Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 2 of 204
Found at i:501603 original size:34 final size:34
Alignment explanation
Indices: 501548--501613 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
501538 CAAACACCAG
*
501548 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
*
501583 AAAACATTTTCCCG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
501614 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:505685 original size:31 final size:32
Alignment explanation
Indices: 505649--505708 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
505639 TTTATATTTA
*
505649 TATTTATAGT-GTTTTCAAATTTTAAAATGTG
1 TATTTAGAGTAGTTTTCAAATTTTAAAATGTG
* **
505680 TATTTAGAGTATTTTTTTAATTTTAAAAT
1 TATTTAGAGTAGTTTTCAAATTTTAAAAT
505709 TTCATATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (32 bp):
TATTTAGAGTAGTTTTCAAATTTTAAAATGTG
Found at i:506704 original size:121 final size:121
Alignment explanation
Indices: 506485--506829 Score: 541
Period size: 121 Copynumber: 2.8 Consensus size: 121
506475 TTATTTCGAG
*
506485 TTGATGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGTTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGC-TCTACCAGGATGTTATTTGAGAAGAAATTGT
* *
506549 GAAATCGCGCCATCGTGGACGCGATTTTGCTACAGTAGGTCATGTAATA-AATATTTT
64 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGATAATATTTT
* *
506606 TTGACGTTTCTGAGCAAATAATATAAAATCGACTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCG-CTCTACCAGGATGTTATTTGAGAAGAAATTGTG
** *
506671 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGATTTTTTTTT
65 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGATAATATTTT
*
506728 TTGACGTTTCTAAGCAAATAGTATAAAATCGCCTCTACCAGGATGTTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCG-CTCTACCAGGATGTTATTTGAGAAGAAATTGTG
* *
506793 AAATCGCGCCCTCGTAGACGCGATTTTTCTACAGTAG
65 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
506830 CAAGTTTGGG
Statistics
Matches: 207, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
121 104 0.50
122 103 0.50
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (121 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTCTACCAGGATGTTATTTGAGAAGAAATTGTGA
AATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGATAATATTTT
Found at i:506797 original size:122 final size:121
Alignment explanation
Indices: 506499--506829 Score: 545
Period size: 122 Copynumber: 2.7 Consensus size: 121
506489 TGTTTCTGGT
* *
506499 CAAATAGTATAAAATCGCTTCTACCAGGATGTTATTTGAGAAGAAATTGTGAAATCGCGCCATCG
1 CAAATAGTATAAAATCGCCTCTACCAGGATGTTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
506564 TGGACGCGATTTTGCTACAGTAGGTCATGTAATAAATATTTTTTGACGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTGACGTTTCTAAG
* * *
506620 CAAATAATATAAAATCGACTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCCTCTACCAGGATGTTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
** *
506685 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGATTTTTTTTTTTGACGTTTCTAAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGA-AATATTTTTTGACGTTTCTAAG
506742 CAAATAGTATAAAATCGCCTCTACCAGGATGTTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCCTCTACCAGGATGTTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
506807 TAGACGCGATTTTTCTACAGTAG
66 TGGACGCGATTTTGCTACAGTAG
506830 CAAGTTTGGG
Statistics
Matches: 194, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
121 93 0.48
122 101 0.52
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (121 bp):
CAAATAGTATAAAATCGCCTCTACCAGGATGTTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTGACGTTTCTAAG
Found at i:508630 original size:22 final size:24
Alignment explanation
Indices: 508575--508630 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
508565 CTTTTATAAC
*
508575 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATAAATAA-TATCTAA
*
508600 AAATAAATAAATAAATAA-ATCT-T
1 AAAT-AATAAATAAATAATATCTAA
508623 AAATAATA
1 AAATAATA
508631 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 4 0.14
24 4 0.14
25 4 0.14
26 12 0.43
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAATAAATAAATAATATCTAA
Found at i:508642 original size:18 final size:18
Alignment explanation
Indices: 508577--508644 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 18
508567 TTTATAACAA
508577 ATAATAAATT-AATAATTAT
1 ATAA-AAATTAAATAA-TAT
* *
508596 CTAAAAA-TAAATAAATAA
1 ATAAAAATTAAAT-AATAT
**
508614 ATAAATCTTAAATAATAT
1 ATAAAAATTAAATAATAT
*
508632 TTAAAAATTAAAT
1 ATAAAAATTAAAT
508645 TTAATACTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
17 1 0.03
18 26 0.70
19 10 0.27
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATTAAATAATAT
Found at i:508763 original size:29 final size:30
Alignment explanation
Indices: 508721--508784 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 30
508711 GCCATTGATG
508721 AAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
508751 AAAATAT-AAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
508780 AAAAT
1 AAAAT
508785 GAAATTGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:508841 original size:51 final size:51
Alignment explanation
Indices: 508785--508897 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
508775 TTTAAAAAAT
* *
508785 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTAGAAG
* *
508836 GAAATTGAGAGGAACTTGAAATTAAATATGGGTTTGAGAGAATTTTAGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTAGAAG
508887 GAAATTGAGAG
1 GAAATTGAGAG
508898 AATTTTGGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.42, C:0.01, G:0.29, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTAGAAG
Found at i:508894 original size:22 final size:22
Alignment explanation
Indices: 508869--508919 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
508859 AAATATGGGT
508869 TTGAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTAGAAGGAAA
*
508891 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTAGAAGGAAA
508913 TTGAGAG
1 TTGAGAG
508920 GATTAGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTAGAAGGAAA
Found at i:517760 original size:163 final size:163
Alignment explanation
Indices: 517488--517817 Score: 615
Period size: 163 Copynumber: 2.0 Consensus size: 163
517478 TTGTAACTTA
*
517488 TTCAACATAATCAGTACAGCATGAGAAGCATTGAACTGAGCACGCATTTTTACATTACAGATAGC
1 TTCAACATAATCAGTACAGCATGAGAAGCATTGAACTGAACACGCATTTTTACATTACAGATAGC
**
517553 GACCGAGTCTATATAGTATTATGTGGGATAAATTTATTAATGGCTGGCTGGTTGGTGTCTAAAGT
66 GACCGAGTCTATATAGTATTATGTGGGATAAATTTACAAATGGCTGGCTGGTTGGTGTCTAAAGT
*
517618 GTAATAAGCTCTTATGAATATACACGCATGTTT
131 GTAATAAGCTCTTATGAATATACACACATGTTT
517651 TTCAACATAATCAGTACAGCATGAGAAGCATTGAACTGAACACGCATTTTTACATTACAGATAGC
1 TTCAACATAATCAGTACAGCATGAGAAGCATTGAACTGAACACGCATTTTTACATTACAGATAGC
*
517716 GACCGAGTCTATTTAGTATTATGTGGGATAAATTTACAAATGGCTGGCTGGTTGGTGTCTAAAGT
66 GACCGAGTCTATATAGTATTATGTGGGATAAATTTACAAATGGCTGGCTGGTTGGTGTCTAAAGT
517781 GTAATAAGCTCTTATGAATATACACACATGTTT
131 GTAATAAGCTCTTATGAATATACACACATGTTT
517814 TTCA
1 TTCA
517818 TCTACTTAAG
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (163 bp):
TTCAACATAATCAGTACAGCATGAGAAGCATTGAACTGAACACGCATTTTTACATTACAGATAGC
GACCGAGTCTATATAGTATTATGTGGGATAAATTTACAAATGGCTGGCTGGTTGGTGTCTAAAGT
GTAATAAGCTCTTATGAATATACACACATGTTT
Found at i:524557 original size:64 final size:64
Alignment explanation
Indices: 524456--524585 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
524446 AAAGGTAACA
524456 CCCTTTCCAAATTGGCCATTTTCTCCAGCTTCTGCCTCCATGGGATCTTTCACTTAAGTTTTGG
1 CCCTTTCCAAATTGGCCATTTTCTCCAGCTTCTGCCTCCATGGGATCTTTCACTTAAGTTTTGG
524520 CCCTTTCCAAATTGGCCATTTTCTCCAGCTTCTGCCTCCATGGGATCTTTCACTTAAGTTTTGG
1 CCCTTTCCAAATTGGCCATTTTCTCCAGCTTCTGCCTCCATGGGATCTTTCACTTAAGTTTTGG
524584 CC
1 CC
524586 TCTAAAGGGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (64 bp):
CCCTTTCCAAATTGGCCATTTTCTCCAGCTTCTGCCTCCATGGGATCTTTCACTTAAGTTTTGG
Found at i:533942 original size:11 final size:11
Alignment explanation
Indices: 533920--533993 Score: 78
Period size: 11 Copynumber: 6.6 Consensus size: 11
533910 AACTAATCCT
533920 CTCTCAAATTTC
1 CTCTC-AATTTC
533932 CTCTCAATTTC
1 CTCTCAATTTC
* *
533943 TTCTAAATTTC
1 CTCTCAATTTC
*
533954 CTCTCAATTTG
1 CTCTCAATTTC
*
533965 CTCTCAAATTC
1 CTCTCAATTTC
*
533976 CTTCACAATTT-
1 C-TCTCAATTTC
533987 CTCTCAA
1 CTCTCAA
533994 ATCCATATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
10 5 0.10
11 34 0.67
12 12 0.24
ACGTcount: A:0.24, C:0.31, G:0.01, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:533950 original size:22 final size:23
Alignment explanation
Indices: 533921--533995 Score: 95
Period size: 22 Copynumber: 3.3 Consensus size: 23
533911 ACTAATCCTC
533921 TCTCAAATTTCCTCTCAATTTCT
1 TCTCAAATTTCCTCTCAATTTCT
533944 TCT-AAATTTCCTCTCAATTTGC-
1 TCTCAAATTTCCTCTCAATTT-CT
*
533966 TCTCAAA-TTCCTTCACAATTTC-
1 TCTCAAATTTCC-TCTCAATTTCT
533988 TCTCAAAT
1 TCTCAAAT
533996 CCATATTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
22 32 0.68
23 15 0.32
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (23 bp):
TCTCAAATTTCCTCTCAATTTCT
Found at i:534064 original size:51 final size:51
Alignment explanation
Indices: 533959--534066 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
533949 ATTTCCTCTC
* **
533959 AATTTGCTCTCAAATTCCTTCACAATTTCTCTCAAATCCATATTTATTTTT
1 AATTTTCTCTCAAATTCCTTCACAATTTCTCTCAAATCCATATTTATTAAT
* * * *
534010 AATTTTCTCTCAAGTTCCTCTTA-AATTTCTCTTAAATCCCTATTT-TTAAAT
1 AATTTTCTCTCAAATTCCT-TCACAATTTCTCTCAAATCCATATTTATT-AAT
534061 AATTTT
1 AATTTT
534067 AAAAATATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.04
51 44 0.92
52 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.02, T:0.49
Consensus pattern (51 bp):
AATTTTCTCTCAAATTCCTTCACAATTTCTCTCAAATCCATATTTATTAAT
Found at i:534083 original size:15 final size:14
Alignment explanation
Indices: 534063--534092 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
534053 TTTTAAATAA
534063 TTTTAAAAATATTTT
1 TTTTAAAAAT-TTTT
534078 TTTTAAAAATTTTT
1 TTTTAAAAATTTTT
534092 T
1 T
534093 AAACCGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTAAAAATTTTT
Found at i:541106 original size:22 final size:21
Alignment explanation
Indices: 541082--541139 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
541072 AATATTTCTA
541082 AAAATGTAAAAATAAAATTTT
1 AAAATGTAAAAATAAAATTTT
* *
541103 AAAATATATAAATACAAATTTT
1 AAAATGTAAAAATA-AAATTTT
*
541125 AAAATGTCAAAATAA
1 AAAATGTAAAAATAA
541140 TATGTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATGTAAAAATAAAATTTT
Found at i:541114 original size:23 final size:23
Alignment explanation
Indices: 541059--541129 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 23
541049 AAAAATATAT
*
541059 TATATAACATATAAATATTTCTAAAA
1 TATATAA-AAATAAA-ATTT-TAAAA
*
541085 -ATGTAAAAATAAAATTTTAAAA
1 TATATAAAAATAAAATTTTAAAA
541107 TATAT--AAATACAAATTTTAAAA
1 TATATAAAAATA-AAATTTTAAAA
541129 T
1 T
541130 GTCAAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.12
22 17 0.43
23 7 0.17
24 6 0.15
25 5 0.12
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (23 bp):
TATATAAAAATAAAATTTTAAAA
Found at i:546167 original size:28 final size:28
Alignment explanation
Indices: 546111--546167 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
546101 ACACAAAGAC
** *
546111 ACACATTCTTACATACATACGTACTTAT
1 ACACATTCTTACATACATACAAACATAT
*
546139 ACACATTCTTACCTACATACAAACATAT
1 ACACATTCTTACATACATACAAACATAT
546167 A
1 A
546168 TGTATATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (28 bp):
ACACATTCTTACATACATACAAACATAT
Found at i:557371 original size:33 final size:33
Alignment explanation
Indices: 557288--557380 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
557278 TTGTTCTGAT
* * * *
557288 GGTGGTGGGTACTGCGGAGGCTGCTGTTGAGCA
1 GGTGGTGGGTATTGCGGTGGCTGTTGCTGAGCA
*
557321 GGTAGTGGGTATTGCGGTGGCTGTTGCTGAGCA
1 GGTGGTGGGTATTGCGGTGGCTGTTGCTGAGCA
*
557354 GGTGGTGGGTATTGCGGTGGTTGTTGC
1 GGTGGTGGGTATTGCGGTGGCTGTTGC
557381 GGCGGGAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.10, C:0.12, G:0.48, T:0.30
Consensus pattern (33 bp):
GGTGGTGGGTATTGCGGTGGCTGTTGCTGAGCA
Found at i:565357 original size:58 final size:59
Alignment explanation
Indices: 565295--565410 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
565285 AATTACCTAG
* * * *
565295 TTTAGGGCTTAACTTGGA-CAAAAAATGTTCAGGCCTTAATATGAGAAT-GCTTGTCAAA
1 TTTAGGGCCTAACTTGGACCAAAAAAAGTTCAGGCCTCAATATAAGAATAG-TTGTCAAA
* *
565353 TTTAGGGCCTAATTTGGACCAAAAAAAGTTTAGGCCTCAATATAAGAATAGTTGTCAA
1 TTTAGGGCCTAACTTGGACCAAAAAAAGTTCAGGCCTCAATATAAGAATAGTTGTCAA
565411 GTTCAGGCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 16 0.32
59 33 0.66
60 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (59 bp):
TTTAGGGCCTAACTTGGACCAAAAAAAGTTCAGGCCTCAATATAAGAATAGTTGTCAAA
Found at i:584413 original size:3 final size:3
Alignment explanation
Indices: 584405--584444 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
584395 TGTCAAATCT
584405 TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
584445 TGGTTACTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.24
3 25 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:584416 original size:6 final size:6
Alignment explanation
Indices: 584405--584444 Score: 52
Period size: 5 Copynumber: 7.3 Consensus size: 6
584395 TGTCAAATCT
584405 TTATTA TTATTA TTATTA TTA-TA TT-TTA TT-TTA TT-TTA TT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
584445 TGGTTACTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 18 0.55
6 15 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (6 bp):
TTATTA
Found at i:585481 original size:12 final size:12
Alignment explanation
Indices: 585465--585516 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
585455 TACATACATA
585465 TATGCATGTATG
1 TATGCATGTATG
* *
585477 CATGCATGCATG
1 TATGCATGTATG
** *
585489 TATATATGTAGG
1 TATGCATGTATG
585501 TATGCATGTATG
1 TATGCATGTATG
585513 TATG
1 TATG
585517 TGTGTATATG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (12 bp):
TATGCATGTATG
Found at i:587461 original size:2 final size:2
Alignment explanation
Indices: 587454--587485 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
587444 AATTAAGTAC
587454 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
587486 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:600627 original size:18 final size:18
Alignment explanation
Indices: 600604--600646 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
600594 TCAATTTCAA
600604 AAATTATAAAATATCACT
1 AAATTATAAAATATCACT
600622 AAATTATAAAATATCACT
1 AAATTATAAAATATCACT
600640 AAATTAT
1 AAATTAT
600647 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTATAAAATATCACT
Found at i:607275 original size:31 final size:31
Alignment explanation
Indices: 607234--607299 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 31
607224 AAATTTTAAA
607234 AAAATAAATAACAAATTATT-ATTTAACT-TTTT
1 AAAATAAAT-A-AAATT-TTGATTTAACTCTTTT
*
607266 AAAAT-AATAAAATTTTGATTTAATTCTTTT
1 AAAATAAATAAAATTTTGATTTAACTCTTTT
607296 AAAA
1 AAAA
607300 ACTATAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 2 0.06
29 12 0.39
30 9 0.29
31 3 0.10
32 5 0.16
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
AAAATAAATAAAATTTTGATTTAACTCTTTT
Found at i:611568 original size:30 final size:30
Alignment explanation
Indices: 611473--611577 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
611463 CCTCTAAAAG
* *
611473 TTTAAGTATCAACTTAAGAAAAAGTGTCAAA
1 TTTAAGTATCAAATTAAGAAAAAAT-TCAAA
* *
611504 TTT-AG-ATGCCAAATTAAGAGAAAATTCAAG
1 TTTAAGTAT--CAAATTAAGAAAAAATTCAAA
*
611534 TTTAAGTATCAAATTAA-AAAAAATATTAAA
1 TTTAAGTATCAAATTAAGAAAAAAT-TCAAA
* *
611564 TTTAAATACCAAAT
1 TTTAAGTATCAAAT
611578 ATTATATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
29 8 0.13
30 32 0.53
31 18 0.30
32 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (30 bp):
TTTAAGTATCAAATTAAGAAAAAATTCAAA
Found at i:622304 original size:151 final size:151
Alignment explanation
Indices: 622031--622318 Score: 418
Period size: 151 Copynumber: 1.9 Consensus size: 151
622021 TAATCCATCT
* * * *
622031 TACCAATTGTTGTATTATCGTTCGGAGATCATTAGTCGAACTTAAAAAAGAAACCTTAACAACCT
1 TACCAATTGTCGTATTATCGTTCGGAGATCATTAGCCGAACTTAAAAAAAAAAACTTAACAACCT
* * *
622096 AGTGACTTAAACAAAAACTTTTAAATAGTGCAGTGACCATATTGTAACTTTTTAAAATTGAGTGA
66 AGTGACTTAAACAAAAAATTTTAAATAGTACAGTAACCATATTGTAACTTTTTAAAATTGAGTGA
622161 C-CAAAACATAAATTTACTAC
131 CACAAAACATAAATTTACTAC
* * * *
622181 TACCAATTGTCGTATTGTCGTTTGGAGATCATTAGCCGAACTTAAAAAAAAAAAACTTAATAACT
1 TACCAATTGTCGTATTATCGTTCGGAGATCATTAGCCGAACTT-AAAAAAAAAAACTTAACAACC
* * *
622246 TAGTGATTTAAACAAAAAATTTTGAATAGTACTA-TAACCATGTTGTAACTTTTTAAAATTGAGT
65 TAGTGACTTAAACAAAAAATTTTAAATAGTAC-AGTAACCATATTGTAACTTTTTAAAATTGAGT
622310 GACACAAAA
129 GACACAAAA
622319 ACACACTAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
150 39 0.32
151 76 0.63
152 6 0.05
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (151 bp):
TACCAATTGTCGTATTATCGTTCGGAGATCATTAGCCGAACTTAAAAAAAAAAACTTAACAACCT
AGTGACTTAAACAAAAAATTTTAAATAGTACAGTAACCATATTGTAACTTTTTAAAATTGAGTGA
CACAAAACATAAATTTACTAC
Found at i:622997 original size:26 final size:27
Alignment explanation
Indices: 622938--623003 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
622928 AAGATTTATA
622938 AATAAATATTATAATTAATTTAAATAT
1 AATAAATATTATAATTAATTTAAATAT
*
622965 AATTAAATA-T-TAATTAATTATAACTAT
1 AA-TAAATATTATAATTAATT-TAAATAT
*
622992 TATAAAT-TTATA
1 AATAAATATTATA
623004 TCATTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 15 0.45
27 12 0.36
28 6 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AATAAATATTATAATTAATTTAAATAT
Found at i:630851 original size:3 final size:3
Alignment explanation
Indices: 630843--630879 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
630833 ATAGAATATT
*
630843 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
630880 ATCCACCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:650426 original size:22 final size:24
Alignment explanation
Indices: 650374--650426 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
650364 ATTCATCGAC
*
650374 ATTAAAT-TATATATTTTTACTATA
1 ATTAAATATATATATTTTTAC-AAA
650398 ATT-AATATATA-ATTTTTA-AAA
1 ATTAAATATATATATTTTTACAAA
650419 ATTAAATA
1 ATTAAATA
650427 AAAATTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 10 0.38
24 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAAATATATATATTTTTACAAA
Found at i:663790 original size:30 final size:30
Alignment explanation
Indices: 663729--663792 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
663719 AGTTTATATC
* *
663729 TTTATAATTTTTAAAGGATCAAATTAAAAT
1 TTTATAATTTTTAAAGGACCAAAGTAAAAT
* * * *
663759 TTTATTATTTTTAAGGGGCCAAAGTATAAT
1 TTTATAATTTTTAAAGGACCAAAGTAAAAT
663789 TTTA
1 TTTA
663793 CTTTAACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGACCAAAGTAAAAT
Found at i:672781 original size:2 final size:2
Alignment explanation
Indices: 672774--672808 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
672764 TAATACCATG
672774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
672809 GTAATAANNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:673827 original size:21 final size:22
Alignment explanation
Indices: 673788--673835 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
673778 TTTATTGAAT
673788 ATAATTAAAATATATTAAT-TA
1 ATAATTAAAATATATTAATATA
673809 ATAATTAAAATAT-TATAATATA
1 ATAATTAAAATATAT-TAATATA
673831 A-AATT
1 ATAATT
673836 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATTAAAATATATTAATATA
Found at i:673831 original size:19 final size:19
Alignment explanation
Indices: 673780--673831 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
673770 AAGCAATCTT
673780 TATTGAATATAATTAAAATA
1 TATT-AATATAATTAAAATA
673800 TATTAATTAATAATTAAAATA
1 TATTAA-T-ATAATTAAAATA
673821 T-TATAATATAA
1 TAT-TAATATAA
673832 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.21
20 7 0.24
21 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TATTAATATAATTAAAATA
Found at i:676645 original size:16 final size:16
Alignment explanation
Indices: 676595--676648 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
676585 TTTGGTTTGC
* *
676595 TGTATTGGAATAGAGA
1 TGTAATGGAATAGAGG
*
676611 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
676627 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
676643 TGTAAT
1 TGTAAT
676649 AGCAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.31, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:677010 original size:120 final size:120
Alignment explanation
Indices: 676865--677207 Score: 659
Period size: 120 Copynumber: 2.9 Consensus size: 120
676855 ATCATATTTA
676865 AACATAATTATTATTAAATATATTATAATTAAAAGATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAAGATATAATTTAATAAAATTCTTAATAATCAA
676930 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
676985 AACATAATTATTATTAAATATATTATAATTAAAAGATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAAGATATAATTTAATAAAATTCTTAATAATCAA
677050 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
677105 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAAGATATAATTTAATAAAATTCTTAATAATCAA
*
677170 TATTCTTATATGAATTTACTCAAATCATAATAAATGAT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
677208 TGTTATTGCT
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 220 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAAGATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:677150 original size:14 final size:15
Alignment explanation
Indices: 677101--677152 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
677091 ATAAAATATA
677101 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
677116 TATTAAATATATTAT
1 AATTAAATATATTAT
677131 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
677144 AATTTAATA
1 AATTAAATA
677153 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:677787 original size:22 final size:22
Alignment explanation
Indices: 677759--677886 Score: 184
Period size: 22 Copynumber: 5.8 Consensus size: 22
677749 GACCATGCTT
677759 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
677781 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
* * * **
677803 AACTAAACCCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
**
677825 TACTAAGCTCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
*
677847 TACTAAGCTCTCATGTTTCACG
1 TACTAAGCTCTCATGTTTAACG
677869 TACTAAGCTCTCATGTTT
1 TACTAAGCTCTCATGTTT
677887 GAACAATAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:679668 original size:15 final size:15
Alignment explanation
Indices: 679645--679685 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
679635 TGAGCAATAC
679645 AAACATACAAAACAG
1 AAACATACAAAACAG
*
679660 AACCATACAAAACAG
1 AAACATACAAAACAG
679675 AAACA-ACAAAA
1 AAACATACAAAA
679686 GCTGCTACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.68, C:0.22, G:0.05, T:0.05
Consensus pattern (15 bp):
AAACATACAAAACAG
Found at i:694486 original size:17 final size:17
Alignment explanation
Indices: 694449--694486 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
694439 TTTTAAGATC
*
694449 AATTAATAAAAATTAAA
1 AATTAATAAAAATAAAA
694466 AATTAA-AAAAATAAAA
1 AATTAATAAAAATAAAA
694482 TAATT
1 -AATT
694487 TCTGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAATAAAAATAAAA
Found at i:696215 original size:16 final size:16
Alignment explanation
Indices: 696196--696232 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
696186 AGAAAAAGTC
*
696196 AATAAAAATCTAAATA
1 AATAAAAATATAAATA
*
696212 AATATAAATATAAATA
1 AATAAAAATATAAATA
696228 AATAA
1 AATAA
696233 CAATTTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAATATAAATA
Found at i:696281 original size:15 final size:15
Alignment explanation
Indices: 696263--696297 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
696253 TTTTTAGAGT
*
696263 GTTTTTTTTATTTGG
1 GTTTTTTTTATTTGA
*
696278 GTTTTTTTTTTTTGA
1 GTTTTTTTTATTTGA
696293 GTTTT
1 GTTTT
696298 ATTGGTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (15 bp):
GTTTTTTTTATTTGA
Found at i:699882 original size:29 final size:31
Alignment explanation
Indices: 699833--699892 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
699823 ACTCCACGTT
*
699833 ATATTTTTAAATTTTATGAATT-TTT-TTAA
1 ATATTTTTAAAATTTATGAATTATTTATTAA
699862 ATATTTTTATAAATTTA-GAATTATTTATTAA
1 ATATTTTTA-AAATTTATGAATTATTTATTAA
699893 TGCGTTCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
ATATTTTTAAAATTTATGAATTATTTATTAA
Found at i:734252 original size:6 final size:6
Alignment explanation
Indices: 734241--734265 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
734231 CGAGGAAGAA
734241 GGAGAT GGAGAT GGAGAT GGAGAT G
1 GGAGAT GGAGAT GGAGAT GGAGAT G
734266 AAGGGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGAGAT
Found at i:742326 original size:2 final size:2
Alignment explanation
Indices: 742321--742355 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
742311 AATTAAAAAA
742321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
742356 AAACTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:743401 original size:22 final size:22
Alignment explanation
Indices: 743373--743416 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
743363 AAGGCATATT
743373 ATTAAGCAGTTAGTATCAAGCA
1 ATTAAGCAGTTAGTATCAAGCA
*
743395 ATTAAGCAGTTAGTATTAAGCA
1 ATTAAGCAGTTAGTATCAAGCA
743417 GTTAGAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (22 bp):
ATTAAGCAGTTAGTATCAAGCA
Found at i:743412 original size:14 final size:14
Alignment explanation
Indices: 743395--743421 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
743385 GTATCAAGCA
743395 ATTAAGCAGTTAGT
1 ATTAAGCAGTTAGT
743409 ATTAAGCAGTTAG
1 ATTAAGCAGTTAG
743422 AAAGTTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (14 bp):
ATTAAGCAGTTAGT
Found at i:746732 original size:21 final size:20
Alignment explanation
Indices: 746702--746745 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
746692 CGAAGATATT
*
746702 TTTATTTTTATATAAAATATAA
1 TTTATTTTTAAAT-AAATA-AA
746724 TTTA-TTTTAAATAAATAAA
1 TTTATTTTTAAATAAATAAA
746743 TTT
1 TTT
746746 TCATTTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 5 0.24
21 7 0.33
22 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATTTTTAAATAAATAAA
Found at i:747324 original size:21 final size:21
Alignment explanation
Indices: 747282--747325 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
747272 TATTGTAATT
* *
747282 AATTTTTAAATTTATTATTCA
1 AATTGTTAAATTGATTATTCA
747303 AATTGTTAAATATGATTA-TCA
1 AATTGTTAAAT-TGATTATTCA
747324 AA
1 AA
747326 CACCATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
AATTGTTAAATTGATTATTCA
Found at i:749073 original size:21 final size:21
Alignment explanation
Indices: 749044--749083 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
749034 AAAGTACAGA
*
749044 GACTTAATTAAATAAGTAGGG
1 GACTAAATTAAATAAGTAGGG
* *
749065 GACTAAATTGAATATGTAG
1 GACTAAATTAAATAAGTAG
749084 CACAATTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (21 bp):
GACTAAATTAAATAAGTAGGG
Found at i:750361 original size:2 final size:2
Alignment explanation
Indices: 750354--750384 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
750344 ATTCTAGTTA
750354 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
750385 GTAAGTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:751755 original size:37 final size:38
Alignment explanation
Indices: 751655--751755 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 38
751645 GACCTTGAGT
**
751655 CGATGAGATACTGGGTGTCATACTATTACTTCGGATAGATT
1 CGATGAGATACTGGGTGTCA-AC--TTACTTCGGATAGAGC
* ** * *
751696 CGATGAGGTACTGGGTACCAACTTACTTCGGCTTG-GC
1 CGATGAGATACTGGGTGTCAACTTACTTCGGATAGAGC
*
751733 CGATGAGACACTGGGTGTCAACT
1 CGATGAGATACTGGGTGTCAACT
751756 ATTGCTTCGA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 19 0.39
38 11 0.22
40 2 0.04
41 17 0.35
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (38 bp):
CGATGAGATACTGGGTGTCAACTTACTTCGGATAGAGC
Found at i:752490 original size:17 final size:17
Alignment explanation
Indices: 752441--752491 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
752431 ATGTGGCATG
*
752441 TACCTAAGTAATGTACA
1 TACCTAAGTAATGTATA
*
752458 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
752475 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
752492 GGGATTAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:755816 original size:19 final size:18
Alignment explanation
Indices: 755773--755810 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
755763 ATATATTATG
*
755773 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATTCATAT
755791 ATTTTATTAAATT-ATAT
1 ATTTTATTAAATTCATAT
755808 ATT
1 ATT
755811 ATTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
ATTTTATTAAATTCATAT
Found at i:755962 original size:39 final size:40
Alignment explanation
Indices: 755917--756021 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 40
755907 TTTCCTTATG
* *
755917 CTATTACACCTCTATTCCATTCAACCAAACACAAGAATAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATAC
* *
755957 C-ATTACGCCTCTATTCCATTACATTCAACCAAATAAAAGATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATAC
756001 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
756022 ACGCATCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
39 13 0.24
40 6 0.11
44 22 0.40
45 14 0.25
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.30
Consensus pattern (40 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATAC
Found at i:756014 original size:45 final size:44
Alignment explanation
Indices: 755934--756023 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
755924 ACCTCTATTC
*
755934 CATTCAACCAAACACAAGAATACCATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTA
* *
755978 CATTCAACCAAATAAAAGATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATACC-ATTACGCCTCTATTCCATTA
756023 C
1 C
756024 GCATCTATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 21 0.50
45 21 0.50
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (44 bp):
CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTA
Found at i:756024 original size:16 final size:16
Alignment explanation
Indices: 756003--756039 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
755993 AAGATTACCT
*
756003 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
756019 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
756035 ATTAC
1 ATTAC
756040 AGCCAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:756202 original size:20 final size:20
Alignment explanation
Indices: 756177--756215 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
756167 AAATTAAAGT
* *
756177 AAAATGAGATTGAAATGAAG
1 AAAATGAAATTCAAATGAAG
756197 AAAATGAAATTCAAATGAA
1 AAAATGAAATTCAAATGAA
756216 ATTTAAAAAG
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:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATGAAATTCAAATGAAG
Found at i:756892 original size:21 final size:20
Alignment explanation
Indices: 756867--756920 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
756857 CTTTACTTTG
*
756867 TAATTATTCTGTTTT-TAATA
1 TAATTATT-TGTTTTCTAAAA
756887 TAAATTTATTT-TTTTCTAAAA
1 T-AA-TTATTTGTTTTCTAAAA
756908 TAATTATTTGTTT
1 TAATTATTTGTTT
756921 GGATAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.21
20 10 0.34
21 8 0.28
22 5 0.17
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (20 bp):
TAATTATTTGTTTTCTAAAA
Found at i:757139 original size:90 final size:88
Alignment explanation
Indices: 756971--757308 Score: 358
Period size: 90 Copynumber: 3.8 Consensus size: 88
756961 TAGAAAAATT
* * ** ** *
756971 AATAATACACAAC-AAATTAAATTTACA-ATACAAGAAAATACAAACATTTTTGAAGATTAATAC
1 AATAATAC-GAACTAAATTAAATTTACAGACACAA-AAAATACAAACATGATAAAAAATTAATAC
757034 ACGAAAATATAAAATTCAAACAACA
64 ACGAAAATATAAAATTCAAACAACA
* * *
757059 AATAATACGAACTAAATTAAATTTACAGACCCAACAAAATACAAATA-GATAGGTAAAATTAATA
1 AATAATACGAACTAAATTAAATTTACAGACACAA-AAAATACAAACATGATA--AAAAATTAATA
* * *
757123 CAAGAAAATTTAAAATTCAAACTACA
63 CACGAAAATATAAAATTCAAACAACA
* * **
757149 AATAATACGAGCTAAATTAAATTTATAGATACAACAAAAAAATACAAACATTCTAAAAAATTAAT
1 AATAATACGAACTAAATTAAATTTACAG--AC-AC-AAAAAATACAAACATGATAAAAAATTAAT
*
757214 ACACGAAAATATAAAATTGAAACAACA
62 ACACGAAAATATAAAATTCAAACAACA
** * ** *
757241 AATAATACCTACTAAATTAAATTTACAGATACAAAAAATACAAACATTCTAAAGAATTAATACAC
1 AATAATACGAACTAAATTAAATTTACAGACACAAAAAATACAAACATGATAAAAAATTAATACAC
757306 GAA
66 GAA
757309 TTTGATTTAT
Statistics
Matches: 211, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
87 3 0.01
88 58 0.27
89 17 0.08
90 59 0.28
92 58 0.27
93 12 0.06
94 4 0.02
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24
Consensus pattern (88 bp):
AATAATACGAACTAAATTAAATTTACAGACACAAAAAATACAAACATGATAAAAAATTAATACAC
GAAAATATAAAATTCAAACAACA
Found at i:757248 original size:92 final size:90
Alignment explanation
Indices: 756984--757308 Score: 371
Period size: 92 Copynumber: 3.6 Consensus size: 90
756974 AATACACAAC
* * ** *
756984 AAATTAAATTTACA-AT--ACAAGAAAATACAAACATTTTTGAAGATTAATACACGAAAATATAA
1 AAATTAAATTTACAGATACACAAAAAAATACAAACATTCTAAAAAATTAATACACGAAAATATAA
757046 AATTCAAACAACAAATAATACGAACT
66 AATTCAAACAACAAATAATACG-ACT
* * * ** * * *
757072 AAATTAAATTTACAG--ACCCAACAAAATACAAATA-GATAGGTAAAATTAATACAAGAAAATTT
1 AAATTAAATTTACAGATACACAAAAAAATACAAACATTCTA--AAAAATTAATACACGAAAATAT
*
757134 AAAATTCAAACTACAAATAATACGAGCT
64 AAAATTCAAACAACAAATAATACGA-CT
*
757162 AAATTAAATTTATAGATACAACAAAAAAATACAAACATTCTAAAAAATTAATACACGAAAATATA
1 AAATTAAATTTACAGATAC-ACAAAAAAATACAAACATTCTAAAAAATTAATACACGAAAATATA
* *
757227 AAATTGAAACAACAAATAATACCTACT
65 AAATTCAAACAACAAATAATA-CGACT
*
757254 AAATTAAATTTACAGAT--AC-AAAAAATACAAACATTCTAAAGAATTAATACACGAA
1 AAATTAAATTTACAGATACACAAAAAAATACAAACATTCTAAAAAATTAATACACGAA
757309 TTTGATTTAT
Statistics
Matches: 201, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
88 50 0.25
89 17 0.08
90 57 0.28
92 59 0.29
93 16 0.08
94 2 0.01
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.24
Consensus pattern (90 bp):
AAATTAAATTTACAGATACACAAAAAAATACAAACATTCTAAAAAATTAATACACGAAAATATAA
AATTCAAACAACAAATAATACGACT
Found at i:760884 original size:18 final size:17
Alignment explanation
Indices: 760851--760889 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
760841 TTTTATAAAT
760851 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
760869 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
760886 TGTG
1 TGTG
760890 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:761142 original size:23 final size:22
Alignment explanation
Indices: 761115--761190 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 22
761105 AGTGTTTTTG
761115 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCG-CTACAT
* *
761138 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTC-GCTACAT
761161 ATCAGTGGTAGCTTCCGCTACAT
1 ATCAGTGGTAGCTT-CGCTACAT
761184 ATCAGTG
1 ATCAGTG
761191 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 45 0.96
24 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (22 bp):
ATCAGTGGTAGCTTCGCTACAT
Found at i:764429 original size:2 final size:2
Alignment explanation
Indices: 764422--764446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
764412 AGCGTCGAGG
764422 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
764447 CATACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:765994 original size:14 final size:14
Alignment explanation
Indices: 765975--766001 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
765965 ATTTTTTTAA
765975 TAATGAGAACAAAG
1 TAATGAGAACAAAG
765989 TAATGAGAACAAA
1 TAATGAGAACAAA
766002 ATGCAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.19, T:0.15
Consensus pattern (14 bp):
TAATGAGAACAAAG
Found at i:772398 original size:31 final size:31
Alignment explanation
Indices: 772356--772418 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
772346 GGCCCATATT
772356 TATTTTAAAAAT-TTTAAAAAAGTAAAAAAAA
1 TATTTTAAAAATATTT-AAAAAGTAAAAAAAA
* * *
772387 TATTTTCAAAATATTTTAAAATTAAAAAAAA
1 TATTTTAAAAATATTTAAAAAGTAAAAAAAA
772418 T
1 T
772419 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAAGTAAAAAAAA
Found at i:772417 original size:10 final size:10
Alignment explanation
Indices: 772404--772506 Score: 59
Period size: 10 Copynumber: 10.2 Consensus size: 10
772394 AAAATATTTT
772404 AAAATTAAAA
1 AAAATTAAAA
772414 AAAATTAAAA
1 AAAATTAAAA
* *
772424 AATATTTTAAA
1 AA-AATTAAAA
* **
772435 AATATT--TT
1 AAAATTAAAA
772443 AAAATTAAAA
1 AAAATTAAAA
772453 AAAATTAAAA
1 AAAATTAAAA
*
772463 AAAGTATTTTAAA
1 AAA--A-TTAAAA
* **
772476 AATATT-TTA
1 AAAATTAAAA
*
772485 AAATTTAAAA
1 AAAATTAAAA
772495 AAAATTAAAA
1 AAAATTAAAA
772505 AA
1 AA
772507 GTATGTAAAA
Statistics
Matches: 68, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
8 5 0.07
9 5 0.07
10 41 0.60
11 9 0.13
12 1 0.01
13 7 0.10
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:772424 original size:39 final size:40
Alignment explanation
Indices: 772356--772537 Score: 258
Period size: 41 Copynumber: 4.5 Consensus size: 40
772346 GGCCCATATT
* * * * *
772356 TATTTTAAAAATTTTAAAAAAGTAAAAAAAATATTTTCAAAA
1 TATTTT-AAAA-TTAAAAAAAATTAAAAAAGTATTTTAAAAA
772398 TATTTTAAAATTAAAAAAAATTAAAAAA-TATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
772437 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTAAAAA
* *
772478 TATTTTAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAA-TTAAAAAAAATTAAAAAAGTATTTTAAAAA
772519 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
772538 TAAATATATT
Statistics
Matches: 131, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
39 32 0.24
40 30 0.23
41 51 0.39
42 18 0.14
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:772446 original size:29 final size:30
Alignment explanation
Indices: 772414--772476 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
772404 AAAATTAAAA
* **
772414 AAAATTAAAAAATATTTTAAAAA-TATTTT
1 AAAATTAAAAAAAATTAAAAAAAGTATTTT
772443 AAAATTAAAAAAAATTAAAAAAAGTATTTT
1 AAAATTAAAAAAAATTAAAAAAAGTATTTT
772473 AAAA
1 AAAA
772477 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAATTAAAAAAAATTAAAAAAAGTATTTT
Found at i:772528 original size:11 final size:11
Alignment explanation
Indices: 772382--772487 Score: 68
Period size: 11 Copynumber: 10.4 Consensus size: 11
772372 AAAAAGTAAA
772382 AAAAATATTTT
1 AAAAATATTTT
*
772393 CAAAATATTTT
1 AAAAATATTTT
772404 --AAA-A--TT
1 AAAAATATTTT
* * *
772410 AAAAAAAATTA
1 AAAAATATTTT
772421 AAAAATATTTT
1 AAAAATATTTT
772432 AAAAATATTTT
1 AAAAATATTTT
*
772443 --AAA-A-TTA
1 AAAAATATTTT
* **
772450 AAAAAAATTAA
1 AAAAATATTTT
772461 AAAAAGTATTTT
1 AAAAA-TATTTT
772473 AAAAATATTTT
1 AAAAATATTTT
772484 AAAA
1 AAAA
772488 TTTAAAAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 5 0.07
9 10 0.13
10 1 0.01
11 47 0.63
12 8 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:787266 original size:17 final size:21
Alignment explanation
Indices: 787216--787261 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
787206 ATTTTTTTTC
787216 TTTTATATTCTTTCAACTTTA
1 TTTTATATTCTTTCAACTTTA
*
787237 TTTTATATTCTTTCAACTTTT
1 TTTTATATTCTTTCAACTTTA
787258 TTTT
1 TTTT
787262 TCTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATTCTTTCAACTTTA
Found at i:789082 original size:2 final size:2
Alignment explanation
Indices: 789069--789101 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
789059 ATCAACTTAA
*
789069 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
789102 ATACAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:793513 original size:6 final size:7
Alignment explanation
Indices: 793498--793522 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
793488 AAGTTGACCG
793498 TTTTCTT
1 TTTTCTT
793505 TTTTCTT
1 TTTTCTT
793512 TTTTCTT
1 TTTTCTT
793519 TTTT
1 TTTT
793523 ACGAGACAAC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:796643 original size:15 final size:15
Alignment explanation
Indices: 796620--796650 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
796610 GGGTAGTAGT
796620 CTAGAAGCGGCGGCA
1 CTAGAAGCGGCGGCA
*
796635 CTAGCAGCGGCGGCA
1 CTAGAAGCGGCGGCA
796650 C
1 C
796651 GAATATCAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.32, G:0.39, T:0.06
Consensus pattern (15 bp):
CTAGAAGCGGCGGCA
Found at i:800780 original size:30 final size:29
Alignment explanation
Indices: 800746--800804 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
800736 GAATTGGATC
* *
800746 AAATCAAAATTTAATGTATAAAATTGCACA
1 AAATC-AAAGTTAATGTATAAAATTACACA
*
800776 AAATCAAAGTTCATGTATAAAATTACACA
1 AAATCAAAGTTAATGTATAAAATTACACA
800805 TTAAACTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATCAAAGTTAATGTATAAAATTACACA
Found at i:803359 original size:7 final size:7
Alignment explanation
Indices: 803347--803375 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
803337 TATAATTTCA
803347 GCAATGG
1 GCAATGG
803354 GCAATGG
1 GCAATGG
803361 GCAATGG
1 GCAATGG
803368 GCAATGG
1 GCAATGG
803375 G
1 G
803376 TGTGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.45, T:0.14
Consensus pattern (7 bp):
GCAATGG
Found at i:816476 original size:22 final size:22
Alignment explanation
Indices: 816446--816487 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
816436 AAATTTGATT
* *
816446 TTTTTAAAAATATGTATATTCA
1 TTTTAAAAAATATATATATTCA
*
816468 TTTTAAAAAATGTATATATT
1 TTTTAAAAAATATATATATT
816488 GAATTTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTAAAAAATATATATATTCA
Found at i:833455 original size:16 final size:18
Alignment explanation
Indices: 833430--833466 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
833420 ATTGACCCAC
*
833430 TATTTTATATT-A-AAAA
1 TATTTCATATTGATAAAA
833446 TATTTCATATTGATAAAA
1 TATTTCATATTGATAAAA
833464 TAT
1 TAT
833467 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTCATATTGATAAAA
Found at i:840787 original size:39 final size:39
Alignment explanation
Indices: 840742--840823 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
840732 AATGATCCAA
840742 CAACTTCTCCAGGAGATGTCTAATAACAACACGGGAGTT
1 CAACTTCTCCAGGAGATGTCTAATAACAACACGGGAGTT
840781 CAACTTCTCCAGGAGATGTCTAATAACAACACGGGAGTT
1 CAACTTCTCCAGGAGATGTCTAATAACAACACGGGAGTT
840820 CAAC
1 CAAC
840824 AGCAGTCCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (39 bp):
CAACTTCTCCAGGAGATGTCTAATAACAACACGGGAGTT
Found at i:853119 original size:32 final size:32
Alignment explanation
Indices: 853083--853154 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
853073 AAAAAACAAT
* **
853083 AATTTAACTT-TTTTTCAAAAGATTGATGGTCA
1 AATTTAACTTCTTTTT-AAAAGATTGAAGACCA
*
853115 AATTTGA-TTCTTTTTAAAAGATTGAAGACCA
1 AATTTAACTTCTTTTTAAAAGATTGAAGACCA
853146 AATTTAACT
1 AATTTAACT
853155 AAAAAAAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (32 bp):
AATTTAACTTCTTTTTAAAAGATTGAAGACCA
Found at i:855778 original size:11 final size:11
Alignment explanation
Indices: 855764--855820 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
855754 ATATTCAAAT
855764 AATAATAACAA
1 AATAATAACAA
855775 AATAATAACAA
1 AATAATAACAA
* ***
855786 TATAATAGTGA
1 AATAATAACAA
*
855797 AATAACAACAA
1 AATAATAACAA
*
855808 AATAGTAACAA
1 AATAATAACAA
855819 AA
1 AA
855821 AAGAACAATT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.67, C:0.09, G:0.05, T:0.19
Consensus pattern (11 bp):
AATAATAACAA
Found at i:855790 original size:22 final size:22
Alignment explanation
Indices: 855765--855829 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
855755 TATTCAAATA
*
855765 ATAATAACAAAATAATAACAAT
1 ATAATAACAAAATAACAACAAT
*** *
855787 ATAATAGTGAAATAACAACAAA
1 ATAATAACAAAATAACAACAAT
* *
855809 ATAGTAACAAAA-AAGAACAAT
1 ATAATAACAAAATAACAACAAT
855830 TTTTGTTTGC
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.18
Consensus pattern (22 bp):
ATAATAACAAAATAACAACAAT
Found at i:856643 original size:15 final size:14
Alignment explanation
Indices: 856618--856646 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
856608 AAAAAAAGAG
856618 ATATATTTATATAT
1 ATATATTTATATAT
856632 ATATATTT-TATAT
1 ATATATTTATATAT
856645 AT
1 AT
856647 GGAAAGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATATTTATATAT
Found at i:864573 original size:3 final size:3
Alignment explanation
Indices: 864565--864589 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
864555 TAAACTCGAA
864565 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
864590 CTGCAAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:868621 original size:178 final size:178
Alignment explanation
Indices: 868316--869014 Score: 1010
Period size: 178 Copynumber: 3.9 Consensus size: 178
868306 TTTTTCAAGC
* *
868316 TGCTATTATCTGTTTTACGACTTTTTACCGGGTAAAGCTGAGTTCTTCCAGCAATGGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAGGTTTGGATT
*
868381 ATGAATGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
868446 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGTTGCTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGTTGCTTTTA
*
868494 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAAGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAGGTTTGGATT
*
868559 ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
* *
868624 CTTTGCCTTAGCTATGATTACAGTATAATCTCTAATGAGCTGCTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGTTGCTTTTA
* *
868672 TGCTATTATCTGTTTTATGACTTTTTTCCGGGTAAAGCTTAGTTCTTCCAGCAAAGGTTTGGATT
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAGGTTTGGATT
868737 ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
66 ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
*
868802 CTTTGCCTTAGCTATGATTACAATATAATCTTTAATGAGCTT-CTTTTA
131 CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAG-TTGCTTTTA
* * * * * * * ** *
868850 T-C--TT-TC----TAACGACGTTTTTCCGGCTGAATGTTCAAGATT-TAT-AAATAAATGTTTG
1 TGCTATTATCTGTTTTACGACTTTTTTCCGGGT-AAAGCT-GAG-TTCT-TCCAGCAAAGGTTTG
*
868905 G-TTTTCGAGTGTTGTTTTGTAGT-AGTTGCAGCGATGATTAAAATGAGGTTTAGGGTTGTAATG
62 GATTAT-GAGTGTTGTTTTGTAGTAAG-TGCAGCGATGATTAAAATGAGGTTTAGGG-T-TAATG
* * *
868968 AGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCTCTAATGAG
123 AGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAG
869015 CTGCCGTATC
Statistics
Matches: 482, Mismatches: 30, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
170 15 0.03
171 9 0.02
172 59 0.12
173 4 0.01
174 50 0.10
175 2 0.00
177 1 0.00
178 341 0.71
179 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (178 bp):
TGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAGCTGAGTTCTTCCAGCAAAGGTTTGGATT
ATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCAAGG
CTTTGCCTTAGCTATGATTACAATATAATCTCTAATGAGTTGCTTTTA
Found at i:869090 original size:173 final size:170
Alignment explanation
Indices: 868313--869119 Score: 805
Period size: 178 Copynumber: 4.6 Consensus size: 170
868303 TTGTTTTTCA
* * ** * *
868313 AGCTGCTATTATCTGTTTTACGAC-TTTTTACCGGGTAAAG--CTGAGTTCTTCCAGC-AATGGT
1 AGCTGCTCTTATCTTTTTTACGACGTTTTT-CCGGG-AAAGTTCAAAGTT-TTCAAACAAAT-GT
*
868374 TTGGATTATGAATGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGA
62 TTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGA
868439 GGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATG
127 GGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATG
* * * ** * *
868483 AGTTGCTTTTATGCTATTATCTGTTTTACGACTTTTTTCCGGGTAAAG--CTGAGTTCTTCCAGC
1 A---GC-----TGCTCTTATCTTTTTTACGACGTTTTTCCGGG-AAAGTTCAAAGTT-TTCAAAC
*
868546 AAAAGTTTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGT
56 AAATGTTTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGT
* *
868611 TAACGAGGCAAGGCTTTGCCTTAGCTATGATTACAGTATAATCTCTAATG
121 TAATGAGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATG
* * * * *
868661 AGCTGCTTTTATGCTATTATCTGTTTTATGACTTTTTTCCGGGTAAAGCTT---AGTTCTTCCAG
1 AGCTGC-----T-C--TTATCTTTTTTACGACGTTTTTCCGGG-AAAG-TTCAAAGTT-TTCAAA
*
868723 CAAAGGTTTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGG
55 CAAATGTTTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGG
*
868788 TTAATGAGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTTTAATG
120 TTAATGAGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATG
* * * * * *
868839 AGCTTCTTTTATCTTTCTAACGACGTTTTTCCGGCTGAATGTTC-AAGATTTAT-AAATAAATGT
1 AGCTGCTCTTATCTTTTTTACGACGTTTTTCCGG--GAAAGTTCAAAG-TTT-TCAAACAAATGT
*
868902 TTGG-TTTTCGAGTGTTGTTTTGTAGT-AGTTGCAGCGATGATTAAAATGAGGTTTAGGGTTGTA
62 TTGGATTAT-GAGTGTTGTTTTGTAGTAAG-TGCAGCGATGATTAAAATGAGGTTTAGGG-T-TA
* * *
868965 ATGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCTCTAATG
123 ATGAGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATG
* * * * * *
869013 AGCTGC-CGTATCTTTTTTACAACGTTTTTCCGACCGAATGTTCAAAATTTTTAAACAAATGTTT
1 AGCTGCTCTTATCTTTTTTACGACGTTTTTCCG--GGAAAGTTCAAAGTTTTCAAACAAATGTTT
* * * *
869077 GGTTTTTGAGTGTTGTTTTGTGGTAATTGCAGCGATGATTAAA
64 GGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAA
869120 GTAAATTAAG
Statistics
Matches: 562, Mismatches: 38, Indels: 71
0.84 0.06 0.11
Matches are distributed among these distances:
170 27 0.05
171 8 0.01
172 61 0.11
173 84 0.15
174 58 0.10
175 3 0.01
178 314 0.56
179 7 0.01
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (170 bp):
AGCTGCTCTTATCTTTTTTACGACGTTTTTCCGGGAAAGTTCAAAGTTTTCAAACAAATGTTTGG
ATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGGCA
AGGCTTTGCCTTAGCTATGATTACAATATAATCTCTAATG
Found at i:869299 original size:180 final size:175
Alignment explanation
Indices: 868723--869300 Score: 530
Period size: 173 Copynumber: 3.3 Consensus size: 175
868713 GTTCTTCCAG
* * * * * *
868723 CAAAGGTTTGGATTATGAGTGTTGTTTTGTAGTAAGTGCAGCGATGATT--AAAATGAGGTTTAG
1 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAAAATAAGGTGTAG
* * * * ** * **
868786 GG-T-TAATGAGGCAAGGCTTTGCCTTAGCTATGATTACAATATAATCTTTAATGAGCTTCTTTT
66 GGTTATAACGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGC-CGT
* * * * ** * *
868849 ATCTTTCTAACGACGTTTTTCCGGCTGAATGTTCAAGATTTAT-AAA
130 ATCTTTTTTACAACGTTCTTCCAACCGAATGTTCAAAATTT-TCAAA
* * * * *
868895 TAAATGTTTGGTTTTCGAGTGTTGTTTTGTAGTAGTTGCAGCGATGATT--AAAATGAGGTTTAG
1 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAAAATAAGGTGTAG
* * *
868958 GGTTGTAATGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCTCTAATGAGCTGCCGTA
66 GGTTATAACGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGCCGTA
* * *
869023 TCTTTTTTACAACGTTTTTCCGACCGAATGTTCAAAATTTTTAAA
131 TCTTTTTTACAACGTTCTTCCAACCGAATGTTCAAAATTTTCAAA
*
869068 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTGGTAATTGCAGCGATGATTAAAGTAAATTAAGGTG
1 CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAA--AAA-TAAGGTG
* * * * * *
869133 TAGGGTTATAACGATCGAA-GTTTGTGCCTAAGCTATGTTTACAATATATTCGCTAATTAGGTGC
63 TAGGGTTATAACGAGCCAAGGTTT-TGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGC
** ** **
869197 CGTAAAGTC-TTTTTACGGCGTTCTTCCAATTGGAA-GTTCAAGGTTTTCAAA
127 CGT--A-TCTTTTTTACAACGTTCTTCCAA-CCGAATGTTCAAAATTTTCAAA
* * *
869248 CAATTGTTCT-GTTTTTGAGTGTTGTCTTGTAGTAATCGCAGCGATGATTAAAA
1 CAAATGTT-TGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAA
869301 TAAGGTTTAC
Statistics
Matches: 344, Mismatches: 48, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
172 59 0.17
173 85 0.25
174 51 0.15
175 1 0.00
177 7 0.02
178 59 0.17
180 76 0.22
181 6 0.02
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (175 bp):
CAAATGTTTGGTTTTTGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAAAATAAGGTGTAG
GGTTATAACGAGCCAAGGTTTTGCCTAAGCTATGATTACAATATAATCGCTAATGAGCTGCCGTA
TCTTTTTTACAACGTTCTTCCAACCGAATGTTCAAAATTTTCAAA
Found at i:871092 original size:25 final size:23
Alignment explanation
Indices: 871044--871091 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
871034 TATTTTAAAA
*
871044 AATATATTATTTTACATTATTTT
1 AATATATTATTTTAAATTATTTT
871067 AATATATTATATTTGAAATGTATTT
1 AATATATTAT-TTT-AAAT-TATTT
871092 AGTTAGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 3 0.14
25 3 0.14
26 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
AATATATTATTTTAAATTATTTT
Found at i:871407 original size:152 final size:151
Alignment explanation
Indices: 871151--872061 Score: 1032
Period size: 152 Copynumber: 6.0 Consensus size: 151
871141 AAAAATAGTT
* * * * * *
871151 GAAATAAGGGTTTTTTTAAAAATTT-AT-T--TAAGCACACTAAATGAAAATATTTTAAATATAA
1 GAAATAAGGGTTTTTTT--AAATTTCATATAAAAAACACACTAAATGAATACATTTCAAACATAA
* * * * *
871212 TGTATTAAAATAATGTAAAATAATAAGATTAGAAAATATTATATTTTTTAAAAGTAATAAAATTT
64 TGTACTAAAATAATGTAAAATAATAAAACTAGAAAATAGTATATTTTTT-AAAGTAATAAAA-TC
* *
871277 GGGGAAAAAATACGAATAAATGGCC
127 GGGGAAAAAATACGAACAAAGGGCC
** * * * * *
871302 GAAATAATAGTTTTTTAAAAATTT-ATTTAAAAAACACAGTAAATTAATACATTTCAAATATAAT
1 GAAATAAGGGTTTTTT-TAAATTTCATATAAAAAACACACTAAATGAATACATTTCAAACATAAT
* * * ***
871366 GTATTAAAATAATAT-AAATAATAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTTAG
65 GTACTAAAATAATGTAAAATAATAAAACTAGAAAATAGTATATTTTTTAAAGTAATAAAATCGGG
* * *
871430 AAAAAAATACGAATAAAGAGCC
130 GAAAAAATACGAACAAAGGGCC
* * * * *
871452 GAAATAA-GGATTTTTTAAATTT-AT-TTAAAAACACAATAAATTAATGCATTTCAAACATAATG
1 GAAATAAGGGTTTTTTTAAATTTCATATAAAAAACACACTAAATGAATACATTTCAAACATAATG
* *
871514 TACTAAAATAATGTAAAATAATAAAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATC
66 TACTAAAATAATGTAAAATAATAAAACTA-GAAAATAGTATA-TTTT-TT-AAAGTAATAAAATC
***
871578 -CAAAAAAAATACGAACAAAGGGCC
127 GGGGAAAAAATACGAACAAAGGGCC
* * *
871602 GAAATAATGGTTTTTTTTAATTTCA-ATAAAAAACACACTAAACGAATACATTTCAAACATAATG
1 GAAATAAGGGTTTTTTTAAATTTCATATAAAAAACACACTAAATGAATACATTTCAAACATAATG
*
871666 TACTAAAATAATGTAAAATAATAAAACTAGAAAAT-G-ATATTTTTTTAAAGTAATAAAATCCGG
66 TACTAAAATAATGTAAAATAATAAAACTAGAAAATAGTATA-TTTTTTAAAGTAATAAAATCGGG
***
871729 GAAAAAATACGAACAATTTGCC
130 GAAAAAATACGAACAAAGGGCC
* *
871751 GAAATAAGGGTTTTTTTTTAATTTCAATAAAAAAAACACACTAAATGAATACATTTCAAACATAA
1 GAAATAAGGG-TTTTTTTAAATTTC-ATATAAAAAACACACTAAATGAATACATTTCAAACATAA
*
871816 TGTATTAAAATAATGTAAAATAATAAAACTAGAAAATA-TAATATTTTTTAAAAGTAATAAAATT
64 TGTACTAAAATAATGTAAAATAATAAAACTAGAAAATAGT-ATATTTTTT-AAAGTAATAAAA-T
* *
871880 CGGGGAAAAAATACGAATAAAGGGCT
126 CGGGGAAAAAATACGAACAAAGGGCC
* *
871906 GAAATGAGGGTTTTTTTTTTAATTTCA-ATAAAAAACACACTAAATGAATACATTT-AAACATAA
1 GAAATAAGGG--TTTTTTTAAATTTCATATAAAAAACACACTAAATGAATACATTTCAAACATAA
*
871969 TGTACTAAAATAATGTAAAATAATAAAAATAGAAAATAGTAT-TTTTTT-AAGTAATAAAATCGG
64 TGTACTAAAATAATGTAAAATAATAAAACTAGAAAATAGTATATTTTTTAAAGTAATAAAATCGG
*
872032 GGAAAAAAATACGAACAAAGGGCT
129 GG-AAAAAATACGAACAAAGGGCC
872056 GAAATA
1 GAAATA
872062 GGAACATGTT
Statistics
Matches: 670, Mismatches: 65, Indels: 51
0.85 0.08 0.06
Matches are distributed among these distances:
147 48 0.07
148 43 0.06
149 45 0.07
150 124 0.19
151 54 0.08
152 172 0.26
153 95 0.14
154 43 0.06
155 31 0.05
156 15 0.02
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (151 bp):
GAAATAAGGGTTTTTTTAAATTTCATATAAAAAACACACTAAATGAATACATTTCAAACATAATG
TACTAAAATAATGTAAAATAATAAAACTAGAAAATAGTATATTTTTTAAAGTAATAAAATCGGGG
AAAAAATACGAACAAAGGGCC
Found at i:878886 original size:22 final size:22
Alignment explanation
Indices: 878861--878903 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
878851 ATTTTAAAAA
878861 ATATTTTTAT-ATTAACATTTAT
1 ATATTTTTATAATTAA-ATTTAT
878883 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
878904 AAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:895233 original size:4 final size:4
Alignment explanation
Indices: 895224--895248 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
895214 CTCCCAGTAC
895224 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
895249 TCTCAAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:898239 original size:19 final size:19
Alignment explanation
Indices: 898215--898256 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
898205 TAAGGACAAG
898215 TTTTAAAGTTATATAT-TAA
1 TTTTAAAGTTA-ATATGTAA
*
898234 TTTT-AATTTAATATGTAA
1 TTTTAAAGTTAATATGTAA
898252 TTTTA
1 TTTTA
898257 TACCAACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTAAAGTTAATATGTAA
Found at i:898525 original size:156 final size:155
Alignment explanation
Indices: 898150--898551 Score: 408
Period size: 156 Copynumber: 2.6 Consensus size: 155
898140 TTGATAGGAA
* ** *
898150 TTAGTTTCTCACTTTGATTTTCAACTTTTACAAAATAATACATTTTTTTAATATTTAAGG-ACAA
1 TTAGTTTCTCACTCTGATTTAGAATTTTTACAAAATAATACA-TTTTTTAATATTTAAGGTA-AA
* * * * * * *
898214 GTTTTAAAGTTATATATTAATTTTAATTTAATATGTAATTTTATACCAACTCAATCATGAGTTCT
64 -TTTTAAAATTATACATGAATTTTAATTTAATATATAATTTTATACCAACTCAATAATAAATTCT
*
898279 ATTAATAGTATAGATATTTCAAGAAAAG
128 ATTAATAGTATAGATATTTCAACAAAAG
* * * * * *
898307 ---GTTTCTCA-TGTCAATTTAGAATTTTCATAAAATGATACA-TTTTTAATATTTAAAGATAAA
1 TTAGTTTCTCACTCT-GATTTAGAATTTTTACAAAATAATACATTTTTTAATATTT-AAGGTAAA
**
898367 TTTTAAAATTATACATGAATTTTAATTTAATATATAATTTTATATACCAACTCGGTTAATAAATT
64 TTTTAAAATTATACATGAATTTTAATTTAATATATAA-TTT-TATACCAACTC-AATAATAAATT
*
898432 -TATT-ATAGTATAGATATTTCAACAAGAG
126 CTATTAATAGTATAGATATTTCAACAAAAG
* * * *
898460 TTAGTTTTTCACTCTGATTTAGAATTTTTACAAAAT-ATGCATTTTTTAATGTTTAACGGTGAAT
1 TTAGTTTCTCACTCTGATTTAGAATTTTTACAAAATAATACATTTTTTAATATTTAA-GGTAAAT
* * *
898524 TTTAAAATTTTACATGATTTTTTATTTA
65 TTTAAAATTATACATGAATTTTAATTTA
898552 TCAAGGTATC
Statistics
Matches: 201, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
152 45 0.22
153 32 0.16
154 44 0.22
155 12 0.06
156 66 0.33
157 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (155 bp):
TTAGTTTCTCACTCTGATTTAGAATTTTTACAAAATAATACATTTTTTAATATTTAAGGTAAATT
TTAAAATTATACATGAATTTTAATTTAATATATAATTTTATACCAACTCAATAATAAATTCTATT
AATAGTATAGATATTTCAACAAAAG
Found at i:912028 original size:103 final size:102
Alignment explanation
Indices: 911818--912186 Score: 555
Period size: 103 Copynumber: 3.6 Consensus size: 102
911808 TGTATATAAA
** * * *
911818 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
911882 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TT-AAA-ATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
911922 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCA-CATATC-
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
911985 TTAAAATGAAAGGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTAAAATGAAA--GGGGGTTGCTATGTGCTGATTCCCCCG
912025 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
* *
912090 TGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TAAAAT-GAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
912128 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
912187 ATAACGGCTA
Statistics
Matches: 247, Mismatches: 11, Indels: 15
0.90 0.04 0.05
Matches are distributed among these distances:
101 5 0.02
102 32 0.13
103 145 0.59
104 37 0.15
105 27 0.11
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TAAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:918576 original size:9 final size:9
Alignment explanation
Indices: 918562--918588 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
918552 TTAGTAACAA
918562 TTTTGAATC
1 TTTTGAATC
918571 TTTTGAATC
1 TTTTGAATC
918580 TTTTGAATC
1 TTTTGAATC
918589 AATCAACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
TTTTGAATC
Found at i:919999 original size:20 final size:20
Alignment explanation
Indices: 919974--920011 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
919964 GTTTTTACAT
919974 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
919994 ATATTAATAAATTTATAT
1 ATATTAATAAATTTATAT
920012 TTTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:920212 original size:41 final size:43
Alignment explanation
Indices: 920166--920246 Score: 148
Period size: 41 Copynumber: 1.9 Consensus size: 43
920156 TATAATTGCA
920166 TTAATAATTTTTTGAGAAA-T-TAAGCTACTTTCTTTGTAATT
1 TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTAATT
920207 TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTA
1 TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTA
920247 CCAATACTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 19 0.50
42 1 0.03
43 18 0.47
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (43 bp):
TTAATAATTTTTTGAGAAATTATAAGCTACTTTCTTTGTAATT
Found at i:920227 original size:21 final size:21
Alignment explanation
Indices: 920166--920227 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
920156 TATAATTGCA
920166 TTAATAATTTTTTGAGAAA--
1 TTAATAATTTTTTGAGAAATT
* *
920185 TTAAGCTACTTTCTTT--GTAATT
1 TTAA--TAATTT-TTTGAGAAATT
920207 TTAATAATTTTTTGAGAAATT
1 TTAATAATTTTTTGAGAAATT
920228 ATAAGCTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
19 7 0.22
20 8 0.25
21 10 0.31
22 7 0.22
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (21 bp):
TTAATAATTTTTTGAGAAATT
Found at i:927480 original size:8 final size:8
Alignment explanation
Indices: 927467--927493 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
927457 ACCTTCAACT
927467 TTTTTTTC
1 TTTTTTTC
927475 TTTTTTTC
1 TTTTTTTC
927483 TTTTTTTC
1 TTTTTTTC
927491 TTT
1 TTT
927494 CGATCATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:927946 original size:47 final size:47
Alignment explanation
Indices: 927895--927986 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
927885 GATTTGGTGA
*
927895 GTTAGTACCCATAAAAAAGTAGAAAAATCCTAAGTCAATTCGACACT
1 GTTAGTACCCATAAAAAAGTAGAAAAATCATAAGTCAATTCGACACT
* *
927942 GTTAGTATCCATAAAAAAGTAGAACAATCATAAGTCAATTCGACA
1 GTTAGTACCCATAAAAAAGTAGAAAAATCATAAGTCAATTCGACA
927987 GTTAGTGTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (47 bp):
GTTAGTACCCATAAAAAAGTAGAAAAATCATAAGTCAATTCGACACT
Found at i:940462 original size:45 final size:46
Alignment explanation
Indices: 940408--940518 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
940398 ATCACTTGTC
*
940408 CTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
*
940453 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
940499 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
940519 CACTTATCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 21 0.33
46 42 0.67
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
Found at i:940501 original size:46 final size:45
Alignment explanation
Indices: 940395--940665 Score: 216
Period size: 37 Copynumber: 6.6 Consensus size: 45
940385 CATATGACCT
* *
940395 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
940438 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
940484 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* **
940521 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* **
940558 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* ** *
940595 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
940641 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTATCACTTGATCAGA
940666 AGTACTCAAA
Statistics
Matches: 206, Mismatches: 9, Indels: 23
0.87 0.04 0.10
Matches are distributed among these distances:
37 101 0.49
39 2 0.01
40 3 0.01
41 1 0.00
42 1 0.00
43 10 0.05
44 5 0.02
45 21 0.10
46 62 0.30
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:940522 original size:37 final size:37
Alignment explanation
Indices: 940480--940627 Score: 260
Period size: 37 Copynumber: 4.0 Consensus size: 37
940470 AGCTGAAGCT
* **
940480 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
940517 GCCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
940554 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
940591 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
940628 GCTAAAACTA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:942139 original size:22 final size:23
Alignment explanation
Indices: 942113--942179 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
942103 TGCACTATTG
942113 AACAGAGAGCACTAAA-GTGCTA
1 AACAGAGAGCACTAAATGTGCTA
*
942135 TACAGAGAGCAC-AAATGTGCTA
1 AACAGAGAGCACTAAATGTGCTA
* *
942157 AACGGAGAGCACT-AATATGCTA
1 AACAGAGAGCACTAAATGTGCTA
942179 A
1 A
942180 TAATCGAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.08
22 36 0.92
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (23 bp):
AACAGAGAGCACTAAATGTGCTA
Found at i:943595 original size:15 final size:15
Alignment explanation
Indices: 943575--943606 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
943565 TTCTTACAAA
943575 AGTCATTTCCAAATT
1 AGTCATTTCCAAATT
*
943590 AGTCATTTTCAAATT
1 AGTCATTTCCAAATT
943605 AG
1 AG
943607 GTACATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (15 bp):
AGTCATTTCCAAATT
Found at i:950109 original size:22 final size:24
Alignment explanation
Indices: 950084--950129 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
950074 AATATATGTA
950084 AATAATTAGGAT-AAA-AATATAT
1 AATAATTAGGATGAAATAATATAT
* *
950106 AATATTTAGGTTGAAATAATATAT
1 AATAATTAGGATGAAATAATATAT
950130 TCTTTCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 3 0.15
24 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (24 bp):
AATAATTAGGATGAAATAATATAT
Found at i:958454 original size:24 final size:23
Alignment explanation
Indices: 958402--958455 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
958392 ATGGATGAGC
* *
958402 CCCGTAAGGTGCCGGTTGAGGGG
1 CCCGTAAGGAGCCGATTGAGGGG
*
958425 CTCCGTAAGGAGCCGATTGAGGATG
1 C-CCGTAAGGAGCCGATTGAGG-GG
958450 CCCGTA
1 CCCGTA
958456 TGAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 23 0.88
25 2 0.08
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (23 bp):
CCCGTAAGGAGCCGATTGAGGGG
Found at i:962136 original size:34 final size:35
Alignment explanation
Indices: 962078--962144 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
962068 CAAACACCAG
962078 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
962113 AAAATATTTTCCCG-AAATCATTTTACAGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
962145 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:964621 original size:32 final size:32
Alignment explanation
Indices: 964585--964648 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
964575 GTTGCTTGCC
964585 TGCATTGCTTTTGGTTG-ATTTGCCTTCCTATT
1 TGCATTGCTTTTGGTTGTATTTG-CTTCCTATT
* *
964617 TGCATTGGTTTTGGTTGTTTTTGCTTCCTATT
1 TGCATTGCTTTTGGTTGTATTTGCTTCCTATT
964649 ATTTGCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (32 bp):
TGCATTGCTTTTGGTTGTATTTGCTTCCTATT
Found at i:964976 original size:218 final size:218
Alignment explanation
Indices: 964598--965022 Score: 715
Period size: 218 Copynumber: 1.9 Consensus size: 218
964588 ATTGCTTTTG
* ** **
964598 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTGCTTCCTATTATTTGCATATGATG
1 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
*
964663 AACTCTACTCGGATTCCCCTTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
66 AACTCTACTCGGATTCCCCTTCAAGACATCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
*
964728 TTAAGTGATAAATTTTACGTAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
131 TTAAGTGATAAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
*
964793 TCATTCTTTCTTTAATTTGGTTT
196 TCATTCATTCTTTAATTTGGTTT
964816 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
1 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
* * * * *
964881 AACTCTACTTGGATTCCTCTTCAAGACATCATGGGTGATGCTAACTTGAGTTTCTGGTGGAAACA
66 AACTCTACTCGGATTCCCCTTCAAGACATCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
* *
964946 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGGAAGTATAAAAAATGTGTTTCT
131 TTAAGTGATAAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
965011 TCATTCATTCTT
196 TCATTCATTCTT
965023 CAATCCTCTA
Statistics
Matches: 192, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
218 192 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (218 bp):
GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACGCATACAATG
AACTCTACTCGGATTCCCCTTCAAGACATCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
TTAAGTGATAAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
TCATTCATTCTTTAATTTGGTTT
Found at i:971403 original size:29 final size:30
Alignment explanation
Indices: 971369--971426 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
971359 TCAAATTTTT
971369 ATAAAATTATACA-AAAGCAAAGTTCATAC
1 ATAAAATTATACATAAAGCAAAGTTCATAC
*
971398 ATAAAATTATACATTAAATCAAAGTTCAT
1 ATAAAATTATACA-TAAAGCAAAGTTCAT
971427 GTATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.29
Consensus pattern (30 bp):
ATAAAATTATACATAAAGCAAAGTTCATAC
Found at i:972497 original size:21 final size:20
Alignment explanation
Indices: 972460--972498 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
972450 CACTTTTGGG
*
972460 CTGAAAAAAGCTAAAAATCT
1 CTGAAAAAAACTAAAAATCT
*
972480 CTGAAAAAACACTTAAAAT
1 CTGAAAAAA-ACTAAAAAT
972499 AAGTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (20 bp):
CTGAAAAAAACTAAAAATCT
Found at i:972718 original size:3 final size:3
Alignment explanation
Indices: 972710--972737 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
972700 ATATAGGAAA
972710 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
972738 AATCTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:979011 original size:17 final size:17
Alignment explanation
Indices: 978974--979011 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
978964 AATACGGCTA
978974 ATTTTAGTAAATTTTAT
1 ATTTTAGTAAATTTTAT
978991 -TTTTAAGT-AATTTTAT
1 ATTTT-AGTAAATTTTAT
979007 ATTTT
1 ATTTT
979012 GTCAACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTTAGTAAATTTTAT
Found at i:989369 original size:14 final size:15
Alignment explanation
Indices: 989347--989423 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
989337 CAATCAAACA
989347 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
989361 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
989376 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
989396 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
989410 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
989424 ACTGACAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:989388 original size:20 final size:20
Alignment explanation
Indices: 989363--989402 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
989353 AATATTTTCC
*
989363 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
989383 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
989403 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:989408 original size:34 final size:35
Alignment explanation
Indices: 989351--989417 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
989341 CAAACACCAG
*
989351 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
989386 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
989418 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1000552 original size:13 final size:13
Alignment explanation
Indices: 1000534--1000559 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1000524 GAAATTAAAA
1000534 TGGAAAAGTAAGG
1 TGGAAAAGTAAGG
1000547 TGGAAAAGTAAGG
1 TGGAAAAGTAAGG
1000560 CCAACATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (13 bp):
TGGAAAAGTAAGG
Found at i:1016296 original size:25 final size:25
Alignment explanation
Indices: 1016248--1016296 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1016238 CAACTATACT
* **
1016248 AATTTTTAACTGTAAAAATGAATTA
1 AATTTTTAACAGTAAAAACCAATTA
*
1016273 AATTTTTAACAGTAAGAACCAATT
1 AATTTTTAACAGTAAAAACCAATT
1016297 TACTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTTTTAACAGTAAAAACCAATTA
Done.