Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 102 of 141
Found at i:28937477 original size:21 final size:20
Alignment explanation
Indices: 28937411--28937478 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
28937401 TTTTTTTATT
28937411 ATTTTTTAA-TTTTAAAAT-
1 ATTTTTTAATTTTTAAAATA
* *
28937429 ATTTTTAAAATATTTTTAAATA
1 ATTTTT-TAAT-TTTTAAAATA
*
28937451 CTTTTTTTAATTTTTAAAATAA
1 -ATTTTTTAATTTTTAAAAT-A
28937473 ATTTTT
1 ATTTTT
28937479 GGTATTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.16
19 2 0.05
21 21 0.55
22 4 0.11
23 5 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTAATTTTTAAAATA
Found at i:28938731 original size:40 final size:40
Alignment explanation
Indices: 28938655--28938740 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
28938645 AAATATATTT
* *
28938655 ATTTTTTTAATTGTAAAATATTTTTACATACTTTTTTAAA
1 ATTTTTTTAATTGTAAAATATTTTTAAATACATTTTTAAA
* **
28938695 ATTTTTTTAATTTTAAAATATTTTTAAAATA-ATTTTTTTA
1 ATTTTTTTAATTGTAAAATATTTTT-AAATACATTTTTAAA
28938735 ATTTTT
1 ATTTTT
28938741 AAAATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (40 bp):
ATTTTTTTAATTGTAAAATATTTTTAAATACATTTTTAAA
Found at i:28938732 original size:31 final size:31
Alignment explanation
Indices: 28938694--28938757 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
28938684 ACTTTTTTAA
28938694 AATTTTTTTAA-TTTTAAAATATTTTTAAAAT
1 AATTTTTTTAATTTTTAAAAT-TTTTTAAAAT
28938725 AATTTTTTTAATTTTTAAAATTTTTTAAAAT
1 AATTTTTTTAATTTTTAAAATTTTTTAAAAT
28938756 AA
1 AA
28938758 AAATAGGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
AATTTTTTTAATTTTTAAAATTTTTTAAAAT
Found at i:28940125 original size:83 final size:83
Alignment explanation
Indices: 28940016--28940181 Score: 262
Period size: 83 Copynumber: 2.0 Consensus size: 83
28940006 TTTCCAAGTC
28940016 TTGTTCACCAATTTTCATATTTTGTTTATTTACCTTGAGCTT-TTACCTTATAATAATTTTTTAT
1 TTGTTCACCAATTTTCATATTTTGTTTATTTACCTTGAGCTTCTTACCTTATAATAA-TTTTTAT
28940080 TCAGTTTTTGTTTGATTTT
65 TCAGTTTTTGTTTGATTTT
* * * * **
28940099 TTGTTGACCAATTTTTATATTTTGTTTATTTGCCTTGTGCTTCTTATTTTATAATAATTTTTATT
1 TTGTTCACCAATTTTCATATTTTGTTTATTTACCTTGAGCTTCTTACCTTATAATAATTTTTATT
28940164 CAGTTTTTGTTTGATTTT
66 CAGTTTTTGTTTGATTTT
28940182 ATATAATAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
83 64 0.84
84 12 0.16
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.61
Consensus pattern (83 bp):
TTGTTCACCAATTTTCATATTTTGTTTATTTACCTTGAGCTTCTTACCTTATAATAATTTTTATT
CAGTTTTTGTTTGATTTT
Found at i:28951867 original size:18 final size:18
Alignment explanation
Indices: 28951844--28951886 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28951834 ACCCAATCTA
**
28951844 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
28951862 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
28951880 AACCCAA
1 AACCCAA
28951887 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:28952042 original size:9 final size:9
Alignment explanation
Indices: 28951991--28952041 Score: 75
Period size: 9 Copynumber: 5.7 Consensus size: 9
28951981 TATGTAGTGA
*
28951991 TTAATTTGG
1 TTAATTCGG
28952000 TTAATTCGG
1 TTAATTCGG
*
28952009 TCAATTCGG
1 TTAATTCGG
28952018 TTAATTCGG
1 TTAATTCGG
*
28952027 TTAATTTGG
1 TTAATTCGG
28952036 TTAATT
1 TTAATT
28952042 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.49
Consensus pattern (9 bp):
TTAATTCGG
Found at i:28952221 original size:12 final size:12
Alignment explanation
Indices: 28952204--28952228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28952194 TATTATTTCG
28952204 GGTCGGTTAACC
1 GGTCGGTTAACC
28952216 GGTCGGTTAACC
1 GGTCGGTTAACC
28952228 G
1 G
28952229 AATGAACACC
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:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:28966929 original size:33 final size:33
Alignment explanation
Indices: 28966875--28966956 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
28966865 TTGTCAGTCC
* *
28966875 AACCAAACACACTAGATGCTCATAAGAGCCAATCC
1 AACC-AACACACCA-ATGCTCATAAGAGCCAATCA
** *
28966910 CTCCAACACACCAATGCTCATAAGAGCTAATCA
1 AACCAACACACCAATGCTCATAAGAGCCAATCA
28966943 AACCAACACACCAA
1 AACCAACACACCAA
28966957 ATCACGACTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 30 0.75
34 8 0.20
35 2 0.05
ACGTcount: A:0.44, C:0.34, G:0.09, T:0.13
Consensus pattern (33 bp):
AACCAACACACCAATGCTCATAAGAGCCAATCA
Found at i:28974188 original size:25 final size:26
Alignment explanation
Indices: 28974155--28974209 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
28974145 GTAGATCTCG
*
28974155 TTTACTTTCTGATTCTTATTTATTTA
1 TTTACTTTCTGATTCTTACTTATTTA
** *
28974181 TTTA-TTTCTTTTTCTTACTTATTTT
1 TTTACTTTCTGATTCTTACTTATTTA
28974206 TTTA
1 TTTA
28974210 GAAGGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTACTTTCTGATTCTTACTTATTTA
Found at i:28982528 original size:24 final size:23
Alignment explanation
Indices: 28982473--28982528 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
28982463 TCCGGGTTGT
* *
28982473 ATAACGGGAAGCTCATAAGAGCT
1 ATAACGGGAAGCTCATAAGACCA
28982496 ATAATCGGGAAGCTCATCCAAG-CCA
1 ATAA-CGGGAAGCTCAT--AAGACCA
28982521 ATAACGGG
1 ATAACGGG
28982529 TAACTCCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 16 0.57
25 5 0.18
26 3 0.11
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (23 bp):
ATAACGGGAAGCTCATAAGACCA
Found at i:28982559 original size:24 final size:25
Alignment explanation
Indices: 28982532--28982583 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
28982522 TAACGGGTAA
*
28982532 CTCCGAAGAGCCATTAATGA-AAAG
1 CTCCGAAGAGCCATTAATCAGAAAG
*
28982556 CTCCGGAGAGCCATTAATCAGAAAG
1 CTCCGAAGAGCCATTAATCAGAAAG
28982581 CTC
1 CTC
28982584 ACATAGAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (25 bp):
CTCCGAAGAGCCATTAATCAGAAAG
Found at i:28982591 original size:26 final size:24
Alignment explanation
Indices: 28982538--28982599 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
28982528 GTAACTCCGA
* *
28982538 AGAGCCATTAATGAAAAGCTCCGG
1 AGAGCCATTAATCAAAAGCTCCAG
*
28982562 AGAGCCATTAATCAGAAAGCTCACAT
1 AGAGCCATTAATCA-AAAGCTC-CAG
*
28982588 AGAGCCTTTAAT
1 AGAGCCATTAAT
28982600 TGGGAAGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 13 0.41
25 7 0.22
26 12 0.38
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
AGAGCCATTAATCAAAAGCTCCAG
Found at i:28986460 original size:44 final size:44
Alignment explanation
Indices: 28986386--28986507 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
28986376 TCGACTTCAA
* ** *
28986386 TCTGCTCCACTGCAACCTCA-GGGAAGTAAGATTTGCTTCT-TCGG
1 TCTGCTCCACTGCAACCTCAGGGGGA-TAAGACCTG-TTCTCTCAG
* * *
28986430 TCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGTTTTCTCAG
1 TCTGCTCCACTGCAACCTCAGGGGGATAAGACCTGTTCTCTCAG
* *
28986474 TCTGCTCCGCTGCAACCTCAGGGAGATAAGACCT
1 TCTGCTCCACTGCAACCTCAGGGGGATAAGACCT
28986508 AATACGATCC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 3 0.05
44 58 0.89
45 4 0.06
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (44 bp):
TCTGCTCCACTGCAACCTCAGGGGGATAAGACCTGTTCTCTCAG
Found at i:28986743 original size:44 final size:43
Alignment explanation
Indices: 28986653--28986931 Score: 218
Period size: 44 Copynumber: 6.1 Consensus size: 43
28986643 CAATCGGATG
* * * * * * *
28986653 CAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTCTGTTT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-TTCGGCTT
* * *
28986697 TAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATCGGCTT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATAAGATT-TCGGCTT
* *
28986741 TAATCTGCTCTACTGTAACTTCAGGGAGATAAGATTTCTGGCTT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTC-GGCTT
* * *
28986785 CAATCGGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT-TGTTT
1 CAATC---T--G--CT-C-C-ACTGTAACTTCAGGGAGATAAGAT--TTCGGCTT
* * *
28986839 TAATCTGCTCTACTGTAACTTCAGGGAGATAGGATTATCGGCTT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATAAGATT-TCGGCTT
* *
28986883 CAATCTACTCCACTGTAACTTCAGGGAAATAAGATTTCTGGCTT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTC-GGCTT
28986927 CAATC
1 CAATC
28986932 GGATGCGATC
Statistics
Matches: 189, Mismatches: 29, Indels: 34
0.75 0.12 0.13
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 141 0.75
46 1 0.01
47 3 0.02
49 2 0.01
51 3 0.02
52 1 0.01
54 30 0.16
56 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (43 bp):
CAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTCGGCTT
Found at i:28986952 original size:98 final size:98
Alignment explanation
Indices: 28986841--28987029 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 98
28986831 CTTTGTTTTA
* * ** * *
28986841 ATCTGCTCTACTGTAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGTAACTTCA
1 ATCTACTCGACTGTAACTTCAAAGAGATAAGATCATCGGCTTCAATCTACTCCACTGTAACTTCA
*
28986906 GGGAAATAAGATT-TCTGGCTTCAATCGGATGCG
66 GGGAAATAAGATTATC-GACTTCAATCGGATGCG
* ** * * *
28986939 ATCTACTCGACTGTAACTTCAAAGAGATAAGATCCTTTGTTTTAATCTACTTCACTGTAACTTCA
1 ATCTACTCGACTGTAACTTCAAAGAGATAAGATCATCGGCTTCAATCTACTCCACTGTAACTTCA
* *
28987004 GGGAGATAGGATTATCGACTTCAATC
66 GGGAAATAAGATTATCGACTTCAATC
28987030 TACTTCCTTA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 73 0.97
99 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (98 bp):
ATCTACTCGACTGTAACTTCAAAGAGATAAGATCATCGGCTTCAATCTACTCCACTGTAACTTCA
GGGAAATAAGATTATCGACTTCAATCGGATGCG
Found at i:28987031 original size:142 final size:142
Alignment explanation
Indices: 28986512--28987033 Score: 701
Period size: 142 Copynumber: 3.7 Consensus size: 142
28986502 AGACCTAATA
* * **
28986512 CGATCCACTCTACTGCAACTTCAGAGAGATAAGAT-CTATTACTTTAATCCACTCCACTGTAACT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTGTTTTAATCCACTCCACTGTAACT
* * * ** * * * * *
28986576 TTAGGGAGATAGGA-TAGT-GTCTTCGATCTGTTTCGCTGTAA-TCTCAAGGAGATAAGATCTCC
65 TCAGGGAGATAGGATTA-TCGGCTTCAATCTACTCCACTGTAACT-TCAGGGAGATAAGATTTCT
**
28986638 ATCTTCAATCGGATG
128 GGCTTCAATCGGATG
* * * *
28986653 CAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTCTGTTTTAATCCGCTCCACTGTAACTT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCACTCCACTGTAACTT
* * *
28986718 CAGGGAGATAGGATTATCGGCTTTAATCTGCTCTACTGTAACTTCAGGGAGATAAGATTTCTGGC
66 CAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTCTGGC
28986783 TTCAATCGGATG
131 TTCAATCGGATG
** *
28986795 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCTGCTCTACTGTAACTT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCACTCCACTGTAACTT
*
28986860 CAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGTAACTTCAGGGAAATAAGATTTCTGGC
66 CAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTCTGGC
28986925 TTCAATCGGATG
131 TTCAATCGGATG
* * * *
28986937 CGATCTACTCGACTGTAACTTCAAAGAGATAAGATCCTTTGTTTTAATCTACTTCACTGTAACTT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCACTCCACTGTAACTT
*
28987002 CAGGGAGATAGGATTATCGACTTCAATCTACT
66 CAGGGAGATAGGATTATCGGCTTCAATCTACT
28987034 TCCTTACACT
Statistics
Matches: 341, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
141 67 0.20
142 273 0.80
143 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCACTCCACTGTAACTT
CAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTCTGGC
TTCAATCGGATG
Found at i:28987222 original size:43 final size:43
Alignment explanation
Indices: 28987149--28987360 Score: 169
Period size: 43 Copynumber: 4.9 Consensus size: 43
28987139 AGGACTTGTG
* * * * *
28987149 GCTTAAATATGTTTCCCTACCCCTGAGGAAGATAAGACTCGCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
* * *
28987192 GTTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGCAA
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGC-C
* * ** * * * * **
28987236 TCTTTA-ACCT-ACTCCGCTGCTGCTCAGGG-AGATAAGGTTCGGTG
1 GC-TTAGATCTGTTTCC-CTACTCCT-GGGGAAGATAAGATTC-GCC
* * *
28987280 GCTTAAATCTATTTCCCTACTCTTGGGGAAGATAAGATTCGCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
28987323 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
28987361 CCGCAATCTT
Statistics
Matches: 127, Mismatches: 34, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
43 80 0.63
44 37 0.29
45 10 0.08
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (43 bp):
GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
Found at i:28988543 original size:7 final size:7
Alignment explanation
Indices: 28988533--28988580 Score: 66
Period size: 6 Copynumber: 7.1 Consensus size: 7
28988523 TTAGCCTTTC
28988533 CATTTTT
1 CATTTTT
28988540 CATTTTT
1 CATTTTT
28988547 CA-TTTT
1 CATTTTT
28988553 CA-TTTT
1 CATTTTT
28988559 CA-TTTT
1 CATTTTT
28988565 CATTTTT
1 CATTTTT
28988572 CATATTTT
1 CAT-TTTT
28988580 C
1 C
28988581 TGACTTAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 18 0.46
7 16 0.41
8 5 0.13
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (7 bp):
CATTTTT
Found at i:28988552 original size:13 final size:13
Alignment explanation
Indices: 28988536--28988574 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
28988526 GCCTTTCCAT
28988536 TTTTCATTTTTCA
1 TTTTCATTTTTCA
28988549 TTTTCA-TTTTCA
1 TTTTCATTTTTCA
28988561 TTTTCATTTTTCA
1 TTTTCATTTTTCA
28988574 T
1 T
28988575 ATTTTCTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:28989504 original size:18 final size:18
Alignment explanation
Indices: 28989483--28989519 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28989473 TCTAAATTTC
28989483 TCTTTTT-TCATTCTTCAT
1 TCTTTTTCTCATT-TTCAT
28989501 TCTTTTTCTCATTTTCAT
1 TCTTTTTCTCATTTTCAT
28989519 T
1 T
28989520 TTGATCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTTTTCTCATTTTCAT
Found at i:28989540 original size:51 final size:47
Alignment explanation
Indices: 28989485--28989597 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 47
28989475 TAAATTTCTC
28989485 TTTTTTCATTCTTCATTCTTTTTCTCATTTTCATTTTGATCTTGA-TTTTGAT
1 TTTTTTCATTCTTCATTC-TTTT-T-ATTTT--TTTT-ATCTTGATTTTTGAT
* *
28989537 TTTTTTC-TTCTCTC-TTCTTTTTGTTTTTTTTATTTTGATTTTTGA-
1 TTTTTTCATTCT-TCATTCTTTTTATTTTTTTTATCTTGATTTTTGAT
28989582 TTTTTTCATT-TTCATT
1 TTTTTTCATTCTTCATT
28989598 TTGACTTTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
44 2 0.04
45 16 0.29
46 12 0.22
48 4 0.07
49 1 0.02
50 4 0.07
51 7 0.13
52 9 0.16
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (47 bp):
TTTTTTCATTCTTCATTCTTTTTATTTTTTTTATCTTGATTTTTGAT
Found at i:28989572 original size:6 final size:6
Alignment explanation
Indices: 28989563--28989623 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
28989553 CTTTTTGTTT
* * * *
28989563 TTTTTA TTTTGA TTTTTGA TTTTTTCA TTTTCA TTTTGA CTTTGA TTTTGA
1 TTTTGA TTTTGA -TTTTGA --TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
28989614 TTTTGA TTTT
1 TTTTGA TTTT
28989624 TCTTTCCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 36 0.75
7 6 0.12
8 6 0.12
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:28989578 original size:21 final size:21
Alignment explanation
Indices: 28989554--28989599 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
28989544 TTCTCTCTTC
* * *
28989554 TTTTTGTTTTTTTTATTTTGA
1 TTTTTGATTTTTTCATTTTCA
28989575 TTTTTGATTTTTTCATTTTCA
1 TTTTTGATTTTTTCATTTTCA
28989596 TTTT
1 TTTT
28989600 GACTTTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTGATTTTTTCATTTTCA
Found at i:28996030 original size:15 final size:15
Alignment explanation
Indices: 28996012--28996065 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
28996002 ATATATTGAA
28996012 TATTTTTATATTATT
1 TATTTTTATATTATT
*
28996027 TATTTTTA-ATATAAT
1 TATTTTTATAT-TATT
*
28996042 TACTTTTATAATTATT
1 TATTTTTAT-ATTATT
*
28996058 TTTTTTTA
1 TATTTTTA
28996066 ATTTATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.06
15 18 0.58
16 9 0.29
17 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTATATTATT
Found at i:28996872 original size:9 final size:9
Alignment explanation
Indices: 28996854--28996943 Score: 67
Period size: 9 Copynumber: 9.7 Consensus size: 9
28996844 ACATGTGGCA
28996854 AAAAAGTTAT
1 AAAAA-TTAT
28996864 AAAAATTAT
1 AAAAATTAT
28996873 AAAAATTATT
1 AAAAATTA-T
*
28996883 AGAAAA-TAA
1 A-AAAATTAT
28996892 AAAAATTAT
1 AAAAATTAT
28996901 AAAAA-TAGT
1 AAAAATTA-T
*
28996910 AAAAAAATAT
1 -AAAAATTAT
* **
28996920 TAAAATGGT
1 AAAAATTAT
*
28996929 AAATATTAT
1 AAAAATTAT
28996938 AAAAAT
1 AAAAAT
28996944 CAATGAGCGT
Statistics
Matches: 63, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
8 6 0.10
9 36 0.57
10 15 0.24
11 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:28996916 original size:28 final size:28
Alignment explanation
Indices: 28996864--28996942 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
28996854 AAAAAGTTAT
* *
28996864 AAAAATTATAAAAATTATTAGAAAATAA
1 AAAAATTATAAAAATTATAAAAAAATAA
*
28996892 AAAAATTATAAAAA-TAGTAAAAAAATAT
1 AAAAATTATAAAAATTA-TAAAAAAATAA
* ** *
28996920 TAAAATGGTAAATATTATAAAAA
1 AAAAATTATAAAAATTATAAAAA
28996943 TCAATGAGCG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
27 2 0.05
28 38 0.90
29 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAAATTATAAAAATTATAAAAAAATAA
Found at i:28996925 original size:19 final size:20
Alignment explanation
Indices: 28996853--28996943 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 20
28996843 GACATGTGGC
*
28996853 AAAAAAGTTATAAAAAT--T
1 AAAAAAATTATAAAAATAGT
* *
28996871 ATAAAAATTATTAGAAA-A-T
1 AAAAAAATTA-TAAAAATAGT
28996890 AAAAAAATTATAAAAATAGT
1 AAAAAAATTATAAAAATAGT
* *
28996910 AAAAAAA-TATTAAAATGGT
1 AAAAAAATTATAAAAATAGT
*
28996929 --AAATATTATAAAAAT
1 AAAAAAATTATAAAAAT
28996944 CAATGAGCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
17 4 0.07
18 21 0.36
19 26 0.44
20 8 0.14
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAATTATAAAAATAGT
Found at i:28998436 original size:33 final size:33
Alignment explanation
Indices: 28998394--28998461 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
28998384 TTTTACATGT
28998394 GATTGCAAATAATGTTGTTTATGGGTATGATGA
1 GATTGCAAATAATGTTGTTTATGGGTATGATGA
28998427 GATTGCAAATAATGTTGTTTATGGGTATGATGA
1 GATTGCAAATAATGTTGTTTATGGGTATGATGA
28998460 GA
1 GA
28998462 ATGTGCATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (33 bp):
GATTGCAAATAATGTTGTTTATGGGTATGATGA
Found at i:29011242 original size:21 final size:21
Alignment explanation
Indices: 29011218--29011268 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
29011208 AAAATAGTAG
*
29011218 TAGTGGTGAAATT-GATTATTA
1 TAGTGATGAAATTGGA-TATTA
*
29011239 TAGTGATGAGATTGGATATTA
1 TAGTGATGAAATTGGATATTA
*
29011260 TAGCGATGA
1 TAGTGATGA
29011269 GATTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.37
Consensus pattern (21 bp):
TAGTGATGAAATTGGATATTA
Found at i:29012716 original size:20 final size:20
Alignment explanation
Indices: 29012693--29012731 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29012683 GCTCTCCCTA
*
29012693 GCCACG-CACACCTCCGTACC
1 GCCACGTCA-ACCCCCGTACC
29012713 GCCACGTCAACCCCCGTAC
1 GCCACGTCAACCCCCGTAC
29012732 GAACGTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.54, G:0.15, T:0.10
Consensus pattern (20 bp):
GCCACGTCAACCCCCGTACC
Found at i:29015875 original size:56 final size:55
Alignment explanation
Indices: 29015808--29015914 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 55
29015798 TATCCATTGG
* *
29015808 ATGATAAATCATCACTTTTAATTTGAATAATGCTTATGAATAATTAAATTTGTAAT
1 ATGATAAATCATCACTTTTAATTTGAATAATGCTCATGAAGAATT-AATTTGTAAT
*
29015864 ATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAAGAATTAATTTG
1 ATGATAAATCATCACTTTTAATTTGAATAATGCTCATGAAGAATTAATTTG
29015915 CAATCTATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 6 0.12
56 42 0.88
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (55 bp):
ATGATAAATCATCACTTTTAATTTGAATAATGCTCATGAAGAATTAATTTGTAAT
Found at i:29018695 original size:30 final size:29
Alignment explanation
Indices: 29018661--29018725 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29018651 TAATCCACCA
29018661 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
29018691 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
29018721 CCCAA
1 CCCAA
29018726 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:29018699 original size:31 final size:30
Alignment explanation
Indices: 29018668--29018725 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29018658 CCACCCAACT
29018668 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
29018698 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
29018726 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:29020778 original size:3 final size:3
Alignment explanation
Indices: 29020723--29020758 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
29020713 ATTATTTTGT
29020723 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
29020759 CCGTCTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29021504 original size:111 final size:111
Alignment explanation
Indices: 29021281--29021672 Score: 626
Period size: 111 Copynumber: 3.5 Consensus size: 111
29021271 TTTCTAATTG
* * * *
29021281 AGGCAATATTTAGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGA-TTTTTC
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTC
* * *
29021345 TCGTTCAACCAAATGGCTTAACATCCTTTTCAAAAATTTTAAAATA
66 TCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTAAAATA
*
29021391 AGGCAATGTTTTGCGTTTGAAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTC
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTC
29021456 TCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTAAAATA
66 TCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTAAAATA
* * * *
29021502 AGGCAATGTTTTGCGTTTGAAAATTTGAGAAACCATGCCCTCAGGTGCCGGGTGTCGATTTTTTC
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTC
29021567 TCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTAAAATA
66 TCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTAAAATA
* * * *
29021613 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGATTT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTT
29021673 CTCGTTTAAC
Statistics
Matches: 262, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
110 78 0.30
111 184 0.70
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (111 bp):
AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTC
TCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTAAAATA
Found at i:29027546 original size:3 final size:3
Alignment explanation
Indices: 29027491--29027526 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
29027481 ATTATTTTGT
*
29027491 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29027527 CCGTCTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:29028274 original size:111 final size:110
Alignment explanation
Indices: 29028048--29028452 Score: 656
Period size: 111 Copynumber: 3.7 Consensus size: 110
29028038 TTTCTAATTG
* *
29028048 AGGCAATATTTAGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
29028113 CGTTCAACCAAATGGCTTAACATCCTTTTCAAAAATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATTTTAAAATA
*
29028158 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTTC
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGA-TTTTTC
*
29028223 TCGTTCGACCAAATGGCTTAATATCCTTTTCAAAAATTTTAAAATA
65 TCGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATTTTAAAATA
29028269 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * * *
29028334 CGTACAACCAAATAGCTAAATATCC-TTTCAAAAATTTCAAAGTA
66 CGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATTTTAAAATA
* *
29028378 AGGCAATGTTTTGCGTTTGGAAATTCGAGG-AACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
29028440 CGTTTAACCAAAT
66 CGTTCAACCAAAT
29028453 TTCCAAATAT
Statistics
Matches: 278, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
106 16 0.06
108 25 0.09
109 47 0.17
110 83 0.30
111 107 0.38
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (110 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATTTTAAAATA
Found at i:29030140 original size:19 final size:17
Alignment explanation
Indices: 29030104--29030148 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
29030094 GCATATGGAT
*
29030104 ATAAAAATAATAAAATA
1 ATAATAATAATAAAATA
29030121 ATAATAATAATAGTAAATA
1 ATAATAATAATA--AAATA
29030140 ATAATAATA
1 ATAATAATA
29030149 CAATGTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.44
19 14 0.56
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAATAATAATAAAATA
Found at i:29030163 original size:3 final size:3
Alignment explanation
Indices: 29030104--29030148 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
29030094 GCATATGGAT
* *
29030104 ATA AAA ATA ATA A-A ATA ATA ATA ATA ATA GTAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
29030149 CAATGTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:29048087 original size:18 final size:17
Alignment explanation
Indices: 29048059--29048093 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29048049 ATTATTAAGA
*
29048059 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29048076 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29048094 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29048098 original size:120 final size:120
Alignment explanation
Indices: 29047952--29048350 Score: 782
Period size: 120 Copynumber: 3.3 Consensus size: 120
29047942 TAATTGAAAA
*
29047952 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
29048016 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
29048071 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
29048136 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
29048191 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
29048256 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
29048311 TATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTT
29048351 TAAATATGAT
Statistics
Matches: 278, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
119 10 0.04
120 268 0.96
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:29048207 original size:18 final size:17
Alignment explanation
Indices: 29048179--29048213 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29048169 ATTATTAAGA
*
29048179 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29048196 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29048214 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29048327 original size:18 final size:17
Alignment explanation
Indices: 29048299--29048333 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29048289 ATTATTAAGA
*
29048299 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29048316 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29048334 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29048547 original size:44 final size:45
Alignment explanation
Indices: 29048498--29048588 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
29048488 ACCTCTATTC
* * *
29048498 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
29048542 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
29048587 CA
1 CA
29048589 CCTCTAATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:29048590 original size:16 final size:16
Alignment explanation
Indices: 29048569--29048637 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
29048559 GATTAGCTAT
29048569 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29048585 TACACCTCTAATCACAA
1 TACACCTCTAATC-CAA
29048602 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
29048618 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
29048634 TACA
1 TACA
29048638 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.38, C:0.36, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:29048611 original size:33 final size:32
Alignment explanation
Indices: 29048569--29048637 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
29048559 GATTAGCTAT
29048569 TACACCTCTAATCCAATACACCTCTAATCACAA
1 TACACCTCTAATCCAATACACCTCTAATC-CAA
*
29048602 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
29048634 TACA
1 TACA
29048638 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.38, C:0.36, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:29049036 original size:65 final size:65
Alignment explanation
Indices: 29048967--29049093 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
29048957 TATTAATTTG
*
29048967 TGTCGAAACCATTTTTATTTTGAAAAACGGGGACGACTTTTAAAAC-AAAAGTGGAGTCGCCAAG
1 TGTCGAAACCATTTTTATTTTGAAAAACGGGCACGACTTTTAAAACGAAAA-TGGAGTCGCCAAG
29049031 C
65 C
*
29049032 TGTCGAAACCATTTTTATTTTGAAAAACGGGCTCGACTTTTAAAACGAAAATGGAGTCGCCA
1 TGTCGAAACCATTTTTATTTTGAAAAACGGGCACGACTTTTAAAACGAAAATGGAGTCGCCA
29049094 CCAATCTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 55 0.93
66 4 0.07
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (65 bp):
TGTCGAAACCATTTTTATTTTGAAAAACGGGCACGACTTTTAAAACGAAAATGGAGTCGCCAAGC
Found at i:29050658 original size:23 final size:22
Alignment explanation
Indices: 29050615--29050672 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
29050605 AAAGGGTACC
* *
29050615 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
29050636 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
29050659 TGCATATCATATCT
1 TACAAATCATATCT
29050673 AAGATTGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:29051105 original size:44 final size:44
Alignment explanation
Indices: 29051056--29051174 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
29051046 TTCTGATCCA
** * *
29051056 CTCCACTACAATTTCAGGGAGATAGGATTGGTTTCTTCAATCTG
1 CTCCACTACAACCTCAGGGAGATAGGATTGGCTTATTCAATCTG
* * *
29051100 TTCCACTACAACCTCAGGGAGATAAGATTGACTTATTCAATCTG
1 CTCCACTACAACCTCAGGGAGATAGGATTGGCTTATTCAATCTG
*
29051144 CTCCACTGCAACCTCAGGGAGAT-GAGATTGG
1 CTCCACTACAACCTCAGGGAGATAG-GATTGG
29051175 ATGCGATCTG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCACTACAACCTCAGGGAGATAGGATTGGCTTATTCAATCTG
Found at i:29053960 original size:18 final size:19
Alignment explanation
Indices: 29053927--29053963 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29053917 CGATCCGATT
*
29053927 AAAAAATTATTTAAAATTC
1 AAAAAATTATTAAAAATTC
29053946 AAAAAATT-TTAAAAATTC
1 AAAAAATTATTAAAAATTC
29053964 TAGTTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATTATTAAAAATTC
Found at i:29063670 original size:51 final size:51
Alignment explanation
Indices: 29063615--29063782 Score: 162
Period size: 51 Copynumber: 3.2 Consensus size: 51
29063605 AGATCTTTTT
* *
29063615 CATTTTCATTTTGGAGAAAACCACATTCATTTTTAAATGATTCCATTTCTC
1 CATTTTCATTTTGGAGAAAACCAAATTCATTTTCAAATGATTCCATTTCTC
* * * *
29063666 CATTTTCATTTTGGAGAAAACTATAA-TCATTTCCAAATGATTTCATTTCTTTATTTT
1 CATTTTCATTTTGGAGAAAACCA-AATTCATTTTCAAATGATTCCATTTC------TC
*
29063723 TATTTTCATTTTGGAGAAAACCATAATT-ATTTTCAAAT-ATTTCTCATTTCTC
1 CATTTTCATTTTGGAGAAAACCA-AATTCATTTTCAAATGA-TTC-CATTTCTC
29063775 CATTTTCA
1 CATTTTCA
29063783 CAATTTTTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
51 42 0.44
52 9 0.09
56 1 0.01
57 36 0.38
58 7 0.07
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (51 bp):
CATTTTCATTTTGGAGAAAACCAAATTCATTTTCAAATGATTCCATTTCTC
Found at i:29067683 original size:103 final size:104
Alignment explanation
Indices: 29067504--29067768 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
29067494 AACCGTTATT
* * * *
29067504 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
29067569 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
29067607 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
29067671 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
29067711 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
29067769 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:29068130 original size:30 final size:29
Alignment explanation
Indices: 29068096--29068160 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29068086 TAATCCACCA
29068096 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
29068126 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
29068156 CCCAA
1 CCCAA
29068161 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:29068134 original size:31 final size:30
Alignment explanation
Indices: 29068103--29068160 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29068093 CCACCCAACT
29068103 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
29068133 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
29068161 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:29075175 original size:103 final size:104
Alignment explanation
Indices: 29074996--29075260 Score: 424
Period size: 103 Copynumber: 2.6 Consensus size: 104
29074986 AACCGTTATT
* * * *
29074996 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
29075061 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
29075099 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
29075164 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
29075203 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
29075261 TTATGTACAA
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:29075622 original size:30 final size:29
Alignment explanation
Indices: 29075588--29075652 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29075578 TAATCCACCA
29075588 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
29075618 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
29075648 CCCAA
1 CCCAA
29075653 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:29075626 original size:31 final size:30
Alignment explanation
Indices: 29075595--29075652 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29075585 CCACCCAACT
29075595 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
29075625 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
29075653 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:29076791 original size:21 final size:22
Alignment explanation
Indices: 29076760--29076803 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29076750 CCTACAAAAG
**
29076760 ACAGAAAAAAGGAAGCAGAGAA
1 ACAGAAAAAAGGAAAAAGAGAA
29076782 ACAG-AAAAAGGAAAAAGAGAA
1 ACAGAAAAAAGGAAAAAGAGAA
29076803 A
1 A
29076804 AATAATATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (22 bp):
ACAGAAAAAAGGAAAAAGAGAA
Found at i:29077486 original size:60 final size:61
Alignment explanation
Indices: 29077392--29077510 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 61
29077382 GGGCTCGAGA
29077392 AAAATAAGAAAGGAAATGAGTTTTTTTAGGCTATTAAAATGATTGTTTTTAGATTTTTTTT
1 AAAATAAGAAAGGAAATGAGTTTTTTTAGGCTATTAAAATGATTGTTTTTAGATTTTTTTT
29077453 AAAA-AAGAAAGGAAATGAGTTTTTTTAGGCTATTAAAATGATTGTTTTTAGATTTTTT
1 AAAATAAGAAAGGAAATGAGTTTTTTTAGGCTATTAAAATGATTGTTTTTAGATTTTTT
29077511 AACTTAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 54 0.93
61 4 0.07
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.45
Consensus pattern (61 bp):
AAAATAAGAAAGGAAATGAGTTTTTTTAGGCTATTAAAATGATTGTTTTTAGATTTTTTTT
Found at i:29079786 original size:14 final size:14
Alignment explanation
Indices: 29079767--29079797 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29079757 AAAATCTTTT
29079767 CAAATTTTCGACAC
1 CAAATTTTCGACAC
29079781 CAAATTTTCGACAC
1 CAAATTTTCGACAC
29079795 CAA
1 CAA
29079798 GGCATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.26
Consensus pattern (14 bp):
CAAATTTTCGACAC
Found at i:29082756 original size:25 final size:27
Alignment explanation
Indices: 29082728--29082785 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
29082718 ATTTAACATT
*
29082728 TTATTTTATTC-AT-TTTTTATTATAA
1 TTATTTTATACTATATTTTTATTATAA
* *
29082753 TTATGTTATACTATGATTTTTATTATTA
1 TTATTTTATACTAT-ATTTTTATTATAA
29082781 TTATT
1 TTATT
29082786 ATCATTCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 9 0.35
26 2 0.08
28 15 0.58
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (27 bp):
TTATTTTATACTATATTTTTATTATAA
Found at i:29084665 original size:19 final size:20
Alignment explanation
Indices: 29084620--29084667 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
29084610 TTAACGTCTC
*
29084620 TATATGCA-TTCATTTCATA
1 TATATGCATTTCATTACATA
* *
29084639 CATTTGCATTTCATTACAT-
1 TATATGCATTTCATTACATA
29084658 TATATGCATT
1 TATATGCATT
29084668 AGACACCGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (20 bp):
TATATGCATTTCATTACATA
Found at i:29086586 original size:18 final size:19
Alignment explanation
Indices: 29086549--29086594 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
29086539 TGAGCAAATG
*
29086549 TTCTTTCATTC-TTTACGA
1 TTCTTTTATTCTTTTACGA
29086567 TTCTTTTATTCTTTTA-GA
1 TTCTTTTATTCTTTTACGA
29086585 TT-TTTT-TTCT
1 TTCTTTTATTCT
29086595 CCTGCCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 14 0.54
19 4 0.15
ACGTcount: A:0.13, C:0.15, G:0.04, T:0.67
Consensus pattern (19 bp):
TTCTTTTATTCTTTTACGA
Found at i:29089068 original size:132 final size:132
Alignment explanation
Indices: 29088830--29090122 Score: 1648
Period size: 132 Copynumber: 9.8 Consensus size: 132
29088820 GGAGCAGGTT
* * *
29088830 GATGGTAGATTTTACCTCCCTGA-GGTTACAGTGGAGTATATTGAAGCCAGTAATTCTA-TCTCT
1 GATGGCAGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCC
* * * *
29088893 CTGGACAGCAGTGGAATAGATTGAATATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
64 CTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGAT
*
29088958 CGAA
129 CAAA
* * * *
29088962 GATGGCGGATTTTCCCTCCCTACGGTTACCGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * * *
29089027 GGGCAGCAGCGGAAGAGATTGGAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTAGAGCAGATAA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
29089092 AA
131 AA
* * * *
29089094 AATGGCAGATTTTATCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTTCCT
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
** * *
29089159 GGGCAGCAGCAGAATAGATTGAATATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
29089224 AA
131 AA
* * *
29089226 GATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * * *
29089291 GGGCAGCAGCGGAATATATTGAATATTTCAGATCTTGTCTCCCTAAGCAGTAGTAGAACAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
29089356 AA
131 AA
* * * *
29089358 GATGACGGATTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCC
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCC
* * * *
29089422 TAGGCAGCAGTGAAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAACAGTAGTGGAGCAGATT
65 TGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
29089487 AAA
130 AAA
* ** *
29089490 GATGGTAGATTTTACCTTTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * * *
29089555 GTGCAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGAAGTAGTGGAACAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
29089620 AA
131 AA
* * * * *
29089622 GATGACGGATTTTACCTCCCTATGGTTACAATGGAGTACATTGAAGCCAGCAATTCTATTTCCCT
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * *
29089687 GGGCGGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGTAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
29089752 AA
131 AA
* * * * *
29089754 GGTGGTAGATTTTACCTCCTTGTGGTTACAGTGGAGTGCATTGAAGCCAGTAATTCTACTTCCCT
1 GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * *
29089819 GGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGGGGAGCAGATC
66 -GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
*
29089884 GAA
130 AAA
* *
29089887 GAGGGCGGATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCC
1 GATGGCAGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCC
* * * * * *
29089950 CTAGGCAACAGTGGAATAGATTGAATATTACAGATCTTATCTCCCTAAGCTGTAGTGGAGCAGAT
64 CTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGAT
*
29090015 AAAA
129 CAAA
* * * * * *
29090019 AATGGCAGACTTTACCTCCTTGA-GGTTGCAGTGGAGTATATT-AAGCCACTAATTCTA-TCTCC
1 GATGGCAGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCC
* * * * * ***
29090081 CCGGTCGGCAGTGGAATCGATCGAAGAAAGCAGATCTTGTCT
64 CTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCT
29090123 TCATGTATTG
Statistics
Matches: 1021, Mismatches: 133, Indels: 15
0.87 0.11 0.01
Matches are distributed among these distances:
131 51 0.05
132 853 0.84
133 117 0.11
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
GATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
AA
Found at i:29090162 original size:44 final size:45
Alignment explanation
Indices: 29090099--29090196 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
29090089 CAGTGGAATC
** * *
29090099 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCACATACTGGTAGTGAAGTA
*
29090143 GATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTAGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCACATACTGGTAGTGAAGTA
29090188 GATCGAAGA
1 GATCGAAGA
29090197 TACAAGTCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 31 0.65
45 17 0.35
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (45 bp):
GATCGAAGAAAGCAGATCTTGTCTTCACATACTGGTAGTGAAGTA
Found at i:29091788 original size:3 final size:3
Alignment explanation
Indices: 29091741--29091814 Score: 57
Period size: 3 Copynumber: 25.7 Consensus size: 3
29091731 ATTTAACATT
* * * * *
29091741 TTA TT- TTA TTCA TTT TTA TTA TAA TTA -TG TTA -TA CTA TGA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29091784 TTA TTA TTA TCA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29091815 CATACATGCG
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
2 7 0.13
3 45 0.82
4 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:29098897 original size:16 final size:16
Alignment explanation
Indices: 29098832--29098890 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
29098822 TTCGCTGTAT
29098832 TGGAATAGAGGCATAA
1 TGGAATAGAGGCATAA
29098848 TGGAATAGAGGCATAA
1 TGGAATAGAGGCATAA
29098864 TGGAATAGAGGCATAA
1 TGGAATAGAGGCATAA
*
29098880 TGGATTAGAGG
1 TGGAATAGAGG
29098891 TGTAATGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.41, C:0.05, G:0.34, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCATAA
Found at i:29098897 original size:32 final size:32
Alignment explanation
Indices: 29098827--29098897 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
29098817 TTTGGTTCGC
*
29098827 TGTATTGGAATAGAGGCATAATGGAATAGAGG
1 TGTAATGGAATAGAGGCATAATGGAATAGAGG
** *
29098859 CATAATGGAATAGAGGCATAATGGATTAGAGG
1 TGTAATGGAATAGAGGCATAATGGAATAGAGG
29098891 TGTAATG
1 TGTAATG
29098898 TAATGGTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.25
Consensus pattern (32 bp):
TGTAATGGAATAGAGGCATAATGGAATAGAGG
Found at i:29099136 original size:16 final size:16
Alignment explanation
Indices: 29099099--29099140 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29099089 TTAATCATAT
*
29099099 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
29099115 TT-AAATATATTATAA
1 TTAAAATATATTATAA
29099130 TTAAAATATAT
1 TTAAAATATAT
29099141 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:29099147 original size:14 final size:15
Alignment explanation
Indices: 29099108--29099149 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29099098 TTTAAACATA
*
29099108 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29099123 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29099137 A-TATAATTTAATA
1 ATTATAATTAAATA
29099150 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29099247 original size:120 final size:121
Alignment explanation
Indices: 29099102--29099784 Score: 1198
Period size: 120 Copynumber: 5.7 Consensus size: 121
29099092 ATCATATTTA
*
29099102 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT-AATCA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
29099166 ATATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
29099222 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT-AATTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
29099286 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
29099342 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAATATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
29099407 A-ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
29099462 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
29099527 AT-TTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
29099582 AACAAAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
29099647 AT-TTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * * * *
29099702 AACATAATTATTATTAAATATATTATAATTAAAATATATTAGTTATTTAAATTCTTGAT-AATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
29099766 ATTTTCTTATATGAATTTA
66 ATATTCTTATATGAATTTA
29099785 TACAATTTAA
Statistics
Matches: 544, Mismatches: 16, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
119 7 0.01
120 532 0.98
121 5 0.01
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:29099267 original size:14 final size:15
Alignment explanation
Indices: 29099218--29099269 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29099208 ATAAAATATA
29099218 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
29099233 TATTAAATATATTAT
1 AATTAAATATATTAT
29099248 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
29099261 AATTTAATA
1 AATTAAATA
29099270 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:29099366 original size:15 final size:15
Alignment explanation
Indices: 29099338--29099394 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
29099328 ATAAAATATA
29099338 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
29099353 TATTAAATATATTAT
1 AATTAAATATATTAT
29099368 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
29099381 AATTTAATAATATT
1 AATTAAAT-ATATT
29099395 CTTAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 9 0.26
14 6 0.17
15 19 0.54
16 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:29099498 original size:16 final size:16
Alignment explanation
Indices: 29099454--29099500 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29099444 TACTATAAAA
*
29099454 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
29099470 TATTATT-AAATATAT
1 TATAATTAAAATATAT
29099485 TATAATTAAAATATAT
1 TATAATTAAAATATAT
29099501 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:29099627 original size:14 final size:15
Alignment explanation
Indices: 29099588--29099629 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29099578 AATTAACAAA
*
29099588 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29099603 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29099617 A-TATAATTTAATA
1 ATTATAATTAAATA
29099630 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29099726 original size:15 final size:15
Alignment explanation
Indices: 29099699--29099753 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
29099689 TAAAATATAA
29099699 ATTAACATA-ATTATT
1 ATTAA-ATATATTATT
*
29099714 ATTAAATATATTATA
1 ATTAAATATATTATT
29099729 ATTAAAATATATTAGTT
1 ATT-AAATATATTA-TT
29099746 ATTTAAAT
1 A-TTAAAT
29099754 TCTTGATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 3 0.09
15 13 0.38
16 10 0.29
17 6 0.18
18 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
ATTAAATATATTATT
Found at i:29102816 original size:23 final size:23
Alignment explanation
Indices: 29102763--29102822 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
29102753 GGTGCAAGAA
*
29102763 ATGAAACAGGAAGAGGCTGAAAG
1 ATGAAACAGGAAGAGGCCGAAAG
**
29102786 -TGAAACAGGAAGAGGCCGATGG
1 ATGAAACAGGAAGAGGCCGAAAG
29102808 ATGAAACAGGAAGAG
1 ATGAAACAGGAAGAG
29102823 AAATTGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.45, C:0.10, G:0.37, T:0.08
Consensus pattern (23 bp):
ATGAAACAGGAAGAGGCCGAAAG
Found at i:29103883 original size:12 final size:12
Alignment explanation
Indices: 29103866--29103890 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29103856 GGTGTTCAGT
29103866 CGGTTAACCGAC
1 CGGTTAACCGAC
29103878 CGGTTAACCGAC
1 CGGTTAACCGAC
29103890 C
1 C
29103891 CGAAATTCTT
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:29104065 original size:9 final size:9
Alignment explanation
Indices: 29104051--29104187 Score: 202
Period size: 9 Copynumber: 14.6 Consensus size: 9
29104041 TTTGGTTAAA
29104051 AATTACCCG
1 AATTACCCG
29104060 AATTACCCG
1 AATTACCCG
29104069 AATTACCCG
1 AATTACCCG
*
29104078 ACTTACCCG
1 AATTACCCG
29104087 AATTACCCG
1 AATTACCCG
29104096 AATTACCCG
1 AATTACCCG
29104105 AATTACCCG
1 AATTACCCG
29104114 AATTACCCG
1 AATTACCCG
*
29104123 AAAATTACCCA
1 --AATTACCCG
29104134 AATTACCCG
1 AATTACCCG
29104143 AATTACCCG
1 AATTACCCG
29104152 AAAATTACCCG
1 --AATTACCCG
29104163 AAAATTACCCG
1 --AATTACCCG
29104174 AATTACCCG
1 AATTACCCG
29104183 AATTA
1 AATTA
29104188 AATCACTACA
Statistics
Matches: 120, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
9 92 0.77
11 28 0.23
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:29104216 original size:17 final size:17
Alignment explanation
Indices: 29104194--29104254 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
29104184 ATTAAATCAC
29104194 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
29104211 TACATAAATCTTTGAATCAC
1 TACAT-AA--TTAAAAACAT
*
29104231 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
29104248 TACATAA
1 TACATAA
29104255 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 2 0.06
19 2 0.06
20 11 0.34
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:29104236 original size:20 final size:20
Alignment explanation
Indices: 29104211--29104274 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
29104201 TTAAAAACAT
29104211 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
29104231 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
29104248 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
29104268 TACATAA
1 TACATAA
29104275 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 7 0.22
20 13 0.41
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:29104294 original size:37 final size:37
Alignment explanation
Indices: 29104188--29104300 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
29104178 ACCCGAATTA
* *
29104188 AATCACTACATAATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
29104225 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
29104262 AATCACTACATAATTAAAAATATTACACAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
29104298 AAT
1 AAT
29104301 TAAAACATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 67 0.92
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:29104368 original size:24 final size:24
Alignment explanation
Indices: 29104341--29104399 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
29104331 ATTCTCCATT
*
29104341 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
29104365 TATATTCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
29104389 TATCTCCATTT
1 TATATCCATTT
29104400 GCATTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:29107486 original size:16 final size:16
Alignment explanation
Indices: 29107465--29107498 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29107455 TTTTTTTTCT
*
29107465 TACATTAATTATAATA
1 TACATTAATTACAATA
29107481 TACATTAATTACAATA
1 TACATTAATTACAATA
29107497 TA
1 TA
29107499 TTCAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TACATTAATTACAATA
Found at i:29108423 original size:16 final size:17
Alignment explanation
Indices: 29108402--29108442 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
29108392 GCCTAAGAGA
29108402 AAATTGGGCT-GGATTT
1 AAATTGGGCTGGGATTT
* *
29108418 AAATTGGGTTGGGTTTT
1 AAATTGGGCTGGGATTT
29108435 AAATTGGG
1 AAATTGGG
29108443 AGGGAGTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.24, C:0.02, G:0.34, T:0.39
Consensus pattern (17 bp):
AAATTGGGCTGGGATTT
Found at i:29110879 original size:53 final size:53
Alignment explanation
Indices: 29110798--29110948 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
29110788 CTTACACGGT
* *
29110798 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
29110853 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
29110906 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
29110949 GCGCACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:29113134 original size:39 final size:39
Alignment explanation
Indices: 29113051--29113144 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
29113041 TGAAACCAAT
*
29113051 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGGTATAA
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
* * * *
29113089 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGG-CATAA
* *
29113128 TTCCAGCACGTAGCCTG
1 TACCAGCACGAAGCCTG
29113145 TGAACCTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 14 0.30
39 32 0.70
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (39 bp):
TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
Found at i:29113201 original size:39 final size:39
Alignment explanation
Indices: 29113118--29113204 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 39
29113108 GGACTTTAGC
* * * * *
29113118 CCGGACATATTTCCAGCACGTAGCCTGTGAACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGAACCCTAAGT
*
29113157 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGAACCCTAAGT
29113196 CCGGATATA
1 CCGGATATA
29113205 GCCTGCGGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGAACCCTAAGT
Found at i:29113205 original size:26 final size:26
Alignment explanation
Indices: 29113176--29113230 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
29113166 ATTCCAGCAC
29113176 ATAGCCTGCGGACCCTAAGTCCGGAT
1 ATAGCCTGCGGACCCTAAGTCCGGAT
*
29113202 ATAGCCTGCGGACCCTAAGTTCGGAT
1 ATAGCCTGCGGACCCTAAGTCCGGAT
29113228 ATA
1 ATA
29113231 CATCACTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (26 bp):
ATAGCCTGCGGACCCTAAGTCCGGAT
Found at i:29122589 original size:56 final size:56
Alignment explanation
Indices: 29122503--29122613 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
29122493 ATGTGAAAGA
29122503 TGATGGGTAATTTTTAAAAGTGGTTTATAATAAAGGTACTAAAAGGAATGATTTTT
1 TGATGGGTAATTTTTAAAAGTGGTTTATAATAAAGGTACTAAAAGGAATGATTTTT
*
29122559 TGATGGGTAATTTTTAAAAGTGGTTTATAATAAAGGTACTAAAAGGAATGGTTTT
1 TGATGGGTAATTTTTAAAAGTGGTTTATAATAAAGGTACTAAAAGGAATGATTTT
29122614 GCATGTCAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (56 bp):
TGATGGGTAATTTTTAAAAGTGGTTTATAATAAAGGTACTAAAAGGAATGATTTTT
Found at i:29123445 original size:19 final size:19
Alignment explanation
Indices: 29123421--29123458 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29123411 ATTCCATTAA
29123421 GTTGAATTGGAAAGTTGTT
1 GTTGAATTGGAAAGTTGTT
29123440 GTTGAATTGGAAAGTTGTT
1 GTTGAATTGGAAAGTTGTT
29123459 ACATGCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
GTTGAATTGGAAAGTTGTT
Found at i:29124312 original size:40 final size:40
Alignment explanation
Indices: 29124250--29124357 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
29124240 TGGAAAAAAA
29124250 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* * *
29124290 TATGACTGGGTTATGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
29124330 TATAACCGGGTTAAGTCTCGAAGGCATT
1 TATAACCGGGTTAAGTCCCGAAGGCATT
29124358 TGTGTTGGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:29133670 original size:27 final size:27
Alignment explanation
Indices: 29133615--29133672 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
29133605 CCACACGACT
* * ** *
29133615 TGGCACACGGCCTACCATACGGTCGTG
1 TGGCACACGACCTACCACACGACCCTG
29133642 TGGCACACGACCTACCACACGACCCTG
1 TGGCACACGACCTACCACACGACCCTG
29133669 TGGC
1 TGGC
29133673 GCTTAAGGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.16
Consensus pattern (27 bp):
TGGCACACGACCTACCACACGACCCTG
Found at i:29134991 original size:17 final size:17
Alignment explanation
Indices: 29134969--29135011 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29134959 GTTTCGCTTG
29134969 AATTAAATTAATTCT-AT
1 AATTAAATTAATT-TGAT
* *
29134986 AATTAATTTAATTTGGT
1 AATTAAATTAATTTGAT
29135003 AATTAAATT
1 AATTAAATT
29135012 TCCAACACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
AATTAAATTAATTTGAT
Found at i:29136136 original size:21 final size:20
Alignment explanation
Indices: 29136105--29136160 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 20
29136095 TTCTTAATCC
29136105 AATATACATTTCAATACCACAAT
1 AATAT-CATTTCAAT-CCA-AAT
*
29136128 AAT-TCATTT-AATTCAAAT
1 AATATCATTTCAATCCAAAT
29136146 AATATCATTTGCAAT
1 AATATCATTT-CAAT
29136161 TTCCATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.21
19 8 0.28
20 3 0.10
21 8 0.28
22 1 0.03
23 3 0.10
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATCATTTCAATCCAAAT
Found at i:29147168 original size:20 final size:20
Alignment explanation
Indices: 29147143--29147196 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
29147133 CGATACCAAT
**
29147143 TAAAAATATCGATAATTTTG
1 TAAAAATATCGATAATCGTG
* *
29147163 TAAAAATATTGATACTCGTG
1 TAAAAATATCGATAATCGTG
*
29147183 TAAATATATCGATA
1 TAAAAATATCGATA
29147197 CCATTGGGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (20 bp):
TAAAAATATCGATAATCGTG
Found at i:29152877 original size:15 final size:16
Alignment explanation
Indices: 29152848--29152877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29152838 CAAACATGCT
29152848 TTAACACATTATCAAA
1 TTAACACATTATCAAA
29152864 TTAACACA-TATCAA
1 TTAACACATTATCAA
29152878 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:29157039 original size:21 final size:24
Alignment explanation
Indices: 29157015--29157061 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
29157005 GATTAGGAGT
29157015 GTTAC-ATTTA-CTGG-TATCAGA
1 GTTACAATTTAGCTGGTTATCAGA
*
29157036 GTTACAATTTAGCTGGTTATTAGA
1 GTTACAATTTAGCTGGTTATCAGA
29157060 GT
1 GT
29157062 AAACGTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 5 0.23
23 4 0.18
24 8 0.36
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (24 bp):
GTTACAATTTAGCTGGTTATCAGA
Found at i:29164000 original size:43 final size:43
Alignment explanation
Indices: 29163871--29164005 Score: 148
Period size: 43 Copynumber: 3.2 Consensus size: 43
29163861 TAATGCCATA
* * * * * *
29163871 TCCCAGATATGGTCTTACATGTTATCACATATTGATGCCATTG
1 TCCCAGACATGGTCTTACATGTAATCTCATATCGATGCTAATG
* * *
29163914 TCCCAGACAGGGTCTTATATG-AA-ATCATATACGATGCTAATG
1 TCCCAGACATGGTCTTACATGTAATCTCATAT-CGATGCTAATG
* *
29163956 TCGCAGACATGGTCTTACACGTAATCTCATATCGATGCTAATG
1 TCCCAGACATGGTCTTACATGTAATCTCATATCGATGCTAATG
29163999 TCCCAGA
1 TCCCAGA
29164006 TGTAACACCC
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
41 5 0.07
42 26 0.35
43 37 0.50
44 6 0.08
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGTAATCTCATATCGATGCTAATG
Found at i:29165589 original size:70 final size:70
Alignment explanation
Indices: 29165504--29165658 Score: 310
Period size: 70 Copynumber: 2.2 Consensus size: 70
29165494 CTCAATAATG
29165504 TCGCACACTTAGTGCCCATATGATTCAAAAATATATATTAAGTCCGCACACTCAGTGCTATATAA
1 TCGCACACTTAGTGCCCATATGATTCAAAAATATATATTAAGTCCGCACACTCAGTGCTATATAA
29165569 TCAAC
66 TCAAC
29165574 TCGCACACTTAGTGCCCATATGATTCAAAAATATATATTAAGTCCGCACACTCAGTGCTATATAA
1 TCGCACACTTAGTGCCCATATGATTCAAAAATATATATTAAGTCCGCACACTCAGTGCTATATAA
29165639 TCAAC
66 TCAAC
29165644 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
29165659 TATATAATCA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 85 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (70 bp):
TCGCACACTTAGTGCCCATATGATTCAAAAATATATATTAAGTCCGCACACTCAGTGCTATATAA
TCAAC
Found at i:29165681 original size:28 final size:28
Alignment explanation
Indices: 29165618--29165715 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
29165608 ATATTAAGTC
*
29165618 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
29165645 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
29165673 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
29165702 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29165716 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:29185718 original size:25 final size:25
Alignment explanation
Indices: 29185681--29185733 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
29185671 CTCAGGGTAC
29185681 TACTAACAAGTTTAAATTTG-AGAAG
1 TACTAACAAGTTTAAATTTGTA-AAG
*
29185706 TACTAACATGTTTAAATTTGTAAAG
1 TACTAACAAGTTTAAATTTGTAAAG
29185731 TAC
1 TAC
29185734 ACCTCCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (25 bp):
TACTAACAAGTTTAAATTTGTAAAG
Found at i:29186361 original size:45 final size:45
Alignment explanation
Indices: 29186291--29186389 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
29186281 CGATGGATGG
* * *
29186291 TTTTATTTTGTTGGATCAGTTTGATGGATGTATTTTGATGTACGA
1 TTTTATTTTGTTGAATCAGTTTGATGGATGTATTTTGATGGACAA
*
29186336 TTTTATTTTGTTGAATCA-TTCTGATGGTTGTATTTTGATGGACAA
1 TTTTATTTTGTTGAATCAGTT-TGATGGATGTATTTTGATGGACAA
29186381 TTTATATTT
1 TTT-TATTT
29186390 ATCCTTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
44 2 0.04
45 41 0.85
46 5 0.10
ACGTcount: A:0.21, C:0.05, G:0.20, T:0.54
Consensus pattern (45 bp):
TTTTATTTTGTTGAATCAGTTTGATGGATGTATTTTGATGGACAA
Found at i:29187285 original size:56 final size:56
Alignment explanation
Indices: 29187204--29187316 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
29187194 GATTGAGACA
*
29187204 AATTTGATAAGATTTTATTTCTTTCTTTATTTAGGATTGAGCCAATCCTTGATTAT
1 AATTTGATAAGACTTTATTTCTTTCTTTATTTAGGATTGAGCCAATCCTTGATTAT
* * ***
29187260 AATTTGATGAGACTTTATTTGTTTCTTTATTTAGGATTGATTTAATCCTTGATTAT
1 AATTTGATAAGACTTTATTTCTTTCTTTATTTAGGATTGAGCCAATCCTTGATTAT
29187316 A
1 A
29187317 GGGATTCTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (56 bp):
AATTTGATAAGACTTTATTTCTTTCTTTATTTAGGATTGAGCCAATCCTTGATTAT
Found at i:29191449 original size:16 final size:16
Alignment explanation
Indices: 29191412--29191453 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29191402 TTAATCATAT
*
29191412 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
29191428 TT-AAATATATTATAA
1 TTAAAATATATTATAA
29191443 TTAAAATATAT
1 TTAAAATATAT
29191454 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:29191460 original size:14 final size:15
Alignment explanation
Indices: 29191421--29191462 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29191411 TTTAAACATA
*
29191421 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29191436 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29191450 A-TATAATTTAATA
1 ATTATAATTAAATA
29191463 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29191558 original size:120 final size:120
Alignment explanation
Indices: 29191410--29191707 Score: 569
Period size: 120 Copynumber: 2.5 Consensus size: 120
29191400 ATTTAATCAT
29191410 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
*
29191475 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTATTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
29191531 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
*
29191596 TCAATATTATTATATGAATTTACTCAAATCGTAATATATGATACTATAAAATATA
66 TCAATATTATTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
29191651 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
29191708 NGTTCTCATC
Statistics
Matches: 175, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 171 0.98
121 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
TCAATATTATTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:29191571 original size:16 final size:16
Alignment explanation
Indices: 29191527--29191573 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29191517 TACTATAAAA
*
29191527 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
29191543 TATTATT-AAATATAT
1 TATAATTAAAATATAT
29191558 TATAATTAAAATATAT
1 TATAATTAAAATATAT
29191574 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:29191645 original size:61 final size:61
Alignment explanation
Indices: 29191460--29191647 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
29191450 ATATAATTTA
*
29191460 ATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTATTAATAATCAATATTATTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * *
29191521 ATAAAA-TA-TAATTTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTATTAA--TAATCAAT-ATTATTATATGAATTTACTCA-AATCATAATATATGATACT
*
29191579 AATAAAATTATTAATAATCAATATTATTATATGAATTTACTCAAATCGTAATATATGATACT
1 -ATAAAATTATTAATAATCAATATTATTATATGAATTTACTCAAATCATAATATATGATACT
29191641 ATAAAAT
1 ATAAAAT
29191648 ATAATTTAAC
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
58 3 0.03
59 33 0.33
60 21 0.21
61 39 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (61 bp):
ATAAAATTATTAATAATCAATATTATTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:29191691 original size:16 final size:16
Alignment explanation
Indices: 29191647--29191693 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29191637 TACTATAAAA
*
29191647 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
29191663 TATTATT-AAATATAT
1 TATAATTAAAATATAT
29191678 TATAATTAAAATATAT
1 TATAATTAAAATATAT
29191694 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:29192830 original size:25 final size:25
Alignment explanation
Indices: 29192796--29192847 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29192786 AAGAATCAGT
29192796 AAACTTAAACAGACGGGACTGGTGA
1 AAACTTAAACAGACGGGACTGGTGA
29192821 AAACTTAAACAGACGGGACTGGTGA
1 AAACTTAAACAGACGGGACTGGTGA
29192846 AA
1 AA
29192848 TACAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (25 bp):
AAACTTAAACAGACGGGACTGGTGA
Found at i:29193197 original size:137 final size:138
Alignment explanation
Indices: 29192948--29193218 Score: 438
Period size: 137 Copynumber: 2.0 Consensus size: 138
29192938 AACTTAAAAT
* * *
29192948 TGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAACACTAG
1 TGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACACTAA
* * *
29193013 CTACAAAAGTAATTTAACAATATCATGTGGTAACAAGTTCACCTGAAAGTG-AGATATGAAAGAT
66 CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCA-ATATGAAAGAC
29193077 ATGCCCAAA
130 ATGCCCAAA
* *
29193086 TGAAATCATTTATGGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAACACTAA
1 TGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACACTAA
*
29193150 CTACAAAATTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAAGACA
66 CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAAGACA
29193215 TGCC
131 TGCC
29193219 ATTTTCTGAA
Statistics
Matches: 123, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
137 85 0.69
138 38 0.31
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (138 bp):
TGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACACTAA
CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAAGACA
TGCCCAAA
Found at i:29196702 original size:32 final size:32
Alignment explanation
Indices: 29196665--29196731 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
29196655 AATTTTAAGA
29196665 GAAAA-CGAAAGAGGAAAGAAAT-GAAAGATGTT
1 GAAAACCGAAAGA-GAAAGAAATGGAAA-ATGTT
* *
29196697 GAAAACCGAAAGAGAAATAGATGGAAAATGTT
1 GAAAACCGAAAGAGAAAGAAATGGAAAATGTT
29196729 GAA
1 GAA
29196732 GATGAAGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 20 0.65
33 11 0.35
ACGTcount: A:0.55, C:0.04, G:0.27, T:0.13
Consensus pattern (32 bp):
GAAAACCGAAAGAGAAAGAAATGGAAAATGTT
Found at i:29200828 original size:20 final size:20
Alignment explanation
Indices: 29200799--29200845 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
29200789 AGTCAGCCCC
29200799 CCATGCAGCAGCCAAGGTGG
1 CCATGCAGCAGCCAAGGTGG
* *
29200819 CCATGTAGCAGTCAAGGTGG
1 CCATGCAGCAGCCAAGGTGG
29200839 CCATGCA
1 CCATGCA
29200846 AGGAACGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.32, T:0.15
Consensus pattern (20 bp):
CCATGCAGCAGCCAAGGTGG
Found at i:29205303 original size:20 final size:20
Alignment explanation
Indices: 29205278--29205325 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
29205268 AGTCAGCCCC
*
29205278 CCATGCAGCAGCCAAGGTGG
1 CCATGCAACAGCCAAGGTGG
*
29205298 CCATGCAACAGTCAAGGTGG
1 CCATGCAACAGCCAAGGTGG
29205318 CCATGCAA
1 CCATGCAA
29205326 GGAACGTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.12
Consensus pattern (20 bp):
CCATGCAACAGCCAAGGTGG
Found at i:29206901 original size:21 final size:22
Alignment explanation
Indices: 29206860--29206916 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
29206850 TTAAAATTAA
*
29206860 AATTTTGTTTT-ATATTCTTTAT
1 AATTTT-TTTTAAAATTCTTTAT
29206882 AATTTTTTTTAAAATT-TTTAT
1 AATTTTTTTTAAAATTCTTTAT
*
29206903 AATTTTTTTGAAAA
1 AATTTTTTTTAAAA
29206917 ATATATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
AATTTTTTTTAAAATTCTTTAT
Found at i:29209950 original size:8 final size:8
Alignment explanation
Indices: 29209937--29209966 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
29209927 ATTTTTACCA
29209937 ATCTCTCT
1 ATCTCTCT
29209945 ATCTCTCT
1 ATCTCTCT
29209953 ATCTCTCT
1 ATCTCTCT
*
29209961 CTCTCT
1 ATCTCT
29209967 TAATCTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (8 bp):
ATCTCTCT
Found at i:29209972 original size:16 final size:17
Alignment explanation
Indices: 29209936--29209973 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
29209926 TATTTTTACC
29209936 AATCTCTCTATCTCTCT
1 AATCTCTCTATCTCTCT
*
29209953 -ATCTCTCTCTCTCT-T
1 AATCTCTCTATCTCTCT
29209968 AATCTC
1 AATCTC
29209974 CTTTGTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (17 bp):
AATCTCTCTATCTCTCT
Found at i:29212945 original size:5 final size:5
Alignment explanation
Indices: 29212920--29212956 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
29212910 TACTTACATG
29212920 TTATA -TATA -TATA TGTATA TTATA TTATA TTATA TTA
1 TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTA
29212957 ACAATTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.27
5 17 0.57
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:29220801 original size:5 final size:5
Alignment explanation
Indices: 29220780--29220818 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
29220770 CACCAACATG
*
29220780 AAAAG AAAAC AATAAC AAAAC AAAAC AAAAC AAAAC AAA
1 AAAAC AAAAC AA-AAC AAAAC AAAAC AAAAC AAAAC AAA
29220819 GAGCAACTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.79, C:0.15, G:0.03, T:0.03
Consensus pattern (5 bp):
AAAAC
Done.