Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 104 of 345
Found at i:28088773 original size:18 final size:19
Alignment explanation
Indices: 28088730--28088798 Score: 79
Period size: 18 Copynumber: 3.7 Consensus size: 19
28088720 GAAAGATCAG
28088730 TTGTTACTGAATAATTTAA
1 TTGTTACTGAATAATTTAA
* *
28088749 TTGTTACTGTAT-ATTTGA
1 TTGTTACTGAATAATTTAA
*
28088767 TTTTTACTGAATAATTT-A
1 TTGTTACTGAATAATTTAA
* *
28088785 CTGTTACTGGATAA
1 TTGTTACTGAATAA
28088799 CCGATCAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 27 0.64
19 15 0.36
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (19 bp):
TTGTTACTGAATAATTTAA
Found at i:28093046 original size:20 final size:20
Alignment explanation
Indices: 28093007--28093046 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28092997 AAATTAAAAA
* *
28093007 TTAAAAATTATTAAAATTAT
1 TTAAAAAGTATGAAAATTAT
*
28093027 TTAAAAAGTATGAAATTTAT
1 TTAAAAAGTATGAAAATTAT
28093047 AGTAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
TTAAAAAGTATGAAAATTAT
Found at i:28094326 original size:27 final size:28
Alignment explanation
Indices: 28094296--28094357 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
28094286 TTTAAGTGTA
28094296 ATTTATAAGAAA-AAGTT-TTTTTTTAAT
1 ATTTAT-AGAAATAAGTTATTTTTTTAAT
* *
28094323 ATTTATAGAAATGAGTTAATTTTTTTATT
1 ATTTATAGAAATAAGTT-ATTTTTTTAAT
28094352 ATTTAT
1 ATTTAT
28094358 TAAAAAGGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.17
27 10 0.33
29 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (28 bp):
ATTTATAGAAATAAGTTATTTTTTTAAT
Found at i:28094864 original size:126 final size:126
Alignment explanation
Indices: 28094724--28095226 Score: 748
Period size: 126 Copynumber: 4.0 Consensus size: 126
28094714 AGAAGACGTA
* * * *
28094724 TCTG-AAAAATAATTTTAAGAAGATGTTTTTAAACAAATAGTATCGAAAACGCTTCAAGCAGGAT
1 TCTGAAAAAATAATTTTAAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGAAT
* * *
28094788 GCA-T-TGCAAGCAAAAGTACTGAAAAAAGCTCCCACGTGGATGTTTTTTTTCTACAGTAGTT
66 GCACTAT-C-AGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
* * *
28094849 TCTGAAAAAATAATTTTGAA-AAGATGTTTTTGAACAAATAGTGTCAAAAACGTTTCAAGCAGAA
1 TCTGAAAAAATAATTTT-AAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGAA
* *
28094913 TGCACTATCAGCAAAAGTACTGAAAAAAGCTCTCACGTGGACGCT-TTTTTCCTACAGTTGTT
65 TGCACTATCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTT-CTACAGTAGTT
28094975 TCTGAAAAAATAATTTTAAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGAAT
1 TCTGAAAAAATAATTTTAAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGAAT
*
28095040 GCACTATCAGCAAAAGTACTGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGTT
66 GCACTATCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
** * *
28095101 TCTGAAAAAATAATTTTGGGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
1 TCTGAAAAAATAATTTTAAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGAAT
* *
28095166 -CTACTATCATCAAAAATACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
66 GC-ACTATCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
28095227 CCTATTTGGC
Statistics
Matches: 348, Mismatches: 22, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
125 12 0.03
126 326 0.94
127 9 0.03
128 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TCTGAAAAAATAATTTTAAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGAAT
GCACTATCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
Found at i:28101291 original size:21 final size:21
Alignment explanation
Indices: 28101267--28101317 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28101257 TTATTTATGT
28101267 TAATGTTATATATT-ATAAAAA
1 TAAT-TTATATATTCATAAAAA
* *
28101288 TAATATATTTATTCATAAAAA
1 TAATTTATATATTCATAAAAA
*
28101309 AAATTTATA
1 TAATTTATA
28101318 ATTTTTTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATTTATATATTCATAAAAA
Found at i:28102067 original size:31 final size:31
Alignment explanation
Indices: 28102030--28102107 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
28102020 GCTTGCCCCC
*
28102030 TAAACTTGTACAAAAA-TACCTAGCTGGTACT
1 TAAACTTGT-CAAAAAGTACATAGCTGGTACT
* *
28102061 TGAACTTGTCCAAAAAGTACATAGTTGGTACT
1 TAAACTTGT-CAAAAAGTACATAGCTGGTACT
*
28102093 TAAAATTGTCAAAAA
1 TAAACTTGTCAAAAA
28102108 AAGTATACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 20 0.50
32 20 0.50
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TAAACTTGTCAAAAAGTACATAGCTGGTACT
Found at i:28102102 original size:32 final size:31
Alignment explanation
Indices: 28102030--28102108 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
28102020 GCTTGCCCCC
* *
28102030 TAAACTTGTACAAAAATACCTAGCTGGTACT
1 TAAACTTGTCCAAAAATACATAGCTGGTACT
* *
28102061 TGAACTTGTCCAAAAAGTACATAGTTGGTACT
1 TAAACTTGTCCAAAAA-TACATAGCTGGTACT
* *
28102093 TAAAATTGTCAAAAAA
1 TAAACTTGTCCAAAAA
28102109 AGTATACTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TAAACTTGTCCAAAAATACATAGCTGGTACT
Found at i:28103209 original size:31 final size:32
Alignment explanation
Indices: 28103154--28103217 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
28103144 TGTAAAACTG
28103154 TTAAAGTTTTAGAAAGTTTAAATTAATA-ATTTC
1 TTAAAGTTTTAG--AGTTTAAATTAATAGATTTC
28103187 TTAAAGTTTTAG-GTGTTAAATTAATAGATTT
1 TTAAAGTTTTAGAGT-TTAAATTAATAGATTT
28103218 TAAGCTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.07
31 11 0.38
32 4 0.14
33 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (32 bp):
TTAAAGTTTTAGAGTTTAAATTAATAGATTTC
Found at i:28104846 original size:51 final size:49
Alignment explanation
Indices: 28104786--28104925 Score: 199
Period size: 49 Copynumber: 2.8 Consensus size: 49
28104776 AAGCTATCTA
* * *
28104786 GTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGG
1 GTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCG
* *
28104837 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCG
1 GTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCG
* *
28104886 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
28104926 TCACAATAGT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 43 0.54
50 1 0.01
51 36 0.45
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (49 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCG
Found at i:28105259 original size:14 final size:16
Alignment explanation
Indices: 28105227--28105265 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
28105217 ATTTACATAA
*
28105227 CATATATCACATATTT
1 CATATATCACATATGT
28105243 CATATATCAC-T-TGT
1 CATATATCACATATGT
28105257 CATATATCA
1 CATATATCA
28105266 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
CATATATCACATATGT
Found at i:28107739 original size:15 final size:15
Alignment explanation
Indices: 28107719--28107770 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28107709 ACTACAAAAC
28107719 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28107734 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
28107753 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
28107768 ATT
1 ATT
28107771 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:28111053 original size:43 final size:43
Alignment explanation
Indices: 28111006--28111139 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 43
28110996 TGTGTATGTT
* * *
28111006 AGTATAATTACTTCGGCTTGTCTGATAATGCACTGTCTGTGCC
1 AGTATAATTACTTCGGCTTATCTGATAATGCACTATGTGTGCC
* * * * * *
28111049 AGTATAATTGCTTTGGCTTACCTGATGATGCATTATGTCTGCC
1 AGTATAATTACTTCGGCTTATCTGATAATGCACTATGTGTGCC
* * * *
28111092 AATAT-ATTTCTTCGGTTTATCCGATAATGCACTATGTGTGCC
1 AGTATAATTACTTCGGCTTATCTGATAATGCACTATGTGTGCC
28111134 AGTATA
1 AGTATA
28111140 TTCCATCAGT
Statistics
Matches: 71, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 33 0.46
43 38 0.54
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (43 bp):
AGTATAATTACTTCGGCTTATCTGATAATGCACTATGTGTGCC
Found at i:28111152 original size:42 final size:42
Alignment explanation
Indices: 28111076--28111158 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
28111066 TTACCTGATG
* * * *
28111076 ATGCATTATGTCTGCCAATATATTTCTTCGGTTTATCCGATA
1 ATGCACTATGTCTGCCAATATATTCCATCAGTTTATCCGATA
* * *
28111118 ATGCACTATGTGTGCCAGTATATTCCATCAGTTTATTCGAT
1 ATGCACTATGTCTGCCAATATATTCCATCAGTTTATCCGAT
28111159 GATGAACGAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (42 bp):
ATGCACTATGTCTGCCAATATATTCCATCAGTTTATCCGATA
Found at i:28114699 original size:31 final size:31
Alignment explanation
Indices: 28114642--28114700 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28114632 ACATAGTAAC
* *
28114642 TTAAATAAAAACTTTCGAATAATTCAATAAT
1 TTAAAGAAAAACTTTCAAATAATTCAATAAT
* *
28114673 TTAAAGAAAAACTTTTAAATAGTTCAAT
1 TTAAAGAAAAACTTTCAAATAATTCAAT
28114701 GACCGTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (31 bp):
TTAAAGAAAAACTTTCAAATAATTCAATAAT
Found at i:28125849 original size:5 final size:5
Alignment explanation
Indices: 28125839--28125864 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28125829 GTGTGTTCTA
28125839 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
28125865 TTCACAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:28128763 original size:46 final size:44
Alignment explanation
Indices: 28128663--28128770 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
28128653 TGTCTTTGAC
** * * *
28128663 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
* *
28128707 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA--TATAAT
28128753 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
28128771 TTTTGTTCTG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
Found at i:28131572 original size:13 final size:13
Alignment explanation
Indices: 28131554--28131598 Score: 90
Period size: 13 Copynumber: 3.5 Consensus size: 13
28131544 ATAGTTTAAT
28131554 AATAAAATAAAGA
1 AATAAAATAAAGA
28131567 AATAAAATAAAGA
1 AATAAAATAAAGA
28131580 AATAAAATAAAGA
1 AATAAAATAAAGA
28131593 AATAAA
1 AATAAA
28131599 TGAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:28131605 original size:9 final size:9
Alignment explanation
Indices: 28131558--28131613 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
28131548 TTTAATAATA
28131558 AAATAAA-G
1 AAATAAATG
28131566 AAATAAAAT-
1 AAAT-AAATG
* *
28131575 AAAGAAATA
1 AAATAAATG
28131584 AAATAAA-G
1 AAATAAATG
28131592 AAATAAATG
1 AAATAAATG
*
28131601 AAATAAAAG
1 AAATAAATG
28131610 AAAT
1 AAAT
28131614 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 15 0.38
9 25 0.62
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (9 bp):
AAATAAATG
Found at i:28132884 original size:15 final size:15
Alignment explanation
Indices: 28132861--28132908 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
28132851 TATCAAATTT
28132861 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
28132876 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
28132891 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
28132905 ATAT
1 ATAT
28132909 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:28133430 original size:23 final size:23
Alignment explanation
Indices: 28133403--28133460 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
28133393 TAATATTCCG
*
28133403 GGTGTGTTTGGGTTGGATATTTT
1 GGTGTGTTTGGGTTGGATATTCT
28133426 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
28133449 GGTGTGTTTGGG
1 GGTGTGTTTGGG
28133461 AGGAATCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.07, C:0.02, G:0.43, T:0.48
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:28139098 original size:13 final size:13
Alignment explanation
Indices: 28139080--28139109 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28139070 CGATCTGTTC
28139080 ATATTAATTTTTT
1 ATATTAATTTTTT
*
28139093 ATATTATTTTTTT
1 ATATTAATTTTTT
28139106 ATAT
1 ATAT
28139110 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:28140612 original size:16 final size:16
Alignment explanation
Indices: 28140581--28140617 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28140571 ATGTGAAGAA
28140581 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
28140597 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
28140613 TATTA
1 TATTA
28140618 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:28147389 original size:2 final size:2
Alignment explanation
Indices: 28147382--28147417 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28147372 CTAATTGCTC
28147382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28147418 GTATTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28147949 original size:16 final size:15
Alignment explanation
Indices: 28147911--28147950 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
28147901 TTGATTTTCC
*
28147911 TTTAATTTTAATTAT
1 TTTAATTTTAATAAT
*
28147926 TTTCATTTTACATAAT
1 TTTAATTTTA-ATAAT
28147942 TTTAATTTT
1 TTTAATTTT
28147951 TAATTTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAATTTTAATAAT
Found at i:28157745 original size:13 final size:13
Alignment explanation
Indices: 28157727--28157752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28157717 CCTATTTCAT
28157727 TCCACCCTTCTCC
1 TCCACCCTTCTCC
28157740 TCCACCCTTCTCC
1 TCCACCCTTCTCC
28157753 CTCTTTTCAG
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:0.08, C:0.62, G:0.00, T:0.31
Consensus pattern (13 bp):
TCCACCCTTCTCC
Found at i:28157759 original size:53 final size:53
Alignment explanation
Indices: 28157687--28157792 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
28157677 CTTCTTTCGT
* * *
28157687 TCCACCCTTCTCCTTCTTTTCAGTCTGGTTCCTATTTCATTCCACCCTTCTCC
1 TCCACCCTTCTCCCTCTTTTCAGTCTGATTCCCATTTCATTCCACCCTTCTCC
* * *
28157740 TCCACCCTTCTCCCTCTTTTCAGTCTTATTCCCATTTCGTTTCACCCTTCTCC
1 TCCACCCTTCTCCCTCTTTTCAGTCTGATTCCCATTTCATTCCACCCTTCTCC
28157793 CTCTTTTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.09, C:0.42, G:0.05, T:0.43
Consensus pattern (53 bp):
TCCACCCTTCTCCCTCTTTTCAGTCTGATTCCCATTTCATTCCACCCTTCTCC
Found at i:28160800 original size:12 final size:12
Alignment explanation
Indices: 28160783--28160809 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28160773 ACAATAATTA
28160783 TTGGGTATTGTT
1 TTGGGTATTGTT
28160795 TTGGGTATTGTT
1 TTGGGTATTGTT
28160807 TTG
1 TTG
28160810 CATAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (12 bp):
TTGGGTATTGTT
Found at i:28161052 original size:32 final size:32
Alignment explanation
Indices: 28161011--28161075 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
28161001 CAAGATGACG
28161011 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
1 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
* *
28161043 AGATAGATGTAAAGGCTAAGGGCAAATATAAA
1 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
28161075 A
1 A
28161076 CAAATTGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (32 bp):
AGATAGATGTAAAAGCCAAGGGCAAATATAAA
Found at i:28161429 original size:2 final size:2
Alignment explanation
Indices: 28161424--28161448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28161414 GTGAAACAGT
28161424 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28161449 TAGTACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28165284 original size:17 final size:17
Alignment explanation
Indices: 28165264--28165296 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28165254 ATTAAGAATG
28165264 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
28165281 TTATTAAATTATATTT
1 TTATTAAATTATATTT
28165297 AATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:28165530 original size:44 final size:46
Alignment explanation
Indices: 28165467--28165556 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 46
28165457 TATTACAACA
* *
28165467 TCATTCCATTTAACCAAACA-TAAGAA-TAC-TATTACAGTTCTATT
1 TCATTCCATTCAACCAAACAGT-AGAATTACTTATTACAGCTCTATT
*
28165511 TCATTCCATTCAACCAAACAGTTGAATTACTTATTACAGCTCTATT
1 TCATTCCATTCAACCAAACAGTAGAATTACTTATTACAGCTCTATT
28165557 CAATTACAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 22 0.55
45 4 0.10
46 14 0.35
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.37
Consensus pattern (46 bp):
TCATTCCATTCAACCAAACAGTAGAATTACTTATTACAGCTCTATT
Found at i:28165564 original size:16 final size:16
Alignment explanation
Indices: 28165543--28165583 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
28165533 TGAATTACTT
*
28165543 ATTACAGCTCTATTCA
1 ATTACAGCCCTATTCA
*
28165559 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCA
*
28165575 ATTATAGCC
1 ATTACAGCC
28165584 AATCTGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCCCTATTCA
Found at i:28168360 original size:57 final size:57
Alignment explanation
Indices: 28168238--28168412 Score: 228
Period size: 57 Copynumber: 3.0 Consensus size: 57
28168228 TAGCCCAATT
* * * *
28168238 ATAAGCTTATAAAGGTAAAAAAAACCAAAATAAAGGTCAAAATTTGCAGTTA-TTTTTGA
1 ATAAGCTTATAAAGGT--GAAAAA-CAAAATAAAGGTCAAAATTTGCAATCACATTTTGA
*
28168297 ATAAGCTTATAAAGGTGAAAAACAAAATAAAGG-CAAAATTTCGCAATCACATTTTGC
1 ATAAGCTTATAAAGGTGAAAAACAAAATAAAGGTCAAAATTT-GCAATCACATTTTGA
* * *
28168354 ATAAGCTTATAATGGTGAAAAACAAAATAAAGGTCAAATTTTGCAACCACATTTTGA
1 ATAAGCTTATAAAGGTGAAAAACAAAATAAAGGTCAAAATTTGCAATCACATTTTGA
28168411 AT
1 AT
28168413 TTTAAGGTTG
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
55 8 0.08
56 16 0.15
57 57 0.55
58 7 0.07
59 16 0.15
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.27
Consensus pattern (57 bp):
ATAAGCTTATAAAGGTGAAAAACAAAATAAAGGTCAAAATTTGCAATCACATTTTGA
Found at i:28170011 original size:20 final size:21
Alignment explanation
Indices: 28169988--28170026 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28169978 TATTATCATT
28169988 AAATAAA-ATAAAAAATTTAA
1 AAATAAATATAAAAAATTTAA
*
28170008 AAATAAATATAAATAATTT
1 AAATAAATATAAAAAATTT
28170027 TATTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATATAAAAAATTTAA
Found at i:28170021 original size:10 final size:10
Alignment explanation
Indices: 28169987--28170073 Score: 54
Period size: 10 Copynumber: 8.7 Consensus size: 10
28169977 ATATTATCAT
28169987 TAAATAAA-A
1 TAAATAAATA
28169996 TAAA-AAATTTA
1 TAAATAAA--TA
*
28170007 AAAATAAATA
1 TAAATAAATA
* *
28170017 TAAATAATTT
1 TAAATAAATA
**
28170027 TATTTAAATA
1 TAAATAAATA
* *
28170037 TAATTAATTA
1 TAAATAAATA
28170047 TAAATAAATA
1 TAAATAAATA
28170057 CT-AATAAATA
1 -TAAATAAATA
*
28170067 TTAATAA
1 TAAATAA
28170074 CTAGTATTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
10 44 0.73
11 5 0.08
12 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAATAAATA
Found at i:28170054 original size:20 final size:20
Alignment explanation
Indices: 28170008--28170061 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
28169998 AAAAATTTAA
* *
28170008 AAATAAATATAAATAATTTT
1 AAATAAATATAATTAATTAT
**
28170028 ATTTAAATATAATTAATTAT
1 AAATAAATATAATTAATTAT
28170048 AAATAAATACTAAT
1 AAATAAATA-TAAT
28170062 AAATATTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAAATATAATTAATTAT
Found at i:28170226 original size:2 final size:2
Alignment explanation
Indices: 28170219--28170254 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28170209 TTATACATAC
28170219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28170255 TGCTGTTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28171131 original size:21 final size:20
Alignment explanation
Indices: 28171076--28171132 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
28171066 CATTTTTCAG
*
28171076 ATTTTATATTAATGATTAAAGA
1 ATTTTATATTAA-AATTAAA-A
* *
28171098 ATTTAAATTTTAAAATTAAAA
1 ATTT-TATATTAAAATTAAAA
28171119 ATTTTGATATTAAA
1 ATTTT-ATATTAAA
28171133 TTAGAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 12 0.43
22 10 0.36
23 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTTTATATTAAAATTAAAA
Found at i:28171740 original size:21 final size:21
Alignment explanation
Indices: 28171697--28171740 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28171687 TTATATTATT
* *
28171697 TATATTATATAAAAATTTCAA
1 TATATTATATAAAAATATAAA
* *
28171718 TATATTATATTATAATATAAA
1 TATATTATATAAAAATATAAA
28171739 TA
1 TA
28171741 AAAATATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATTATATAAAAATATAAA
Found at i:28173087 original size:34 final size:33
Alignment explanation
Indices: 28173023--28173087 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
28173013 TAAAGTTTTT
***
28173023 AAAAATTTTAAGAGTTTAATGAATTTTTTTAAA
1 AAAAATTTTAAGAGTTTAATGAAAAATTTTAAA
*
28173056 AAAAATTATTAAGAGTTTAATTAAAAATTTTA
1 AAAAATT-TTAAGAGTTTAATGAAAAATTTTA
28173088 TATGATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (33 bp):
AAAAATTTTAAGAGTTTAATGAAAAATTTTAAA
Found at i:28177799 original size:44 final size:44
Alignment explanation
Indices: 28177749--28177832 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
28177739 GCAACACTAC
* *
28177749 TTTTGTATCTAAAGATAAGACCTCTAGCTTTTAATTTCATTTAA
1 TTTTGTATCTAAAGATAAGACCTCTAGCCTTTAAATTCATTTAA
* *
28177793 TTTTGTATCTAAAGATAAGATCTCTCGCCTTTAAATTCAT
1 TTTTGTATCTAAAGATAAGACCTCTAGCCTTTAAATTCAT
28177833 CACAAAGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (44 bp):
TTTTGTATCTAAAGATAAGACCTCTAGCCTTTAAATTCATTTAA
Found at i:28178875 original size:49 final size:49
Alignment explanation
Indices: 28178822--28178918 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
28178812 GTCCCGCATA
28178822 CTCATATACAGATATCATACATGTTATTACAAAGTAGTCAAATCATATT
1 CTCATATACAGATATCATACATGTTATTACAAAGTAGTCAAATCATATT
*
28178871 CTCATATACAGATATCATACATGTTATTACAAAGTAGTTAAATCATAT
1 CTCATATACAGATATCATACATGTTATTACAAAGTAGTCAAATCATAT
28178919 ATATAAACTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (49 bp):
CTCATATACAGATATCATACATGTTATTACAAAGTAGTCAAATCATATT
Found at i:28184175 original size:28 final size:28
Alignment explanation
Indices: 28184111--28184176 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
28184101 TACATGTTAT
* *
28184111 AAAAGTATTATAATATATTCTTAGTCTAA
1 AAAATTATTATAATATATTCTTA-TATAA
28184140 AAATATTATTATAATATATTCATT-TATAA
1 AAA-ATTATTATAATATATTC-TTATATAA
28184169 AAAATTAT
1 AAAATTAT
28184177 GGCCAAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 5 0.15
29 10 0.30
30 16 0.48
31 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (28 bp):
AAAATTATTATAATATATTCTTATATAA
Found at i:28186563 original size:21 final size:20
Alignment explanation
Indices: 28186519--28186563 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28186509 TATAAAAAAG
* * *
28186519 GAAAAAAGAAATAAAGGAGA
1 GAAAAAAGAAACAAAGCAAA
28186539 GAAAAAAGAAACAAAGCAAA
1 GAAAAAAGAAACAAAGCAAA
28186559 CGAAA
1 -GAAA
28186564 CAGAAAGCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.71, C:0.07, G:0.20, T:0.02
Consensus pattern (20 bp):
GAAAAAAGAAACAAAGCAAA
Found at i:28186612 original size:21 final size:21
Alignment explanation
Indices: 28186580--28186642 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
28186570 GCAGGGGAAG
*
28186580 GAAAGAGAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
28186601 GAAGGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
* *
28186622 GAAAGAAAAAAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
28186643 TCAAAGATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:28188619 original size:46 final size:46
Alignment explanation
Indices: 28188567--28188793 Score: 323
Period size: 46 Copynumber: 5.0 Consensus size: 46
28188557 AGTGTGCTCT
28188567 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28188613 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28188659 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
28188705 ATGACATGAAATGAATAAGACCATGGTTGAAAGATA-CATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
28188750 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
28188794 TCATGTCAAA
Statistics
Matches: 169, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
44 1 0.01
45 39 0.23
46 129 0.76
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:28194861 original size:12 final size:12
Alignment explanation
Indices: 28194844--28194868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28194834 TGCAAATGGA
28194844 TCATTTCCATTT
1 TCATTTCCATTT
28194856 TCATTTCCATTT
1 TCATTTCCATTT
28194868 T
1 T
28194869 TGGAAACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:28197845 original size:27 final size:28
Alignment explanation
Indices: 28197806--28197860 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
28197796 TATAACAGTT
28197806 TGCTCTTTCGGGTTAT-AAAAAAACCAC
1 TGCTCTTTCGGGTTATAAAAAAAACCAC
*
28197833 TGCTCTTTTGGGTTATAAAAAAAACCAC
1 TGCTCTTTCGGGTTATAAAAAAAACCAC
28197861 CCTTTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (28 bp):
TGCTCTTTCGGGTTATAAAAAAAACCAC
Found at i:28202616 original size:46 final size:46
Alignment explanation
Indices: 28202561--28202788 Score: 332
Period size: 46 Copynumber: 5.0 Consensus size: 46
28202551 AGTGTGCTCT
*
28202561 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28202607 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
28202653 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** * *
28202699 GTGATATGAAATGAATAAGACCATGGTTGAAATATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
28202745 ATGATA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
28202789 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:28203097 original size:16 final size:17
Alignment explanation
Indices: 28203076--28203108 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28203066 ATGATGGAGC
28203076 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
28203092 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
28203109 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:28203685 original size:46 final size:45
Alignment explanation
Indices: 28203618--28203738 Score: 156
Period size: 46 Copynumber: 2.6 Consensus size: 45
28203608 CGAGAGCTAG
*
28203618 TGTAAGACATGTCTAGGACATGCATCGGCCT-CGAGATGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTGCGAGATGT--GCCAA
* *
28203664 TGTAAGACATGTCTGGGACATGCATCGG-CTGTGAGATGTGTCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTGCGAGATGTGCCAA
*
28203708 TGTAATACCATGTCTGGGACATGGCATCGGC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC
28203739 ACGAACATGT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
44 10 0.15
45 16 0.24
46 41 0.61
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTGCGAGATGTGCCAA
Found at i:28204254 original size:12 final size:12
Alignment explanation
Indices: 28204237--28204261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28204227 GGTTTTATTA
28204237 TTTTGAATATGG
1 TTTTGAATATGG
28204249 TTTTGAATATGG
1 TTTTGAATATGG
28204261 T
1 T
28204262 ATGTGTAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TTTTGAATATGG
Found at i:28207377 original size:34 final size:34
Alignment explanation
Indices: 28207332--28207421 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 34
28207322 CAACTTGTCT
* *
28207332 AACTAGTGCTGGGCACACAATCGTCGATTTATCC
1 AACTAGAGCTGGGCACACAATCGTCGATTCATCC
* * * * *
28207366 AACTAGCGCTGGGCACAAACACCGTTGGTTCATCC
1 AACTAGAGCTGGGCACACA-ATCGTCGATTCATCC
*
28207401 AACTAGAGCTGGGCTCACAAT
1 AACTAGAGCTGGGCACACAAT
28207422 TATTATCATC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
34 18 0.40
35 27 0.60
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (34 bp):
AACTAGAGCTGGGCACACAATCGTCGATTCATCC
Found at i:28210311 original size:26 final size:26
Alignment explanation
Indices: 28210275--28210331 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
28210265 CATGAAATTC
28210275 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28210301 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28210327 TTATC
1 TTATC
28210332 GATTTGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28212167 original size:23 final size:22
Alignment explanation
Indices: 28212098--28212173 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
28212088 ACCTGATCAG
**
28212098 AATACGACACATAAAGTGCCTA
1 AATACGACACACGAAGTGCCTA
28212120 AA-ACGACACACGAAGTGCCT-
1 AATACGACACACGAAGTGCCTA
* *
28212140 GATACGACACACGAGGTGCCTAA
1 AATACGACACACGAAGTGCCT-A
28212163 AATACGACACA
1 AATACGACACA
28212174 TAAAGTGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 33 0.72
22 2 0.04
23 10 0.22
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (22 bp):
AATACGACACACGAAGTGCCTA
Found at i:28212186 original size:44 final size:42
Alignment explanation
Indices: 28212099--28212186 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 42
28212089 CCTGATCAGA
* *
28212099 ATACGACACATAAAGTGCCTAAAACGACACACGAAGTGCCTG
1 ATACGACACACAAAGTGCCTAAAACGACACACAAAGTGCCTG
* * * *
28212141 ATACGACACACGAGGTGCCTAAAATACGACACATAAAGTGTCTG
1 ATACGACACACAAAGTGCCT-AAA-ACGACACACAAAGTGCCTG
28212185 AT
1 AT
28212187 CGGTAAAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 17 0.45
43 3 0.08
44 18 0.47
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (42 bp):
ATACGACACACAAAGTGCCTAAAACGACACACAAAGTGCCTG
Found at i:28213639 original size:3 final size:3
Alignment explanation
Indices: 28213631--28213671 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28213621 ATATGAAACC
28213631 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28213672 TTAATATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28214498 original size:19 final size:19
Alignment explanation
Indices: 28214439--28214497 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
28214429 TTTGTTAAAT
28214439 ATTTTAATTAAATTTT-TTA
1 ATTTTAATT-AATTTTATTA
* *
28214458 GTTTTAGTT-A-TTTATTA
1 ATTTTAATTAATTTTATTA
28214475 ATTTTAATTAATTTTATT-
1 ATTTTAATTAATTTTATTA
28214493 ATTTT
1 ATTTT
28214498 TTTATTACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 6 0.18
19 13 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTAATTAATTTTATTA
Found at i:28219099 original size:19 final size:19
Alignment explanation
Indices: 28219077--28219121 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28219067 TTTTAGAATT
*
28219077 TTTTTTATTGT-ACTAATAA
1 TTTTTTATAGTAACTAAT-A
*
28219096 TTTTTTATAGTAATTAATA
1 TTTTTTATAGTAACTAATA
28219115 TTTTTTA
1 TTTTTTA
28219122 AAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTTATAGTAACTAATA
Found at i:28227531 original size:10 final size:10
Alignment explanation
Indices: 28227502--28227546 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
28227492 AATGACATTC
28227502 TAAATGATAAA
1 TAAA-GATAAA
28227513 TACAA-ATAAA
1 TA-AAGATAAA
*
28227523 TAAAGATAAT
1 TAAAGATAAA
28227533 TAAAGATAAA
1 TAAAGATAAA
28227543 TAAA
1 TAAA
28227547 TCCTAGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.07
10 24 0.80
11 2 0.07
12 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (10 bp):
TAAAGATAAA
Found at i:28228377 original size:96 final size:97
Alignment explanation
Indices: 28228207--28228393 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 97
28228197 ATTCTATTTA
* * * *
28228207 TTTATTTTTACTTAGGAATATATTGAACCTTTTGAAGTGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCACCCCA
* *
28228272 CCCCGGTTACTCAACCCAATACATTCGTAATT
66 CCCCAGTTACTCAACCCAACACATTCGTAATT
* * *
28228304 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGTCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCACCCCA
*
28228368 CCCCAGTTACTCAGCCCAACACATTC
66 CCCCAGTTACTCAACCCAACACATTC
28228394 TTAAAAATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
96 71 0.89
97 9 0.11
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCACCCCA
CCCCAGTTACTCAACCCAACACATTCGTAATT
Found at i:28229172 original size:18 final size:15
Alignment explanation
Indices: 28229139--28229179 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
28229129 TTAATATCTG
28229139 AAAATAATAAATAAT
1 AAAATAATAAATAAT
*
28229154 AAAATAAT-AA-GAT
1 AAAATAATAAATAAT
28229167 AAAATAA-AAATAA
1 AAAATAATAAATAA
28229180 AAATTGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:28235601 original size:10 final size:10
Alignment explanation
Indices: 28235582--28235641 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
28235572 TGAAATTCTA
28235582 AAAGATAAAT
1 AAAGATAAAT
28235592 ACAA-ATAAAT
1 A-AAGATAAAT
*
28235602 AAAGATAATT
1 AAAGATAAAT
28235612 AAAGATAAAT
1 AAAGATAAAT
28235622 AAAGATAAAT
1 AAAGATAAAT
28235632 GAAA-ATAAAT
1 -AAAGATAAAT
28235642 CCTAGAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:28237939 original size:30 final size:30
Alignment explanation
Indices: 28237892--28237964 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
28237882 ATTATGGAGC
* * *
28237892 ACACGATCGTGTTACACATACGGCCTGGCT
1 ACACGGTCGTGTGACACACACGGCCTGGCT
* *
28237922 ACACTGTCGTGTGACACACATGGCCTGGCT
1 ACACGGTCGTGTGACACACACGGCCTGGCT
28237952 ACACGGTCGTGTG
1 ACACGGTCGTGTG
28237965 TCACTTGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (30 bp):
ACACGGTCGTGTGACACACACGGCCTGGCT
Found at i:28240186 original size:92 final size:92
Alignment explanation
Indices: 28240024--28240208 Score: 316
Period size: 92 Copynumber: 2.0 Consensus size: 92
28240014 ACCAAACAAC
* * *
28240024 ACTTCCATCAACCAGCCACTATAAATTTAGTTACCAATCATCATTTTCATGCAAATAGCAACCCA
1 ACTTCCATCAACCAACCACCATAAATTTAGTTACCAATCATCATTTTCATGCAAATAACAACCCA
*
28240089 ACACATAATCAAGTCATACATTAAAAT
66 ACACATAATAAAGTCATACATTAAAAT
*
28240116 ACTTTCATCAACCAACCACCATAAATTTAGTTACCAATCATCATTTTCATGCAAATAACAACCCA
1 ACTTCCATCAACCAACCACCATAAATTTAGTTACCAATCATCATTTTCATGCAAATAACAACCCA
*
28240181 ACACATACTAAAGTCATACATTAAAAT
66 ACACATAATAAAGTCATACATTAAAAT
28240208 A
1 A
28240209 AGCACAAGAG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.27
Consensus pattern (92 bp):
ACTTCCATCAACCAACCACCATAAATTTAGTTACCAATCATCATTTTCATGCAAATAACAACCCA
ACACATAATAAAGTCATACATTAAAAT
Found at i:28240330 original size:27 final size:27
Alignment explanation
Indices: 28240292--28240346 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
28240282 ATGGAGGTGA
*
28240292 AAATACAAATAGAGTTCATATTTTTAT
1 AAATACAAATAGACTTCATATTTTTAT
28240319 AAATACAAATAGACTTCATATTTTTAT
1 AAATACAAATAGACTTCATATTTTTAT
28240346 A
1 A
28240347 CTTTGAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (27 bp):
AAATACAAATAGACTTCATATTTTTAT
Found at i:28242763 original size:30 final size:31
Alignment explanation
Indices: 28242726--28242802 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
28242716 ATCTACCGGC
* *
28242726 TATTATAAAAAATTATGA-AAATATTAATTAA
1 TATTATAAAAAATTA-AATAAATATTAAATAA
28242757 -ATTAT-AAAAATTAAATAAATATTAAATAA
1 TATTATAAAAAATTAAATAAATATTAAATAA
*
28242786 TATTA-AAAAAATAAAAT
1 TATTATAAAAAATTAAAT
28242803 TAATCCTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.03
29 20 0.50
30 19 0.47
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (31 bp):
TATTATAAAAAATTAAATAAATATTAAATAA
Found at i:28242782 original size:18 final size:19
Alignment explanation
Indices: 28242731--28242776 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
28242721 CCGGCTATTA
28242731 TAAA-AAATTATGAAAATAT
1 TAAATAAATTAT-AAAATAT
*
28242750 TAATTAAATTATAAAA-AT
1 TAAATAAATTATAAAATAT
28242768 TAAATAAAT
1 TAAATAAAT
28242777 ATTAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAATAAATTATAAAATAT
Found at i:28248334 original size:14 final size:15
Alignment explanation
Indices: 28248315--28248370 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
28248305 AATCTTCAAT
28248315 GATATG-CAATCTTA
1 GATATGACAATCTTA
28248329 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
28248346 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
28248364 GATATGA
1 GATATGA
28248371 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:28248359 original size:35 final size:37
Alignment explanation
Indices: 28248313--28248391 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
28248303 ATAATCTTCA
28248313 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
28248349 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
28248385 A-GATATG
1 ATGATATG
28248392 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:28248391 original size:17 final size:19
Alignment explanation
Indices: 28248313--28248384 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
28248303 ATAATCTTCA
28248313 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28248332 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28248349 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28248367 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
28248385 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:28248410 original size:22 final size:22
Alignment explanation
Indices: 28248313--28248407 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
28248303 ATAATCTTCA
28248313 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
28248332 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
28248349 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
28248367 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
28248389 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
28248408 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:28248697 original size:17 final size:17
Alignment explanation
Indices: 28248672--28248707 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28248662 ATATTTCCCA
*
28248672 AATTTTTTTATATATTTT
1 AATTTTTTAATA-ATTTT
28248690 AATTTTTTAATAATTTT
1 AATTTTTTAATAATTTT
28248707 A
1 A
28248708 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTTAATAATTTT
Found at i:28251147 original size:14 final size:14
Alignment explanation
Indices: 28251128--28251164 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28251118 TCGATACCTT
*
28251128 TTTGCATTCATGCA
1 TTTGCATTAATGCA
28251142 TTTGCATTAATGCA
1 TTTGCATTAATGCA
*
28251156 TTTTCATTA
1 TTTGCATTA
28251165 CATTACATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (14 bp):
TTTGCATTAATGCA
Found at i:28258050 original size:24 final size:24
Alignment explanation
Indices: 28258005--28258051 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28257995 ATATTAAAAG
*
28258005 ATATATATATAAAATGTATACATA
1 ATATATATATAAAATATATACATA
*
28258029 ATATA-ATATTAAAATATTTACAT
1 ATATATATA-TAAAATATATACAT
28258052 GGTATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATATATATAAAATATATACATA
Found at i:28258600 original size:39 final size:39
Alignment explanation
Indices: 28258557--28258631 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
28258547 AAGCTGATCT
*
28258557 CACTCCCCCATGCTACTTTGTTTTATTATTAATTAATCC
1 CACTCCCCCATGCCACTTTGTTTTATTATTAATTAATCC
28258596 CACTCCCCCATGCCACTTTGTTTTATTATTAATTAA
1 CACTCCCCCATGCCACTTTGTTTTATTATTAATTAA
28258632 AACCATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.24, C:0.28, G:0.05, T:0.43
Consensus pattern (39 bp):
CACTCCCCCATGCCACTTTGTTTTATTATTAATTAATCC
Found at i:28260124 original size:44 final size:44
Alignment explanation
Indices: 28260070--28260361 Score: 381
Period size: 44 Copynumber: 6.6 Consensus size: 44
28260060 TGTTATTTTT
* * *
28260070 GATCTGCTCTCTACCAATACAAAGACGCCAAATCTGTCATCTTC
1 GATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGTCATCTTC
* * * *
28260114 GATCTACTCTCCGCCACTACAGAGACGTCAAATCTGTTATCTTC
1 GATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGTCATCTTC
* * *
28260158 GATCTGCTCT-TCGCCACCACAAAGACGCCAAATCTGTTATCTTC
1 GATCTGCTCTCT-GCCACTACAGAGACGCCAAATCTGTCATCTTC
* *
28260202 GATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTC
1 GATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGTCATCTTC
* * *
28260246 GATCTGCTCTCTGCCGCTACAGAGACGCTAAATCTG-CTAACTTC
1 GATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGTC-ATCTTC
*
28260290 GATCTGCTCTCTACCACTACAGAGACGCCAAATCTGTCATCTTC
1 GATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGTCATCTTC
* * *
28260334 GATCTGCTCTCCGCCGCTGCAGAGACGC
1 GATCTGCTCTCTGCCACTACAGAGACGC
28260362 TCTTCGATCT
Statistics
Matches: 218, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
44 216 0.99
45 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (44 bp):
GATCTGCTCTCTGCCACTACAGAGACGCCAAATCTGTCATCTTC
Found at i:28260434 original size:44 final size:44
Alignment explanation
Indices: 28260375--28260568 Score: 343
Period size: 44 Copynumber: 4.4 Consensus size: 44
28260365 TCGATCTGCT
* *
28260375 CTACAAAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
1 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
*
28260419 CTACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
1 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
*
28260463 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCG
1 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
*
28260507 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCG
1 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
28260551 CTACAGAGACGCCAAATC
1 CTACAGAGACGCCAAATC
28260569 ATCTTGGATC
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 145 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.27
Consensus pattern (44 bp):
CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG
Found at i:28260507 original size:157 final size:157
Alignment explanation
Indices: 28260218--28260518 Score: 485
Period size: 157 Copynumber: 1.9 Consensus size: 157
28260208 CTCTCTGCCG
* * * *
28260218 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCTAAATCTGC
1 CTACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGC
*
28260283 TAACTTCGATCTGCTCTCTACCACTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGC
66 TAACTTCGATCTGCTCTCCACCACTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGC
*
28260348 CGCTGCAGAGACGCTCTTCGATCTGCT
131 CGCTACAGAGACGCTCTTCGATCTGCT
* *
28260375 CTACAAAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGT
1 CTACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGC
* * * * *
28260440 TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGC
66 TAACTTCGATCTGCTCTCCACCACTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGC
28260505 CGCTACAGAGACGC
131 CGCTACAGAGACGC
28260519 CAAATCTGTT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
157 131 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (157 bp):
CTACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGC
TAACTTCGATCTGCTCTCCACCACTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGC
CGCTACAGAGACGCTCTTCGATCTGCT
Found at i:28260521 original size:201 final size:201
Alignment explanation
Indices: 28260176--28260562 Score: 666
Period size: 201 Copynumber: 1.9 Consensus size: 201
28260166 CTTCGCCACC
* *
28260176 ACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTA
1 ACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGTTA
* *
28260241 TCTTCGATCTGCTCTCTGCCGCTACAGAGACGCTAAATCTGCTAACTTCGATCTGCTCTCTACCA
66 TCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTAACTTCGATCTGCTCTCTACCA
*
28260306 CTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGCCGCTGCAGAGACGCTCTTCGATC
131 CTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCTCTTCGATC
28260371 TGCTCT
196 TGCTCT
*
28260377 ACAAAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGTTA
1 ACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGTTA
* * * *
28260442 TCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCG
66 TCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTAACTTCGATCTGCTCTCTACCA
* *
28260507 CTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGC
131 CTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
28260563 CAAATCATCT
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 174 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.28
Consensus pattern (201 bp):
ACAAAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACACCAAATCTGTTA
TCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTAACTTCGATCTGCTCTCTACCA
CTACAGAGACGCCAAATCTGTCATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCTCTTCGATC
TGCTCT
Found at i:28260801 original size:61 final size:62
Alignment explanation
Indices: 28260687--28260809 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 62
28260677 TCATGTATCC
28260687 ATGCTTATGCCAAATAATTAGGATGCTATTATTGAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAGGATG--ATTATTGAAATGAATCAAATGCTCCTAACTAAATGTG
* *
28260751 ATGCTTTATGTCAAATAATTAGGATG-TTA-TGAAATGAATCAAATGTTCCTAACTAAATG
1 ATGC-TTATGCCAAATAATTAGGATGATTATTGAAATGAATCAAATGCTCCTAACTAAATG
28260810 AATGGTTATG
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 29 0.52
62 3 0.05
64 4 0.07
65 20 0.36
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (62 bp):
ATGCTTATGCCAAATAATTAGGATGATTATTGAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:28265022 original size:27 final size:27
Alignment explanation
Indices: 28264992--28265332 Score: 353
Period size: 27 Copynumber: 12.6 Consensus size: 27
28264982 TTAGTTTACC
28264992 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
28265019 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
28265046 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * **
28265073 AAATTACCAAAATACCCTTGGATTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
28265100 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * ** * *
28265127 AAATTACTAAAATAACTTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
28265154 AAATTACCAAAATACCACTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
28265181 AAATTACCAAAATACGCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
28265208 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** * *
28265235 AAATTACCAAAATAAACCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
** ***
28265262 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*** *
28265289 AAATTATGGAAATA-CCCTGGACTTGTA
1 AAATTACCAAAATACCCCTGG-TTTGTA
*
28265316 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
28265333 TTAATTTACA
Statistics
Matches: 260, Mismatches: 51, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
26 4 0.02
27 254 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:28265345 original size:27 final size:27
Alignment explanation
Indices: 28265315--28265376 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
28265305 CTGGACTTGT
*
28265315 AAAATTACCAAAGTACCCTTAATTTAC
1 AAAATTACCAAAGTACCCTCAATTTAC
*** *
28265342 AAAATTACCATTTTACCCTCGATTTAC
1 AAAATTACCAAAGTACCCTCAATTTAC
28265369 AAAATTAC
1 AAAATTAC
28265377 TGAAATACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAGTACCCTCAATTTAC
Found at i:28265385 original size:27 final size:27
Alignment explanation
Indices: 28265262--28265387 Score: 78
Period size: 27 Copynumber: 4.7 Consensus size: 27
28265252 CTGATTTGTG
* **
28265262 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACTTACA
* **
28265289 AAATTA-TGGAAATACCCTGGACTTGTA
1 AAATTACT-GAAATACCCTCGACTTACA
* ** *
28265316 AAATTAC-CAAAGTACCCTTAATTTACA
1 AAATTACTGAAA-TACCCTCGACTTACA
* ** *
28265343 AAATTAC-CATTTTACCCTCGATTTACA
1 AAATTACTGA-AATACCCTCGACTTACA
28265370 AAATTACTGAAATACCCT
1 AAATTACTGAAATACCCT
28265388 TGTAGGGTAG
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
26 4 0.05
27 74 0.94
28 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACTTACA
Found at i:28265528 original size:81 final size:81
Alignment explanation
Indices: 28265380--28265537 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
28265370 AAATTACTGA
* * *
28265380 AATACCCTTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTGT
1 AATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCTGT
28265445 AGGGTAGAATTATCGC
66 AGGGTAGAATTATCGC
*
28265461 AATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCTGT
1 AATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCTGT
*
28265526 AGGGTGGAATTA
66 AGGGTAGAATTA
28265538 CCGAGATACT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (81 bp):
AATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCTGT
AGGGTAGAATTATCGC
Found at i:28265546 original size:27 final size:27
Alignment explanation
Indices: 28265371--28265546 Score: 235
Period size: 27 Copynumber: 6.5 Consensus size: 27
28265361 CGATTTACAA
* *
28265371 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28265398 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
28265425 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28265452 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28265479 AATTATCGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
28265506 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28265533 AATTACCGAGATAC
1 AATTACCGAAATAC
28265547 TTTGTGGGGT
Statistics
Matches: 131, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 131 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28266044 original size:22 final size:22
Alignment explanation
Indices: 28265992--28266056 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28265982 TTAAAGCCTT
* *
28265992 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
28266014 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
28266036 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
28266057 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:28266251 original size:26 final size:27
Alignment explanation
Indices: 28266214--28266288 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
28266204 TATTCCGTTA
* *
28266214 AGTGGCTTTGCCACATTATCTGT-TCT
1 AGTGGCTCTGCCACAATATCTGTATCT
* *
28266240 GGTGGCTCTGCCATAATATCTGTATCT
1 AGTGGCTCTGCCACAATATCTGTATCT
* *
28266267 AGTGACTCTGTCACAATATCTG
1 AGTGGCTCTGCCACAATATCTG
28266289 ATAACTGAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 19 0.47
27 21 0.52
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (27 bp):
AGTGGCTCTGCCACAATATCTGTATCT
Found at i:28266458 original size:19 final size:19
Alignment explanation
Indices: 28266436--28266493 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
28266426 TTCTGACTTT
28266436 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
28266455 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
28266467 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
28266486 TGATTCTG
1 TGATTCTG
28266494 ATTCTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:28266463 original size:6 final size:6
Alignment explanation
Indices: 28266425--28266544 Score: 68
Period size: 6 Copynumber: 19.3 Consensus size: 6
28266415 TTGCATTCAC
* * *
28266425 ATTCTG ACTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
28266475 -TTACCTG ATACTG ATTCTG ATTCTG ATTTTG -TCACCTG ATTTTA ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
28266525 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
28266545 AATGTTTCTT
Statistics
Matches: 86, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
5 6 0.07
6 63 0.73
7 14 0.16
8 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28266470 original size:31 final size:31
Alignment explanation
Indices: 28266425--28266560 Score: 150
Period size: 31 Copynumber: 4.4 Consensus size: 31
28266415 TTGCATTCAC
*
28266425 ATTCTGACTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTTACCTGATACTG
*
28266457 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * ** *
28266488 ATTCTGATTCTGATTTTGTCACCTGATTTTA
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
28266519 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTCTGATTCT-GTTACCTGATACTG
* *
28266549 TTTCTTATTCTG
1 ATTCTGATTCTG
28266561 TAATGGGTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
30 16 0.18
31 65 0.72
32 9 0.10
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:28268515 original size:27 final size:27
Alignment explanation
Indices: 28268485--28268843 Score: 326
Period size: 27 Copynumber: 13.3 Consensus size: 27
28268475 TTAGTTTACC
*
28268485 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
28268512 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
28268539 AAATCACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * **
28268566 AAATTACCAAAATACCATTGGATTACA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
28268593 AAATTACCAAAATACCCTTGGTTTGAA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * * * *
28268620 AAATTACTAAAATAACTTTTGTTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * * *
28268647 AAATTACTAAAATACCTTTTGTTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
28268674 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
28268701 AAATTACCAAAATACTCC-TAGTTTGTA
1 AAATTACCAAAATAC-CCTTGGTTTGTA
* * *
28268728 AAATTACCAAAATAAACC-TGATTTGTT
1 AAATTACCAAAAT-ACCCTTGGTTTGTA
** * *** *
28268755 AAATTACTGAAATACCCTCGACCTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*** * **
28268782 AAATTATGGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
28268809 AAATTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
28268836 GAATTACC
1 AAATTACC
28268844 GTTTTACCCT
Statistics
Matches: 277, Mismatches: 52, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
26 3 0.01
27 271 0.98
28 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTGTA
Found at i:28268894 original size:27 final size:27
Alignment explanation
Indices: 28268864--28269057 Score: 225
Period size: 27 Copynumber: 7.2 Consensus size: 27
28268854 TGATTTACAA
*
28268864 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
28268891 AATTA-TCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
28268918 AATTACTGAAATACCCTTGTAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
*
28268945 AATTA-TCGCAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
28268972 AATTA-TCGAAATACCTCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
28268999 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
28269026 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
28269052 AATTAC
1 AATTAC
28269058 CATTTTACCC
Statistics
Matches: 145, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
26 17 0.12
27 126 0.87
28 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:28269030 original size:81 final size:81
Alignment explanation
Indices: 28268873--28269023 Score: 266
Period size: 81 Copynumber: 1.9 Consensus size: 81
28268863 AAATTACTGA
* *
28268873 AATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGT
1 AATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGT
28268938 AGGGTAAAATTATCGC
66 AGGGTAAAATTATCGC
* *
28268954 AATACCCCTGTAGGGTAGAATTATCGAAATACCTCTGTAGGGTAGAATTACTAAAATACCCCTGT
1 AATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGT
28269019 AGGGT
66 AGGGT
28269024 GGAATTACCG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (81 bp):
AATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGT
AGGGTAAAATTATCGC
Found at i:28269040 original size:81 final size:80
Alignment explanation
Indices: 28268862--28269040 Score: 259
Period size: 81 Copynumber: 2.2 Consensus size: 80
28268852 CTTGATTTAC
* *
28268862 AAAATTACTGAAATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTGA
1 AAAATTACCG-AATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAA
*
28268927 AATACCCTTGTAGGGT
65 AATACCCCTGTAGGGT
* * *
28268943 AAAATTATCGCAATACCCCTGTAGGGTAGAATTATCGAAATACCTCTGTAGGGTAGAATTACTAA
1 AAAATTACCG-AATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAA
28269008 AATACCCCTGTAGGGT
65 AATACCCCTGTAGGGT
**
28269024 GGAATTACCGAGATACC
1 AAAATTACCGA-ATACC
28269041 TTGTGGGGTA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 1 0.01
81 86 0.99
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (80 bp):
AAAATTACCGAATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTAAA
ATACCCCTGTAGGGT
Found at i:28269537 original size:22 final size:22
Alignment explanation
Indices: 28269485--28269549 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28269475 TTAAAGCCTT
* *
28269485 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
28269507 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
28269529 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
28269550 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:28269744 original size:26 final size:27
Alignment explanation
Indices: 28269708--28269781 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
28269698 ATTCTGTTAA
* *
28269708 GTGGCTTTGCCACATTATCTGT-TCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
28269734 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
* *
28269761 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
28269782 ATGACTGAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 20 0.47
27 23 0.53
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:28269956 original size:6 final size:6
Alignment explanation
Indices: 28269918--28270074 Score: 117
Period size: 6 Copynumber: 25.3 Consensus size: 6
28269908 TTGCATTCAC
* * *
28269918 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
28269968 -TTACCTG ATACTG ATTTTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
*
28270018 ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTG ATTCT-
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
28270066 AGTTCTG AT
1 A-TTCTG AT
28270075 AATGTTTCTT
Statistics
Matches: 122, Mismatches: 14, Indels: 30
0.73 0.08 0.18
Matches are distributed among these distances:
5 8 0.07
6 92 0.75
7 18 0.15
8 4 0.03
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28269964 original size:31 final size:31
Alignment explanation
Indices: 28269918--28270060 Score: 202
Period size: 31 Copynumber: 4.6 Consensus size: 31
28269908 TTGCATTCAC
28269918 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
28269950 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
28269981 ATTTTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
28270012 ATTCTGATTCTGATTCTGATT--CTG-TCACCTG
1 ATTCTGATTTTGATTCTG-TTACCTGAT-A-CTG
*
28270043 ATTCTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTG
28270061 ATTCTAGTTC
Statistics
Matches: 105, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.01
30 4 0.04
31 91 0.87
32 9 0.09
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:28269982 original size:37 final size:37
Alignment explanation
Indices: 28269941--28270063 Score: 159
Period size: 37 Copynumber: 3.5 Consensus size: 37
28269931 ATTCTGTTAC
28269941 CTGATACTGATTCTGATTTTGATTCTGTTACCTGATA
1 CTGATACTGATTCTGATTTTGATTCTGTTACCTGATA
28269978 CTG--A-T--TT-TGATTTTGATTCTGTTACCTGATA
1 CTGATACTGATTCTGATTTTGATTCTGTTACCTGATA
* * * *
28270009 CTGATTCTGATTCTGATTCTGATTCTGTCACCTGATT
1 CTGATACTGATTCTGATTTTGATTCTGTTACCTGATA
*
28270046 CTGATTCTGATTCTGATT
1 CTGATACTGATTCTGATT
28270064 CTAGTTCTGA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
31 27 0.36
32 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 42 0.55
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (37 bp):
CTGATACTGATTCTGATTTTGATTCTGTTACCTGATA
Found at i:28270006 original size:25 final size:24
Alignment explanation
Indices: 28269941--28270075 Score: 96
Period size: 25 Copynumber: 5.5 Consensus size: 24
28269931 ATTCTGTTAC
* *
28269941 CTGATACTGATTCTGATTTTGATT
1 CTGATTCTGATACTGATTTTGATT
28269965 CTG-TTACCTGATACTGATTTTGATT
1 CTGATT--CTGATACTGATTTTGATT
* * **
28269990 TTGATTCTGTTACCTGATACTGATT
1 CTGATTCTGATA-CTGATTTTGATT
* * *
28270015 CTGATTCTGATTCTGATTCTG-TCAC
1 CTGATTCTGATACTGATTTTGAT--T
* *
28270040 CTGATTCTGATTCTGATTCTGATT
1 CTGATTCTGATACTGATTTTGATT
28270064 CT-AGTTCTGATA
1 CTGA-TTCTGATA
28270076 ATGTTTCTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.03
24 25 0.28
25 59 0.66
26 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.47
Consensus pattern (24 bp):
CTGATTCTGATACTGATTTTGATT
Found at i:28276196 original size:21 final size:22
Alignment explanation
Indices: 28276162--28276206 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28276152 TTTCCATTTC
* *
28276162 TCAGCCTCTGACCTTTGA-GCA
1 TCAGCCTCTAACCTTAGATGCA
*
28276183 TCAGCGTCTAACCTTAGATGCA
1 TCAGCCTCTAACCTTAGATGCA
28276205 TC
1 TC
28276207 TTCTCTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (22 bp):
TCAGCCTCTAACCTTAGATGCA
Found at i:28279655 original size:10 final size:10
Alignment explanation
Indices: 28279644--28279678 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
28279634 ATATTAAAAG
* *
28279644 ATATATATAG
1 ATATAGATAT
28279654 ATATAGATAT
1 ATATAGATAT
28279664 ATATAGATAT
1 ATATAGATAT
28279674 ATATA
1 ATATA
28279679 AAATGTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (10 bp):
ATATAGATAT
Found at i:28279663 original size:16 final size:16
Alignment explanation
Indices: 28279642--28279674 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28279632 CAATATTAAA
28279642 AGATATATATAGATAT
1 AGATATATATAGATAT
28279658 AGATATATATAGATAT
1 AGATATATATAGATAT
28279674 A
1 A
28279675 TATAAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (16 bp):
AGATATATATAGATAT
Found at i:28279700 original size:23 final size:24
Alignment explanation
Indices: 28279661--28279706 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
28279651 TAGATATAGA
*
28279661 TATATATAGATATATA-TAAAATG
1 TATACATAGATATATATTAAAATG
28279684 TATACATA-ATATAATATTAAAAT
1 TATACATAGATAT-ATATTAAAAT
28279707 ATTTACATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACATAGATATATATTAAAATG
Found at i:28281797 original size:78 final size:78
Alignment explanation
Indices: 28281513--28281796 Score: 435
Period size: 78 Copynumber: 3.6 Consensus size: 78
28281503 CGAAGAAACA
** * * * * *
28281513 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGTAGATCTAACCTTCATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
28281578 GCAGATCCAAGAT
66 GCAGATCCAAGAT
28281591 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
28281656 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * *
28281669 GATTTGGCATCTTTGTATTAGACGGGGTGAAGATCGAAGACATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
*
28281733 AGCAGATCCAAAAT
65 AGCAGATCCAAGAT
*
28281747 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAGCAGAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGAT
28281797 TTGGCTTTCA
Statistics
Matches: 188, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
77 1 0.01
78 187 0.99
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:28281988 original size:78 final size:78
Alignment explanation
Indices: 28281878--28282172 Score: 466
Period size: 78 Copynumber: 3.8 Consensus size: 78
28281868 CGAAGAAACA
** * * * * * *
28281878 GATTTGGCATCTCCATATTCGATGGAGAGCAGATCAAAGACATAGCAGATTTGACCTTCATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
28281943 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
28281956 GATTTGGCATCTCTGTAATAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
28282021 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
28282034 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGAT-TGGACCTTTATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
28282098 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
28282112 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
28282173 GTGTTTACAT
Statistics
Matches: 199, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
77 1 0.01
78 197 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:28282099 original size:365 final size:365
Alignment explanation
Indices: 28281418--28282201 Score: 1302
Period size: 365 Copynumber: 2.2 Consensus size: 365
28281408 GTAGCAGGCT
* * * *
28281418 AAAG-CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAAGCGGATCCAAGATAATTTAACATCT
1 AAAGACATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCT
* *
28281482 CTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGAT
66 CTGTACTGTCAAAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGAT
* * *
28281547 CGAAGACATAGTAGATCTAACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAG
131 CAAAGACATAGCAGATCTAACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTAATAG
*
28281612 ACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
196 ACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
* *
28281677 ATCTTTGTATTAGACGGGGTGAAGATCGAAGACATAACAGATTGGACCTTCATTGAAGCAGATCC
261 ATCTCTGTATTAGACGGGGAGAAGATCGAAGACATAACAGATTGGACCTTCATTGAAGCAGATCC
28281742 AAAATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
326 AAAATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* * **
28281782 AAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCT
1 AAAGACATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCT
* *
28281847 TTGTACTGTCAAAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGAT
66 CTGTACTGTCAAAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGAT
* *
28281912 CAAAGACATAGCAGATTTGACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTAATAG
131 CAAAGACATAGCAGATCTAACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTAATAG
28281977 ACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
196 ACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
* *
28282042 ATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGATTGGACCTTTATTGAAGCAGATCC
261 ATCTCTGTATTAGACGGGGAGAAGATCGAAGACATAACAGATTGGACCTTCATTGAAGCAGATCC
*
28282107 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
326 AAAATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* * * *
28282147 GAAGACATAGCAGATCTGACCTTCATGTGTTTAC-ATAGAAGCAGATCTAAGATGA
1 AAAGACATAGCAGATTTGACCTTCACGTGTTTACGCT-GAAGCAGATCTAAGATGA
28282202 CAGATTTGGC
Statistics
Matches: 389, Mismatches: 29, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
364 5 0.01
365 384 0.99
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (365 bp):
AAAGACATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCT
CTGTACTGTCAAAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGAT
CAAAGACATAGCAGATCTAACCTTCATTAAAGCAGATCCAAGATGATTTGGCATCTCTGTAATAG
ACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
ATCTCTGTATTAGACGGGGAGAAGATCGAAGACATAACAGATTGGACCTTCATTGAAGCAGATCC
AAAATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
Found at i:28282265 original size:45 final size:45
Alignment explanation
Indices: 28282112--28282385 Score: 293
Period size: 45 Copynumber: 6.1 Consensus size: 45
28282102 GATCCAAGAT
*
28282112 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATAACA
* * * * * ** * * *
28282159 GATCTGACCT-TCATGTGTT-TACATAGAAGCAGATCTAAGATGACA
1 GATTTGGCATCTC-TGTATTAGAC-GGGGAGCAGATCGAAGATAACA
* *
28282204 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
** * *
28282249 GATTTGGCATCTCTGTATTAGACGATGAGCAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
*
28282293 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* * * *
28282338 GATTCGGCCTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
28282383 GAT
1 GAT
28282386 ATCGCCTTCC
Statistics
Matches: 184, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
44 39 0.21
45 113 0.61
46 8 0.04
47 24 0.13
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
Found at i:28282322 original size:89 final size:90
Alignment explanation
Indices: 28282112--28282385 Score: 297
Period size: 89 Copynumber: 3.0 Consensus size: 90
28282102 GATCCAAGAT
* * * *
28282112 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA-TCTG-ACCTTCATGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAG--ATAACAGATTCGGCATC-TC-TGT
* * * * *
28282175 GTT-TACATAGAAGCAGATCTAAGAT-GACA
62 ATTAGAC-GAGGAGCAGATCAAAGATAG-CA
* *
28282204 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTCGGCATCTCTGTATTA
* **
28282269 GACGATGAGCAGATTGAAGA-AGCA
66 GACGAGGAGCAGATCAAAGATAGCA
* * *
28282293 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTCGGCCTCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTCGGCATCTCTGTATTA
*
28282358 GACGGGGAGCAGATCAAAGATAGCA
66 GACGAGGAGCAGATCAAAGATAGCA
28282383 GAT
1 GAT
28282386 ATCGCCTTCC
Statistics
Matches: 155, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
89 78 0.50
90 32 0.21
91 6 0.04
92 39 0.25
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (90 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTCGGCATCTCTGTATTA
GACGAGGAGCAGATCAAAGATAGCA
Found at i:28282757 original size:14 final size:15
Alignment explanation
Indices: 28282738--28282793 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
28282728 AATCTTCAAT
28282738 GATATG-CAATCTTA
1 GATATGACAATCTTA
28282752 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
28282769 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
28282787 GATATGA
1 GATATGA
28282794 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:28282782 original size:35 final size:37
Alignment explanation
Indices: 28282736--28282814 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
28282726 ATAATCTTCA
28282736 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
28282772 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
28282808 A-GATATG
1 ATGATATG
28282815 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:28282814 original size:17 final size:19
Alignment explanation
Indices: 28282736--28282807 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
28282726 ATAATCTTCA
28282736 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28282755 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28282772 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28282790 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
28282808 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:28282833 original size:22 final size:22
Alignment explanation
Indices: 28282736--28282830 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
28282726 ATAATCTTCA
28282736 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
28282755 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
28282772 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
28282790 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
28282812 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
28282831 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:28283131 original size:17 final size:19
Alignment explanation
Indices: 28283099--28283133 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28283089 TTCCCAGATT
28283099 TTTTTTATATATATTTTAA
1 TTTTTTATATATATTTTAA
28283118 TTTTTTA-ATA-ATTTTA
1 TTTTTTATATATATTTTA
28283134 GTATCATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTATATATATTTTAA
Found at i:28287544 original size:31 final size:30
Alignment explanation
Indices: 28287509--28287580 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
28287499 AATTAGGTCG
**
28287509 GGACTAAATTTTCAAATTTCAAAAAGTACAA
1 GGACTAAATTAACAAATTTCAAAAA-TACAA
* *
28287540 GGACTAAAATTAACCAATTTGAAAAATACAA
1 GGACT-AAATTAACAAATTTCAAAAATACAA
*
28287571 GAACTAAATT
1 GGACTAAATT
28287581 GGGTCAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 5 0.14
31 14 0.40
32 16 0.46
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.26
Consensus pattern (30 bp):
GGACTAAATTAACAAATTTCAAAAATACAA
Found at i:28289995 original size:21 final size:21
Alignment explanation
Indices: 28289969--28290008 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28289959 TTACTGATGT
*
28289969 TAATATCTACACATGGATTAA
1 TAATATATACACATGGATTAA
28289990 TAATATATACACATGGATT
1 TAATATATACACATGGATT
28290009 GCCATATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (21 bp):
TAATATATACACATGGATTAA
Found at i:28290278 original size:6 final size:7
Alignment explanation
Indices: 28290267--28290291 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28290257 TTTAAAATCT
28290267 TAAAAAA
1 TAAAAAA
28290274 TAAAAAA
1 TAAAAAA
28290281 TAAAAAA
1 TAAAAAA
28290288 TAAA
1 TAAA
28290292 TATTTTTATA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:28291102 original size:20 final size:21
Alignment explanation
Indices: 28291077--28291116 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28291067 TATAAATTTT
28291077 TAAATTTATAAAA-TAAAAAC
1 TAAATTTATAAAATTAAAAAC
28291097 TAAATTTATAAAATTAAAAA
1 TAAATTTATAAAATTAAAAA
28291117 TACACGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATTTATAAAATTAAAAAC
Found at i:28291864 original size:3 final size:3
Alignment explanation
Indices: 28291856--28291932 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
28291846 CTTGTTTCCT
28291856 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
28291904 TTA TTT TTA TTT TTA TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28291933 TTAGCTTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Done.