Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 106 of 259
Found at i:34241553 original size:25 final size:25
Alignment explanation
Indices: 34241503--34241553 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
34241493 CCCTTATAAT
* *
34241503 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
*
34241528 GTGAAAATGA-CTATTATACCCTTAG
1 GTGAAAATGACCT-TTATACCCCTAG
34241553 G
1 G
34241554 GTTATGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:34241608 original size:10 final size:10
Alignment explanation
Indices: 34241597--34241641 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
34241587 TTTGTACATA
*
34241597 ATATGCCATA
1 ATATGCCATG
34241607 ATATGCCATG
1 ATATGCCATG
34241617 ATATGCACATG
1 ATATGC-CATG
34241628 ATATGCCATG
1 ATATGCCATG
34241638 ATAT
1 ATAT
34241642 ATGTATATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
10 23 0.70
11 10 0.30
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:34241633 original size:21 final size:20
Alignment explanation
Indices: 34241597--34241641 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
34241587 TTTGTACATA
34241597 ATATGCCATAATATGCCATG
1 ATATGCCATAATATGCCATG
*
34241617 ATATGCACATGATATGCCATG
1 ATATGC-CATAATATGCCATG
34241638 ATAT
1 ATAT
34241642 ATGTATATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
ATATGCCATAATATGCCATG
Found at i:34241714 original size:25 final size:24
Alignment explanation
Indices: 34241686--34241754 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 24
34241676 AGGAAGTGAT
*
34241686 AAAGGGCTATGCCCTAGTTTACCGA
1 AAAGGGCTTTGCCCTAGTTTACC-A
* *
34241711 AAAGGGCTTTGCCCCAGTTTATCA
1 AAAGGGCTTTGCCCTAGTTTACCA
34241735 AAATGGGCTTTGCCCTAGTT
1 AAA-GGGCTTTGCCCTAGTT
34241755 ATTTAAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.10
25 35 0.90
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAGGGCTTTGCCCTAGTTTACCA
Found at i:34243415 original size:30 final size:31
Alignment explanation
Indices: 34243351--34243418 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
34243341 ACCCTTAAAA
* * *
34243351 TATTTACACTATTAGTCCTTCAAAATTTTTG
1 TATTTACACTATTAATCCCTCAAAATTTTAG
34243382 TATTTACACT-TTAATCCCTC-AAATTTTGAG
1 TATTTACACTATTAATCCCTCAAAATTTT-AG
34243412 TATTTAC
1 TATTTAC
34243419 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 7 0.21
30 16 0.48
31 10 0.30
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAAATTTTAG
Found at i:34245708 original size:27 final size:26
Alignment explanation
Indices: 34245677--34245746 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
34245667 CTTCATAATT
* *
34245677 ATTTCATGCAACTATTTTTGTATAAAC
1 ATTTCATACAACCA-TTTTGTATAAAC
* *
34245704 ATTTCACACAACCATTTTGTATAACC
1 ATTTCATACAACCATTTTGTATAAAC
* *
34245730 AATTCATATAACCATTT
1 ATTTCATACAACCATTT
34245747 GTCATCTGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 25 0.69
27 11 0.31
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTCATACAACCATTTTGTATAAAC
Found at i:34245894 original size:46 final size:46
Alignment explanation
Indices: 34245829--34246187 Score: 409
Period size: 46 Copynumber: 7.8 Consensus size: 46
34245819 TTATCTTCGA
* * * *
34245829 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* * ***
34245875 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTT-CATAT
* * *
34245922 TATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
** *
34245968 CACATTGCCATGGTATCTTTCAACCATTGTCTTACAT-ATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCATAT
* *
34246014 CATGTTGCCATGGTATCTTTCAACCAGGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
34246060 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACGCATTTCATAA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
34246106 CATGTTGCCATGGTATCTTTCAACCATTGTCTTACACATTTGA-AT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
** * * * * *
34246151 CGCGATGCCATAGCATCTTTCAGCTATGGTCTTACTC
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC
34246188 GTCTGAATCA
Statistics
Matches: 270, Mismatches: 39, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
45 32 0.12
46 197 0.73
47 41 0.15
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:34246183 original size:45 final size:45
Alignment explanation
Indices: 34246111--34246230 Score: 132
Period size: 45 Copynumber: 2.7 Consensus size: 45
34246101 CATAACATGT
* * * * * * *
34246111 TGCCATGGTATCTTTCAACCATTGTCTTACACATTTGAATCGCGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACACATCTGAATCACGA
* * *
34246156 TGCCATAGCATCTTTCAGCTATGGTCTTACTCGTCTGAATCATGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACACATCTGAATCACGA
* *
34246201 TGCCATAGCGTCTTTTAGCTATGGTCTTAC
1 TGCCATAGCATCTTTCAGCTATGGTCTTAC
34246231 TCGTTTCTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (45 bp):
TGCCATAGCATCTTTCAGCTATGGTCTTACACATCTGAATCACGA
Found at i:34248914 original size:20 final size:20
Alignment explanation
Indices: 34248889--34248942 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
34248879 ATATATATAC
34248889 TAAATAAAATAATAAAATAT
1 TAAATAAAATAATAAAATAT
*** *
34248909 TAAATATCTTATTAAAATAT
1 TAAATAAAATAATAAAATAT
34248929 TAAAT-AAATAATAA
1 TAAATAAAATAATAA
34248943 TTATCTAATT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATAAAATAATAAAATAT
Found at i:34249223 original size:30 final size:31
Alignment explanation
Indices: 34249168--34249226 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
34249158 CACCCTTAAA
* * *
34249168 ATATTTGCACTATTAGTCCTTCAAATTTTTT
1 ATATTTACACTATTAATCCCTCAAATTTTTT
34249199 ATATTTACACT-TTAATCCCTCAAATTTT
1 ATATTTACACTATTAATCCCTCAAATTTT
34249227 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (31 bp):
ATATTTACACTATTAATCCCTCAAATTTTTT
Found at i:34249234 original size:30 final size:31
Alignment explanation
Indices: 34249168--34249236 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
34249158 CACCCTTAAA
* * * *
34249168 ATATTTGCACTATTAGTCCTTCAAATTTTTT
1 ATATTTACACTATTAATCCCTCAAATTTTTG
34249199 ATATTTACACT-TTAATCCCTCAAA-TTTTG
1 ATATTTACACTATTAATCCCTCAAATTTTTG
34249228 AGTATTTAC
1 A-TATTTAC
34249237 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 10 0.30
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (31 bp):
ATATTTACACTATTAATCCCTCAAATTTTTG
Found at i:34255621 original size:11 final size:11
Alignment explanation
Indices: 34255606--34255677 Score: 71
Period size: 11 Copynumber: 6.7 Consensus size: 11
34255596 AAAAAACATG
34255606 CAAAAAAAGTT
1 CAAAAAAAGTT
*
34255617 -TAAAAAA-TT
1 CAAAAAAAGTT
34255626 CGAAAAAAAGTT
1 C-AAAAAAAGTT
34255638 CAAAAAAA-TT
1 CAAAAAAAGTT
*
34255648 CGAAAAAA-TT
1 CAAAAAAAGTT
*
34255658 CGGAAAAAAGTT
1 C-AAAAAAAGTT
34255670 CAAAAAAA
1 CAAAAAAA
34255678 AGTTTGAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.04
10 18 0.35
11 26 0.50
12 6 0.12
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (11 bp):
CAAAAAAAGTT
Found at i:34255633 original size:12 final size:12
Alignment explanation
Indices: 34255618--34255712 Score: 67
Period size: 12 Copynumber: 8.1 Consensus size: 12
34255608 AAAAAAGTTT
34255618 AAAAAATTCGAA
1 AAAAAATTCGAA
*
34255630 AAAAAGTTC--A
1 AAAAAATTCGAA
34255640 AAAAAATTCG--
1 AAAAAATTCGAA
*
34255650 AAAAAATTCGGA
1 AAAAAATTCGAA
*
34255662 AAAAAGTTC-AA
1 AAAAAATTCGAA
*
34255673 AAAAAAGTTTGAAGA
1 AAAAAA-TTCG-A-A
34255688 AAAAAATTTC-AA
1 AAAAAA-TTCGAA
*
34255700 AAAAAATTTGAA
1 AAAAAATTCGAA
34255712 A
1 A
34255713 TTAGAACATT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
10 19 0.29
11 8 0.12
12 28 0.42
13 1 0.02
14 1 0.02
15 9 0.14
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (12 bp):
AAAAAATTCGAA
Found at i:34255645 original size:22 final size:22
Alignment explanation
Indices: 34255607--34255681 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
34255597 AAAAACATGC
*
34255607 AAAAAAAGTT-TAAAAAATTCG
1 AAAAAAAGTTCAAAAAAATTCG
34255628 AAAAAAAGTTCAAAAAAATTCG
1 AAAAAAAGTTCAAAAAAATTCG
* *
34255650 -AAAAAA-TTCGGAAAAAAGTTCA
1 AAAAAAAGTTC--AAAAAAATTCG
34255672 AAAAAAAGTT
1 AAAAAAAGTT
34255682 TGAAGAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 3 0.07
21 16 0.35
22 19 0.41
23 6 0.13
24 2 0.04
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAAAAGTTCAAAAAAATTCG
Found at i:34255692 original size:15 final size:13
Alignment explanation
Indices: 34255661--34255705 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
34255651 AAAAATTCGG
*
34255661 AAAAAAGTTCAAA
1 AAAAAATTTCAAA
* *
34255674 AAAAAGTTTGAAGA
1 AAAAAATTTCAA-A
34255688 AAAAAATTTCAAA
1 AAAAAATTTCAAA
34255701 AAAAA
1 AAAAA
34255706 TTTGAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAAAATTTCAAA
Found at i:34255701 original size:26 final size:27
Alignment explanation
Indices: 34255661--34255711 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
34255651 AAAAATTCGG
*
34255661 AAAAAAGTTCAAAAAAAAGTTTGAAGA
1 AAAAAAGTTCAAAAAAAAATTTGAAGA
*
34255688 AAAAAATTTC-AAAAAAAATTTGAA
1 AAAAAAGTTCAAAAAAAAATTTGAA
34255712 ATTAGAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.22
Consensus pattern (27 bp):
AAAAAAGTTCAAAAAAAAATTTGAAGA
Found at i:34257826 original size:16 final size:17
Alignment explanation
Indices: 34257807--34257842 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
34257797 GAAGATTGTC
*
34257807 AAAAAATAA-AAGAAGA
1 AAAAAATAAGAAAAAGA
34257823 AAAAAATAAGAAAAAGA
1 AAAAAATAAGAAAAAGA
34257840 AAA
1 AAA
34257843 CAAAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAATAAGAAAAAGA
Found at i:34260871 original size:100 final size:98
Alignment explanation
Indices: 34260744--34261368 Score: 723
Period size: 100 Copynumber: 6.3 Consensus size: 98
34260734 CTAGTACGCA
* * *
34260744 TAGTAGCCTGTACTTAGTACTACACATGCAACCGATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
* * *
34260809 GTACTACACACGTGATCGAAGTTATCGGGTACACA
66 GTACTACACACGTGA-CCAA-TTATCTGGTACACG
34260844 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
** *
34260909 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACC-AATTATCTGGTACACG
* * * * * * *
34260943 TAGTAGGCTTCACTTAGTACTACACACGTGATCGAAGTTAT-CGAGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCG-GTACACGTAGTAGCCTGCAC
* * *
34261007 TTAGTACTACACATGCGACCAATTATCTGATACACG
63 TTAGTACTACACACGTGACCAATTATCTGGTACACG
* * ** * *
34261043 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACACGTAGTAGCCTGCACTT
* * *
34261108 AGTACTACACACGTGATCAAAGTTAT-TGGGTACGCA
65 AGTACTACACACGTGA-CCAA-TTATCT-GGTACACG
* *
34261144 TAGTAGCCTGTACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
** *
34261209 GTACTACACACGTGACCTAACAATCTGATACACG
66 GTACTACACACGTGACC-AATTATCTGGTACACG
* * * * * * *
34261243 TAGTAGCCTGCACTTAGTACTACAGACGTGATCAAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACACGTAGTAGCCTGCACT
* * * *
34261308 TAGTACTACACATGCGACCAATAATCCGGTACACG
64 TAGTACTACACACGTGACCAATTATCTGGTACACG
34261343 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
34261369 CGTGACCTCA
Statistics
Matches: 449, Mismatches: 63, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
99 108 0.24
100 221 0.49
101 120 0.27
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
GTACTACACACGTGACCAATTATCTGGTACACG
Found at i:34260970 original size:150 final size:150
Alignment explanation
Indices: 34260787--34261376 Score: 1054
Period size: 150 Copynumber: 3.9 Consensus size: 150
34260777 GATTATCCGG
* *
34260787 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACATAGTAGCC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCC
*
34260852 TGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
66 TGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
34260917 CACGTGACCTAACCATCTGA
131 CACGTGACCTAACCATCTGA
* * * *
34260937 TACACGTAGTAGGCTTCACTTAGTACTACACACGTGATCGAAGTTATCGAGTACGCATAGTAGCC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCC
* * *
34261002 TGCACTTAGTACTACACATGCGACCAATTATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
66 TGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
34261067 CACGTGACCTAACCATCTGA
131 CACGTGACCTAACCATCTGA
*
34261087 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATTGGGTACGCATAGTAGCC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCC
*
34261152 TGTACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
66 TGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
*
34261217 CACGTGACCTAACAATCTGA
131 CACGTGACCTAACCATCTGA
*
34261237 TACACGTAGTAGCCTGCACTTAGTACTACAGACGTGATCAAAGTTATCGGGTACGCATAGTAGCC
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCC
34261302 TGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
66 TGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
34261367 CACGTGACCT
131 CACGTGACCT
34261377 CATAATAGAT
Statistics
Matches: 421, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 421 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (150 bp):
TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCC
TGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
CACGTGACCTAACCATCTGA
Found at i:34264580 original size:39 final size:40
Alignment explanation
Indices: 34264463--34264647 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
34264453 GCTACTCGTT
* *
34264463 CAAATGCTTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
34264503 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
34264543 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
34264582 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
34264623 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
34264648 CATCATTCGA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 75 0.61
41 13 0.11
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:34264631 original size:79 final size:80
Alignment explanation
Indices: 34264471--34264647 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
34264461 TTCAAATGCT
* * *
34264471 TTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGT
1 TTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGT
* *
34264535 AACTCGCACCAATGCC
65 AACTAGCACCAAAGCC
* ** * *
34264551 TTCGGG-CTTAGCCCGGAATTAGTAGCTCGCACAAATGCCTTC-GGATCTTAGTCTGGATATGGT
1 TTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGT
*
34264614 CACTTAGCA-CAAAGCC
65 AAC-TAGCACCAAAGCC
34264630 TTCGGGACTTAGCCCGGA
1 TTCGGGACTTAGCCCGGA
34264648 CATCATTCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.04
79 57 0.70
80 22 0.27
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (80 bp):
TTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTA
ACTAGCACCAAAGCC
Found at i:34268971 original size:39 final size:39
Alignment explanation
Indices: 34268850--34269059 Score: 316
Period size: 39 Copynumber: 5.3 Consensus size: 39
34268840 GCTCCTCGTT
* *
34268850 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
34268890 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
34268930 CAAATGCCTTCGGGCTTAGCCCTGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
34268969 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
34269008 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
34269047 CAAATGCCTTCGG
1 CAAATGCCTTCGG
34269060 ATCTTAGTCC
Statistics
Matches: 160, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 112 0.70
40 46 0.29
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:34269095 original size:78 final size:78
Alignment explanation
Indices: 34268850--34269111 Score: 302
Period size: 78 Copynumber: 3.3 Consensus size: 78
34268840 GCTCCTCGTT
* * *
34268850 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCC
* * *
34268913 GGATTTAGTAACTCGCA
62 GGAATTAGTATCTAGCA
*
34268930 CAAATGCCTTCGGGCTTAGCCCTGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
*
34268995 TTAGTATCTCGCA
66 TTAGTATCTAGCA
* *
34269008 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCC-GA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
*
34269072 ATATTGTCA-CTTAGCA
65 AT-TAGT-ATC-TAGCA
34269088 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
34269112 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
78 88 0.54
79 55 0.34
80 21 0.13
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTAGCA
Found at i:34276136 original size:40 final size:40
Alignment explanation
Indices: 34275954--34276176 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
34275944 TCCTCGTTCA
* * * * *
34275954 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34275993 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34276033 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34276073 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
34276113 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
34276153 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34276177 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34276185 original size:41 final size:41
Alignment explanation
Indices: 34276108--34276185 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
34276098 TTAGTATCTC
* * *
34276108 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
34276149 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
34276186 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:34296630 original size:40 final size:40
Alignment explanation
Indices: 34296448--34296670 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
34296438 TCCTCGTTCA
* * * * *
34296448 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34296487 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34296527 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34296567 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
34296607 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
34296647 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34296671 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34296679 original size:41 final size:41
Alignment explanation
Indices: 34296602--34296679 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
34296592 TTAGTATCTC
* * *
34296602 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
34296643 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
34296680 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:34303934 original size:79 final size:80
Alignment explanation
Indices: 34303823--34304003 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 80
34303813 GCTCCTCGTT
* **
34303823 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGT-ATCTCGCACAAATGCCTTCGGG-CTTAACCCG
*
34303887 GAT-TTAGTAAC-TCGCA
64 GATATT-GTAACTTAGCA
*
34303903 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTATCTCGCACAAATGCCTTCGGGCTTAACCCGG
*
34303966 ATATTGTCACTTAGCA
65 ATATTGTAACTTAGCA
34303982 C-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
34304004 GACATCATTC
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
77 10 0.11
78 27 0.30
79 37 0.41
80 16 0.18
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTATCTCGCACAAATGCCTTCGGGCTTAACCCGGA
TATTGTAACTTAGCA
Found at i:34304004 original size:39 final size:41
Alignment explanation
Indices: 34303823--34304005 Score: 215
Period size: 39 Copynumber: 4.6 Consensus size: 41
34303813 GCTCCTCGTT
* * *
34303823 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTACTTCGCA
*
34303863 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGT-ACTTCGCA
*
34303903 CAAATGCCTTCGGG-CTTAGCCCAGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTACT-TCGCA
*
34303942 CAAATGCCTTCGGG-CTTAGCCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGT-ACTTCGCA
34303982 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
34304006 CATCATTCAA
Statistics
Matches: 126, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
38 10 0.08
39 58 0.46
40 56 0.44
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTAGTACTTCGCA
Found at i:34318427 original size:10 final size:10
Alignment explanation
Indices: 34318412--34318437 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34318402 TGGAAACTTT
34318412 AAACTACACA
1 AAACTACACA
34318422 AAACTACACA
1 AAACTACACA
34318432 AAACTA
1 AAACTA
34318438 TACGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.27, G:0.00, T:0.12
Consensus pattern (10 bp):
AAACTACACA
Found at i:34319622 original size:15 final size:15
Alignment explanation
Indices: 34319602--34319630 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34319592 CTCGGTTCAT
34319602 TAACCCAATTTTTAA
1 TAACCCAATTTTTAA
34319617 TAACCCAATTTTTA
1 TAACCCAATTTTTA
34319631 GGATGTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
TAACCCAATTTTTAA
Found at i:34321672 original size:27 final size:27
Alignment explanation
Indices: 34321642--34321719 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
34321632 CTTTTAGAGA
34321642 TTTCCACAAATGCTATTCTTTCATAAT
1 TTTCCACAAATGCTATTCTTTCATAAT
*
34321669 TTTCCACAAAAT-TTATTCTTTCATAAT
1 TTTCCAC-AAATGCTATTCTTTCATAAT
*
34321696 TTTCCACAAAAGCTATTCTTTCAT
1 TTTCCACAAATGCTATTCTTTCAT
34321720 GACATGTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 39 0.85
28 4 0.09
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.45
Consensus pattern (27 bp):
TTTCCACAAATGCTATTCTTTCATAAT
Found at i:34323460 original size:29 final size:29
Alignment explanation
Indices: 34323428--34323557 Score: 131
Period size: 29 Copynumber: 4.5 Consensus size: 29
34323418 TTTATCAAGC
34323428 ACTATGTACTGGTGTTATATTTATTAGGT
1 ACTATGTACTGGTGTTATATTTATTAGGT
** *
34323457 ACTATGTA-TCGGTGACCATA-TTATCAGGT
1 ACTATGTACT-GGTG-TTATATTTATTAGGT
* *
34323486 ACTTTGTA-TCGGTGTTATATTTATTAGGC
1 ACTATGTACT-GGTGTTATATTTATTAGGT
* * * *
34323515 ATTATATGCTGGTGTTATATTTATAAGGT
1 ACTATGTACTGGTGTTATATTTATTAGGT
34323544 ACTATGTACTGGTG
1 ACTATGTACTGGTG
34323558 GTGGATACCA
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
28 4 0.05
29 72 0.90
30 4 0.05
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.44
Consensus pattern (29 bp):
ACTATGTACTGGTGTTATATTTATTAGGT
Found at i:34331548 original size:30 final size:30
Alignment explanation
Indices: 34331512--34331574 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
34331502 CCTTTTCATA
34331512 TTTCATATTTCATAACACTGGGCCGAAACC
1 TTTCATATTTCATAACACTGGGCCGAAACC
**
34331542 TTTCATATTTCATATTACTGGGCCGAAACC
1 TTTCATATTTCATAACACTGGGCCGAAACC
34331572 TTT
1 TTT
34331575 ACTATAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (30 bp):
TTTCATATTTCATAACACTGGGCCGAAACC
Found at i:34331842 original size:23 final size:23
Alignment explanation
Indices: 34331788--34331906 Score: 202
Period size: 23 Copynumber: 5.1 Consensus size: 23
34331778 CCTAGCCTCT
*
34331788 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
34331811 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
34331835 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
34331858 TTTAATAACTGGGGCATAAGCTC
1 TTTAATAACTGGGGCATAAGCCC
34331881 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
34331904 TTT
1 TTT
34331907 TACACTTCCT
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
23 68 0.76
24 22 0.24
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:34331982 original size:20 final size:20
Alignment explanation
Indices: 34331957--34332023 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
34331947 TTATGATTAC
34331957 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
34331977 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
34331997 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
34332017 ACCATGT
1 ATCATGT
34332024 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:34331988 original size:11 final size:11
Alignment explanation
Indices: 34331957--34332012 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
34331947 TTATGATTAC
34331957 ATCATGTGCAT
1 ATCATGTGCAT
*
34331968 ATCA--TACAT
1 ATCATGTGCAT
34331977 ATCATGTGCAT
1 ATCATGTGCAT
*
34331988 ATCA--TACAT
1 ATCATGTGCAT
*
34331997 GTCATGTGCAT
1 ATCATGTGCAT
34332008 ATCAT
1 ATCAT
34332013 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:34336602 original size:73 final size:73
Alignment explanation
Indices: 34336497--34336636 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
34336487 AGGTTTTTGC
* * * * * * **
34336497 GTATAGTAGTAAAATAGTTTGTCTAGCGAAGTGTAATCTACCCAATTTCATATTGTGGTGTATAC
1 GTATAGTAGTAAAATAATCTGTCTAGCAAAGTGCAATCCACCCAAGTTCATATTGTGGCATATAC
34336562 GTGTGGGT
66 GTGTGGGT
* * *
34336570 GTATAGTAGTAAAATAATCTGTCTGGCAAAGTGCAATCCGCCCAAGTTCATGTTGTGGCATATAC
1 GTATAGTAGTAAAATAATCTGTCTAGCAAAGTGCAATCCACCCAAGTTCATATTGTGGCATATAC
34336635 GT
66 GT
34336637 AATCAAATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (73 bp):
GTATAGTAGTAAAATAATCTGTCTAGCAAAGTGCAATCCACCCAAGTTCATATTGTGGCATATAC
GTGTGGGT
Found at i:34338550 original size:13 final size:13
Alignment explanation
Indices: 34338479--34338513 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
34338469 CAAAAACAAC
*
34338479 TTAATAAGCTTAA
1 TTAATAAACTTAA
*
34338492 TTAATAGACTTAA
1 TTAATAAACTTAA
34338505 TTAATAAAC
1 TTAATAAAC
34338514 ACATTTAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (13 bp):
TTAATAAACTTAA
Found at i:34342578 original size:11 final size:11
Alignment explanation
Indices: 34342550--34342584 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
34342540 ATCAACCAAA
*
34342550 AAATTTATTTT
1 AAATTGATTTT
34342561 AAA-TGATTTT
1 AAATTGATTTT
34342571 AAATTGATTTT
1 AAATTGATTTT
34342582 AAA
1 AAA
34342585 AACCACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (11 bp):
AAATTGATTTT
Found at i:34350119 original size:23 final size:23
Alignment explanation
Indices: 34350092--34350137 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
34350082 TTGCAAACTC
34350092 CTTATTGTATACTCTTTATGAAA
1 CTTATTGTATACTCTTTATGAAA
34350115 CTTATTGTATACTCTTTATGAAA
1 CTTATTGTATACTCTTTATGAAA
34350138 GCAATTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (23 bp):
CTTATTGTATACTCTTTATGAAA
Found at i:34359431 original size:50 final size:48
Alignment explanation
Indices: 34359306--34359481 Score: 174
Period size: 51 Copynumber: 3.5 Consensus size: 48
34359296 TGAGGTCACG
* * * * *
34359306 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAA-TT-GGTC-CA
** * * **
34359357 TGTGTAGTACTAAGTGCAACCTACTACGTGTATCAGATGGTTAGGT-CA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAATT-GGTCCA
*
34359405 TGTGGGTAGTACTAAGTGCAGGCTACTACGTGCACCGGATAATTGGTCGCA
1 TGT--GTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAATTGGTC-CA
34359456 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
34359482 TGCGTACCAG
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
48 5 0.05
49 26 0.25
50 36 0.35
51 37 0.36
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAATTGGTCCA
Found at i:34365837 original size:43 final size:42
Alignment explanation
Indices: 34365790--34365889 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
34365780 TCCCAAACGT
* *
34365790 GGTCTTACATGTAATCAAATATCGATGC-CACTATCCCAGACAG
1 GGTCTTACAAGAAATCAAATA-CGATGCTCA-TATCCCAGACAG
* * * *
34365833 GGTCTTACAAGAAATCATATACGATGCTGATGTCCCAGACAT
1 GGTCTTACAAGAAATCAAATACGATGCTCATATCCCAGACAG
*
34365875 GGTCTTACACGAAAT
1 GGTCTTACAAGAAAT
34365890 ATCAAGTTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.61
43 19 0.39
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (42 bp):
GGTCTTACAAGAAATCAAATACGATGCTCATATCCCAGACAG
Found at i:34367012 original size:39 final size:39
Alignment explanation
Indices: 34366959--34367081 Score: 158
Period size: 39 Copynumber: 3.2 Consensus size: 39
34366949 GGACTTTAGC
* * *
34366959 CCGGACATATTTCCAGCACGTAGCCTGCTGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCTGACCTTAAGT
* *
34366998 CCGGTTATAATTCCAGCACATAGCCT-ATGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCT-GACCTTAAGT
* * *
34367037 CCGGATATAATTCTAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCTGACCTTAAGT
34367076 CCGGAT
1 CCGGAT
34367082 GAACATCACT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 71 0.99
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCTGACCTTAAGT
Found at i:34368386 original size:27 final size:27
Alignment explanation
Indices: 34368325--34368454 Score: 217
Period size: 27 Copynumber: 4.9 Consensus size: 27
34368315 ATTACCAAAG
34368325 TACCCTCGATTTATAGAA-TACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* *
34368351 TACCATCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
34368378 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
34368405 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* *
34368432 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTATAGAATTACT
34368455 AAAATACCCT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
26 17 0.18
27 80 0.82
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTGTTT
Found at i:34368462 original size:27 final size:27
Alignment explanation
Indices: 34368286--34368706 Score: 158
Period size: 27 Copynumber: 15.6 Consensus size: 27
34368276 TTAGTTTACC
* * * *
34368286 AAATTACTAAAATGCCCTCAAATTGTA
1 AAATTACTAAAATACCCTCGATTTATA
* *
34368313 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* **** *
34368340 GAA-TACTGTTTTACCATCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* *****
34368366 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* ****
34368393 GAATTACTGTTTTACCCTCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* **** *
34368420 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACTAAAATACCCTCGATTTATA
* * *
34368447 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACTAAAATACCCTCGATTTATA
* * * * *
34368474 AAATTACCAAAAAAACCTC-AATCAGTA
1 AAATTACTAAAATACCCTCGATTTA-TA
* * * *
34368501 AAATTACCAAAATACCCTAG-TCTGTA
1 AAATTACTAAAATACCCTCGATTTATA
* * *
34368527 AAATTGCTAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GATTTATA
* * *
34368554 AAATTACCAAAATACCACT-GGTTTGTA
1 AAATTACTAAAATACC-CTCGATTTATA
* * *
34368581 AAATTA-TCGAAATACCCTCAATTTGTA
1 AAATTACT-AAAATACCCTCGATTTATA
* *
34368608 AAATTACCAAAATACCC-CTGATTTACA
1 AAATTACTAAAATACCCTC-GATTTATA
* * *
34368635 AAGTTAC-AGAAATACCCTTGACTTTCTAA
1 AAATTACTA-AAATACCCTCGA-TTTAT-A
* * * *
34368664 AAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACTA-AAATACCCTCGATTTATA
*
34368691 AAATTACTGAAATACC
1 AAATTACTAAAATACC
34368707 ATTGGTTTGT
Statistics
Matches: 313, Mismatches: 64, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
26 44 0.14
27 243 0.78
28 8 0.03
29 18 0.06
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTATA
Found at i:34368479 original size:81 final size:80
Alignment explanation
Indices: 34368325--34368480 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 80
34368315 ATTACCAAAG
* * ****
34368325 TACCCTCGATTTATAGAATACTGTTTTACCATCGATTTATAGAATTACCGTTTTACCCTCGATTT
1 TACCCTCGATTTATAGAATACTGTTTTACCATCGATTTACAAAATTACCAAAATACCCTCGATTT
* *
34368390 ATAGAATTACTGTTT
66 ACAAAATTACTGTTT
* * * *
34368405 TACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTT
1 TACCCTCGATTTATAGAA-TACTGTTTTACCATCGATTTACAAAATTACCAAAATACCCTCGATT
34368470 TACAAAATTAC
65 TACAAAATTAC
34368481 CAAAAAAACC
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
80 18 0.29
81 45 0.71
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (80 bp):
TACCCTCGATTTATAGAATACTGTTTTACCATCGATTTACAAAATTACCAAAATACCCTCGATTT
ACAAAATTACTGTTT
Found at i:34368549 original size:80 final size:81
Alignment explanation
Indices: 34368446--34368641 Score: 216
Period size: 80 Copynumber: 2.4 Consensus size: 81
34368436 CTCGATTTAC
* *
34368446 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAAAAAC-CTCAATCAGTAAAATTACCA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAAAACCACT-AATCAGTAAAATTACCA
*
34368510 AAATACCCT-AGTCTGT
65 AAATACCCTCAATCTGT
* ** * ** ** * *
34368526 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTATCGA
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAAAACCACTAATCAGTAAAATTACCAA
*
34368591 AATACCCTCAATTTGT
66 AATACCCTCAATCTGT
* * *
34368607 AAAATTACCAAAATACCCCTGATTTACAAAGTTAC
1 AAAATTACTAAAATACCCCTGGTTTACAAAATTAC
34368642 AGAAATACCC
Statistics
Matches: 94, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
80 58 0.62
81 36 0.38
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (81 bp):
AAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAAAACCACTAATCAGTAAAATTACCAA
AATACCCTCAATCTGT
Found at i:34368606 original size:54 final size:53
Alignment explanation
Indices: 34368432--34368624 Score: 190
Period size: 54 Copynumber: 3.6 Consensus size: 53
34368422 ATTACTGTTT
* ** * **
34368432 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCC-TGGTTTGTAAAATTACCAAAA
* * ** * * * *
34368486 AAACCTCAATCAGTAAAATTACCAAAATACCCTAGTCTGTAAAATTGCTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTGGTTTGTAAAATTACCAAAA
** * *
34368539 TACCC-CTGGTTTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTATCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACC-CTGGTTTGTAAAATTACCAAAA
34368593 TACCCTCAATTTGTAAAATTACCAAAATACCC
1 TACCCTCAATTTGTAAAATTACCAAAATACCC
34368625 CTGATTTACA
Statistics
Matches: 108, Mismatches: 28, Indels: 7
0.76 0.20 0.05
Matches are distributed among these distances:
52 1 0.01
53 39 0.36
54 67 0.62
55 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (53 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTGGTTTGTAAAATTACCAAAA
Found at i:34368724 original size:27 final size:27
Alignment explanation
Indices: 34368663--34368714 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
34368653 TGACTTTCTA
34368663 AAAATTA-TAGAAATACCATTGGTTTAC
1 AAAATTACT-GAAATACCATTGGTTTAC
34368690 AAAATTACTGAAATACCATTGGTTT
1 AAAATTACTGAAATACCATTGGTTT
34368715 GTAGATTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTACTGAAATACCATTGGTTTAC
Found at i:34368859 original size:27 final size:27
Alignment explanation
Indices: 34368769--34368859 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
34368759 CCCCAATTAA
*
34368769 GTAAAAAGACCGTAAAGCCCCTGTAGG
1 GTAAAATGACCGTAAAGCCCCTGTAGG
*
34368796 GTAAAGA-GACCGTAAAGCTCCTGTAGG
1 GTAAA-ATGACCGTAAAGCCCCTGTAGG
* *
34368823 GTAAAGTGACCGTAATA-CCCCTGTATG
1 GTAAAATGACCGTAA-AGCCCCTGTAGG
34368850 GTAAAATGAC
1 GTAAAATGAC
34368860 GAATATGCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 54 0.96
28 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GTAAAATGACCGTAAAGCCCCTGTAGG
Found at i:34369687 original size:26 final size:26
Alignment explanation
Indices: 34369658--34369845 Score: 258
Period size: 26 Copynumber: 7.3 Consensus size: 26
34369648 GAGGAAGTGC
34369658 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
34369684 AAAAGGGCTTATACCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
34369710 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
***
34369736 AAAAGGGCTTATGCCCCAGTTTGCCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
34369762 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
34369788 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
34369813 AAAAGGG-TTTTGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
34369836 AAAAGAGGCT
1 AAAAG-GGCT
34369846 AGGCCTCCAG
Statistics
Matches: 143, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
23 5 0.03
24 7 0.05
25 29 0.20
26 102 0.71
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:34369720 original size:52 final size:52
Alignment explanation
Indices: 34369658--34369845 Score: 312
Period size: 52 Copynumber: 3.7 Consensus size: 52
34369648 GAGGAAGTGC
*
34369658 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATACCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
34369710 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTGCCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
34369762 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
34369813 AAAAGGG-TTTTGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
34369846 AGGCCTCCAG
Statistics
Matches: 131, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
48 5 0.04
49 9 0.07
50 10 0.08
51 21 0.16
52 86 0.66
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:34370128 original size:31 final size:31
Alignment explanation
Indices: 34370051--34370129 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
34370041 CGTTTACAAT
*
34370051 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
34370082 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
34370113 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
34370130 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:34376499 original size:46 final size:46
Alignment explanation
Indices: 34376432--34376606 Score: 155
Period size: 46 Copynumber: 3.8 Consensus size: 46
34376422 TGTAACCCGC
*
34376432 CCATAAGCGAACTCGGACTCAACTCAACGAACTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAATTCGGGCGTTCGCAT
* * *
34376478 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAATTCGG--G-C--GTTCGCAT
* * ** *
34376528 -C-TCA-CGAACTTGGACTCAACTCAAC-AAGTTCGTACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAA-TTCGGGCGTTCGCAT
*
34376571 CCATAAGTGAACTCGGACTCAACTCAAC-AAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAA-TTCGG
34376607 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 16, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.58
47 23 0.22
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAATTCGGGCGTTCGCAT
Found at i:34376552 original size:93 final size:93
Alignment explanation
Indices: 34376439--34376610 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
34376429 CGCCCATAAG
* *
34376439 CGAACTCGGACTCAACTCAACGAA-CTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAAC-AAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
*
34376503 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACAAGTTCGGATGCCTAGTTACATCTCA
* * *
34376532 CGAACTTGGACTCAACTCAACAAGTTCGTACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
34376597 ACAAGTTCGGATGC
66 ACAAGTTCGGATGC
34376611 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATCTCA
Found at i:34376626 original size:46 final size:44
Alignment explanation
Indices: 34376483--34376626 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 44
34376473 CGCATCCATA
*
34376483 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACAAGTTCGGATGCC-A---ACCATCT
* * * * * *
34376530 CA-CGAACTTGGACTCAACTCAACAAGTTCGTACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACAAGTTCG--GATGC-CAACCATCT
34376576 AGTGAACTCGGACTCAACTCAACAAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACAAGTTCGGATGC-CAACCAT-CT
34376622 AGTGA
1 AGTGA
34376627 CATGTCACTT
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 31 0.41
47 28 0.37
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCAACCATCT
Found at i:34377964 original size:26 final size:27
Alignment explanation
Indices: 34377894--34377973 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
34377884 TGGGATATTA
* *
34377894 CAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTCATTAATTTTACAAAC
*
34377921 CAAGGGTATTTCATTAATTTTACAATC
1 CAAGGGTATTTCATTAATTTTACAAAC
*
34377948 C-GGGGTATTTCGA-TAATTTTACAAAC
1 CAAGGGTATTTC-ATTAATTTTACAAAC
34377974 TGGGGTCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
26 21 0.45
27 26 0.55
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTCATTAATTTTACAAAC
Found at i:34377978 original size:26 final size:26
Alignment explanation
Indices: 34377897--34377979 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
34377887 GATATTACAA
* * *
34377897 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTCATTAATTTTACAAA-CAG
* *
34377924 GGGTATTTCATTAATTTTACAATCCG
1 GGGTATTTCATTAATTTTACAAACAG
*
34377950 GGGTATTTCGA-TAATTTTACAAACTG
1 GGGTATTTC-ATTAATTTTACAAACAG
34377976 GGGT
1 GGGT
34377980 CTTAACGACC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 27 0.56
27 21 0.44
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (26 bp):
GGGTATTTCATTAATTTTACAAACAG
Found at i:34380953 original size:14 final size:15
Alignment explanation
Indices: 34380934--34380962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34380924 TTACATTCTT
34380934 TTTAG-TTATTTTTA
1 TTTAGTTTATTTTTA
34380948 TTTAGTTTATTTTTA
1 TTTAGTTTATTTTTA
34380963 GTGAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTAGTTTATTTTTA
Found at i:34382780 original size:184 final size:184
Alignment explanation
Indices: 34382272--34382828 Score: 803
Period size: 185 Copynumber: 3.0 Consensus size: 184
34382262 GAGATAATAA
* * * *
34382272 TAAATTACAATTATTTCTAGAAATCACAACTTTGGAAAAATTACTTTATCATCCACAGCAATAAA
1 TAAATTACATTTATTTCTAGGAATCACAAATTTGGAAAAATTACTTTATCATCCATAGCAATAAA
* * * ** * *
34382337 ATAATTGCATATATTCATTCATATGCATTCCCTGAAACATGCATACAATTACAAGAATGTCACAT
66 TTAATTACATACATTCATTCGCATACATTCCCCGAAACATGCATACAATTACAAGAATGTCACAT
* * *
34382402 CTTATCAAAAATAATCATACATAAAGAAGAGAGAATTTTGGTCTCAGTTTACAC
131 CTTATCAAATATAATCATACATGAAGAAGAGAGAATTTTGGTCTAAGTTTACAC
* * ** *
34382456 TAAATTACATTTAATCTCTAGGAATCATAAATTTGGAAATTTTACTTTATCTTCCATAGCAATAA
1 TAAATTACATTT-ATTTCTAGGAATCACAAATTTGGAAAAATTACTTTATCATCCATAGCAATAA
* *
34382521 ATTAATTACATACATTCATTCGCATACATTCCTCAAAACATGCATACAATTACAAGAATGTCACA
65 ATTAATTACATACATTCATTCGCATACATTCCCCGAAACATGCATACAATTACAAGAATGTCACA
*
34382586 TCTTATCAAATATAATCATACATGAAGAATAGAGAATTTTGGTCTAAGTTTACAC
130 TCTTATCAAATATAATCATACATGAAGAAGAGAGAATTTTGGTCTAAGTTTACAC
* * *
34382641 TAAATTACATTTATTTTCTAGGAATCACAAATTT-AAAAAATTACTTTATCAGCTATAGCAATAA
1 TAAATTACATTTA-TTTCTAGGAATCACAAATTTGGAAAAATTACTTTATCATCCATAGCAATAA
*
34382705 ATTAATTACATACATTCATTCGCATACATTCCCCGAAACATGCATACAATTATAAGAATGTCACA
65 ATTAATTACATACATTCATTCGCATACATTCCCCGAAACATGCATACAATTACAAGAATGTCACA
* *
34382770 TCTTATCAAATATACTCATACATGAAGAAGAGAAAGAATTTTTGTCTCAA-TTTACAC
130 TCTTATCAAATATAATCATACATGAAGAAGAG--AGAATTTTGGTCT-AAGTTTACAC
34382827 TA
1 TA
34382829 TAAACATAGC
Statistics
Matches: 332, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
184 128 0.39
185 181 0.55
186 21 0.06
187 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (184 bp):
TAAATTACATTTATTTCTAGGAATCACAAATTTGGAAAAATTACTTTATCATCCATAGCAATAAA
TTAATTACATACATTCATTCGCATACATTCCCCGAAACATGCATACAATTACAAGAATGTCACAT
CTTATCAAATATAATCATACATGAAGAAGAGAGAATTTTGGTCTAAGTTTACAC
Found at i:34386947 original size:21 final size:18
Alignment explanation
Indices: 34386921--34386967 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
34386911 TTTTCCGTTA
34386921 TTTATAAATTGTAAAGTTATT
1 TTTATAAATT-TAAA--TATT
34386942 TTTATAATATTTAAATATT
1 TTTATAA-ATTTAAATATT
34386961 TTT-TAAA
1 TTTATAAA
34386968 AAAATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 3 0.12
19 7 0.28
21 11 0.44
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTATAAATTTAAATATT
Found at i:34387010 original size:27 final size:27
Alignment explanation
Indices: 34386976--34387031 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
34386966 AAAAAATTAT
*
34386976 ATTTT-AT-TTTTAA-TTTATAATATA
1 ATTTTAATATTTTAATTTTACAATATA
*
34387000 ATTTTAATATTTTAATTTTACAATATC
1 ATTTTAATATTTTAATTTTACAATATA
34387027 ATTTT
1 ATTTT
34387032 TATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 5 0.19
25 2 0.07
26 6 0.22
27 14 0.52
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTTAATATTTTAATTTTACAATATA
Found at i:34388499 original size:8 final size:9
Alignment explanation
Indices: 34388469--34388530 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 9
34388459 TTAAAAATTT
34388469 AAAAATTACA
1 AAAAATTA-A
34388479 AAAAATTACA
1 AAAAATTA-A
34388489 AAAAATTAA
1 AAAAATTAA
34388498 AATAAATTAA
1 AA-AAATTAA
*
34388508 TTCAAAAAATAA
1 ---AAAAATTAA
*
34388520 AAAAACTAA
1 AAAAATTAA
34388529 AA
1 AA
34388531 TTCATCAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
9 13 0.28
10 25 0.54
12 6 0.13
13 2 0.04
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATTAA
Found at i:34388507 original size:10 final size:10
Alignment explanation
Indices: 34388469--34388506 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
34388459 TTAAAAATTT
34388469 AAAAATTACA
1 AAAAATTACA
34388479 AAAAATTACA
1 AAAAATTACA
34388489 AAAAATTA-A
1 AAAAATTACA
34388498 AATAAATTA
1 AA-AAATTA
34388507 ATTCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 3 0.11
10 24 0.89
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTACA
Found at i:34388532 original size:23 final size:24
Alignment explanation
Indices: 34388480--34388534 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
34388470 AAAATTACAA
34388480 AAAATTACAAAAAATTAAAATAAAT
1 AAAATT-CAAAAAATTAAAATAAAT
*
34388505 -TAATTCAAAAAA-TAAAA-AAACT
1 AAAATTCAAAAAATTAAAATAAA-T
34388527 AAAATTCA
1 AAAATTCA
34388535 TCAAACTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 6 0.23
23 13 0.50
24 4 0.15
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATTCAAAAAATTAAAATAAAT
Found at i:34393153 original size:63 final size:63
Alignment explanation
Indices: 34393054--34393180 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
34393044 TTACCATTCA
34393054 ACCCAATACTTACAGAGTTGCCCCCTCACATTTTGTAAAGATTAAATTAAGCTATGAAATGTG
1 ACCCAATACTTACAGAGTTGCCCCCTCACATTTTGTAAAGATTAAATTAAGCTATGAAATGTG
* * *
34393117 ACCCAATACTTACAGAGTTGTCCCCTCATATTTTGTAAAGATTAAATTAAGCTATGAAGTGTG
1 ACCCAATACTTACAGAGTTGCCCCCTCACATTTTGTAAAGATTAAATTAAGCTATGAAATGTG
34393180 A
1 A
34393181 TACATCAAGC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (63 bp):
ACCCAATACTTACAGAGTTGCCCCCTCACATTTTGTAAAGATTAAATTAAGCTATGAAATGTG
Found at i:34410049 original size:15 final size:16
Alignment explanation
Indices: 34410029--34410058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34410019 ACTATTTAAG
34410029 TTTAAT-AATAAATTA
1 TTTAATAAATAAATTA
34410044 TTTAATAAATAAATT
1 TTTAATAAATAAATT
34410059 TAAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAATAAATAAATTA
Found at i:34413722 original size:28 final size:28
Alignment explanation
Indices: 34413682--34413741 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
34413672 GTCATTATCA
34413682 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * *
34413710 ACCCCATAAGTTATGAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
34413738 ACCC
1 ACCC
34413742 TATTAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:34419140 original size:28 final size:28
Alignment explanation
Indices: 34419100--34419162 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
34419090 GTCATTATCA
34419100 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * * *
34419128 ACCCCATAAGTTATGAGACTTTTTCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
34419156 ACCCCAT
1 ACCCCAT
34419163 TAATATGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:34419506 original size:35 final size:38
Alignment explanation
Indices: 34419437--34419507 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
34419427 TAAATATAAA
* * *
34419437 AATAATTATATTAAGAATGTTATTAAGTTATATTTAAT
1 AATAATTATATTAAGAATATGATTAAGATATATTTAAT
34419475 AATAATTATATTAA-AATATGATTAA-AT-TATTTA
1 AATAATTATATTAAGAATATGATTAAGATATATTTA
34419508 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 6 0.20
36 1 0.03
37 9 0.30
38 14 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (38 bp):
AATAATTATATTAAGAATATGATTAAGATATATTTAAT
Found at i:34419731 original size:16 final size:16
Alignment explanation
Indices: 34419710--34419760 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
34419700 TGAATTACTG
34419710 ATTACAGGCCTATTCC
1 ATTACAGGCCTATTCC
34419726 ATTACA-GCTCTATTCC
1 ATTACAGGC-CTATTCC
34419742 ATTAC-GGCCCTATTCC
1 ATTACAGG-CCTATTCC
34419758 ATT
1 ATT
34419761 CCAGTGAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.35
Consensus pattern (16 bp):
ATTACAGGCCTATTCC
Found at i:34420379 original size:21 final size:21
Alignment explanation
Indices: 34420340--34420383 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
34420330 TAGTCAATGG
34420340 GATTAAAATTAACTTTTTATAT
1 GATTAAAATTAACTTTTTA-AT
34420362 GATTAAAATTAA-TTTTTAAT
1 GATTAAAATTAACTTTTTAAT
34420382 GA
1 GA
34420384 AAATAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
GATTAAAATTAACTTTTTAAT
Found at i:34420486 original size:53 final size:53
Alignment explanation
Indices: 34420383--34420489 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 53
34420373 ATTTTTAATG
* * **
34420383 AAAATAGTAAAGAAGTGAGTTATGGAGTATTCTTTAATGGATGGGAGATTAAA
1 AAAATAGCAAAGAAGTGAGTTATGGAGTATTCTCTAATCAATGGGAGATTAAA
* *
34420436 AAAATAGCGAAGAAGTGAGTTGTGGAGTATTCTCTAATCAATGTGG-GATTAAA
1 AAAATAGCAAAGAAGTGAGTTATGGAGTATTCTCTAATCAATG-GGAGATTAAA
34420489 A
1 A
34420490 TTAACTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 45 0.96
54 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.29
Consensus pattern (53 bp):
AAAATAGCAAAGAAGTGAGTTATGGAGTATTCTCTAATCAATGGGAGATTAAA
Found at i:34424689 original size:52 final size:52
Alignment explanation
Indices: 34424611--34424715 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
34424601 AAATGTGAAA
34424611 GTGGTGACATTCTTCGGGTTGAATTAGATGAATCGGATAGCTTGCCTGTAGT
1 GTGGTGACATTCTTCGGGTTGAATTAGATGAATCGGATAGCTTGCCTGTAGT
*
34424663 GTGGTGGCATTCTTCGGGTTGAATTAGATGAATCGGATAGCTTGCCTGTAGT
1 GTGGTGACATTCTTCGGGTTGAATTAGATGAATCGGATAGCTTGCCTGTAGT
34424715 G
1 G
34424716 ATTTCTTCTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.20, C:0.13, G:0.32, T:0.34
Consensus pattern (52 bp):
GTGGTGACATTCTTCGGGTTGAATTAGATGAATCGGATAGCTTGCCTGTAGT
Found at i:34429406 original size:29 final size:29
Alignment explanation
Indices: 34429374--34429433 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
34429364 AATATTAGCG
34429374 AAAATAACCTATACACT-CCATTATAACCA
1 AAAATAACCTATACA-TGCCATTATAACCA
34429403 AAAATAACCTATACATGCCATTATAACCA
1 AAAATAACCTATACATGCCATTATAACCA
34429432 AA
1 AA
34429434 CTCAAACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (29 bp):
AAAATAACCTATACATGCCATTATAACCA
Found at i:34429793 original size:30 final size:30
Alignment explanation
Indices: 34429738--34429799 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
34429728 CACTAAGCAA
34429738 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
34429767 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
34429798 GT
1 GT
34429800 ATTTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:34429984 original size:25 final size:25
Alignment explanation
Indices: 34429956--34430004 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
34429946 ATGTATGCTC
34429956 TCACGAGCTGTGAATCGATAAGCTT
1 TCACGAGCTGTGAATCGATAAGCTT
* *
34429981 TCACGAGTTGTGAATCGGTAAGCT
1 TCACGAGCTGTGAATCGATAAGCT
34430005 CATATGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (25 bp):
TCACGAGCTGTGAATCGATAAGCTT
Found at i:34430017 original size:25 final size:25
Alignment explanation
Indices: 34429956--34430017 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
34429946 ATGTATGCTC
*
34429956 TCACGAGCTGTGAATCGATAAGCTT
1 TCACGAGCTGTGAATCGATAAGCTA
* *
34429981 TCACGAGTTGTGAATCGGTAAGCTCA
1 TCACGAGCTGTGAATCGATAAGCT-A
*
34430007 T-ATGAGCTGTG
1 TCACGAGCTGTG
34430018 GTGTGTCTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (25 bp):
TCACGAGCTGTGAATCGATAAGCTA
Found at i:34432500 original size:17 final size:17
Alignment explanation
Indices: 34432480--34432513 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34432470 TGGCAGATAG
* *
34432480 TATCGTGTGGCGGACAC
1 TATCGTCTGGCGAACAC
34432497 TATCGTCTGGCGAACAC
1 TATCGTCTGGCGAACAC
34432514 GGTCGCAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (17 bp):
TATCGTCTGGCGAACAC
Found at i:34433487 original size:17 final size:17
Alignment explanation
Indices: 34433453--34433493 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34433443 GACTGACAAA
*
34433453 AGACTCACACAAGCTGG
1 AGACTCACACAAACTGG
* *
34433470 ATACTCACACAAATTGG
1 AGACTCACACAAACTGG
34433487 AGACTCA
1 AGACTCA
34433494 AAGAAGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (17 bp):
AGACTCACACAAACTGG
Found at i:34435341 original size:21 final size:20
Alignment explanation
Indices: 34435316--34435377 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
34435306 CCCAAACCAT
*
34435316 GCATATAATGAGTATATCATA
1 GCATATCATG-GTATATCATA
*
34435337 GCATATCATGTTCATATCATA
1 GCATATCATGGT-ATATCATA
* *
34435358 ACATATCATGTGCATATCAT
1 GCATATCATG-GTATATCAT
34435378 GTCCTATCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (20 bp):
GCATATCATGGTATATCATA
Found at i:34435354 original size:11 final size:11
Alignment explanation
Indices: 34435338--34435389 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
34435328 TATATCATAG
34435338 CATATCATGTT
1 CATATCATGTT
**
34435349 CATATCAT-AA
1 CATATCATGTT
*
34435359 CATATCATGTG
1 CATATCATGTT
34435370 CATATCATG-T
1 CATATCATGTT
*
34435380 CCTATCATGT
1 CATATCATGT
34435390 ATAACAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (11 bp):
CATATCATGTT
Found at i:34435385 original size:10 final size:11
Alignment explanation
Indices: 34435315--34435389 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
34435305 ACCCAAACCA
*
34435315 TGCATATAATG
1 TGCATATCATG
* *
34435326 AGTATATCAT-
1 TGCATATCATG
*
34435336 AGCATATCATG
1 TGCATATCATG
*
34435347 TTCATATCAT-
1 TGCATATCATG
**
34435357 AACATATCATG
1 TGCATATCATG
34435368 TGCATATCATG
1 TGCATATCATG
*
34435379 T-CCTATCATG
1 TGCATATCATG
34435389 T
1 T
34435390 ATAACAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
10 26 0.51
11 25 0.49
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (11 bp):
TGCATATCATG
Found at i:34435389 original size:21 final size:21
Alignment explanation
Indices: 34435329--34435377 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
34435319 TATAATGAGT
* *
34435329 ATATCATAGCATATCATGTTC
1 ATATCATAACATATCATGTGC
34435350 ATATCATAACATATCATGTGC
1 ATATCATAACATATCATGTGC
34435371 ATATCAT
1 ATATCAT
34435378 GTCCTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATCATAACATATCATGTGC
Found at i:34435642 original size:27 final size:27
Alignment explanation
Indices: 34435501--34435630 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
34435491 GGGGCAAAAT
* * * * *
34435501 GGTAATTTTACCCCACAAAGTTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
34435528 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
34435555 GGTATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
34435582 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
34435609 GGTAATTCTACCCTACAAGGGT
1 GGTAATTCTACCCTACAAGGGT
34435631 GCTTTGGTAA
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:34435642 original size:54 final size:54
Alignment explanation
Indices: 34435501--34435630 Score: 179
Period size: 54 Copynumber: 2.4 Consensus size: 54
34435491 GGGGCAAAAT
* * * * * *
34435501 GGTAATTTTACCCCACAAAGTTATCTCAGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * *
34435555 GGTATTTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
34435609 GGTAATTCTACCCTACAAGGGT
1 GGTAATTCTACCCTACAAGGGT
34435631 GCTTTGGTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
Found at i:34435783 original size:27 final size:27
Alignment explanation
Indices: 34435687--34435912 Score: 226
Period size: 27 Copynumber: 8.4 Consensus size: 27
34435677 TCAGAAGTAC
* *
34435687 TTTGGTAATTTTACAAGTCGAGGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTAT
** * ** *
34435714 TTCAGTAATTTTATAGGTCGAGGGTA-
1 TTTGGTAATTTTACAAATCAAGGGTAT
* *
34435740 TTCGGTAATTTCACAAATCAAGGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTAT
*
34435767 TTTGGTAATTTTACAAA-CTAGGGGTAT
1 TTTGGTAATTTTACAAATC-AAGGGTAT
* *
34435794 TTTGGTAATTTTATAAA-CTAGGGGTAT
1 TTTGGTAATTTTACAAATC-AAGGGTAT
* * *
34435821 TTTGGTAATTTTATAAACCAAAGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTAT
*
34435848 TTTGGTAATTTTACAAGTCAAGGGTAT
1 TTTGGTAATTTTACAAATCAAGGGTAT
*
34435875 TTTGGTAATTTTACAAA-CTAGGGGTAT
1 TTTGGTAATTTTACAAATC-AAGGGTAT
*
34435902 TTTGATAATTT
1 TTTGGTAATTT
34435913 GGTAAACTAA
Statistics
Matches: 172, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 22 0.13
27 149 0.87
28 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
TTTGGTAATTTTACAAATCAAGGGTAT
Found at i:34435919 original size:81 final size:80
Alignment explanation
Indices: 34435687--34435912 Score: 267
Period size: 81 Copynumber: 2.8 Consensus size: 80
34435677 TCAGAAGTAC
* ** * ** * *
34435687 TTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTATAGGTCGAGGGTA-TTCGGTAATTT
1 TTTGGTAATTTTACAAGTCAAGGGTATTTTGGTAATTTTAAAACTAG-GGGTATTTTGGTAATTT
* * *
34435751 CACAAATCAAGGGTAT
65 CATAAACCAAAGGTAT
* *
34435767 TTTGGTAATTTTACAA-ACTAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATT
1 TTTGGTAATTTTACAAGTC-AAGGGTATTTTGGTAATTTTA-AAACTAGGGGTATTTTGGTAATT
*
34435831 TTATAAACCAAAGGTAT
64 TCATAAACCAAAGGTAT
*
34435848 TTTGGTAATTTTACAAGTCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTT
1 TTTGGTAATTTTACAAGTCAAGGGTATTTTGGTAATTTTA-AAACTAGGGGTATTTTGGTAATTT
34435913 GGTAAACTAA
Statistics
Matches: 124, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
79 1 0.01
80 38 0.31
81 84 0.68
82 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (80 bp):
TTTGGTAATTTTACAAGTCAAGGGTATTTTGGTAATTTTAAAACTAGGGGTATTTTGGTAATTTC
ATAAACCAAAGGTAT
Found at i:34440969 original size:31 final size:32
Alignment explanation
Indices: 34440885--34440971 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
34440875 TCATAAATTT
* * * *
34440885 ATAAATTGATTACTTAAATTTAATAACTCATG
1 ATAAATTAATTAATTTAATTAAATAACTCATG
34440917 ATAAATTAATTAATTTAATTAAATAACTCAT-
1 ATAAATTAATTAATTTAATTAAATAACTCATG
* *
34440948 ATAGATTAATTGATCTT-ATTAAAT
1 ATAAATTAATTAAT-TTAATTAAAT
34440972 TTATGAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 19 0.40
32 29 0.60
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTTAATTAAATAACTCATG
Found at i:34443116 original size:116 final size:116
Alignment explanation
Indices: 34442912--34443147 Score: 427
Period size: 116 Copynumber: 2.0 Consensus size: 116
34442902 CCAAGAAAAG
34442912 AATTTCCACCCCCACATAATGACTAGTATTACATTTAGTTGTATGAGATTTGCAGATTCATACTT
1 AATTTCCACCCCCACATAATGACTAGTATTACATTTAGTTGTATGAGATTTGCAGATTCATACTT
* * *
34442977 AGGTATTAGTTTTAATTTTCAAATAAGTAATCTTATAATCAATTCAAATAT
66 AAGTATTAGTTTTAATTATCAAATAAGTAATATTATAATCAATTCAAATAT
*
34443028 AATTTCCAGCCCCACATAATGACTAGTATTACATTTAGTTGTATGAGATTTGCAGATTCATACTT
1 AATTTCCACCCCCACATAATGACTAGTATTACATTTAGTTGTATGAGATTTGCAGATTCATACTT
*
34443093 AAGTATTAGTTTTAATTATCAAATAAGTAATATTCTAATCAATTCAAATAT
66 AAGTATTAGTTTTAATTATCAAATAAGTAATATTATAATCAATTCAAATAT
34443144 AATT
1 AATT
34443148 CCCTTTTAAA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (116 bp):
AATTTCCACCCCCACATAATGACTAGTATTACATTTAGTTGTATGAGATTTGCAGATTCATACTT
AAGTATTAGTTTTAATTATCAAATAAGTAATATTATAATCAATTCAAATAT
Found at i:34456247 original size:40 final size:40
Alignment explanation
Indices: 34456149--34456372 Score: 317
Period size: 40 Copynumber: 5.6 Consensus size: 40
34456139 TCCTCGTTCA
* * * * *
34456149 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34456188 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34456228 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34456268 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34456308 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34456348 AAGGCCTTC-GGATCTTAATCCGGAT
1 AATGCCTTCGGGA-CTTAACCCGGAT
34456373 ATATTGACTT
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 37 0.22
40 134 0.78
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34456395 original size:80 final size:80
Alignment explanation
Indices: 34456152--34456410 Score: 274
Period size: 80 Copynumber: 3.3 Consensus size: 80
34456142 TCGTTCAAAT
* * * * * * * *
34456152 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* * *
34456216 ACAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * *
34456231 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
34456296 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * *
34456311 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
* *
34456375 ATTGACTTAGCAC-AAA
65 AATAAC-TAGCACGAAA
*
34456391 GCCTTC-GGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
34456411 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
79 47 0.30
80 107 0.67
81 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:34456395 original size:120 final size:118
Alignment explanation
Indices: 34456147--34456410 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 118
34456137 GCTCCTCGTT
* * *
34456147 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
* * * *
34456212 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * *
34456266 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGG
** * * * *
34456331 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGATATATTGACTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
34456387 CAAAGCCTTC-GGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
34456411 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
119 48 0.39
120 69 0.57
121 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:34459653 original size:1 final size:1
Alignment explanation
Indices: 34459605--34459638 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
34459595 TCTATGATTC
34459605 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34459639 CGCTGATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34459729 original size:1 final size:1
Alignment explanation
Indices: 34459723--34459773 Score: 102
Period size: 1 Copynumber: 51.0 Consensus size: 1
34459713 GTCAGGAAAC
34459723 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34459774 CCGTTTCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34463245 original size:40 final size:40
Alignment explanation
Indices: 34463147--34463409 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
34463137 TCCTCGTTCA
* * * * *
34463147 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
34463186 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34463226 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
34463266 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
34463306 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
34463346 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
34463386 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34463410 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:34468675 original size:20 final size:20
Alignment explanation
Indices: 34468652--34468690 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34468642 AAGACTTCAC
* *
34468652 TTTATTTTTATTTTTATTTG
1 TTTACTTTTATCTTTATTTG
34468672 TTTACTTTTATCTTTATTT
1 TTTACTTTTATCTTTATTT
34468691 ACCTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTACTTTTATCTTTATTTG
Found at i:34484416 original size:6 final size:7
Alignment explanation
Indices: 34484400--34484424 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34484390 CTAAAAGTAT
34484400 AAAATTA
1 AAAATTA
34484407 AAAATTA
1 AAAATTA
34484414 AAAATTA
1 AAAATTA
34484421 AAAA
1 AAAA
34484425 GTAGTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:34496913 original size:49 final size:49
Alignment explanation
Indices: 34496849--34497023 Score: 242
Period size: 49 Copynumber: 3.5 Consensus size: 49
34496839 CTGGTACGCA
* * *
34496849 TAGTAGCCTGCACTTAGTGCTACACATGCGACCAATAATCGGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGGGTACACG
* * * * *
34496898 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCG
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATTATCGGGTACACG
*
34496949 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGGGTACACG
*
34496998 TAGTAGCTTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
34497024 CGTGACCTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 66 0.61
50 2 0.02
51 41 0.38
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGGGTACACG
Found at i:34496956 original size:100 final size:100
Alignment explanation
Indices: 34496841--34497028 Score: 322
Period size: 100 Copynumber: 1.9 Consensus size: 100
34496831 GAAGCTATCT
* *
34496841 GGTACGCATAGTAGCCTGCACTTAGTGCTACACATGCGACCAATAATCGGGTACATGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCGGGTACACGTAGTAGCC
34496906 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* * * *
34496941 GGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCGGGTACACGTAGTAGCC
34497006 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
34497029 CCTCACAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCGGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:34499082 original size:15 final size:15
Alignment explanation
Indices: 34499059--34499103 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
34499049 AAGAAAATCG
34499059 AATAAAGAAATCCAA
1 AATAAAGAAATCCAA
* *
34499074 AATAGAGAAA-CCTAT
1 AATAAAGAAATCC-AA
34499089 AATAAAGAAATCCAA
1 AATAAAGAAATCCAA
34499104 GATACGATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.16
Consensus pattern (15 bp):
AATAAAGAAATCCAA
Found at i:34501488 original size:49 final size:49
Alignment explanation
Indices: 34501430--34501619 Score: 209
Period size: 49 Copynumber: 3.8 Consensus size: 49
34501420 TAGCTGAAGC
* *
34501430 TATCTGGTACGCATAATAGCCTGCACTTAGTACTACACATGAGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGAGACCAAT
* ** * * *
34501479 AATCTGGTACATGTAGTAGCCTGCACTTAGTAATATACATGTGATCACAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGAGA-C-CAAT
* * * *
34501530 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGAGACCAAT
* * * * *
34501579 TATCCGATACACGTAGTAACCAGCACTTAGTACTACACATG
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATG
34501620 TGAGCTCACA
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 74 0.64
50 2 0.02
51 39 0.34
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGAGACCAAT
Found at i:34501557 original size:100 final size:101
Alignment explanation
Indices: 34501435--34501631 Score: 288
Period size: 100 Copynumber: 2.0 Consensus size: 101
34501425 GAAGCTATCT
* * * *
34501435 GGTACGCATAATAGCCTGCACTTAGTACTACACATGAGACCAATAATCTGGTACATGTAGTAGCC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGAGACCAATAATCCGATACACGTAGTAACC
* *
34501500 TGCACTTAGTAATATACATGTGA-TCACAATTTTCG
66 AGCACTTAGTAATACACATGTGACTCACAATTTTCG
* * *
34501535 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACGTAGTAACC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGAGACCAATAATCCGATACACGTAGTAACC
*
34501600 AGCACTTAGTACTACACATGTGAGCTCACAAT
66 AGCACTTAGTAATACACATGTGA-CTCACAAT
34501632 AGTTTATTTG
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 78 0.92
102 7 0.08
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (101 bp):
GGTACGCATAATAGCCTGCACTTAGTACTACACATGAGACCAATAATCCGATACACGTAGTAACC
AGCACTTAGTAATACACATGTGACTCACAATTTTCG
Found at i:34503870 original size:11 final size:11
Alignment explanation
Indices: 34503854--34503878 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34503844 ATTTTGTCCC
34503854 TTTTTGGCTCA
1 TTTTTGGCTCA
34503865 TTTTTGGCTCA
1 TTTTTGGCTCA
34503876 TTT
1 TTT
34503879 CCCTCTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTTGGCTCA
Found at i:34506808 original size:46 final size:46
Alignment explanation
Indices: 34506758--34506886 Score: 186
Period size: 46 Copynumber: 2.8 Consensus size: 46
34506748 TGGCTGAGCA
* * *
34506758 TCCGAGCTCGTTGAGTTGAGTTCGAATTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
34506804 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
34506850 CCCAAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
34506887 GTGGGTTACA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:34510240 original size:37 final size:37
Alignment explanation
Indices: 34510181--34510252 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
34510171 AGCTCAGACG
* *
34510181 AAATCTCCACACGAAGTTATCGGGTCTTACTCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
34510218 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
34510253 ATATATTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:34510514 original size:98 final size:96
Alignment explanation
Indices: 34510398--34510581 Score: 316
Period size: 98 Copynumber: 1.9 Consensus size: 96
34510388 GCACATCACC
*
34510398 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--ATACATATTTCACATT
34510463 -GACCATTCGGCTTTACCACATATGCATATCTCA
64 AG-CCATTCGGCTTTACCACATATGCATATCTCA
*
34510496 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
34510561 CCATTCGGCTTTACCACATAT
66 CCATTCGGCTTTACCACATAT
34510582 AAGCATGTTC
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
96 36 0.43
97 1 0.01
98 46 0.55
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (96 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGGCTTTACCACATATGCATATCTCA
Found at i:34510522 original size:48 final size:48
Alignment explanation
Indices: 34510398--34510582 Score: 309
Period size: 48 Copynumber: 3.8 Consensus size: 48
34510388 GCACATCACC
*
34510398 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
34510448 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
34510496 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
34510544 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
34510583 AGCATGTTCA
Statistics
Matches: 128, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
48 84 0.66
49 2 0.02
50 42 0.33
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:34510688 original size:47 final size:47
Alignment explanation
Indices: 34510552--34510698 Score: 170
Period size: 47 Copynumber: 3.1 Consensus size: 47
34510542 CATACATATT
* * * *
34510552 TCACATTAGCCATTCGGCTTTACCACATATA-AGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCATTATCACATATATA-CATGTTCACATTCA
* * * * *
34510599 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCATTATCACATATATACATGTTCACATTCA
* **
34510646 TCACATTGGCCATTCGGCATTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCATTATCACATATATACATGTTCACATTCA
34510693 TCACAT
1 TCACAT
34510699 AAAATCCTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
47 83 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCATTATCACATATATACATGTTCACATTCA
Found at i:34518559 original size:33 final size:34
Alignment explanation
Indices: 34518491--34518560 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
34518481 GTGGCAATAA
* * *
34518491 CAGTGTGGGCCTTAGCCCATTACAATAACAGTAT
1 CAGTATGGGCCTTAGCCCAATACAAGAACAGTAT
34518525 CAGTATGGGCCTTAGCCCAA-ATC-AGAACAGTAT
1 CAGTATGGGCCTTAGCCCAATA-CAAGAACAGTAT
34518558 CAG
1 CAG
34518561 AGATGCAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (34 bp):
CAGTATGGGCCTTAGCCCAATACAAGAACAGTAT
Found at i:34524046 original size:28 final size:28
Alignment explanation
Indices: 34524014--34524136 Score: 165
Period size: 28 Copynumber: 4.4 Consensus size: 28
34524004 TCGATATTTT
*
34524014 GCACACTAAGTGCCATACCCAATGTCTC
1 GCACACTAAGTGCCATACTCAATGTCTC
** *
34524042 GCACACTAAGTGTTATATTCAATGTCTC
1 GCACACTAAGTGCCATACTCAATGTCTC
*
34524070 GCACACTAAGTGCCATGCTCAATGTCTC
1 GCACACTAAGTGCCATACTCAATGTCTC
* * * *
34524098 ACACACTAAGTGCCACAATCAATGTATC
1 GCACACTAAGTGCCATACTCAATGTCTC
34524126 GCACACTAAGT
1 GCACACTAAGT
34524137 TCCGCACATA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 81 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (28 bp):
GCACACTAAGTGCCATACTCAATGTCTC
Found at i:34524189 original size:40 final size:40
Alignment explanation
Indices: 34524145--34524226 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
34524135 GTTCCGCACA
* *
34524145 TAGCCAAAACTATCTCAAATCGCACACTAAGTGCCAAATT
1 TAGCCAAAACTATATCAAACCGCACACTAAGTGCCAAATT
* * ** * *
34524185 TAGCCGAAGCTATATTGAACCGCACATTAAGTGCCACATT
1 TAGCCAAAACTATATCAAACCGCACACTAAGTGCCAAATT
34524225 TA
1 TA
34524227 ACTGATATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (40 bp):
TAGCCAAAACTATATCAAACCGCACACTAAGTGCCAAATT
Found at i:34542086 original size:40 final size:40
Alignment explanation
Indices: 34541895--34542079 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
34541885 TCGAATGATG
* * * *
34541895 TCCGGGCTAAGTCCCGAAGGC-TTCGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
34541935 TCCGAACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
34541975 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34542014 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
34542055 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
34542080 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 33 0.27
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34542101 original size:79 final size:79
Alignment explanation
Indices: 34541951--34542102 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 79
34541941 CTAAGATCCA
* **
34541951 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTCACTAAATC
1 AAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGCCCGAAGGCATTGGAACGAGTCACTAAATC
34542016 CGGGTTAAGTCCCG
66 CGGGTTAAGTCCCG
* * *
34542030 AAGGCATTTGTGCGAGTTACTATAAT-CGGGCTATGTCCCGAAGGCATTTGAACGAGT-AGCTAT
1 AAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAG-CCCGAAGGCATTGGAACGAGTCA-CTAA
34542093 ATCC-GGTTAA
63 ATCCGGGTTAA
34542103 ATTTCGAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 37 0.58
80 27 0.42
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGCCCGAAGGCATTGGAACGAGTCACTAAATC
CGGGTTAAGTCCCG
Found at i:34544262 original size:28 final size:28
Alignment explanation
Indices: 34544222--34544322 Score: 157
Period size: 28 Copynumber: 3.6 Consensus size: 28
34544212 TTTAAATTGC
34544222 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
*
34544250 ATAGCACTAAGTGTGCCAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
* *
34544278 GTAAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCAAGTTTGATTAT
*
34544307 ATAACACTAAGTGTGC
1 ATAGCACTAAGTGTGC
34544323 GGACTTACTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
28 41 0.61
29 26 0.39
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCAAGTTTGATTAT
Found at i:34544323 original size:28 final size:28
Alignment explanation
Indices: 34544197--34544323 Score: 155
Period size: 28 Copynumber: 4.5 Consensus size: 28
34544187 ATGAGATTGG
* * ** *
34544197 CACTAAGTGTGCGGGTTTAAATTGCATAG
1 CACTAAGTGTGCGAGTTT-GATTATATAA
* *
34544226 CACTAAGTGTGCAAGTTTGATTATATAG
1 CACTAAGTGTGCGAGTTTGATTATATAA
* *
34544254 CACTAAGTGTGCCAGTTTGATTATGTAA
1 CACTAAGTGTGCGAGTTTGATTATATAA
34544282 GCACTAAGTGTGCGAGTTTGATTATATAA
1 -CACTAAGTGTGCGAGTTTGATTATATAA
34544311 CACTAAGTGTGCG
1 CACTAAGTGTGCG
34544324 GACTTACTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 45 0.52
29 42 0.48
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATATAA
Found at i:34552305 original size:28 final size:28
Alignment explanation
Indices: 34552239--34552366 Score: 184
Period size: 28 Copynumber: 4.5 Consensus size: 28
34552229 CATGAGATTG
* **
34552239 GCACTAAGTGTGCGAGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
34552268 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
34552296 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
34552325 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
34552353 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
34552367 GACTTACTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
28 45 0.50
29 45 0.50
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:34552328 original size:57 final size:57
Alignment explanation
Indices: 34552239--34552366 Score: 195
Period size: 57 Copynumber: 2.2 Consensus size: 57
34552229 CATGAGATTG
34552239 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
34552296 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
34552353 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
34552367 GACTTACTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 62 0.95
58 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:34558615 original size:13 final size:13
Alignment explanation
Indices: 34558597--34558625 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
34558587 GGTTATTTAT
34558597 TAAACTAATTAAC
1 TAAACTAATTAAC
34558610 TAAACTAATTAAC
1 TAAACTAATTAAC
34558623 TAA
1 TAA
34558626 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Done.