
43502812 GAGCAGACTTGCGGACAACAATGGTGC-GAGCTATCAGGCAAACAGACCAAAAGC
1 GAGCAGACTCGCGGACAACAATGGTGCAGAGCTGTCATGCGAACAGACCAAATGC
* * **
43502866 GAGCAGACTCGCGGACAGCAAT-G-GCACGAGTTGTCATGCGAACAG-CCACGGTGC
1 GAGCAGACTCGCGGACAACAATGGTGCA-GAGCTGTCATGCGAACAGACCA-AATGC
* **
43502920 TG-GCAGACTCGCGGACAACAATGGTGCAG-GCTGTCATGCGGACAGACCATTTGC
1 -GAGCAGACTCGCGGACAACAATGGTGCAGAGCTGTCATGCGAACAGACCAAATGC
* *
43502974 GAGCAAACTCGTGGAC
1 GAGCAGACTCGCGGAC
43502990 GAAAAAAGGT
Statistics
Matches: 100, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
52 2 0.02
53 5 0.05
54 84 0.84
55 6 0.06
56 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.31, T:0.14
Consensus pattern (55 bp):
GAGCAGACTCGCGGACAACAATGGTGCAGAGCTGTCATGCGAACAGACCAAATGC
Found at i:43506236 original size:9 final size:9
Alignment explanation
Indices: 43506219--43506252 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
43506209 TAAAAATACT
*
43506219 TTTTTATAA
1 TTTTAATAA
43506228 TTTTAATAA
1 TTTTAATAA
43506237 TTTTAATAA
1 TTTTAATAA
43506246 TTTTAAT
1 TTTTAAT
43506253 TTTTAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTAATAA
Found at i:43506264 original size:26 final size:25
Alignment explanation
Indices: 43506228--43506299 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 25
43506218 TTTTTTATAA
*
43506228 TTTTAATAATTTTAATAATTTTAAT
1 TTTTAAAAATTTTAATAATTTTAAT
**
43506253 TTTTAAAGAATTTTTGTAATTTTTTAAT
1 TTTTAAA-AATTTTAATAA--TTTTAAT
*
43506281 TTTTTAAAATTTTAA-AATT
1 TTTTAAAAATTTTAATAATT
43506300 AATTAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
24 2 0.05
25 6 0.16
26 11 0.29
27 6 0.16
28 13 0.34
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTTAAAAATTTTAATAATTTTAAT
Found at i:43516357 original size:50 final size:50
Alignment explanation
Indices: 43516215--43516547 Score: 253
Period size: 50 Copynumber: 6.6 Consensus size: 50
43516205 GAATATAACA
* * * ** * * *
43516215 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * ** *
43516264 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** ** *
43516314 TGCCCATGCCCCGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
43516364 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * **
43516414 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATTTCAATAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
43516470 TGCCAATC-CCATGTCCCAGACATGGTCTTACATTGG--CTCACATATCGA
1 TGCCAA-CGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
43516518 TGTCGATGCCATGTCCTAGACATGGTCTTA
1 TGCCAACGCCATGTCCCAGACATGGTCTTA
43516548 TACGAGATCG
Statistics
Matches: 231, Mismatches: 43, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
48 27 0.12
49 36 0.16
50 125 0.54
51 2 0.01
53 3 0.01
54 6 0.03
56 31 0.13
57 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:43519982 original size:20 final size:21
Alignment explanation
Indices: 43519944--43519982 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
43519934 TTAATGTATG
* *
43519944 ATCATATTAAATTATTTAAAT
1 ATCATATTAAAGTAATTAAAT
43519965 ATCAT-TTAAAGTAATTAA
1 ATCATATTAAAGTAATTAA
43519983 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (21 bp):
ATCATATTAAAGTAATTAAAT
Found at i:43533694 original size:22 final size:22
Alignment explanation
Indices: 43533669--43533712 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43533659 ATCATGGATC
*
43533669 TCCTTAAGAATAATCTTCCTAA
1 TCCTAAAGAATAATCTTCCTAA
43533691 TCCTAAAGAATAATCTTCCTAA
1 TCCTAAAGAATAATCTTCCTAA
43533713 CACTGATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (22 bp):
TCCTAAAGAATAATCTTCCTAA
Found at i:43536651 original size:2 final size:2
Alignment explanation
Indices: 43536644--43536672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43536634 TGATAACATT
43536644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43536673 CTCAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43537086 original size:41 final size:41
Alignment explanation
Indices: 43537025--43537128 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
43537015 ACTGGCCTTT
* * * *
43537025 AGCCTGCTAGACCTATAGTCTGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAAATATATCACCGGCATCA
* *
43537066 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAATATATCACCGGCATCA
*
43537107 AGCCTACTAGACGTAAAGTCTG
1 AGCCTGCTAGACGTAAAGTCTG
43537129 TATTACATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAATATATCACCGGCATCA
Found at i:43537402 original size:12 final size:12
Alignment explanation
Indices: 43537387--43537440 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
43537377 ACTCATAACT
43537387 TATATATATACA
1 TATATATATACA
*
43537399 TATATATATTCGA
1 TATATATATAC-A
*
43537412 GTATTATACATACA
1 -TA-TATATATACA
43537426 TATATATATACA
1 TATATATATACA
43537438 TAT
1 TAT
43537441 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:43542797 original size:14 final size:15
Alignment explanation
Indices: 43542770--43542798 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43542760 TTGATGACTT
43542770 CCTAAGGTTTTCAAG
1 CCTAAGGTTTTCAAG
43542785 CCTAAGG-TTTCAAG
1 CCTAAGGTTTTCAAG
43542799 TTCTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (15 bp):
CCTAAGGTTTTCAAG
Found at i:43544983 original size:238 final size:238
Alignment explanation
Indices: 43544562--43545041 Score: 750
Period size: 238 Copynumber: 2.0 Consensus size: 238
43544552 TAAGGTTAAA
* *
43544562 TTAGTAAATTAGTTAATAAGTGAATTAAAACAAAAGAAATAATGTATCATCTTCTTTAATTTGTT
1 TTAGTAAATTAGTTAATAAGTGAACTAAAACAAAAGAAATAATGTATAATCTTCTTTAATTTGTT
* * *
43544627 AAACACCATCGAAAATTGAACGAAAAGAAACCATAGAAGCTTGAACATTTGGCCATCCTTATTTT
66 AAACACCACCGAAAATTCAACGAAAAGAAACCATAGAAGCTTGAACATTCGGCCATCCTTATTTT
*
43544692 GCTTGCATGTGAGTATTTTTCGTCCTATTTTTAATTATTTCTATGTTTTAGAATCGTTGTAGCTT
131 GCTTGCATGTGAGTATTTTTCGTCCTATTTTTAATGATTTCTATGTTTTAGAATCGTTGTAGCTT
43544757 AATCTAGCAAGCCCGGGGACTAATTTGCAAACCTGTTAATAA-G
196 AATCTAGCAAGCCCGGGGACTAATTTGCAAACCTGTTAA-AAGG
* * * *
43544800 TTAGTAACTTAGTTAATAAGTGAACTAAAATAAAATAAATAATGTATAATCTTTTTTAATTTGTT
1 TTAGTAAATTAGTTAATAAGTGAACTAAAACAAAAGAAATAATGTATAATCTTCTTTAATTTGTT
* * *
43544865 AAACACCACCGAAAGTTCAAGGAAAAGAAACTA-AGAAGCTTGAACATTCGGCCATCCTTATTTT
66 AAACACCACCGAAAATTCAACGAAAAGAAACCATAGAAGCTTGAACATTCGGCCATCCTTATTTT
*
43544929 GCTTGCATGTGAGTATTTTTCGTCCTGA-TTTTAATGATTTCTATGTTTTTAGAATCGTTTTAGC
131 GCTTGCATGTGAGTATTTTTCGTCCT-ATTTTTAATGATTTCTATG-TTTTAGAATCGTTGTAGC
* ** *
43544993 TTAATCTAGCTAGCTTGGGTACTAATTTGCAAACCTGTTAAAAGG
194 TTAATCTAGCAAGCCCGGGGACTAATTTGCAAACCTGTTAAAAGG
43545038 TTAG
1 TTAG
43545042 GGTTTTGCCA
Statistics
Matches: 221, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
237 74 0.33
238 147 0.67
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (238 bp):
TTAGTAAATTAGTTAATAAGTGAACTAAAACAAAAGAAATAATGTATAATCTTCTTTAATTTGTT
AAACACCACCGAAAATTCAACGAAAAGAAACCATAGAAGCTTGAACATTCGGCCATCCTTATTTT
GCTTGCATGTGAGTATTTTTCGTCCTATTTTTAATGATTTCTATGTTTTAGAATCGTTGTAGCTT
AATCTAGCAAGCCCGGGGACTAATTTGCAAACCTGTTAAAAGG
Found at i:43545341 original size:21 final size:20
Alignment explanation
Indices: 43545312--43545364 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
43545302 ATTTTGATAA
43545312 AATATGAATTTTGATTGAATTG
1 AATA-GAATTTT-ATTGAATTG
*
43545334 AATAGAATAATTATTGAATTG
1 AATAGAAT-TTTATTGAATTG
*
43545355 AATTGAATTT
1 AATAGAATTT
43545365 GTTCATTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 20 0.74
22 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (20 bp):
AATAGAATTTTATTGAATTG
Found at i:43551859 original size:26 final size:26
Alignment explanation
Indices: 43551829--43551880 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
43551819 TTAGGTCCAG
43551829 TCTGATGTACTGTTAGTCACATGTAT
1 TCTGATGTACTGTTAGTCACATGTAT
*
43551855 TCTGATGTACTGTTAGTCATATGTAT
1 TCTGATGTACTGTTAGTCACATGTAT
43551881 GTCTCTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.44
Consensus pattern (26 bp):
TCTGATGTACTGTTAGTCACATGTAT
Found at i:43563639 original size:61 final size:66
Alignment explanation
Indices: 43563545--43563693 Score: 182
Period size: 61 Copynumber: 2.3 Consensus size: 66
43563535 AAAGAAATCC
* *
43563545 TTTTCAAATTTTGATTATTTTAGTTTACCCAAATTATAAACGGTAATT-AAAAAAAA-C-TT-TT
1 TTTTCAAATTTT-AATATTTTAGTTTACCCAAATTATAAACCGTAATTAAAAAAAAACCTTTCTT
43563606 -T
65 CT
* ** *
43563607 TTTTCAAATTTTAATATTTTGGTTTGTCCAAATTATAAACCGTAGTTAAAAAAAAACTCTTTCTT
1 TTTTCAAATTTTAATATTTTAGTTTACCCAAATTATAAACCGTAATTAAAAAAAAAC-CTTTCTT
43563672 CT
65 CT
*
43563674 TTTTCAAATTTTAATTTTTT
1 TTTTCAAATTTTAATATTTT
43563694 TCAATCCAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
61 29 0.39
62 20 0.27
64 1 0.01
65 2 0.03
66 2 0.03
67 20 0.27
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (66 bp):
TTTTCAAATTTTAATATTTTAGTTTACCCAAATTATAAACCGTAATTAAAAAAAAACCTTTCTTC
T
Found at i:43563825 original size:33 final size:33
Alignment explanation
Indices: 43563783--43563849 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
43563773 ATTTCACTTG
43563783 ATTTCCTCTGACTATTAATTGAAAATCTATGGA
1 ATTTCCTCTGACTATTAATTGAAAATCTATGGA
43563816 ATTTCCTCTGACTATTAATTGAAAATCTATGGA
1 ATTTCCTCTGACTATTAATTGAAAATCTATGGA
43563849 A
1 A
43563850 GATTAATGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (33 bp):
ATTTCCTCTGACTATTAATTGAAAATCTATGGA
Found at i:43565122 original size:9 final size:9
Alignment explanation
Indices: 43565102--43565143 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
43565092 TAGTAACATT
*
43565102 ACAAAATGA
1 ACAAAATAA
*
43565111 ACAAAGTAA
1 ACAAAATAA
43565120 ACAAAATAA
1 ACAAAATAA
43565129 ACAAAATGAA
1 ACAAAAT-AA
43565139 ACAAA
1 ACAAA
43565144 CTGCTCCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.71, C:0.12, G:0.07, T:0.10
Consensus pattern (9 bp):
ACAAAATAA
Found at i:43569650 original size:9 final size:9
Alignment explanation
Indices: 43569630--43569671 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
43569620 TAGTAACATT
*
43569630 ACAAAATGA
1 ACAAAATAA
*
43569639 ACAAAGTAA
1 ACAAAATAA
43569648 ACAAAATAA
1 ACAAAATAA
43569657 ACAAAATGAA
1 ACAAAAT-AA
43569667 ACAAA
1 ACAAA
43569672 TTGCTCCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.71, C:0.12, G:0.07, T:0.10
Consensus pattern (9 bp):
ACAAAATAA
Found at i:43585695 original size:34 final size:34
Alignment explanation
Indices: 43585652--43585719 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
43585642 CAAAGTAAAC
43585652 ATGGTACATAAGATAGTAAATTTAAATCAATCTA
1 ATGGTACATAAGATAGTAAATTTAAATCAATCTA
43585686 ATGGTACATAAGATAGTAAATTTAAATCAATCTA
1 ATGGTACATAAGATAGTAAATTTAAATCAATCTA
43585720 CTGGAAGTTT
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:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (34 bp):
ATGGTACATAAGATAGTAAATTTAAATCAATCTA
Found at i:43591393 original size:15 final size:15
Alignment explanation
Indices: 43591373--43591407 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43591363 CATACATTTA
*
43591373 TTGTTCTTTTCTACT
1 TTGTTCTGTTCTACT
*
43591388 TTGTTCTGTTCTATT
1 TTGTTCTGTTCTACT
43591403 TTGTT
1 TTGTT
43591408 GTACTACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.14, G:0.11, T:0.69
Consensus pattern (15 bp):
TTGTTCTGTTCTACT
Found at i:43594039 original size:37 final size:37
Alignment explanation
Indices: 43593994--43594083 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
43593984 TTCCAAAAAT
43593994 AATATTATTTTAATAGT-TTAATATTAAATTAA-ATTA
1 AATATTATTTTAATAGTATT-ATATTAAATTAATATTA
* *
43594030 AATACTTATTTTAATAGTATTTTATTAATTTAATATTA
1 AATA-TTATTTTAATAGTATTATATTAAATTAATATTA
*
43594068 AAGTGATTATCTTAAT
1 AA-T-ATTATTTTAAT
43594084 TTAATATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
36 4 0.09
37 23 0.50
38 8 0.17
39 10 0.22
40 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (37 bp):
AATATTATTTTAATAGTATTATATTAAATTAATATTA
Found at i:43594066 original size:11 final size:11
Alignment explanation
Indices: 43593993--43594121 Score: 56
Period size: 11 Copynumber: 11.4 Consensus size: 11
43593983 ATTCCAAAAA
*
43593993 TAATATTATTT
1 TAATATTAATT
43594004 TAATAGTTTAATAT
1 TAATA--TTAAT-T
43594018 TAA-ATTAAATT
1 TAATATT-AATT
* *
43594029 AAATACTTATTT
1 TAATA-TTAATT
*
43594041 TAATAGT-ATT
1 TAATATTAATT
43594051 T--TATTAATT
1 TAATATTAATT
43594060 TAATATTAAAGTGAT
1 TAATATT-AA-T--T
*
43594075 T-ATCTTAATT
1 TAATATTAATT
*
43594085 TAATATTATTT
1 TAATATTAATT
43594096 TAATA--AGATT
1 TAATATTA-ATT
43594106 TAATATTAAATT
1 TAATATT-AATT
43594118 TAAT
1 TAAT
43594122 CTAATATTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 35
0.66 0.08 0.26
Matches are distributed among these distances:
8 3 0.03
9 5 0.06
10 12 0.13
11 27 0.30
12 21 0.24
13 11 0.12
14 8 0.09
15 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (11 bp):
TAATATTAATT
Found at i:43594167 original size:95 final size:92
Alignment explanation
Indices: 43593993--43594171 Score: 263
Period size: 95 Copynumber: 1.9 Consensus size: 92
43593983 ATTCCAAAAA
* *
43593993 TAATATTATTTTAATAGTTTAATATTAAATTAAATTAAATACTTATTTTAATAGTATTTTATTAA
1 TAATATTATTTTAATAGTTTAATATTAAATTAAATTAAATACTTATTTTAATAATATTATATTAA
43594058 TTTAATATTAAAGTGATTATCTTAATT
66 TTTAATATTAAAGTGATTATCTTAATT
* *
43594085 TAATATTATTTTAATAAGATTTAATATTAAATTTAATCT-AATATTTATTTTGACA-AATATTAT
1 TAATATTATTTTAAT-AG-TTTAATATTAAATTAAAT-TAAATACTTATTTT-A-ATAATATTAT
43594148 ATTAATTTAATATTAAAGTGATTA
61 ATTAATTTAATATTAAAGTGATTA
43594172 AGTTTAATCG
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
92 15 0.19
93 2 0.03
94 28 0.36
95 32 0.41
96 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (92 bp):
TAATATTATTTTAATAGTTTAATATTAAATTAAATTAAATACTTATTTTAATAATATTATATTAA
TTTAATATTAAAGTGATTATCTTAATT
Found at i:43600234 original size:13 final size:13
Alignment explanation
Indices: 43600216--43600240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43600206 CATGGGCATA
43600216 TGGACCATACGGG
1 TGGACCATACGGG
43600229 TGGACCATACGG
1 TGGACCATACGG
43600241 CCCCTCACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (13 bp):
TGGACCATACGGG
Found at i:43601644 original size:91 final size:91
Alignment explanation
Indices: 43601458--43601663 Score: 234
Period size: 91 Copynumber: 2.2 Consensus size: 91
43601448 TATTAATGAT
** * *
43601458 TAAATATATTAGTGGATGAACCATCTGTCTATGTAGATAAAAGCTGCTAATACGTTGTGGATGAA
1 TAAA-ATATTAGTGGATGAACCATCCATCTATGCAGATAAAAGCTGCGAATACGTTGTGGATGAA
* *
43601523 CCATTGGTCGAGCAGGTGACTGTCGGC
65 CCATTGGTCGAGCAGATGACTGTCGAC
* * * *
43601550 TAAAATATTGGTGGATGAACCATCCATTTGTGCAGATAAAAGCTGCGAATATGTTGTGGATGAAC
1 TAAAATATTAGTGGATGAACCATCCATCTATGCAGATAAAAGCTGCGAATACGTTGTGGATGAAC
* * * *
43601615 CATTGGTTGAGTATATGATTG-CTGAC
66 CATTGGTCGAGCAGATGACTGTC-GAC
* *
43601641 TAAAATATGTTGTGGATAAACCA
1 TAAAATAT-TAGTGGATGAACCA
43601664 CTGGTCTAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
90 1 0.01
91 79 0.82
92 16 0.17
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (91 bp):
TAAAATATTAGTGGATGAACCATCCATCTATGCAGATAAAAGCTGCGAATACGTTGTGGATGAAC
CATTGGTCGAGCAGATGACTGTCGAC
Found at i:43606253 original size:41 final size:41
Alignment explanation
Indices: 43606196--43606489 Score: 471
Period size: 41 Copynumber: 7.1 Consensus size: 41
43606186 TATCTTATGC
* *
43606196 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
* * *
43606237 GATCTGTATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
*
43606278 GATCTGAATCAGGCTATAAGCCTATCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
* *
43606319 GATCTAAATCAGGCTATAAGCCTATCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
*
43606360 GATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
* *
43606401 GATCTAAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
*
43606442 GATCTGAATCAGGCTATATGCCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
43606483 GAATCTG
1 G-ATCTG
43606490 TTAAATTAAG
Statistics
Matches: 241, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
41 236 0.98
42 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (41 bp):
GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
Found at i:43610727 original size:30 final size:31
Alignment explanation
Indices: 43610688--43610747 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
43610678 TGGGATGGGA
43610688 TGGGAAGGGA-AAAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAGAAAAAA-TTTTAGGGGAAAAG
* *
43610719 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAGAAAAAATTTTAGGGGAAAA
43610748 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAGAAAAAATTTTAGGGGAAAAG
Found at i:43610941 original size:9 final size:9
Alignment explanation
Indices: 43610927--43610972 Score: 92
Period size: 9 Copynumber: 5.1 Consensus size: 9
43610917 TATAGTTTGA
43610927 TATTCGAAT
1 TATTCGAAT
43610936 TATTCGAAT
1 TATTCGAAT
43610945 TATTCGAAT
1 TATTCGAAT
43610954 TATTCGAAT
1 TATTCGAAT
43610963 TATTCGAAT
1 TATTCGAAT
43610972 T
1 T
43610973 TGAAAACTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43611226 original size:33 final size:36
Alignment explanation
Indices: 43611167--43611240 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 36
43611157 AAAATGGAAT
* * *
43611167 ATATAGACACATATGTAGGTATGTATA-A-AT-AAA
1 ATATAGAAACATATATAGGTACGTATATATATAAAA
43611200 ATATAGAAACATATAT-GTGTACGTATATATATAAAA
1 ATATAGAAACATATATAG-GTACGTATATATATAAAA
43611236 ATATA
1 ATATA
43611241 CATGGGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 1 0.03
33 22 0.65
34 1 0.03
35 2 0.06
36 8 0.24
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.32
Consensus pattern (36 bp):
ATATAGAAACATATATAGGTACGTATATATATAAAA
Found at i:43611365 original size:3 final size:3
Alignment explanation
Indices: 43611347--43611420 Score: 103
Period size: 3 Copynumber: 24.3 Consensus size: 3
43611337 GAAATAAAAC
* * * *
43611347 TAA TAA CAA TTAA TAA TAA TAG CAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43611393 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43611421 GATGATGATG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 62 0.97
4 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:43613146 original size:44 final size:43
Alignment explanation
Indices: 43613092--43613295 Score: 153
Period size: 44 Copynumber: 4.7 Consensus size: 43
43613082 GCCATATTCG
* ** *
43613092 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCCCAGGGAGATAAAATCTG-AATCTTCA
* *
43613136 ATCTATTCCACTACTGCCCAGGGAGATAAAATTACTG--GCTTCA
1 ATCTACTCCACTACTGCCCAGGGAGATAAAA-T-CTGAATCTTCA
* * * * * * *
43613179 ATGTACACCACTA-TAACCACAGGGAGGTAAAATCCGCCATCTTCG
1 ATCTACTCCACTACT-GCC-CAGGGAGATAAAATCTG-AATCTTCA
* ** * *
43613224 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTTA
1 ATCTACTCCACTACTGCCCAGGGAGATAAAATCTG-AATCTTCA
*
43613268 ATCTATTCCACTACTGCCCAGGGAGATA
1 ATCTACTCCACTACTGCCCAGGGAGATA
43613296 GAATTATCGG
Statistics
Matches: 121, Mismatches: 31, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
42 3 0.02
43 18 0.15
44 80 0.66
45 16 0.13
46 4 0.03
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
ATCTACTCCACTACTGCCCAGGGAGATAAAATCTGAATCTTCA
Found at i:43613427 original size:126 final size:126
Alignment explanation
Indices: 43613024--43613807 Score: 1097
Period size: 126 Copynumber: 6.1 Consensus size: 126
43613014 AGCAACATCG
* **
43613024 GGGAGATAGAATTA-CTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAAT-TCGCCAT
1 GGGAGATAGAATTATC-GGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCT-GCCAT
* * * **
43613087 ATTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTG
64 CTTCAATCTGCT-C-C-ACT--TT-GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCA
*
43613152 CCCA
123 ACCA
* * * * *
43613156 GGGAGATAAAATTA-CTGGCTTCAATGTACACCACTATAACCACAGGGAGGTAAAATCCGCCATC
1 GGGAGATAGAATTATC-GGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATC
* * ***
43613220 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTACTGC
65 TTCAATCTGCT-C-C-ACT--TT-GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCAA
43613285 CCA
124 CCA
* * * *
43613288 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCATAGGTAGGTAAAATTTGCCATCT
1 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
*
43613353 TCAATCTGCTCCACTTTGGGAGATAAGATATGAAATCTTCAATCTATTCCACTACCAACCA
66 TCAATCTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCAACCA
*
43613414 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
* * *
43613479 TCAATCTGCTCCACTTTAGGAAATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCA
66 TCAATCTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCAACCA
*
43613540 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTGAAATCTGCCATCT
1 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
*
43613605 TCAATCTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCA
66 TCAATCTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCAACCA
* * *
43613666 GGGAGGTAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTTCCATCT
1 GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
* *
43613731 TCAATTTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCA
66 TCAATCTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCAACCA
43613792 GGGAGATAGAATTATC
1 GGGAGATAGAATTATC
43613808 AATCTTCTCC
Statistics
Matches: 609, Mismatches: 41, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
126 416 0.68
127 2 0.00
129 3 0.00
130 1 0.00
131 1 0.00
132 185 0.30
133 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (126 bp):
GGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCT
TCAATCTGCTCCACTTTGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACCAACCA
Found at i:43613482 original size:45 final size:44
Alignment explanation
Indices: 43613432--43613745 Score: 156
Period size: 38 Copynumber: 7.4 Consensus size: 44
43613422 GAATTATCGG
* *
43613432 CTTCAATGTACTCCACTGTAATCATAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAATC-CAGGGAGGTAAAATCTGCCAT
* ** * **
43613477 CTTCAATCTGCTCCACT-T--T--A-GGAAATAAGATCTGAAAT
1 CTTCAATCTACTCCACTGTAATCCAGGGAGGTAAAATCTGCCAT
* * * * ** **
43613515 CTTCAATCTATTCCACTGCCAA-CCAGGGAGATAGAAT-TATCGG
1 CTTCAATCTACTCCACTG-TAATCCAGGGAGGTAAAATCTGCCAT
* *
43613558 CTTCAATGTACTCCACTGTAATCACAGGGAGGTGAAATCTGCCAT
1 CTTCAATCTACTCCACTGTAATC-CAGGGAGGTAAAATCTGCCAT
* * * **
43613603 CTTCAATCTGCTCCACT-T--T---GGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTGTAATCCAGGGAGGTAAAATCTGCCAT
* * * ** **
43613641 CTTCAATCTATTCCACTGCCAA-CCAGGGAGGTAGAAT-TATCGG
1 CTTCAATCTACTCCACTG-TAATCCAGGGAGGTAAAATCTGCCAT
* * *
43613684 CTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTTTCCAT
1 CTTCAATCTACTCCACTGTAATC-CAGGGAGGTAAAATCTGCCAT
* *
43613729 CTTCAATTTGCTCCACT
1 CTTCAATCTACTCCACT
43613746 TTGGGAGATA
Statistics
Matches: 193, Mismatches: 56, Indels: 40
0.67 0.19 0.14
Matches are distributed among these distances:
38 57 0.30
39 1 0.01
42 6 0.03
43 37 0.19
44 43 0.22
45 49 0.25
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTAATCCAGGGAGGTAAAATCTGCCAT
Found at i:43615081 original size:12 final size:12
Alignment explanation
Indices: 43615061--43615135 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
43615051 TCCTTTTTCT
*
43615061 TTTCATTTCTTC
1 TTTCTTTTCTTC
43615073 TTTCTTTTCTTC
1 TTTCTTTTCTTC
* *
43615085 TTTCCTTTCTTT
1 TTTCTTTTCTTC
43615097 TTTCTCTTT-TCTC
1 TTTCT-TTTCT-TC
* *
43615110 TTT-TTTTTTTT
1 TTTCTTTTCTTC
*
43615121 TTTCTTTTTTTC
1 TTTCTTTTCTTC
43615133 TTT
1 TTT
43615136 TTTGAATATG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.13
12 38 0.73
13 7 0.13
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTTTCTTC
Found at i:43615104 original size:9 final size:8
Alignment explanation
Indices: 43615054--43615138 Score: 77
Period size: 8 Copynumber: 10.5 Consensus size: 8
43615044 TGGCCTCTCC
43615054 TTTTTCTT
1 TTTTTCTT
43615062 TTCATTTC-T
1 TT--TTTCTT
*
43615071 TCTTTCTT
1 TTTTTCTT
*
43615079 TTCTTCTT
1 TTTTTCTT
*
43615087 TCCTTTC-T
1 T-TTTTCTT
43615095 TTTTTCTCT
1 TTTTTCT-T
*
43615104 TTTCTCTT
1 TTTTTCTT
43615112 TTTTT-TT
1 TTTTTCTT
43615119 TTTTTCTT
1 TTTTTCTT
43615127 TTTTTCTT
1 TTTTTCTT
43615135 TTTT
1 TTTT
43615139 GAATATGAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
7 15 0.24
8 31 0.50
9 12 0.19
10 4 0.06
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:43615111 original size:16 final size:15
Alignment explanation
Indices: 43615053--43615136 Score: 64
Period size: 15 Copynumber: 5.3 Consensus size: 15
43615043 TTGGCCTCTC
43615053 CTTTT-TCTTTTCATTT
1 CTTTTCTCTTTT--TTT
*
43615069 CTTCTT-TCTTTTCTT
1 CTT-TTCTCTTTTTTT
*
43615084 CTTTCCTTTCTTTTTTCT
1 CTTT--TCTCTTTTTT-T
43615102 CTTTTCTCTTTTTTT
1 CTTTTCTCTTTTTTT
* *
43615117 TTTTTTTCTTTTTTT
1 CTTTTCTCTTTTTTT
43615132 CTTTT
1 CTTTT
43615137 TTGAATATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.02
15 23 0.40
16 13 0.23
17 15 0.26
18 5 0.09
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTCTCTTTTTTT
Found at i:43615130 original size:7 final size:7
Alignment explanation
Indices: 43615066--43615138 Score: 65
Period size: 7 Copynumber: 9.4 Consensus size: 7
43615056 TTTCTTTTCA
*
43615066 TTTCTTC
1 TTTCTTT
43615073 TTTCTTT
1 TTTCTTT
43615080 TCTTCTTT
1 T-TTCTTT
43615088 CCTTTCTTT
1 --TTTCTTT
43615097 TTTCTCTT
1 TTTCT-TT
43615105 TTCTCTTTT
1 TT-TC-TTT
*
43615114 TTTTTTT
1 TTTCTTT
43615121 TTTCTTTT
1 TTTC-TTT
43615129 TTTCTTT
1 TTTCTTT
43615136 TTT
1 TTT
43615139 GAATATGAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
7 24 0.43
8 18 0.32
9 12 0.21
10 2 0.04
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:43618265 original size:13 final size:13
Alignment explanation
Indices: 43618247--43618271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43618237 CATGGGCATA
43618247 TGGACCATACGGG
1 TGGACCATACGGG
43618260 TGGACCATACGG
1 TGGACCATACGG
43618272 CCCCTCACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (13 bp):
TGGACCATACGGG
Found at i:43619652 original size:91 final size:91
Alignment explanation
Indices: 43619466--43619671 Score: 252
Period size: 91 Copynumber: 2.2 Consensus size: 91
43619456 TATTAATGAT
**
43619466 TAAATATATTAGTGGATGAACCATCTGTCTATGTAGATAAAAGCTGCTAATACGTTGTGGATGAA
1 TAAA-ATATTAGTGGATGAACCATCCATCTATGTAGATAAAAGCTGCTAATACGTTGTGGATGAA
* *
43619531 CCATTGGTCGAACAGGTGACTGTCGGC
65 CCATTGGTCGAACAGATGACTGTCGAC
* * * *
43619558 TAAAATATTGGTGGATGAACCATCCATTTGTGTAGATAAAAGCTGCTAATATGTTGTGGATGAAC
1 TAAAATATTAGTGGATGAACCATCCATCTATGTAGATAAAAGCTGCTAATACGTTGTGGATGAAC
* ** *
43619623 CATTGGTTGAGTAGATGATTG-CTGAC
66 CATTGGTCGAACAGATGACTGTC-GAC
* *
43619649 TAAAATATGTTGTGGATAAACCA
1 TAAAATAT-TAGTGGATGAACCA
43619672 CTGGTCTAGC
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
90 1 0.01
91 81 0.83
92 16 0.16
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (91 bp):
TAAAATATTAGTGGATGAACCATCCATCTATGTAGATAAAAGCTGCTAATACGTTGTGGATGAAC
CATTGGTCGAACAGATGACTGTCGAC
Found at i:43624144 original size:20 final size:20
Alignment explanation
Indices: 43624122--43624322 Score: 64
Period size: 21 Copynumber: 10.8 Consensus size: 20
43624112 GATCCGATTT
43624122 AAACACGAGAAATTTTTTTTA
1 AAACACGAG-AATTTTTTTTA
*
43624143 AAACACGAGAA----TTTTG
1 AAACACGAGAATTTTTTTTA
* * *
43624159 AAGCATGA-AATTTTTTTAAAA
1 AAACACGAGAATTTTTTT--TA
* * *
43624180 AAAAAC-AAAAGTTTTTTTA
1 AAACACGAGAATTTTTTTTA
* **
43624199 AAACACGA-AA-ATTTTTGC
1 AAACACGAGAATTTTTTTTA
43624217 AAACACGAGAA---TTTTTA
1 AAACACGAGAATTTTTTTTA
** *
43624234 AAACAC-A-AA--AATTTTG
1 AAACACGAGAATTTTTTTTA
* *
43624250 AAACACGACAA--T-TTTTG
1 AAACACGAGAATTTTTTTTA
43624267 AAACACGAGAATTTTTTTTA
1 AAACACGAGAATTTTTTTTA
43624287 AAA-ACGCA-AATTTTTTTTTTA
1 AAACACG-AGAA--TTTTTTTTA
*
43624308 AAACACGAAAATTTT
1 AAACACGAGAATTTT
43624323 GGAAACACGA
Statistics
Matches: 139, Mismatches: 21, Indels: 41
0.69 0.10 0.20
Matches are distributed among these distances:
15 4 0.03
16 21 0.15
17 26 0.19
18 15 0.11
19 19 0.14
20 16 0.12
21 33 0.24
22 5 0.04
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (20 bp):
AAACACGAGAATTTTTTTTA
Found at i:43624213 original size:17 final size:17
Alignment explanation
Indices: 43624193--43624428 Score: 172
Period size: 18 Copynumber: 13.2 Consensus size: 17
43624183 AACAAAAGTT
43624193 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
43624210 TTTTTGCAAACACGAGAA
1 TTTTT-AAAACACGAAAA
43624228 TTTTTAAAACAC-AAAA
1 TTTTTAAAACACGAAAA
* * *
43624244 ATTTTGAAACACGACAA
1 TTTTTAAAACACGAAAA
* *
43624261 TTTTTGAAACACGAGAATTT
1 TTTTTAAAACACGA-AA--A
*
43624281 TTTTTAAAA-ACGCAAATTTTT
1 TTTTTAAAACACG-AAA----A
43624302 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
** *
43624319 TTTTGGAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
43624336 TTGTTGAAAACACGAAAA
1 TT-TTTAAAACACGAAAA
* *
43624354 TTTTTGAAAATATGAAAA
1 TTTTT-AAAACACGAAAA
43624372 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* *
43624390 TTTTTGAAACA-TAGAAA
1 TTTTTAAAACACGA-AAA
43624407 TTTTTAGAAAACACGAAAA
1 TTTTT--AAAACACGAAAA
43624426 TTT
1 TTT
43624429 GAATTTTTTT
Statistics
Matches: 178, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
16 14 0.08
17 58 0.33
18 62 0.35
19 16 0.09
20 10 0.06
21 15 0.08
22 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:43624291 original size:21 final size:20
Alignment explanation
Indices: 43624267--43624322 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
43624257 ACAATTTTTG
43624267 AAACACGAGAATTTTTTTTAA
1 AAACACGA-AATTTTTTTTAA
* *
43624288 AAACGC-AAATTTTTTTTTTA
1 AAACACGAAA-TTTTTTTTAA
43624308 AAACACGAAAATTTT
1 AAACACG-AAATTTT
43624323 GGAAACACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 9 0.31
22 3 0.10
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (20 bp):
AAACACGAAATTTTTTTTAA
Found at i:43624306 original size:22 final size:22
Alignment explanation
Indices: 43624261--43624322 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
43624251 AACACGACAA
* *
43624261 TTTTTGAAACACGAGAA--TTT
1 TTTTTAAAACACGAAAATTTTT
*
43624281 TTTTTAAAA-ACGCAAATTTTT
1 TTTTTAAAACACGAAAATTTTT
43624302 TTTTTAAAACACGAAAATTTT
1 TTTTTAAAACACGAAAATTTT
43624323 GGAAACACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 5 0.14
20 8 0.23
21 12 0.34
22 10 0.29
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
TTTTTAAAACACGAAAATTTTT
Found at i:43624379 original size:36 final size:36
Alignment explanation
Indices: 43624192--43624428 Score: 211
Period size: 36 Copynumber: 6.6 Consensus size: 36
43624182 AAACAAAAGT
* * *
43624192 TTTTTTAAAACACGAAAATTTTTGCAAACACGAGAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACACGAAAA
* *
43624228 TTTTT-AAAACAC-AAAAATTTTG-AAACACGACAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACACGAAAA
* * *
43624261 TTTTTG-AAACACGAGAATTTTTTTTAAAA-ACGCAAATTTT
1 TTTTTGAAAACACGA-AA-ATTTTTGAAAACACG-AAA---A
* * *
43624301 TTTTTTAAAACACGAAAA-TTTTGGAAACACGAGAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACACGAAAA
* * *
43624336 TTGTTGAAAACACGAAAATTTTTGAAAATATGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACACGAAAA
*
43624372 TTTTTGAAAACACGAAAATTTTTG-AAACA-TAGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACACGA-AAA
43624407 TTTTTAGAAAACACGAAAATTT
1 TTTTT-GAAAACACGAAAATTT
43624429 GAATTTTTTT
Statistics
Matches: 165, Mismatches: 22, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
33 21 0.13
34 11 0.07
35 37 0.22
36 64 0.39
37 5 0.03
38 9 0.05
39 3 0.02
40 7 0.04
41 8 0.05
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:43624434 original size:42 final size:40
Alignment explanation
Indices: 43624390--43624468 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
43624380 AACACGAAAA
43624390 TTTTTGAAACATAGAAATTTTTAGAAAACACGAAAATTTGAAT
1 TTTTTGAAAC-TAGAAATTTTT--AAAACACGAAAATTTGAAT
** *
43624433 TTTTTTTAACTAGAAATTTTTAAAACACGAGAATTT
1 TTTTTGAAACTAGAAATTTTTAAAACACGAAAATTT
43624469 TTTCTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 14 0.42
42 11 0.33
43 8 0.24
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (40 bp):
TTTTTGAAACTAGAAATTTTTAAAACACGAAAATTTGAAT
Found at i:43625265 original size:28 final size:28
Alignment explanation
Indices: 43625232--43625299 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
43625222 ATATTATTTT
* *
43625232 TCTTTTTTCTTTCTTTCCCTTTT-TTCTC
1 TCTTTTTTCCTTCCTT-CCTTTTCTTCTC
* *
43625260 TCTTTTTTCCTTCCTTCTTTTTCTTCTT
1 TCTTTTTTCCTTCCTTCCTTTTCTTCTC
43625288 TC-TTTTTCCTTC
1 TCTTTTTTCCTTC
43625300 TTCGTTCGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (28 bp):
TCTTTTTTCCTTCCTTCCTTTTCTTCTC
Done.