Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 130 of 211
Found at i:41284465 original size:3 final size:3
Alignment explanation
Indices: 41284444--41284503 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
41284434 AGAGTTCATT
* * *
41284444 TTC TTC CTC TTC CTC TTC TTC TTC TTC TTC TTCC TT- TTC CTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC
*
41284489 TTC TTC TTT TTC TTC
1 TTC TTC TTC TTC TTC
41284504 GTCGTCGTCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:41284470 original size:21 final size:21
Alignment explanation
Indices: 41284445--41284496 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
41284435 GAGTTCATTT
* *
41284445 TCTTCCTCTTCCTCTTCTTCT
1 TCTTCTTCTTCCTCTTCCTCT
*
41284466 TCTTCTTCTTCCTTTTCCTCT
1 TCTTCTTCTTCCTCTTCCTCT
41284487 TCTTCTTCTT
1 TCTTCTTCTT
41284497 TTTCTTCGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTTCTTCTTCCTCTTCCTCT
Found at i:41284483 original size:27 final size:27
Alignment explanation
Indices: 41284444--41284503 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
41284434 AGAGTTCATT
41284444 TTCTTCCTCTTCCTCTTCTTCTTCTTC
1 TTCTTCCTCTTCCTCTTCTTCTTCTTC
* *
41284471 TTCTTCCTTTTCCTCTTCTTCTTCTTT
1 TTCTTCCTCTTCCTCTTCTTCTTCTTC
41284498 TTCTTC
1 TTCTTC
41284504 GTCGTCGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (27 bp):
TTCTTCCTCTTCCTCTTCTTCTTCTTC
Found at i:41287012 original size:15 final size:17
Alignment explanation
Indices: 41286977--41287009 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41286967 TTCTAATACT
41286977 ATATAAAATATTCTAAA
1 ATATAAAATATTCTAAA
*
41286994 ATATGAAATATT-TAAA
1 ATATAAAATATTCTAAA
41287010 TATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATAAAATATTCTAAA
Found at i:41288171 original size:12 final size:12
Alignment explanation
Indices: 41288154--41288181 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41288144 AATTTTTTTC
41288154 TTTTTTTCTTTA
1 TTTTTTTCTTTA
41288166 TTTTTTTCTTTA
1 TTTTTTTCTTTA
41288178 TTTT
1 TTTT
41288182 CCCTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTTA
Found at i:41288189 original size:20 final size:20
Alignment explanation
Indices: 41288145--41288192 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
41288135 CAATTTTTAA
**
41288145 ATTTTTTTCTTTTTTTCTTT
1 ATTTTTTTCTTTTTTTCCCT
41288165 ATTTTTTTCTTTATTTTCCCT
1 ATTTTTTTCTTT-TTTTCCCT
41288186 -TTTTTTT
1 ATTTTTTT
41288193 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (20 bp):
ATTTTTTTCTTTTTTTCCCT
Found at i:41297461 original size:27 final size:27
Alignment explanation
Indices: 41297430--41297484 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
41297420 CCTAGACATG
41297430 TATATATCTATTGCCACACTTTGTACT
1 TATATATCTATTGCCACACTTTGTACT
*
41297457 TATATATCTATTGTCACACTTTGTACT
1 TATATATCTATTGCCACACTTTGTACT
41297484 T
1 T
41297485 TGCAACTTGT
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:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (27 bp):
TATATATCTATTGCCACACTTTGTACT
Found at i:41298958 original size:25 final size:26
Alignment explanation
Indices: 41298929--41298984 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
41298919 TTAATTAGTA
*
41298929 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
41298953 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
41298979 TAAAAT
1 TAAAAT
41298985 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:41310206 original size:36 final size:37
Alignment explanation
Indices: 41310164--41310256 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
41310154 TCATAAGATT
* * * *
41310164 TAATCCAACC-AATACACGCCAATTGCTTTGAAGAGC
1 TAATCCAACCAAAAACACACCAATTGCTCTAAAGAGC
41310200 TAATCCAACCAAAAACACACCAATTGCTCTAAAGAGC
1 TAATCCAACCAAAAACACACCAATTGCTCTAAAGAGC
* *
41310237 TAGTCCAACCGAAAACACAC
1 TAATCCAACCAAAAACACAC
41310257 TAAAACAGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 10 0.20
37 40 0.80
ACGTcount: A:0.42, C:0.30, G:0.11, T:0.17
Consensus pattern (37 bp):
TAATCCAACCAAAAACACACCAATTGCTCTAAAGAGC
Found at i:41310675 original size:23 final size:24
Alignment explanation
Indices: 41310647--41310701 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
41310637 AATTATTAGC
*
41310647 TTACATTTCATATTCCAATTT-AT
1 TTACATTTCATATTCCAATTTAAG
41310670 TTACATTTCATATTCCAATTTAAG
1 TTACATTTCATATTCCAATTTAAG
41310694 TTACATTT
1 TTACATTT
41310702 TATACCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (24 bp):
TTACATTTCATATTCCAATTTAAG
Found at i:41310690 original size:13 final size:13
Alignment explanation
Indices: 41310651--41310690 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
41310641 ATTAGCTTAC
41310651 ATTTCATATTCCA
1 ATTTCATATTCCA
*
41310664 ATTT-AT-TTAC-
1 ATTTCATATTCCA
41310674 ATTTCATATTCCA
1 ATTTCATATTCCA
41310687 ATTT
1 ATTT
41310691 AAGTTACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.18
11 5 0.23
12 5 0.23
13 8 0.36
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTCATATTCCA
Found at i:41316603 original size:25 final size:25
Alignment explanation
Indices: 41316547--41316603 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
41316537 GACATATATC
* *
41316547 TTGATTTGATTTGATTTGGTTCCAA
1 TTGATTTGATTTGATTTGATTCAAA
** * *
41316572 TCAATTTGATTTTATTTTATTCAAA
1 TTGATTTGATTTGATTTGATTCAAA
41316597 TTGATTT
1 TTGATTT
41316604 AAAGGCTCAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (25 bp):
TTGATTTGATTTGATTTGATTCAAA
Found at i:41317882 original size:114 final size:113
Alignment explanation
Indices: 41317696--41318184 Score: 564
Period size: 114 Copynumber: 4.3 Consensus size: 113
41317686 AAAATAAGCA
*
41317696 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCG-TTTCTCGAGCT
1 TTAGCGGCGTTTTTG-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT-GAGCT
* *
41317759 TTC-GAGGATTTAGAGGAGTTTATAAG-AAAGCGTCGCTAATGCTCAGGGCT
64 TTCAG-GGATTTAGCGGAGTTT-TAAGTAAAGCGCCGCTAATGCTCAGGGCT
* * *
41317809 TTAGCGGCGTTTTTGGGAAGCGCCGCAAAAAAAACCTAAGCCCAACGATGCCATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
41317874 TCGGGGATTTAGCGGCGTTTTTAAG-GAAGCGCCGCTAATGC-CTAAGGCT
65 TCAGGGATTTAGCGGAG-TTTTAAGTAAAGCGCCGCTAATGCTC-AGGGCT
* * * *
41317923 TTAGCGGCGTTTTTGATAAAGTGTCGCAAAAAAACCTAAG-CCAACGACGCCGTTTCCTGAGCTT
1 TTAGCGGCGTTTTTG-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* **
41317987 TCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATG-TCCAGGGCT
65 TCAGGGATTTAGCGGAGTTTTAAGTAAAGCGCCGCTAATGCT-CAGGGCT
* * *
41318036 TTAGCGGAGTTTTTGGAAAAGCGCCGCAAAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGT
1 TTAGCGGCGTTTTTGG-AAAGCGCCGC--AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
** *
41318101 TTTCAGGGATTTAGC-GACGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
63 TTTCAGGGATTTAGCGGA-GTTTTAAGTAAAGCGCCGCTAATGCTCAGGGCT
* *
41318152 TTAGCGGCGTTTTTTGAAAAGCGCCGCTAAAAA
1 TTAGCGGCG-TTTTTGGAAAGCGCCGCAAAAAA
41318185 TATTTTATCT
Statistics
Matches: 326, Mismatches: 33, Indels: 33
0.83 0.08 0.08
Matches are distributed among these distances:
112 15 0.05
113 94 0.29
114 98 0.30
115 30 0.09
116 83 0.25
117 6 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CAGGGATTTAGCGGAGTTTTAAGTAAAGCGCCGCTAATGCTCAGGGCT
Found at i:41318018 original size:113 final size:114
Alignment explanation
Indices: 41317696--41318184 Score: 597
Period size: 113 Copynumber: 4.3 Consensus size: 114
41317686 AAAATAAGCA
*
41317696 TTAGCGGCGTTTTTGAGAAAGCGCCGC--AAAAAACCTAAGCCCAACGACGTCG-TTTCTCGAGC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCT-GAGC
* * ** *
41317758 TTTC-GAGGATTTAGAGGAGTTTATAAGAAAGCGTCGCTAATG-CTCAGGGCT
65 TTTCAG-GGATTTAGCGGCGTTT-TTGGAAAGCGCCGCTAATGCCT-AGGGCT
* * *
41317809 TTAGCGGCGTTTTTG-GGAAGCGCCGCAAAAAAAACCTAAGCCCAACGATGCCATTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
41317873 TTCGGGGATTTAGCGGCGTTTTTAAGG-AAGCGCCGCTAATGCCTAAGGCT
66 TTCAGGGATTTAGCGGCGTTTTT--GGAAAGCGCCGCTAATGCCTAGGGCT
* * * *
41317923 TTAGCGGCGTTTTTGATAAAGTGTCGC-AAAAAAACCTAAG-CCAACGACGCCGTTTCCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
41317986 TTCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGTCC-AGGGCT
66 TTCAGGGATTTAGCGGCGTTTTTGG-AAAGCGCCGCTAATG-CCTAGGGCT
* *
41318036 TTAGCGGAGTTTTTG-GAAAAGCGCCGCAAAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAG
1 TTAGCGGCGTTTTTGAG-AAAGCGCCGC-AAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAG
* * *
41318100 TTTTCAGGGATTTAGCGACGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
64 CTTTCAGGGATTTAGCGGCGTTTTTGG-AAAGCGCCGCTAATGCCTAGGGCT
*
41318152 TTAGCGGCGTTTTTTGA-AAAGCGCCGCTAAAAA
1 TTAGCGGCG-TTTTTGAGAAAGCGCCGCAAAAAA
41318185 TATTTTATCT
Statistics
Matches: 329, Mismatches: 29, Indels: 34
0.84 0.07 0.09
Matches are distributed among these distances:
111 2 0.01
112 10 0.03
113 99 0.30
114 92 0.28
115 36 0.11
116 84 0.26
117 6 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCAGGGATTTAGCGGCGTTTTTGGAAAGCGCCGCTAATGCCTAGGGCT
Found at i:41318163 original size:41 final size:41
Alignment explanation
Indices: 41318104--41318181 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
41318094 TCTGAGTTTT
*
41318104 CAGGGATTTAGCGACGTTTTTGGTAAAGCGCCGCTAATGCC
1 CAGGGATTTAGCGACGTTTTTGGAAAAGCGCCGCTAATGCC
* * *
41318145 CAGGGCTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAA
1 CAGGGATTTAGCGACGTTTTTGGAAAAGCGCCGCTAA
41318182 AAATATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (41 bp):
CAGGGATTTAGCGACGTTTTTGGAAAAGCGCCGCTAATGCC
Found at i:41318449 original size:15 final size:15
Alignment explanation
Indices: 41318429--41318459 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41318419 CATATTTTAA
41318429 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
41318444 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
41318459 G
1 G
41318460 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:41318773 original size:7 final size:7
Alignment explanation
Indices: 41318763--41318811 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
41318753 GATTTAAGGT
41318763 TTAGGGG
1 TTAGGGG
41318770 TTAGGGG
1 TTAGGGG
41318777 TTTAGGGG
1 -TTAGGGG
**
41318785 TTAGATG
1 TTAGGGG
41318792 TTAGGGG
1 TTAGGGG
* *
41318799 TTAAGAG
1 TTAGGGG
41318806 TTAGGG
1 TTAGGG
41318812 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:41318780 original size:15 final size:15
Alignment explanation
Indices: 41318759--41318826 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
41318749 TTGAGATTTA
41318759 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
41318774 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
41318789 ATG-TTAGGGGTTA-
1 AGGTTTAGGGGTTAG
*
41318802 AGAG-TTAGGGATTTA-
1 AG-GTTTAGGG-GTTAG
41318817 AGGTTTAGGG
1 AGGTTTAGGG
41318827 ATTCAGGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.02
14 18 0.40
15 26 0.58
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:41318824 original size:268 final size:263
Alignment explanation
Indices: 41318329--41318824 Score: 649
Period size: 268 Copynumber: 1.8 Consensus size: 263
41318319 ATTATTTAAA
* *
41318329 ATAATTGTAAAAGAGATAATAATAAAATTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTT
1 ATAATTGTAAAAGAGATAATAATAAAATTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
* * *
41318394 AAGATTTAAGGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGGTTTAGGGATTATG
66 AAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATTATG
* * *
41318459 GATTAGGGGTTGGGATTTAAGGTTTATGGGTTAGAGGGTTAGGGGTTTATGGATTAAAAGTTAGG
131 GATTAGGGGTTGGGA-TTAAGATTTAAGGGTTAGAGGGTTAGGGGTTTAGGGATTAAAAGTTAGG
* **
41318524 GATTCAGGGGTCGAGTTAGAGTTTTGGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATAT
195 GATTCA---G-AGAGTTAGAGTTTAAGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATAT
41318589 GTTCTTAT
256 GTTCTTAT
*
41318597 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
1 ATAATTGTAAAAGAGATAATAATAAAATTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
41318662 AAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGGTTATA
66 AAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTA-GGG-----
* * * * * *
41318727 ATTATGGATTATGGTTTAAGGG-TTGAGATTTAAGGTTTAG-GGGTTAGGGGTTTAGGGGTTAGA
125 ATTATGGATTAGGGGTT--GGGATTAAGATTTAAGGGTTAGAGGGTTAGGGGTTTAGGGATTAAA
* * *
41318790 TGTTAGGGGTT-A-AGAGTTAGGGATTTAAGGTTTAG
188 AGTTAGGGATTCAGAGAGTTAGAG-TTTAAGGTTTAG
41318825 GGATTCAGGG
Statistics
Matches: 198, Mismatches: 21, Indels: 18
0.84 0.09 0.08
Matches are distributed among these distances:
267 8 0.04
268 125 0.63
269 3 0.02
272 1 0.01
273 29 0.15
274 29 0.15
276 3 0.02
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.41
Consensus pattern (263 bp):
ATAATTGTAAAAGAGATAATAATAAAATTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
AAGATTTAAAGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATTATG
GATTAGGGGTTGGGATTAAGATTTAAGGGTTAGAGGGTTAGGGGTTTAGGGATTAAAAGTTAGGG
ATTCAGAGAGTTAGAGTTTAAGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCT
TAT
Found at i:41318923 original size:3 final size:3
Alignment explanation
Indices: 41318910--41318948 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
41318900 ATAATTGTAA
41318910 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41318949 ATCAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41319191 original size:23 final size:23
Alignment explanation
Indices: 41319147--41319191 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41319137 TTGATATATT
* *
41319147 TAAATTAGTTTAAATAGAATTAA
1 TAAATAAGTTTAAAAAGAATTAA
*
41319170 TAAATAAGTTTAAAAAGTATTA
1 TAAATAAGTTTAAAAAGAATTA
41319192 GATTGATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (23 bp):
TAAATAAGTTTAAAAAGAATTAA
Found at i:41319809 original size:147 final size:146
Alignment explanation
Indices: 41319414--41320603 Score: 1983
Period size: 146 Copynumber: 8.1 Consensus size: 146
41319404 TATTTTATAA
* * * *
41319414 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAA-ATAA-AAAAAA--TTTAGAATAGCAAAACGGCGTCGTTTTGTTCAA
41319479 AATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCT
62 AATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCT
41319544 ATAAAAACGCCGCAAAAAAT
127 ATAAAAACGCCGCAAAAAAT
* *
41319564 AAATCAATTTATAAAAAAAT-AAAAAATTTTAGAATAGCAAAACGGCGTCGTTTGGTTCAAAATG
1 AAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
* * *
41319628 AAAAAATTTTGCGGCGCTTTACAAGAAGCACCGCTAAAGGTAACCAATAACGGCGTTTTCTATAA
66 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATAA
41319693 AAACGCCGCAAAAAAT
131 AAACGCCGCAAAAAAT
41319709 AAATCAATTTATAAAAAAATAAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT
1 AAATCAATTTATAAAAAAAT-AAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT
*
41319774 GAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATA
65 GAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATA
41319839 AAAACGCCGCAAAAAAT
130 AAAACGCCGCAAAAAAT
* *
41319856 AAATCAATTTATAAAAAAA-ATAAAAAATTTCTAGAATAGCAAAATGGCGTCGTTTTGTTCAAAA
1 AAATCAATTTATAAAAAAATA-AAAAAAATT-TAGAATAGCAAAACGGCGTCGTTTTGTTCAAAA
*
41319920 TGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTAT
64 TGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTAT
41319985 AAAAACGCCGCAAAAAAT
129 AAAAACGCCGCAAAAAAT
41320003 AAATCAATTTATAAAAAAAATAAAAAAAA-TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT
1 AAATCAATTTAT-AAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT
* * *
41320067 GAAAAAATTTTGCGGCACTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGTCGTTTTCTATA
65 GAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATA
*
41320132 AAAACGCCACAAAAAAT
130 AAAACGCCGCAAAAAAT
* * *
41320149 AAATAAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCATCATTTTGTTCAAAATG
1 AAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
*
41320214 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCAGCGTTTTCTATAA
66 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATAA
41320279 AAACGCCGCAAAAAAT
131 AAACGCCGCAAAAAAT
* *
41320295 AAATCAATTTATAAAAAAAT-AAAAAATTTTAGAATAGCAAAACGGCGTCGTTTGGTTCAAAATG
1 AAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
* *
41320359 AAAAAATTTTGCGGCGCTTTACAAGAAGCGCCGCTAAAGGTAACCAATAACGGCGTTTTCTATAA
66 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATAA
41320424 AAACGCCGCAAAAAAT
131 AAACGCCGCAAAAAAT
* *
41320440 AAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAACAAAACGACGTCGTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
* * * * *
41320505 AAAAAAATTTGCGGCACTTTATAACAAGCGCCGTTAAAGGTAACCAATAGCGGTGTTTTCTATAA
66 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATAA
*
41320570 AAATGCCGCAAAAAAT
131 AAACGCCGCAAAAAAT
41320586 AAATCAATTTATAAAAAA
1 AAATCAATTTATAAAAAA
41320604 TTTCCCAAAA
Statistics
Matches: 982, Mismatches: 50, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
145 286 0.29
146 391 0.40
147 271 0.28
148 14 0.01
149 2 0.00
150 18 0.02
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (146 bp):
AAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAACCAATAGCGGCGTTTTCTATAA
AAACGCCGCAAAAAAT
Found at i:41320177 original size:21 final size:20
Alignment explanation
Indices: 41320142--41320180 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41320132 AAAACGCCAC
*
41320142 AAAAAATAAATAAATTTATA
1 AAAAAATAAAAAAATTTATA
41320162 AAAAAATAAAAAAAATTTA
1 AAAAAAT-AAAAAAATTTA
41320181 GAATAGCAAA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATAAAAAAATTTATA
Found at i:41320896 original size:15 final size:15
Alignment explanation
Indices: 41320876--41320905 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41320866 AAATCTCCCT
41320876 AAATCGATTCCCCAG
1 AAATCGATTCCCCAG
41320891 AAATCGATTCCCCAG
1 AAATCGATTCCCCAG
41320906 TAATGCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
AAATCGATTCCCCAG
Found at i:41322192 original size:16 final size:16
Alignment explanation
Indices: 41322171--41322203 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41322161 CAGCTGTAAG
41322171 TGTTCTTAACAATTCT
1 TGTTCTTAACAATTCT
41322187 TGTTCTTAACAATTCT
1 TGTTCTTAACAATTCT
41322203 T
1 T
41322204 TGCTTCTCTT
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:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
TGTTCTTAACAATTCT
Found at i:41325076 original size:13 final size:13
Alignment explanation
Indices: 41325058--41325100 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
41325048 TTTTATTTTG
*
41325058 ATTTAAAATTAGA
1 ATTTAAAATTAAA
*
41325071 ATTTAAAAATAAA
1 ATTTAAAATTAAA
* *
41325084 ATTCAAAATTACA
1 ATTTAAAATTAAA
41325097 ATTT
1 ATTT
41325101 TGCATTGAGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (13 bp):
ATTTAAAATTAAA
Found at i:41326677 original size:44 final size:44
Alignment explanation
Indices: 41326617--41326782 Score: 176
Period size: 43 Copynumber: 3.8 Consensus size: 44
41326607 TTTTTGGCAG
* * *
41326617 AAGCGCCGCAAAAGGTCATAATCTTTTAGCGGCGTTTGTAATAA
1 AAGCGCCGCTAAAGGTCATGATCTTTTAGCGGCGTTTGTAAGAA
* * * *
41326661 ATGCGTCGCTAAAGGTCCTGA-CCTTTAGCGGCGTTTGTAAGAA
1 AAGCGCCGCTAAAGGTCATGATCTTTTAGCGGCGTTTGTAAGAA
* * * ** **
41326704 AAGTGCCACTAAAGGTCCTGGCCTTTT-GCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGATCTTTTAGCGGCGTTTGTAAGAA
*
41326747 AAGCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCATGATCTTTTAGCGGCGTTT
41326783 TTTAAAAGCG
Statistics
Matches: 101, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
42 3 0.03
43 78 0.77
44 20 0.20
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (44 bp):
AAGCGCCGCTAAAGGTCATGATCTTTTAGCGGCGTTTGTAAGAA
Found at i:41326690 original size:43 final size:43
Alignment explanation
Indices: 41326641--41326782 Score: 185
Period size: 43 Copynumber: 3.3 Consensus size: 43
41326631 GTCATAATCT
* * * *
41326641 TTTAGCGGCGTTTGTAATAAATGCGTCGCTAAAGGTCCTGACC
1 TTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCCTGGCC
* *
41326684 TTTAGCGGCGTTTGTAAGAAAAGTGCCACTAAAGGTCCTGGCC
1 TTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCCTGGCC
* ** * *
41326727 TTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCCTGGCC
41326770 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
41326783 TTTAAAAGCG
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCCTGGCC
Found at i:41333891 original size:128 final size:128
Alignment explanation
Indices: 41333663--41333914 Score: 495
Period size: 128 Copynumber: 2.0 Consensus size: 128
41333653 AACTTACTGG
41333663 CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
1 CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
41333728 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGCACTT
66 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGCACTT
*
41333791 CAATTGTTGAGAAAATGTTATATGGCTTATTTTACTAAATACCATCTGACTCTTAGCACAATACA
1 CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
41333856 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGC
66 GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGC
41333915 TTTGAAGTGC
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (128 bp):
CAATTGTTGAGAAAATGTTATATGGCATATTTTACTAAATACCATCTGACTCTTAGCACAATACA
GACTAGGTGGTTCTAGATCAAAGGGGTAGAAATAGATTCAAGGGATAAAAAGTTTGAGCACTT
Found at i:41355946 original size:16 final size:16
Alignment explanation
Indices: 41355925--41355957 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41355915 TCTGCTTTTA
41355925 AAAAAAAAGAGAAAAT
1 AAAAAAAAGAGAAAAT
*
41355941 AAAAAAAAGGGAAAAT
1 AAAAAAAAGAGAAAAT
41355957 A
1 A
41355958 GAGAAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAAAAGAGAAAAT
Found at i:41359063 original size:17 final size:17
Alignment explanation
Indices: 41359043--41359081 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
41359033 TTGTTAGTTT
41359043 TTGATTAAAGGATT-GAA
1 TTGATTAAAGG-TTAGAA
*
41359060 TTGATTAAATGTTAGAA
1 TTGATTAAAGGTTAGAA
41359077 TTGAT
1 TTGAT
41359082 AGGGAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (17 bp):
TTGATTAAAGGTTAGAA
Found at i:41359762 original size:20 final size:20
Alignment explanation
Indices: 41359730--41359805 Score: 95
Period size: 19 Copynumber: 3.9 Consensus size: 20
41359720 TTATATGGGA
41359730 TTGCA-TTTCGGTGCCTCTGT
1 TTGCACTTT-GGTGCCTCTGT
41359750 TTGCACTTTGGTGCCTCTG-
1 TTGCACTTTGGTGCCTCTGT
* * *
41359769 TTACACTTCGGTTCC-CTGT
1 TTGCACTTTGGTGCCTCTGT
41359788 TTGCACTTTGGTGCCTCT
1 TTGCACTTTGGTGCCTCT
41359806 ATTACGCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.06
19 24 0.51
20 17 0.36
21 3 0.06
ACGTcount: A:0.07, C:0.28, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTGT
Found at i:41359789 original size:38 final size:39
Alignment explanation
Indices: 41359736--41359810 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
41359726 GGGATTGCAT
*
41359736 TTCGGTGCCTCTGTTTGCACTTTGGTGCCTCTGTTACAC
1 TTCGGTGCCTCTGTTTGCACTTTGGTGCCTCTATTACAC
*
41359775 TTCGGTTCC-CTGTTTGCACTTTGGTGCCTCTATTAC
1 TTCGGTGCCTCTGTTTGCACTTTGGTGCCTCTATTAC
41359811 GCATCTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.08, C:0.28, G:0.21, T:0.43
Consensus pattern (39 bp):
TTCGGTGCCTCTGTTTGCACTTTGGTGCCTCTATTACAC
Found at i:41367122 original size:12 final size:12
Alignment explanation
Indices: 41367092--41367124 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
41367082 ATAACTAATA
*
41367092 CTAACTACTCTG
1 CTAACTGCTCTG
41367104 CTAACTGCTCTG
1 CTAACTGCTCTG
41367116 CTAACTGCT
1 CTAACTGCT
41367125 AACTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (12 bp):
CTAACTGCTCTG
Found at i:41371773 original size:12 final size:12
Alignment explanation
Indices: 41371743--41371775 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
41371733 ATGACTAATA
*
41371743 CTAACTACTCTG
1 CTAACTGCTCTG
41371755 CTAACTGCTCTG
1 CTAACTGCTCTG
41371767 CTAACTGCT
1 CTAACTGCT
41371776 AACTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (12 bp):
CTAACTGCTCTG
Found at i:41376419 original size:24 final size:24
Alignment explanation
Indices: 41376379--41376427 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
41376369 ACTATTAAGA
*
41376379 TAAATATTAAATTTAAT-TTAATAT
1 TAAATATTAAATATAATATT-ATAT
41376403 TAAACTATTAAA-ATAATATTATAT
1 TAAA-TATTAAATATAATATTATAT
41376427 T
1 T
41376428 TGGAATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATATTAAATATAATATTATAT
Found at i:41379045 original size:51 final size:51
Alignment explanation
Indices: 41378981--41379197 Score: 353
Period size: 51 Copynumber: 4.3 Consensus size: 51
41378971 GATCACATTT
* *
41378981 ATCACTTGCCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
41379032 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
* * ** *
41379083 ATCACTTGTCACTTGTCACCGATCAGATAAGCGTAGCTAAAGCTGTCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
41379134 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
41379185 ATCTCTTGTCACT
1 ATCACTTGTCACT
41379198 GATCAGAAGT
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 154 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:41382297 original size:30 final size:30
Alignment explanation
Indices: 41382262--41382320 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
41382252 TCTAATTTGA
41382262 ACACAATAATCACTTGTTCATCCTAAAAAC
1 ACACAATAATCACTTGTTCATCCTAAAAAC
*
41382292 ACACAATAATCATTTGTTCATCCTAAAAA
1 ACACAATAATCACTTGTTCATCCTAAAAA
41382321 AAGACCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (30 bp):
ACACAATAATCACTTGTTCATCCTAAAAAC
Found at i:41384213 original size:12 final size:12
Alignment explanation
Indices: 41384196--41384239 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
41384186 AGAAGCTATT
*
41384196 AATTAAAATATA
1 AATTAAAAAATA
41384208 AATTAAAAAATA
1 AATTAAAAAATA
*
41384220 AAATAAAAAA-A
1 AATTAAAAAATA
41384231 AATTTAAAA
1 AA-TTAAAA
41384240 CATGTTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 3 0.11
12 25 0.89
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AATTAAAAAATA
Found at i:41387174 original size:2 final size:2
Alignment explanation
Indices: 41387167--41387198 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41387157 AGGTTTTTGC
41387167 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41387199 TTACTTCCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41389830 original size:12 final size:12
Alignment explanation
Indices: 41389813--41389839 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41389803 TAAGCCCTTT
41389813 TCAATATCAGTA
1 TCAATATCAGTA
41389825 TCAATATCAGTA
1 TCAATATCAGTA
41389837 TCA
1 TCA
41389840 GTTTAGCCTT
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:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (12 bp):
TCAATATCAGTA
Found at i:41391384 original size:28 final size:28
Alignment explanation
Indices: 41391352--41391425 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
41391342 TGACTTTCGA
*
41391352 CACTAAGTGTGAGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGGTAAAG
41391380 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGGTAAAG
*
41391408 TACTAAGTGTGCGAGTTT
1 CACTAAGTGTGCGAGTTT
41391426 GATTATTGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATGGTAAAG
Found at i:41391440 original size:28 final size:28
Alignment explanation
Indices: 41391352--41391447 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
41391342 TGACTTTCGA
* *
41391352 CACTAAGTGTGAGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGATAAAG
*
41391380 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGATAAAG
* * * **
41391408 TACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATGATAAAG
41391436 CACTAAGTGTGC
1 CACTAAGTGTGC
41391448 AAACTTATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATGATAAAG
Found at i:41392281 original size:93 final size:93
Alignment explanation
Indices: 41392184--41392772 Score: 1097
Period size: 93 Copynumber: 6.3 Consensus size: 93
41392174 AAATGCTGCT
* *
41392184 CAAATTGGTATATATATGCTACCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATATATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
41392249 CGGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
*
41392277 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
41392342 CTGTCAAATTTTGTGTATAAGTGTTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
41392370 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
41392435 CTGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
* *
41392463 CAAATTGGTATATATATGCCGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATATATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
41392528 CTGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
41392556 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
41392621 CTGTCAAATTTTGTGTATAAGTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
41392649 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
1 CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
*
41392714 CTGTCAAATTTTGTGTATAATTGCTGTC
66 CTGTCAAATTTTGTGTATAAGTGCTGTC
*
41392742 CAAATTGGTATATATATGCTGTCCAATTTTG
1 CAAATTGGTATATATATGCTGCCCAATTTTG
41392773 TATATATATA
Statistics
Matches: 483, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 483 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (93 bp):
CAAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATG
CTGTCAAATTTTGTGTATAAGTGCTGTC
Found at i:41392807 original size:27 final size:27
Alignment explanation
Indices: 41392191--41392819 Score: 168
Period size: 23 Copynumber: 26.7 Consensus size: 27
41392181 GCTCAAATTG
** *
41392191 GTATATATATGCTACCCAATTTTG-GT
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392217 G-A-ATAAATGCTGTCCAA--TT-T-T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392238 GTATATATATGCGGTCAAATTTTG--T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392263 GTATA-A-GTGCTGTCCAA-ATTG---
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392284 GTATATATATGCTGCCCAATTTTG-GT
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392310 G-A-ATAAATGTTGTCCAA--TT-T-T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392331 GTATATACATGCTGTCAAATTTTG--T
1 GTATATATATGCTGTCCAATTTTGTAT
* * *
41392356 GTATA-A-GTGTTGTCCAA-ATTG---
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392377 GTATATATATGCTGCCCAATTTTG-GT
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392403 G-A-ATAAATGCTGTCCAA--TT-T-T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392424 GTATATACATGCTGTCAAATTTTG--T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392449 GTATA-A-GTGCTGTCCAA-ATTG---
1 GTATATATATGCTGTCCAATTTTGTAT
* * *
41392470 GTATATATATGCCGCCCAATTTTG-GT
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392496 G-A-ATAAATGCTGTCCAA--TT-T-T
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392517 GTATATATATGCTGTCAAATTTTG--T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392542 GTATA-A-GTGCTGTCCAA-ATTG---
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392563 GTATATATATGCTGCCCAATTTTG-GT
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392589 G-A-ATAAATGCTGTCCAA--TT-T-T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392610 GTATATACATGCTGTCAAATTTTG--T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392635 GTATA-A-GTGCTGTCCAA-ATTG---
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392656 GTATATATATGCTGCCCAATTTTG-GT
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392682 G-A-ATAAATGCTGTCCAA--TT-T-T
1 GTATATATATGCTGTCCAATTTTGTAT
* *
41392703 GTATATACATGCTGTCAAATTTTG--T
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392728 GTATA-AT-TGCTGTCCAA-ATTG---
1 GTATATATATGCTGTCCAATTTTGTAT
41392749 GTATATATATGCTGTCCAATTTTGTAT
1 GTATATATATGCTGTCCAATTTTGTAT
*
41392776 ATATATATATGCTG-CTCAATTTCTG-AT
1 GTATATATATGCTGTC-CAATTT-TGTAT
*
41392803 GTATA-AGA-GCTGTCCAA
1 GTATATATATGCTGTCCAA
41392820 ACATGGTAGA
Statistics
Matches: 463, Mismatches: 70, Indels: 141
0.69 0.10 0.21
Matches are distributed among these distances:
21 42 0.09
22 43 0.09
23 181 0.39
24 99 0.21
25 61 0.13
26 10 0.02
27 25 0.05
28 2 0.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (27 bp):
GTATATATATGCTGTCCAATTTTGTAT
Found at i:41399620 original size:25 final size:25
Alignment explanation
Indices: 41399592--41399640 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41399582 TACAGTCTAT
* *
41399592 CTATAGTAGTCTCAGTATATACTAC
1 CTATAATAGTCTCAGGATATACTAC
*
41399617 CTATAATAGTTTCAGGATATACTA
1 CTATAATAGTCTCAGGATATACTA
41399641 TCAAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (25 bp):
CTATAATAGTCTCAGGATATACTAC
Found at i:41399649 original size:25 final size:25
Alignment explanation
Indices: 41399598--41399655 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
41399588 CTATCTATAG
* * * *
41399598 TAGTCTCAGTATATACTACCTATAA
1 TAGTTTCAGGATATACTACCAAAAA
*
41399623 TAGTTTCAGGATATACTATCAAAAA
1 TAGTTTCAGGATATACTACCAAAAA
41399648 TAGTTTCA
1 TAGTTTCA
41399656 AGAAACTTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (25 bp):
TAGTTTCAGGATATACTACCAAAAA
Found at i:41406256 original size:32 final size:30
Alignment explanation
Indices: 41406220--41406288 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
41406210 ATTGTAAAAC
*
41406220 AAAATAATACAAATGTGTTAAAATCATTAATT
1 AAAATAACACAAATGTGTTAAAATC--TAATT
* *
41406252 AAAATAACACAACTGTGTTAATATCTAATT
1 AAAATAACACAAATGTGTTAAAATCTAATT
41406282 ACAAATA
1 A-AAATA
41406289 TTTAATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 6 0.18
31 5 0.15
32 22 0.67
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (30 bp):
AAAATAACACAAATGTGTTAAAATCTAATT
Found at i:41409549 original size:4 final size:4
Alignment explanation
Indices: 41409533--41409581 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
41409523 ATGGCAATAG
* *
41409533 AAAT AATAT AAAT AAAT AAGT AAAT AAAT AAAT -AA- AAAT AAAT CAAT
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
41409580 AA
1 AA
41409582 CATGCGAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 4 0.11
4 30 0.79
5 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41410068 original size:23 final size:26
Alignment explanation
Indices: 41410042--41410092 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
41410032 TTTTAAATGT
41410042 ATGTATAT-TAT-TATAA-AAAAATA
1 ATGTATATGTATATATAATAAAAATA
* *
41410065 ATGTGTATGTATATATAATAATAATA
1 ATGTATATGTATATATAATAAAAATA
41410091 AT
1 AT
41410093 AATAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 3 0.13
25 5 0.22
26 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
ATGTATATGTATATATAATAAAAATA
Found at i:41410072 original size:29 final size:29
Alignment explanation
Indices: 41410039--41410095 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
41410029 TTTTTTTAAA
*
41410039 TGTATGTATATTATTATAA-AAAAATAATG
1 TGTATGTATA-TATAATAATAAAAATAATG
*
41410068 TGTATGTATATATAATAATAATAATAAT
1 TGTATGTATATATAATAATAAAAATAAT
41410096 AATAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
TGTATGTATATATAATAATAAAAATAATG
Found at i:41410087 original size:3 final size:3
Alignment explanation
Indices: 41410079--41410115 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41410069 GTATGTATAT
41410079 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41410116 ATAGGGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41411487 original size:43 final size:44
Alignment explanation
Indices: 41411423--41411534 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 44
41411413 CTTGGGTCTA
* * * *
41411423 CTCCACTGCAACTTCAAGGAGATAAAATTATCGG-TTTTATCTG
1 CTCCACTGCAACTTCAGGGAGATAAAATTATCGGCCTTAATATG
* * *
41411466 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCCTTAATATT
1 CTCCACTGCAACTTCAGGGAGATAAAATTATCGGCCTTAATATG
* *
41411510 CTCCACTGCAACTTTAGGGAAATAA
1 CTCCACTGCAACTTCAGGGAGATAA
41411535 GATTCGCCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 31 0.53
44 28 0.47
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAAATTATCGGCCTTAATATG
Found at i:41411529 original size:44 final size:43
Alignment explanation
Indices: 41411423--41411538 Score: 142
Period size: 44 Copynumber: 2.7 Consensus size: 43
41411413 CTTGGGTCTA
* * * * *
41411423 CTCCACTGCAACTTCAAGGAGATAAAATTATCGGTTTTATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTAATATG
* *
41411466 CTCCACTGCAACTTCAGGGAGATAAGATTATTGGCCTTAATATT
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGG-CTTAATATG
* *
41411510 CTCCACTGCAACTTTAGGGAAATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
41411539 CGCCCACTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
43 31 0.49
44 32 0.51
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTAATATG
Found at i:41411800 original size:132 final size:132
Alignment explanation
Indices: 41411563--41412028 Score: 706
Period size: 132 Copynumber: 3.5 Consensus size: 132
41411553 TGCCTCACTG
* * * *
41411563 CCAATATAAGAAGACAGGATCTGTTAT-TTTCGATCCACTTCATGCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAGGATCTGCTATCTTT-GATCTACTTCACGCCAATACATGAAGACAAGAT
* *
41411627 CTAG-TTTCTTCGATCCACTTCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCTACTT
65 CT-GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCTACTT
41411691 CCTA
129 CCTA
* *
41411695 CCAATATAGGAAGACAGGATCTG-TAATCTTTGATCTATTTCAAGCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAGGATCTGCT-ATCTTTGATCTACTTCACGCCAATACATGAAGACAAGAT
*
41411759 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC
65 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCTACTTC
41411824 CTA
130 CTA
* *
41411827 CCAATATAGGAAGACAGGATCTGCTACCTTTGATCTACTTCACGCCAATACATGAAGACGAGATC
1 CCAATATAGGAAGACAGGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
* * * * *
41411892 TGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCTTAGAT-TCATTTC
66 TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCT-ACTTC
41411956 CTA
130 CTA
* *
41411959 CAAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
1 CCAATATAGGAAGACAGGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
41412024 TGCTT
66 TGCTT
41412029 CTTTTTAGCC
Statistics
Matches: 308, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
131 2 0.01
132 302 0.98
133 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (132 bp):
CCAATATAGGAAGACAGGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCTACTTCC
TA
Found at i:41412026 original size:44 final size:44
Alignment explanation
Indices: 41411563--41412031 Score: 402
Period size: 44 Copynumber: 10.7 Consensus size: 44
41411553 TGCCTCACTG
* * * * * **
41411563 CCAATATAAGAAGACAGGATCTGTTATTTTCGATCCACTTCATG
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
* * * * *
41411607 CCAATACATGAAGACAAGATCTAG-TTTCTTCGATCCACTTCGCCA
1 CCAATATAGGAAGACAAGATCT-GCTATCTTCGATCTACTTC-ACA
* *
41411652 CCAATATGGGAAGACAAGATCTAC-ATCTTCGATCTACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-A
* * *
41411695 CCAATATAGGAAGACAGGATCTG-TAATCTTTGATCTATTTCA-A
1 CCAATATAGGAAGACAAGATCTGCT-ATCTTCGATCTACTTCACA
* * * *
41411738 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 -CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACA
* *
41411784 CCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-A
* * * *
41411827 CCAATATAGGAAGACAGGATCTGCTACCTTTGATCTACTTCACG
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
* * * *
41411871 CCAATACATGAAGACGAGATCTGCTTTCTTCGATCTACTTCACCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CA
* * * * *
41411916 CCAGTATGGGAAGACAAAATCTGC-ATCTTAGAT-TCATTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCT-ACTTCAC-A
* * *
41411959 CAAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
* *
41412003 CCAATACATGAAGACAAGATCTGCT-TCTT
1 CCAATATAGGAAGACAAGATCTGCTATCTT
41412032 TTTAGCCTGC
Statistics
Matches: 339, Mismatches: 66, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
42 3 0.01
43 70 0.21
44 201 0.59
45 64 0.19
46 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACA
Found at i:41422997 original size:38 final size:38
Alignment explanation
Indices: 41422955--41423030 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
41422945 CAAGTACTTG
41422955 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
1 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
41422993 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
1 ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
41423031 TTCGATTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (38 bp):
ATCTGGATCTCACAATTTTGCAGTGTTGTTTCTAGTTC
Found at i:41426781 original size:25 final size:25
Alignment explanation
Indices: 41426753--41426803 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
41426743 TTTTAAATGT
41426753 ATGTATAT-TATTATAAAAAATAATA
1 ATGTATATGTA-TATAAAAAATAATA
* * *
41426778 ATGTGTATGTATATATATAATAATA
1 ATGTATATGTATATAAAAAATAATA
41426803 A
1 A
41426804 AAATAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (25 bp):
ATGTATATGTATATAAAAAATAATA
Found at i:41426788 original size:31 final size:34
Alignment explanation
Indices: 41426750--41426813 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
41426740 TTTTTTTAAA
*
41426750 TGTATGTATAT-TATTAT-A-AAAAATAATAATG
1 TGTATGTATATATATAATAATAAAAATAATAATG
41426781 TGTATGTATATATATAATAATAAAAATAATAAT
1 TGTATGTATATATATAATAATAAAAATAATAAT
41426814 AATAACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 11 0.38
32 5 0.17
33 1 0.03
34 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.41
Consensus pattern (34 bp):
TGTATGTATATATATAATAATAAAAATAATAATG
Found at i:41429970 original size:41 final size:41
Alignment explanation
Indices: 41429925--41430004 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
41429915 TCGAAGCCTA
*
41429925 ATATAACACACCGGCACAAAGCCTACTAGGCACAAAACCTG
1 ATATAACACACCGGCACAAAGCCTACTAGACACAAAACCTG
* * * * *
41429966 ATATAATACATCGGCACGAAGCCTGCTAGACACATAACC
1 ATATAACACACCGGCACAAAGCCTACTAGACACAAAACC
41430005 CGAATATCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.15
Consensus pattern (41 bp):
ATATAACACACCGGCACAAAGCCTACTAGACACAAAACCTG
Found at i:41430067 original size:38 final size:38
Alignment explanation
Indices: 41430016--41430102 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
41430006 GAATATCATT
41430016 GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
1 GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
*
41430054 GGCACAGAGCCCGAATATCACCGGCACAAAGCCTGCTA
1 GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
*
41430092 GGCACAAAGCC
1 GGCACAGAGCC
41430103 TAAATAATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.33, C:0.34, G:0.23, T:0.09
Consensus pattern (38 bp):
GGCACAGAGCCCGAATATCACCAGCACAAAGCCTGCTA
Found at i:41430086 original size:22 final size:22
Alignment explanation
Indices: 41430003--41430086 Score: 63
Period size: 22 Copynumber: 4.1 Consensus size: 22
41429993 AGACACATAA
** *
41430003 CCCGAATATCATTGGCACAGAG
1 CCCGAATATCACCGGCACAAAG
*
41430025 CCCGAATATCACCAGCACAAAG
1 CCCGAATATCACCGGCACAAAG
* * *
41430047 CCTG---CT-A--GGCACAGAG
1 CCCGAATATCACCGGCACAAAG
41430063 CCCGAATATCACCGGCACAAAG
1 CCCGAATATCACCGGCACAAAG
41430085 CC
1 CC
41430087 TGCTAGGCAC
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
16 10 0.22
18 1 0.02
19 2 0.04
20 1 0.02
22 31 0.69
ACGTcount: A:0.33, C:0.35, G:0.20, T:0.12
Consensus pattern (22 bp):
CCCGAATATCACCGGCACAAAG
Found at i:41433470 original size:18 final size:19
Alignment explanation
Indices: 41433447--41433487 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
41433437 TTCATTTCGA
41433447 AAAATAATTAAA-TATTAT
1 AAAATAATTAAATTATTAT
*
41433465 AAAATAATTAAATTATTTT
1 AAAATAATTAAATTATTAT
41433484 AAAA
1 AAAA
41433488 ATATGAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATTAAATTATTAT
Found at i:41437917 original size:22 final size:22
Alignment explanation
Indices: 41437892--41437948 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 22
41437882 CCCTTTTGAC
41437892 ATTAAAATATTATTTTTAATTT
1 ATTAAAATATTATTTTTAATTT
*
41437914 ATT---AT-TT-TATTT-ATTT
1 ATTAAAATATTATTTTTAATTT
41437930 ATTAAAAATATTATTTTTA
1 ATT-AAAATATTATTTTTA
41437949 TAGTTGGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 13
0.63 0.05 0.32
Matches are distributed among these distances:
16 7 0.27
17 4 0.15
18 2 0.08
19 2 0.08
20 2 0.08
21 2 0.08
22 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTAAAATATTATTTTTAATTT
Found at i:41439181 original size:18 final size:19
Alignment explanation
Indices: 41439144--41439184 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
41439134 TAAATCTTAC
*
41439144 CAAACTAATTATAATAATT
1 CAAACTAATAATAATAATT
*
41439163 CAAAC-AATAATAATCATT
1 CAAACTAATAATAATAATT
41439181 CAAA
1 CAAA
41439185 AGAAACCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (19 bp):
CAAACTAATAATAATAATT
Found at i:41440918 original size:10 final size:10
Alignment explanation
Indices: 41440905--41441013 Score: 65
Period size: 10 Copynumber: 11.5 Consensus size: 10
41440895 TAAAAAAAAT
41440905 AAAATTTATA
1 AAAATTTATA
*
41440915 AAAA-TTATT
1 AAAATTTATA
*
41440924 AAATTTTAATA
1 AAAATTT-ATA
41440935 AATAA-TT-TA
1 AA-AATTTATA
*
41440944 AAATTTTATTA
1 AAAATTTA-TA
41440955 AAAA-TTAT-
1 AAAATTTATA
41440963 --AATTTA-A
1 AAAATTTATA
*
41440970 AAAAATTATA
1 AAAATTTATA
*
41440980 AAAAATTATA
1 AAAATTTATA
*
41440990 AAATTTTATA
1 AAAATTTATA
*
41441000 AAAA-TCATA
1 AAAATTTATA
41441009 AAAAT
1 AAAAT
41441014 AATTATAAGT
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 1 0.01
9 27 0.36
10 31 0.41
11 11 0.14
12 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATTTATA
Found at i:41440947 original size:20 final size:20
Alignment explanation
Indices: 41440903--41440982 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
41440893 TATAAAAAAA
41440903 ATAAAA-TTT-ATAAAAATT
1 ATAAAATTTTAATAAAAATT
*
41440921 ATTAAATTTTAATAAATAATT
1 ATAAAATTTTAATAAA-AATT
*
41440942 -TAAAATTTTATTAAAAATT
1 ATAAAATTTTAATAAAAATT
41440961 AT--AA-TTTAA-AAAAATT
1 ATAAAATTTTAATAAAAATT
41440977 ATAAAA
1 ATAAAA
41440983 AATTATAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
16 9 0.17
17 4 0.08
18 9 0.17
19 7 0.13
20 19 0.37
21 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAATTTTAATAAAAATT
Found at i:41440966 original size:25 final size:26
Alignment explanation
Indices: 41440936--41440990 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
41440926 ATTTTAATAA
** *
41440936 ATAATTT-AAAATTTTATTAAAAATT
1 ATAATTTAAAAAAATTATAAAAAATT
41440961 ATAATTTAAAAAAATTATAAAAAATT
1 ATAATTTAAAAAAATTATAAAAAATT
41440987 ATAA
1 ATAA
41440991 AATTTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAATTTAAAAAAATTATAAAAAATT
Found at i:41440967 original size:38 final size:36
Alignment explanation
Indices: 41440890--41440992 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 36
41440880 TGTGGCAAAA
*
41440890 AAATATAAAAAAA--ATAAAATTTATAAAAATTATT
1 AAATTTAAAAAAATTATAAAATTTATAAAAATTATT
41440924 AAATTTTAATAAATAATT-TAAAATTTTATTAAAAATTA-T
1 AAA-TTTAA-AAA-AATTATAAAA-TTTA-TAAAAATTATT
*
41440963 -AATTTAAAAAAATTATAAAAAATTATAAAA
1 AAATTTAAAAAAATTAT-AAAATTTATAAAA
41440993 TTTTATAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
34 3 0.05
35 13 0.22
36 10 0.17
37 11 0.19
38 7 0.12
39 5 0.09
40 9 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (36 bp):
AAATTTAAAAAAATTATAAAATTTATAAAAATTATT
Found at i:41440992 original size:8 final size:9
Alignment explanation
Indices: 41440887--41441013 Score: 71
Period size: 9 Copynumber: 13.7 Consensus size: 9
41440877 ACATGTGGCA
*
41440887 AAAAAATAT
1 AAAAATTAT
**
41440896 AAAAAAAAT
1 AAAAATTAT
*
41440905 AAAATTTAT
1 AAAAATTAT
41440914 AAAAATTATT
1 AAAAATTA-T
**
41440924 AAATTTTAAT
1 AAAAATT-AT
41440934 AAATAATT-T
1 AAA-AATTAT
*
41440943 AAAATTTTATT
1 AAAA-ATTA-T
41440954 AAAAATTAT
1 AAAAATTAT
* *
41440963 --AATTTAA
1 AAAAATTAT
41440970 AAAAATTAT
1 AAAAATTAT
41440979 AAAAAATTAT
1 -AAAAATTAT
*
41440989 AAAATTTTAT
1 AAAA-ATTAT
*
41440999 AAAAATCAT
1 AAAAATTAT
41441008 AAAAAT
1 AAAAAT
41441014 AATTATAAGT
Statistics
Matches: 90, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
9 46 0.51
10 30 0.33
11 8 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41441009 original size:19 final size:18
Alignment explanation
Indices: 41440971--41441011 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
41440961 ATAATTTAAA
*
41440971 AAAATTATAAAAAATTAT
1 AAAATTATAAAAAATCAT
*
41440989 AAAATTTTATAAAAATCAT
1 AAAATTATA-AAAAATCAT
41441008 AAAA
1 AAAA
41441012 ATAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATTATAAAAAATCAT
Found at i:41441009 original size:29 final size:29
Alignment explanation
Indices: 41440954--41441021 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
41440944 AAATTTTATT
*
41440954 AAAAATTAT--AATTTAAAAAAATTAT-A
1 AAAAATTATAAAATTTAAAAAAATCATAA
*
41440980 AAAAATTATAAAATTTTATAAAAATCATAA
1 AAAAATTATAAAA-TTTAAAAAAATCATAA
41441010 AAATAATTATAA
1 AAA-AATTATAA
41441022 GTGCATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 9 0.26
28 2 0.06
29 12 0.34
30 4 0.11
31 8 0.23
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAATTATAAAATTTAAAAAAATCATAA
Found at i:41441920 original size:20 final size:20
Alignment explanation
Indices: 41441895--41441949 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
41441885 TACGATAATG
41441895 TTTATAATTTTTTTACGA-AT
1 TTTATAATTTTTTTAC-ATAT
* *
41441915 TTTAT-ATTTCTTTACATTT
1 TTTATAATTTTTTTACATAT
*
41441934 TTTATAATTTTCTTAC
1 TTTATAATTTTTTTAC
41441950 CACTTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTATAATTTTTTTACATAT
Found at i:41442044 original size:18 final size:19
Alignment explanation
Indices: 41442023--41442069 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
41442013 TTTATAAAAA
41442023 TTACATTTTTTATA-TTTT
1 TTACATTTTTTATACTTTT
41442041 TTACGA-TTTTTATACTTTT
1 TTAC-ATTTTTTATACTTTT
* *
41442060 ATATATTTTT
1 TTACATTTTT
41442070 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (19 bp):
TTACATTTTTTATACTTTT
Found at i:41442069 original size:36 final size:39
Alignment explanation
Indices: 41441985--41442071 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 39
41441975 TTCTATATTC
*
41441985 ATATATATTTTATAATTATTTTATGATTTTTATAAAAATT
1 ATATAT-TTTTATAATTATTTTACGATTTTTATAAAAATT
* ***
41442025 ACAT-TTTTTAT-ATT-TTTTACGATTTTTAT-ACTTTT
1 ATATATTTTTATAATTATTTTACGATTTTTATAAAAATT
41442060 ATATATTTTTAT
1 ATATATTTTTAT
41442072 TAAAATTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
35 6 0.15
36 21 0.52
37 3 0.08
38 6 0.15
39 1 0.03
40 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.62
Consensus pattern (39 bp):
ATATATTTTTATAATTATTTTACGATTTTTATAAAAATT
Found at i:41442094 original size:19 final size:19
Alignment explanation
Indices: 41442064--41442110 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
41442054 ACTTTTATAT
41442064 ATTTTTATTAAAATTTAATC
1 ATTTTTA-TAAAATTTAATC
* * *
41442084 ATTTTTATAAATTTTATTG
1 ATTTTTATAAAATTTAATC
41442103 ATTTTTAT
1 ATTTTTAT
41442111 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTTATAAAATTTAATC
Found at i:41442097 original size:18 final size:18
Alignment explanation
Indices: 41441953--41442110 Score: 56
Period size: 19 Copynumber: 8.3 Consensus size: 18
41441943 TTCTTACCAC
*
41441953 TTTATAAAATTTTATAATTTT
1 TTTAT-AAA-TTTAT-ATATT
* * *
41441974 TTTCTATATTCATATATAT
1 TTTATAAATTTATATAT-T
41441993 TTTATAATTATTT-TATGATT
1 TTTATAA--ATTTATAT-ATT
* *
41442013 TTTATAAAAATTACAT-TT
1 TTTAT-AAATTTATATATT
* * *
41442031 TTTAT-ATTTTTTACGATT
1 TTTATAAATTTATA-TATT
**
41442049 TTTATACTTTTATATATT
1 TTTATAAATTTATATATT
41442067 TTTATTAAAATTTA-ATCATT
1 TTTA-T-AAATTTATAT-ATT
41442087 TTTATAAATTT-TATTGATT
1 TTTATAAATTTATA-T-ATT
41442106 TTTAT
1 TTTAT
41442111 TTTTTATTAT
Statistics
Matches: 103, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
16 4 0.04
18 31 0.30
19 32 0.31
20 25 0.24
21 11 0.11
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTATAAATTTATATATT
Found at i:41444798 original size:31 final size:33
Alignment explanation
Indices: 41444763--41444831 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
41444753 AAATATTATT
* *
41444763 TTTAAGTA-ATTAGTATTAATTAT-TTTTAAA-A
1 TTTAAGTAGAATA-TATAAATTATATTTTAAATA
*
41444794 TTTAATTAGAATATATAAATTATATTTTAAATA
1 TTTAAGTAGAATATATAAATTATATTTTAAATA
41444827 TTTAA
1 TTTAA
41444832 ATATAATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.50
32 10 0.31
33 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (33 bp):
TTTAAGTAGAATATATAAATTATATTTTAAATA
Found at i:41444846 original size:33 final size:31
Alignment explanation
Indices: 41444780--41444850 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
41444770 AATTAGTATT
*
41444780 AATTATTTTTAAAATTTAATTAGAATATATA
1 AATTATTTTTAAAATTTAAATAGAATATATA
*
41444811 AATTATATTTTAAATATTTAAATATAATCAT-TA
1 AATTAT-TTTTAAA-ATTTAAATAGAAT-ATATA
41444844 AA-TATTT
1 AATTATTT
41444851 ATAATTAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 8 0.23
32 10 0.29
33 15 0.43
34 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
AATTATTTTTAAAATTTAAATAGAATATATA
Found at i:41444864 original size:21 final size:19
Alignment explanation
Indices: 41444798--41444865 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
41444788 TTAAAATTTA
*
41444798 ATTAGAATATATAAATTATAT
1 ATTA-AATATTTAAATTA-AT
*
41444819 TTTAAATATTTAAATATAAT
1 ATTAAATATTTAAAT-TAAT
41444839 CATTAAATATTTATAATTAGAT
1 -ATTAAATATTTA-AATTA-AT
41444861 ATTAA
1 ATTAA
41444866 TACAGTTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 12 0.30
21 23 0.57
22 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTAAATATTTAAATTAAT
Found at i:41447906 original size:38 final size:38
Alignment explanation
Indices: 41447860--41447958 Score: 191
Period size: 37 Copynumber: 2.6 Consensus size: 38
41447850 ACCAAAAATT
41447860 TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
41447898 TATTTTAAAATTAAAAAAT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
41447935 TATTTTAAAATTAAAAAATAAAAA
1 TATTTTAAAATTAAAAAATAAAAA
41447959 TATTTATTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
37 37 0.62
38 23 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (38 bp):
TATTTTAAAATTAAAAAATAAAAAAAGTATTTTAAAAA
Found at i:41447916 original size:18 final size:18
Alignment explanation
Indices: 41447893--41447954 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
41447883 AAAGTATTTT
41447893 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
** *
41447911 AAAAATA--AAAAAGTATTTT
1 AAAAATATTTTAAA--A-TTA
41447930 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
41447948 AAAAATA
1 AAAAATA
41447955 AAAATATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
16 3 0.09
18 17 0.52
19 10 0.30
21 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAATATTTTAAAATTA
Found at i:41453871 original size:17 final size:18
Alignment explanation
Indices: 41453837--41453882 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
41453827 CCGTTATGTC
41453837 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
41453852 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
41453869 CGCGACCGCGACCG
1 CGCGACCGCGACCG
41453883 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:41456536 original size:92 final size:91
Alignment explanation
Indices: 41456379--41456587 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
41456369 TTGATTTTAG
** *
41456379 TAAATTCATATAAGAACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
41456444 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
41456471 TAAATTCATATAAGAAAATTTATTATCAAGTATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
41456535 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
41456563 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
41456588 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 28 0.27
92 70 0.69
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:41456749 original size:120 final size:120
Alignment explanation
Indices: 41456610--41457255 Score: 1172
Period size: 120 Copynumber: 5.4 Consensus size: 120
41456600 TTAAATTATT
* * * *
41456610 TTAAATCATATATTATAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTATAG
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
* *
41456672 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
41456730 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
41456795 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
41456850 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
*
41456915 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
41456970 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
*
41457035 CATATATTATGATTTCTGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
41457090 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
41457155 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
41457210 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
41457256 TAAATATGAT
Statistics
Matches: 513, Mismatches: 10, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
119 6 0.01
120 505 0.98
121 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
Found at i:41456752 original size:18 final size:17
Alignment explanation
Indices: 41456724--41456758 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41456714 ATTATTAAGA
*
41456724 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41456741 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41456759 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:41456872 original size:18 final size:17
Alignment explanation
Indices: 41456844--41456878 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41456834 ATTATTAAGA
*
41456844 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41456861 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41456879 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:41457112 original size:18 final size:17
Alignment explanation
Indices: 41457084--41457118 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41457074 ATTATTAAGA
*
41457084 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41457101 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41457119 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:41457232 original size:18 final size:17
Alignment explanation
Indices: 41457204--41457238 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41457194 ATTATTAAGA
*
41457204 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41457221 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41457239 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:41457452 original size:44 final size:45
Alignment explanation
Indices: 41457403--41457493 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
41457393 ACCTCTATTC
* * *
41457403 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
41457447 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
41457492 CA
1 CA
41457494 CCTCTAATCC
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:41457495 original size:16 final size:16
Alignment explanation
Indices: 41457474--41457542 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
41457464 GATTAGCTAT
41457474 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41457490 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
41457507 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
41457523 TACGCCTTTAATCCAA
1 TACACCTCTAATCCAA
41457539 TACA
1 TACA
41457543 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
16 33 0.67
17 16 0.33
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:41457516 original size:33 final size:32
Alignment explanation
Indices: 41457474--41457542 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
41457464 GATTAGCTAT
41457474 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
* *
41457507 TACACCTCTAATCCAATACGCCTTTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
41457539 TACA
1 TACA
41457543 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:41465991 original size:39 final size:39
Alignment explanation
Indices: 41465882--41465998 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 39
41465872 TAGCAACTAT
* **
41465882 CAAAATCTCTCAACTATTACTAAATTCCCTATTGGAAAC
1 CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAAC
*
41465921 CAAAATCTCTCAAATCATCACTAAATTTTCTATTGGAAAC
1 CAAAATCTCTCAACT-ATCACTAAATTTTCTATTGGAAAC
41465961 CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAA
1 CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAA
41465999 ATAAATTCCA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 37 0.51
40 35 0.49
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.32
Consensus pattern (39 bp):
CAAAATCTCTCAACTATCACTAAATTTTCTATTGGAAAC
Found at i:41466131 original size:39 final size:38
Alignment explanation
Indices: 41466011--41466152 Score: 124
Period size: 39 Copynumber: 3.7 Consensus size: 38
41466001 AAATTCCATA
* * * * *
41466011 ACTAAAATTCCTACTGGAAAATCAATTTTGTAACAAAAT
1 ACTAAAATTCCTATTGAAAAAAC-ATTTTTTAACCAAAT
* * * * * *
41466050 ACTAAAATTTCTATTGAAAAACAAAATCTTTCAA-CTATT
1 ACTAAAATTCCTATTG-AAAA-AACATTTTTTAACCAAAT
41466089 ACTAAAATTCCTATTGAAAAAACATTTTTATAACCAAAT
1 ACTAAAATTCCTATTGAAAAAACATTTTT-TAACCAAAT
* *
41466128 ACTATAATTCCTATTGAAAACACAT
1 ACTAAAATTCCTATTGAAAAAACAT
41466153 GTGACTAGGT
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
37 7 0.09
38 6 0.08
39 57 0.71
40 9 0.11
41 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.33
Consensus pattern (38 bp):
ACTAAAATTCCTATTGAAAAAACATTTTTTAACCAAAT
Found at i:41466246 original size:21 final size:21
Alignment explanation
Indices: 41466220--41466268 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41466210 ATTCTAGAAA
41466220 TTATAATGTCAAAAATTAATT
1 TTATAATGTCAAAAATTAATT
* ** *
41466241 TTATAATTTGTAAAATTATTT
1 TTATAATGTCAAAAATTAATT
41466262 TTATAAT
1 TTATAAT
41466269 TTTCATACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
TTATAATGTCAAAAATTAATT
Found at i:41466269 original size:21 final size:21
Alignment explanation
Indices: 41466231--41466270 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41466221 TATAATGTCA
41466231 AAAATTAATTTTATAATTTGT
1 AAAATTAATTTTATAATTTGT
*
41466252 AAAATTATTTTTATAATTT
1 AAAATTAATTTTATAATTT
41466271 TCATACAATT
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:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AAAATTAATTTTATAATTTGT
Found at i:41466287 original size:22 final size:20
Alignment explanation
Indices: 41466231--41466294 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
41466221 TATAATGTCA
*
41466231 AAAATTAATTTTATAATTTGT
1 AAAATTATTTTTATAATTT-T
41466252 AAAATTATTTTTATAATTTT
1 AAAATTATTTTTATAATTTT
*
41466272 CATACAATT-TTTTTATGATTTT
1 -A-A-AATTATTTTTATAATTTT
41466294 A
1 A
41466295 TATAATACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.03
21 20 0.53
22 13 0.34
23 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
AAAATTATTTTTATAATTTT
Found at i:41469914 original size:15 final size:15
Alignment explanation
Indices: 41469896--41469925 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41469886 TCTCTTTTCT
41469896 TTATACAAATAAGCA
1 TTATACAAATAAGCA
41469911 TTATACAAATAAGCA
1 TTATACAAATAAGCA
41469926 AGTACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
TTATACAAATAAGCA
Found at i:41470128 original size:3 final size:3
Alignment explanation
Indices: 41470120--41470153 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41470110 CTAAAAATAG
41470120 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41470154 TTTGCTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41471626 original size:31 final size:30
Alignment explanation
Indices: 41471588--41471733 Score: 116
Period size: 31 Copynumber: 5.0 Consensus size: 30
41471578 GGCCCATTTT
41471588 TATTTTAAAAATTTTTAAAAATTAAAAAAA
1 TATTTTAAAAATTTTTAAAAATTAAAAAAA
**
41471618 GTATTTTAAAAATATTTTTAAAATATT--TTAAA
1 -TATTTT-AAAA-ATTTTTAAAA-ATTAAAAAAA
*
41471650 -A-TTTAAAAA-ATTT---AA--AAAAAAA
1 TATTTTAAAAATTTTTAAAAATTAAAAAAA
41471672 TATTTTAAAAATATTTT-AAAATTAAAAAAA
1 TATTTTAAAAAT-TTTTAAAAATTAAAAAAA
*
41471702 GTATTTTAAAAATATTTTAAAATTTAAAAAAA
1 -TATTTTAAAAAT-TTTTAAAAATTAAAAAAA
41471734 ATTAAAAAAG
Statistics
Matches: 93, Mismatches: 7, Indels: 29
0.72 0.05 0.22
Matches are distributed among these distances:
22 4 0.04
23 2 0.02
24 8 0.09
26 6 0.06
27 1 0.01
28 6 0.06
29 3 0.03
30 8 0.09
31 23 0.25
32 19 0.20
33 10 0.11
34 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
TATTTTAAAAATTTTTAAAAATTAAAAAAA
Found at i:41471650 original size:53 final size:52
Alignment explanation
Indices: 41471588--41471693 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 52
41471578 GGCCCATTTT
* *
41471588 TATTTTAAAAATTTTTAAAAA-TT-AAAAAAAGTATTTTAAAAATATTTTTAAAA
1 TATTTT-AAAA-TTTAAAAAATTTAAAAAAAAATATTTTAAAAATA-TTTTAAAA
41471641 TATTTTAAAATTTAAAAAATTTAAAAAAAAATATTTTAAAAATATTTTAAAA
1 TATTTTAAAATTTAAAAAATTTAAAAAAAAATATTTTAAAAATATTTTAAAA
41471693 T
1 T
41471694 TAAAAAAAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
51 8 0.16
52 15 0.31
53 26 0.53
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (52 bp):
TATTTTAAAATTTAAAAAATTTAAAAAAAAATATTTTAAAAATATTTTAAAA
Found at i:41471651 original size:42 final size:41
Alignment explanation
Indices: 41471588--41471766 Score: 179
Period size: 42 Copynumber: 4.3 Consensus size: 41
41471578 GGCCCATTTT
* *
41471588 TATTTTAAAAATTTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTTAAAATTTTT-AAAATTAAAAAAAGTATTTAAAAAA
* *
41471630 TATTTTTAAAATATTTTAAAATTTAAAAAA-T-TTAAAAAAAAA
1 TATTTTTAAAAT-TTTTAAAATTAAAAAAAGTATT--TAAAAAA
* *
41471672 TATTTTAAAAATATTTTAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTTAAAAT-TTTTAAAATTAAAAAAAGTATTTAAAAAA
** *
41471714 TA-TTTTAAAATTTAAAAAAAATT-AAAAAAGTATGTAAAAAA
1 TATTTTTAAAATTT--TTAAAATTAAAAAAAGTATTTAAAAAA
41471755 TA-TTTTAAAATT
1 TATTTTTAAAATT
41471767 AAAAAAATAA
Statistics
Matches: 117, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
40 4 0.03
41 37 0.32
42 69 0.59
43 5 0.04
44 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (41 bp):
TATTTTTAAAATTTTTAAAATTAAAAAAAGTATTTAAAAAA
Found at i:41471735 original size:84 final size:83
Alignment explanation
Indices: 41471588--41471764 Score: 236
Period size: 84 Copynumber: 2.1 Consensus size: 83
41471578 GGCCCATTTT
* *
41471588 TATTTTAAAAATTTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATTTTAAAATT
1 TATTTTAAAAATTTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATA-TTAAAAAAT
*
41471653 TAAAAAA-TTTAAAAAAAAA
65 TAAAAAAGTAT-AAAAAAAA
41471672 TATTTTAAAAATATTTT-AAAATTAAAAAAAGTATTTTAAAAATA-TTTTAAAAT-TTAAAAAAA
1 TATTTTAAAAAT-TTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATT--AAAAA
**
41471734 ATTAAAAAAGTATGTAAAAAA
63 ATTAAAAAAGTATAAAAAAAA
41471755 TATTTTAAAA
1 TATTTTAAAA
41471765 TTAAAAAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
81 2 0.02
83 37 0.44
84 41 0.49
85 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (83 bp):
TATTTTAAAAATTTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATTAAAAAATT
AAAAAAGTATAAAAAAAA
Found at i:41471766 original size:41 final size:41
Alignment explanation
Indices: 41471604--41471773 Score: 94
Period size: 41 Copynumber: 4.1 Consensus size: 41
41471594 AAAAATTTTT
* * ***
41471604 AAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATTTT
1 AAAAATTAAAAAAAGTATGTAAAAAATA-TTTTAAAAT-TAAA
* ** ** * **
41471647 AAAATTTAAAAAATTTA-AAAAAAAATATTTTAAAAATATTT
1 AAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTA-AA
* * * * ** *
41471688 TAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTTAAA
1 AAAAATTAAAAAAAGTA-TGT-AAAAAATATTTTAAAATTAAA
41471730 AAAAATT-AAAAAAGTATGTAAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
41471770 AAAA
1 AAAA
41471774 TAAATATATT
Statistics
Matches: 93, Mismatches: 29, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
39 10 0.11
40 12 0.13
41 32 0.34
42 13 0.14
43 16 0.17
44 10 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (41 bp):
AAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
Found at i:41475328 original size:17 final size:18
Alignment explanation
Indices: 41475290--41475328 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41475280 AGAATTCATA
*
41475290 AAAATACAAAATATTATT
1 AAAATACAAAACATTATT
*
41475308 AAAATTCAAAACATT-TT
1 AAAATACAAAACATTATT
41475325 AAAA
1 AAAA
41475329 AGTTGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATACAAAACATTATT
Found at i:41479204 original size:15 final size:15
Alignment explanation
Indices: 41479184--41479214 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41479174 AAAGATTTTT
*
41479184 TTTAAAAACAATTTC
1 TTTAAAAAAAATTTC
41479199 TTTAAAAAAAATTTC
1 TTTAAAAAAAATTTC
41479214 T
1 T
41479215 CTACAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAAAAAATTTC
Found at i:41479424 original size:61 final size:56
Alignment explanation
Indices: 41479321--41479509 Score: 173
Period size: 61 Copynumber: 3.2 Consensus size: 56
41479311 ATTACTTTAA
* * * *
41479321 TATTAAATTAAGATAATGCTCATTAAGATAAATATTAGATTAAATTTAAAATTAAATC
1 TATTAAATTAATAAAATACT-ATTAAGATAAATATTAAATTAAATTTAAAATTAAA-C
* * ** *
41479379 TATTAAATTAATAGAATATTTATATACAAGATAAATATTAAATTAAAGATAATCAATTTAA-
1 TATTAAATTAATAAAATA-CTAT-T--AAGATAAATATTAAATTAAATTTAA--AATTAAAC
* * * *
41479440 TATTAAATTAATAAAATACTATTAATATAAATATTTAATTTAATTTAATATTAAACC
1 TATTAAATTAATAAAATACTATTAAGATAAATATTAAATTAAATTTAAAATTAAA-C
41479497 TATTAAATTAATA
1 TATTAAATTAATA
41479510 TTATTTTTGG
Statistics
Matches: 106, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
55 5 0.05
57 33 0.31
58 17 0.16
59 3 0.03
60 3 0.03
61 39 0.37
63 6 0.06
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (56 bp):
TATTAAATTAATAAAATACTATTAAGATAAATATTAAATTAAATTTAAAATTAAAC
Found at i:41483863 original size:44 final size:42
Alignment explanation
Indices: 41483768--41483887 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 42
41483758 ACAACGCTAT
* * *
41483768 CGTCCCAGACGTGGTCTTACATGTAATCACATATTGATGCCA
1 CGTCCCAGACGTGGTCTTACACGTAACCACATATCGATGCCA
41483810 CTGTCCCAGACAG-GGTCTTACACGTAAGCCACA-AGTCGATGCCAA
1 C-GTCCCAGAC-GTGGTCTTACACGTAA-CCACATA-TCGATGCC-A
41483855 CGTCCCAGACGTGGTCTTACACGATAA-CACATA
1 CGTCCCAGACGTGGTCTTACACG-TAACCACATA
41483888 ACACAATTCT
Statistics
Matches: 67, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
42 1 0.01
43 28 0.42
44 33 0.49
45 5 0.07
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (42 bp):
CGTCCCAGACGTGGTCTTACACGTAACCACATATCGATGCCA
Found at i:41485824 original size:20 final size:20
Alignment explanation
Indices: 41485799--41485839 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41485789 TGTTAAGTGT
41485799 AAGTTAATATTAATTATTGA
1 AAGTTAATATTAATTATTGA
41485819 AAGTTAATATTAATTATTGA
1 AAGTTAATATTAATTATTGA
41485839 A
1 A
41485840 GTAAGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
AAGTTAATATTAATTATTGA
Found at i:41485848 original size:20 final size:20
Alignment explanation
Indices: 41485799--41485848 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
41485789 TGTTAAGTGT
*
41485799 AAGTTAATATTAATTATTGA
1 AAGTAAATATTAATTATTGA
*
41485819 AAGTTAATATTAATTATTG-
1 AAGTAAATATTAATTATTGA
41485838 AAGTAAGATAT
1 AAGTAA-ATAT
41485849 ATTAAATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
AAGTAAATATTAATTATTGA
Found at i:41486518 original size:63 final size:63
Alignment explanation
Indices: 41486384--41486532 Score: 174
Period size: 63 Copynumber: 2.4 Consensus size: 63
41486374 TATCTCTAGA
* * * *** *
41486384 GAAGGTGTTGATATAGGGAATGATTGCACGTGTTGTGGTGCTTGTGTAAAATAAATTGGTGTT
1 GAAGGTGTTGATACAGAGAATGATTGCACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
* * * *
41486447 AAATGTGTTGATGCAGAGAATGATTGTACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
1 GAAGGTGTTGATACAGAGAATGATTGCACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
*
41486510 GAAGGTGTTTATAC-GAGGAATGA
1 GAAGGTGTTGATACAGA-GAATGA
41486533 GTGTGTGTAC
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
62 2 0.03
63 68 0.97
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.33
Consensus pattern (63 bp):
GAAGGTGTTGATACAGAGAATGATTGCACGTGATGTGGTGCTTGTGTAAAATAAACCAGAGTT
Found at i:41490437 original size:13 final size:13
Alignment explanation
Indices: 41490416--41490449 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41490406 TATTTGATTT
41490416 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
41490430 GTTATTTATTTTA
1 ATTATTTATTTTA
41490443 ATTATTT
1 ATTATTT
41490450 TATCTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:41495131 original size:21 final size:20
Alignment explanation
Indices: 41495091--41495139 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
41495081 ATAAATGAAA
*
41495091 TCATTCATGTCAATTCCCTG
1 TCATTCATGACAATTCCCTG
*
41495111 TCATTCACTGACAATTTCCTG
1 TCATTCA-TGACAATTCCCTG
41495132 TCATTCAT
1 TCATTCAT
41495140 AACTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (20 bp):
TCATTCATGACAATTCCCTG
Found at i:41495358 original size:21 final size:21
Alignment explanation
Indices: 41495312--41495421 Score: 107
Period size: 21 Copynumber: 5.3 Consensus size: 21
41495302 CGAATACGCC
* *
41495312 AACAGAAGCTC-GAA-AGCTT
1 AACAGAAGCTCATAAGAGCTA
* *
41495331 AATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
**
41495352 AACAGAAGCTTGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
41495373 AATAGAAACTCATAGGAGTTT
1 AACAGAAGCTCATAAGAGCTA
41495394 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
41495415 AACAGAA
1 AACAGAA
41495422 AGTAAAACAT
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
19 10 0.14
20 2 0.03
21 58 0.83
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:41495385 original size:42 final size:42
Alignment explanation
Indices: 41495312--41495422 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
41495302 CGAATACGCC
* *
41495312 AACAGAAGCTCG-AA-AGCTTAATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTAAATAGAAACTCATAAGAGCTG
* * * *
41495352 AACAGAAGCTTGTAAGAGCTAAATAGAAACTCATAGGAGTTT
1 AACAGAAGCTCGTAAGAGCTAAATAGAAACTCATAAGAGCTG
* *
41495394 AACAGAAGCTCATAAGAGCTAAACAGAAA
1 AACAGAAGCTCGTAAGAGCTAAATAGAAA
41495423 GTAAAACATG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 11 0.18
41 2 0.03
42 47 0.78
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAATAGAAACTCATAAGAGCTG
Found at i:41497364 original size:18 final size:18
Alignment explanation
Indices: 41497341--41497380 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
41497331 AAATCATATC
41497341 TTTGATCTTAAAGATAGT
1 TTTGATCTTAAAGATAGT
*
41497359 TTTGATTTTAAAGATAGT
1 TTTGATCTTAAAGATAGT
41497377 TTTG
1 TTTG
41497381 GTGCATAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTGATCTTAAAGATAGT
Found at i:41504674 original size:125 final size:126
Alignment explanation
Indices: 41504437--41504707 Score: 465
Period size: 125 Copynumber: 2.2 Consensus size: 126
41504427 GTGAAACTGC
41504437 ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGT
1 ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGT
*
41504502 ATAAAATCGCTTCTAGCAAGATGCTATTTTGAGAAGAATTTGTAAAATCGAGCCCTCGTGG
66 ATAAAATCGCTTCGAGCAAGATGCTATTTTGAGAAGAATTTGTAAAATCGAGCCCTCGTGG
* *
41504563 ACGCACTTTTGCTACTGTAGGTCATGGAAGAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGT
1 ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGT
* * *
41504627 ATAAAATCGCTTCGAGTAGGATGCTA-TTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGG
66 ATAAAATCGCTTCGAGCAAGATGCTATTTTGAGAAGAATTTGT-AAAATCGAGCCCTCGTGG
41504688 ACGCGCTTTTGCTACAGTAG
1 ACGCGCTTTTGCTACAGTAG
41504708 CATGTTTGGG
Statistics
Matches: 136, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
124 16 0.12
125 86 0.63
126 34 0.25
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (126 bp):
ACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGT
ATAAAATCGCTTCGAGCAAGATGCTATTTTGAGAAGAATTTGTAAAATCGAGCCCTCGTGG
Found at i:41507880 original size:23 final size:23
Alignment explanation
Indices: 41507854--41508463 Score: 687
Period size: 23 Copynumber: 27.5 Consensus size: 23
41507844 AGTTTAGGAC
* * *
41507854 TTTTAATTAAATTAGTTTAGGTT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41507877 TTTTAAGTTAA--GGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
*
41507898 TTTTAATTAAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41507921 TTTTAAGTTAA--GGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41507942 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41507965 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41507988 TTTTAAGTTAA--GGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508009 TTTTAATTTAAATAGGTTAGAGT
1 TTTTAATTTAATTAGGTTAGGGT
41508032 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508055 TTTTAAGTTAA--GGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41508076 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508099 TTTTAAGTTAA--GGGTTTAGGGT
1 TTTTAATTTAATTAGG-TTAGGGT
* *
41508121 TTTTAAGTTAA--GGGTTAGGG-
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508141 TTTTAAGTTAA--GGGTTTAGGGT
1 TTTTAATTTAATTAGG-TTAGGGT
* *
41508163 TTTTTATTTAATTAGGTTGGGGT
1 TTTTAATTTAATTAGGTTAGGGT
*
41508186 TTTTAATTTAATTGGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41508209 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
*
41508232 TTTTAATTAAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508255 TTTTAAGTTAA--GGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41508276 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41508299 TTTTAATTTAATTAGGTTAGGG-
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508321 TTTTAAGTTAA--GGGTTTAGGGT
1 TTTTAATTTAATTAGG-TTAGGGT
*
41508343 TTTTAATTAAATT--GTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
41508364 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
* *
41508387 TTTTAAGTTAA--GGGTTTAGGGT
1 TTTTAATTTAATTAGG-TTAGGGT
* * *
41508409 TTTTAAGTTAA--GGGTTAGTGT
1 TTTTAATTTAATTAGGTTAGGGT
41508430 TTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGT
*
41508453 TTTTAAGTTAA
1 TTTTAATTTAA
41508464 GGGTATTAAT
Statistics
Matches: 511, Mismatches: 52, Indels: 48
0.84 0.09 0.08
Matches are distributed among these distances:
20 16 0.03
21 149 0.29
22 71 0.14
23 273 0.53
24 2 0.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (23 bp):
TTTTAATTTAATTAGGTTAGGGT
Found at i:41507910 original size:44 final size:44
Alignment explanation
Indices: 41507854--41508467 Score: 741
Period size: 44 Copynumber: 13.9 Consensus size: 44
41507844 AGTTTAGGAC
* * *
41507854 TTTTAATTAAATTAGTTTAGGTTTTTTAAGTTAAGGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
*
41507898 TTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
* *
41507942 TTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGT
* * * * *
41507988 TTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAAATAGGTTAGAGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-AA-GGGTTAGGGT
41508032 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
41508076 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGT
* *
41508121 TTTTAAGTTAA--GGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGT
* * *
41508163 TTTTTATTTAATTAGGTTGGGGTTTTTAATTTAATTGGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGT
*
41508209 TTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-AA--GGGTTAGGGT
* * * *
41508255 TTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGT
41508299 TTTTAATTTAATTAGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGT
* * *
41508343 TTTTAATTAAATT--GTTAGGGTTTTTAATTTAATTAGGTTAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGT
* * *
41508387 TTTTAAGTTAA--GGGTTTAGGGTTTTTAAGTTAAGGGTTAGTGT
1 TTTTAATTTAATTAGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGT
41508430 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGT
1 TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGT
41508468 ATTAATGGTT
Statistics
Matches: 507, Mismatches: 39, Indels: 48
0.85 0.07 0.08
Matches are distributed among these distances:
42 38 0.07
43 38 0.07
44 261 0.51
45 66 0.13
46 101 0.20
47 3 0.01
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (44 bp):
TTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
Found at i:41507960 original size:67 final size:67
Alignment explanation
Indices: 41507889--41508467 Score: 899
Period size: 67 Copynumber: 8.7 Consensus size: 67
41507879 TTAAGTTAAG
*
41507889 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
41507954 TA
66 TA
*
41507956 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
41508021 TA
66 TA
*
41508023 GGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
41508088 TA
66 TA
* * *
41508090 GGTTAGGGTTTTTAAGTTAA--GGGTTTAGGGTTTTTAAGTTAAGGGTTAGGG-TTTTAAGTTAA
1 GGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAA
*
41508152 --G
65 TTA
* * *
41508153 GGTTTAGGGTTTTTTATTTAATTAGGTTGGGGTTTTTAATTTAATTGGGTTAGGGTTTTTAATTT
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTT
41508218 AATTA
63 AATTA
*
41508223 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
41508288 TA
66 TA
*
41508290 GGTTAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAATTTAA
41508354 TT-
65 TTA
*
41508356 -GTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAATTTAA
*
41508420 --G
65 TTA
*
41508421 GGTTAGTGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGT
41508468 ATTAATGGTT
Statistics
Matches: 474, Mismatches: 25, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
63 2 0.00
64 16 0.03
65 59 0.12
66 118 0.25
67 230 0.49
68 10 0.02
69 37 0.08
70 2 0.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.48
Consensus pattern (67 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAT
TA
Done.