Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold276
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: 761718
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
File 5 of 6
Found at i:604808 original size:15 final size:14
Alignment explanation
Indices: 604782--604817 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
604772 TGAGTCGGAT
604782 TTATTATAATTTAAA
1 TTATT-TAATTTAAA
604797 TTGATTTAATTTAAA
1 TT-ATTTAATTTAAA
604812 TTATTT
1 TTATTT
604818 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 13 0.65
16 3 0.15
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTATTTAATTTAAA
Found at i:605425 original size:17 final size:17
Alignment explanation
Indices: 605375--605426 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
605365 TCAATTGAGT
605375 TTTTTATTTTTTAC-AA
1 TTTTTATTTTTTACAAA
** *
605391 TAAATTAATTTTTA-AAA
1 T-TTTTATTTTTTACAAA
605408 TTTTTATTTTTTACAAA
1 TTTTTATTTTTTACAAA
605425 TT
1 TT
605427 AAGTTTATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTATTTTTTACAAA
Found at i:606412 original size:11 final size:10
Alignment explanation
Indices: 606387--606438 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 10
606377 TGTAAAATAC
606387 AAAATA-AATT
1 AAAATATAA-T
606397 AAAATATAAT
1 AAAATATAAT
606407 ACAAATATAATAT
1 A-AAATAT-A-AT
606420 AAAATAATAAT
1 AAAAT-ATAAT
606431 AAAATATA
1 AAAATATA
606439 GCGAGACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 11 0.30
11 15 0.41
12 6 0.16
13 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATATAAT
Found at i:606422 original size:23 final size:24
Alignment explanation
Indices: 606382--606438 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
606372 AATTATGTAA
606382 AATACAAA-ATAAATTAAAAT-AT
1 AATACAAATATAAATTAAAATAAT
606404 AATACAAATAT-AATATAAAATAAT
1 AATACAAATATAAAT-TAAAATAAT
606428 AATA-AAATATA
1 AATACAAATATA
606439 GCGAGACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 11 0.35
23 14 0.45
24 6 0.19
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
AATACAAATATAAATTAAAATAAT
Found at i:606495 original size:18 final size:19
Alignment explanation
Indices: 606450--606495 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
606440 CGAGACACAA
606450 AAAATACTATGACATGATAT
1 AAAATA-TATGACATGATAT
606470 AAAA-ATATGAACAT-AT-T
1 AAAATATATG-ACATGATAT
606487 AAAATATAT
1 AAAATATAT
606496 ATAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 5 0.21
20 4 0.17
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAATATATGACATGATAT
Found at i:607296 original size:14 final size:13
Alignment explanation
Indices: 607266--607302 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
607256 AAAATATAAA
607266 TTTTTT-TTTCTT
1 TTTTTTCTTTCTT
607278 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
607291 TCTTTTTCTTTC
1 T-TTTTTCTTTC
607303 CATTTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 7 0.30
14 10 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTCTT
Found at i:607309 original size:13 final size:13
Alignment explanation
Indices: 607265--607311 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
607255 TAAAATATAA
607265 ATTTTTT-TTTCT
1 ATTTTTTCTTTCT
*
607277 TTTTTTTCTTTCT
1 ATTTTTTCTTTCT
* *
607290 TTCTTTTTCTTTCC
1 AT-TTTTTCTTTCT
607304 ATTTTTTC
1 ATTTTTTC
607312 CATTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 6 0.20
13 13 0.43
14 11 0.37
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTTTTCTTTCT
Found at i:607342 original size:26 final size:26
Alignment explanation
Indices: 607289--607342 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
607279 TTTTTCTTTC
* * **
607289 TTTCTTTTTCTTTCCATTTTTTCCAT
1 TTTCTTTCTCTGTCCATTCCTTCCAT
*
607315 TTTCTTTCTCTGTCCATTCCTTCTAT
1 TTTCTTTCTCTGTCCATTCCTTCCAT
607341 TT
1 TT
607343 CAACCTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.07, C:0.26, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTCTTTCTCTGTCCATTCCTTCCAT
Found at i:608031 original size:21 final size:22
Alignment explanation
Indices: 608006--608047 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
607996 TATAATTATT
608006 TTTATAAAATAATA-TTATAAC
1 TTTATAAAATAATATTTATAAC
**
608027 TTTATAATTTAATATTTATAA
1 TTTATAAAATAATATTTATAA
608048 ATATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATAAAATAATATTTATAAC
Found at i:615738 original size:14 final size:14
Alignment explanation
Indices: 615719--615746 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
615709 ACCTTTTGGC
615719 AGGAGTTTATCAAT
1 AGGAGTTTATCAAT
615733 AGGAGTTTATCAAT
1 AGGAGTTTATCAAT
615747 CATTAAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
AGGAGTTTATCAAT
Found at i:617915 original size:7 final size:7
Alignment explanation
Indices: 617903--617932 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
617893 ACAACAACTT
*
617903 AAAAAAA
1 AAAAAAG
617910 AAAAAAG
1 AAAAAAG
617917 AAAAAAG
1 AAAAAAG
617924 AAAAAAG
1 AAAAAAG
617931 AA
1 AA
617933 TGTGTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:622175 original size:209 final size:209
Alignment explanation
Indices: 621815--622232 Score: 746
Period size: 209 Copynumber: 2.0 Consensus size: 209
621805 ACTTTACAAA
621815 TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
1 TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
**
621880 TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGGTTATTGAAACTAAAAGTATAGTATTC
66 TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
*
621945 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAATGTTAAGTAATAAAA
131 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAAGTAATAAAA
*
622010 CTTTTATATACTTT
196 CTTTTATACACTTT
* *
622024 TTATATTACTTTCAGATATGATTAATTTTAGGTTTAAAAATTACATATGATGTGAGTTTACTTAA
1 TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
* * *
622089 TTTTTTTTATAATTAAGCTTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
66 TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
*
622154 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAGGTAATAAAA
131 TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAAGTAATAAAA
622219 CTTTTATACACTTT
196 CTTTTATACACTTT
622233 AATATTAAAT
Statistics
Matches: 199, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 199 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (209 bp):
TTATATTACTTTCAGATATGATTAATTTTAAGTTTAAAAATTACATATAATGTGAGTTTACTTAA
TTTTTCTCATAATTAAGATTGTTAAGTTTTGATATCTGACTATTGAAACTAAAAGTATAGTATTC
TATCAACAAATCACATAACTGTTGACAAATTTATTGAAAATTTACAAAAACGTTAAGTAATAAAA
CTTTTATACACTTT
Found at i:622262 original size:14 final size:14
Alignment explanation
Indices: 622245--622272 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
622235 TATTAAATCC
622245 TTAATAGATAACAT
1 TTAATAGATAACAT
622259 TTAATAGATAACAT
1 TTAATAGATAACAT
622273 GACAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TTAATAGATAACAT
Found at i:626448 original size:6 final size:6
Alignment explanation
Indices: 626437--626467 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
626427 TTCGTCTCTT
626437 AGGCTC AGGCTC AGGCTC AGGCTC AGGCTC A
1 AGGCTC AGGCTC AGGCTC AGGCTC AGGCTC A
626468 ACTCATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
AGGCTC
Found at i:630941 original size:2 final size:2
Alignment explanation
Indices: 630934--630971 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
630924 ATGCAAATAC
630934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
630972 GTTCGTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631361 original size:2 final size:2
Alignment explanation
Indices: 631356--631396 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
631346 TACATATAAT
631356 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
631397 CTCTGTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:632610 original size:20 final size:20
Alignment explanation
Indices: 632537--632613 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
632527 TACATAAGTA
632537 AATGTATCGATACATTTACT-
1 AATGTATCGATACATTT-CTC
* * * *
632557 ATTTATATCGATAAATTTTTC
1 A-ATGTATCGATACATTTCTC
*
632578 ATTGTATCGATACATTTCTC
1 AATGTATCGATACATTTCTC
632598 AATGTATCGATACATT
1 AATGTATCGATACATT
632614 CAAGCATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 33 0.70
21 14 0.30
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.44
Consensus pattern (20 bp):
AATGTATCGATACATTTCTC
Found at i:634908 original size:79 final size:78
Alignment explanation
Indices: 634775--635163 Score: 358
Period size: 79 Copynumber: 5.0 Consensus size: 78
634765 TCATTGATGT
* * *
634775 TTTTATTTCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCTATTATTTTTTA-GAGG
1 TTTTATTTCTAAAACAC-GATTTTCCACCATCGAGGATACTCCAACCCTGTTATTTTTGAGGA-G
* * *
634839 ATACTCTAATCCAAA
64 ATACTCCAACCCCAA
* * *
634854 TTTTATTTCTAAAAGATCGATTTTTCACCATCGAGGATACTCCAACTCTGTTATTTTTGAGGAGA
1 TTTTATTTCTAAAACA-CGATTTTCCACCATCGAGGATACTCCAACCCTGTTATTTTTGAGGAGA
* * *
634919 TGCTTCAACCCCGA
65 TACTCCAACCCCAA
* * * * **
634933 TTTTATTCCTAAACCACTGATTTTCCACCATCG-GAGATACTCCAACCCCGTTACTTTCAAGG-G
1 TTTTATTTCTAAAACAC-GATTTTCCACCATCGAG-GATACTCCAACCCTGTTATTTTTGAGGAG
634996 ATACTCCAACCCCAA
64 ATACTCCAACCCCAA
* * * * * * * *
635011 TTTTATTTCTAAAATACCA-ATTCCATCATCGGGGATATTACAACCCCGTTATTTTTGAGGAGAT
1 TTTTATTTCTAAAACACGATTTTCCACCATCGAGGATACTCCAACCCTGTTATTTTTGAGGAGAT
*
635075 ACTCCAA-CCCAT
66 ACTCCAACCCCAA
* * * * * * *
635087 TTTTATTTCCAAAATATCGATTTTTCATCATTGAGGATACTCCAACCCTATTATTTTCGA-GAGA
1 TTTTATTTCTAAAACA-CGATTTTCCACCATCGAGGATACTCCAACCCTGTTATTTTTGAGGAG-
*
635151 ATATTCCAACCCC
64 ATACTCCAACCCC
635164 CTTTTATCTC
Statistics
Matches: 252, Mismatches: 48, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
76 51 0.20
77 17 0.07
78 67 0.27
79 114 0.45
80 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (78 bp):
TTTTATTTCTAAAACACGATTTTCCACCATCGAGGATACTCCAACCCTGTTATTTTTGAGGAGAT
ACTCCAACCCCAA
Found at i:635059 original size:76 final size:76
Alignment explanation
Indices: 634955--635102 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 76
634945 ACCACTGATT
*
634955 TTCCACCATCGGAGATACTCCAACCCCGTTACTTTCAAGG-GATACTCCAACCCCAATTTTATTT
1 TTCCACCATCGGAGATACTACAACCCCGTTACTTTCAAGGAGATACTCCAA-CCCAATTTTATTT
*
635019 CTAAAATACCAA
65 CCAAAATACCAA
* * * * ** *
635031 TTCCATCATCGGGGATATTACAACCCCGTTATTTTTGAGGAGATACTCCAACCCATTTTTATTTC
1 TTCCACCATCGGAGATACTACAACCCCGTTACTTTCAAGGAGATACTCCAACCCAATTTTATTTC
635096 CAAAATA
66 CAAAATA
635103 TCGATTTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 52 0.84
77 10 0.16
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (76 bp):
TTCCACCATCGGAGATACTACAACCCCGTTACTTTCAAGGAGATACTCCAACCCAATTTTATTTC
CAAAATACCAA
Found at i:635112 original size:155 final size:158
Alignment explanation
Indices: 634775--635162 Score: 396
Period size: 155 Copynumber: 2.5 Consensus size: 158
634765 TCATTGATGT
* * * * **
634775 TTTTATTTCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCTATTATTTTTTAGAGGA
1 TTTTATTCCTAAAACACTGATTTTCCACCATCGAGGATACTCCAACCCCATTACTTTCAAGAGGA
* * * * * * * *
634840 TACTCTAATCCAAATTTTATTTCTAAAAGATCGATTTTTCACCATCGAGGATACTCCAACTCTGT
66 TACTCCAACCCAAATTTTATTTCTAAAAGATCCATATTCCACCATCGAGGATACTACAACCCCGT
* *
634905 TATTTTTGAGGAGATGCTTCAACCCCGA
131 TATTTTTGAGGAGATACTCCAACCCCGA
* *
634933 TTTTATTCCTAAACCACTGATTTTCCACCATCG-GAGATACTCCAACCCCGTTACTTTCAAG-GG
1 TTTTATTCCTAAAACACTGATTTTCCACCATCGAG-GATACTCCAACCCCATTACTTTCAAGAGG
* * * * *
634996 ATACTCCAACCCCAATTTTATTTCTAAAATA-CCA-ATTCCATCATCGGGGATATTACAACCCCG
65 ATACTCCAACCCAAATTTTATTTCTAAAAGATCCATATTCCACCATCGAGGATACTACAACCCCG
635059 TTATTTTTGAGGAGATACTCCAA-CCC-A
130 TTATTTTTGAGGAGATACTCCAACCCCGA
* * * * * * *
635086 TTTTTATTTCC-AAAATA-TCGATTTTTCATCATTGAGGATACTCCAACCCTATTATTTTCGAGA
1 -TTTTA-TTCCTAAAACACT-GATTTTCCACCATCGAGGATACTCCAACCCCATTACTTTCAAGA
* *
635149 GAATATTCCAACCC
63 GGATACTCCAACCC
635163 CCTTTTATCT
Statistics
Matches: 190, Mismatches: 34, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
153 2 0.01
154 46 0.24
155 59 0.31
156 2 0.01
157 30 0.16
158 51 0.27
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (158 bp):
TTTTATTCCTAAAACACTGATTTTCCACCATCGAGGATACTCCAACCCCATTACTTTCAAGAGGA
TACTCCAACCCAAATTTTATTTCTAAAAGATCCATATTCCACCATCGAGGATACTACAACCCCGT
TATTTTTGAGGAGATACTCCAACCCCGA
Found at i:636189 original size:2 final size:2
Alignment explanation
Indices: 636184--636208 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
636174 TCTCTCTTTG
636184 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
636209 GAAGCAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:641236 original size:299 final size:298
Alignment explanation
Indices: 640635--641236 Score: 1064
Period size: 299 Copynumber: 2.0 Consensus size: 298
640625 AAAACTAGAG
*
640635 GAAATTCATAATGAGACCTATGAAAATTCAAGGATTTACAAGGAAAGAATTAAGGACTTCCATGA
1 GAAATTCACAATGAGACCTATGAAAATTCAAGGATTTACAAGGAAAGAATTAAGGACTTCCATGA
* * *
640700 CCAGATGATTGCAAGAAAAACATTTACCATTGGTAAAAAAGTTCTACTTTTCCATGTAAAACTTT
66 CCAGATGATTGCAAGAAAAACATTTACCATTAGTAAAAAAGTTCTACTTTTCCATGCAAAACTTA
* **
640765 AAATCTTTCTAGTAAGTTACGTTCTCGATAGATTGGTCCATTTATTATAACTACTGTGTTTCTTA
131 AAATCTTTCTAGTAAGTTACGTTCTCGATAGATTGGTCCATTTATTATAACTAATGTGTTTCCCA
*
640830 TGGTGCAGTTGAAATCTAAAGTTCAAGTACTAGAAAATTTTTTAAGGTGAATGGACATTGTTTCA
196 TGGTGCAGTTGAAATCAAAAGTTCAAGTACTAGAAAATTTTTTAAGGTGAATGGACATTGTTTCA
640895 AGCCTTTTTACGAAGGTTTCCAAGCATTTAAGGTGGAA
261 AGCCTTTTTACGAAGGTTTCCAAGCATTTAAGGTGGAA
640933 GAAATTCACAATGAGACCTATGAAAATTCAAGGATTTACAAGGAAAGAATTAA-GACTTCCATGA
1 GAAATTCACAATGAGACCTATGAAAATTCAAGGATTTACAAGGAAAGAATTAAGGACTTCCATGA
*
640997 CCAGATGATTGCAAGAAAAACATTTACCATTAGTCAAAAAGTTCTACTTTTCCATGCAAAACTTA
66 CCAGATGATTGCAAGAAAAACATTTACCATTAGTAAAAAAGTTCTACTTTTCCATGCAAAACTTA
* *
641062 AAATTTTTCCTAGTAAGTTACGTTCTCGATGGATTGGTCCATTTATTATAACTAATGTGTTTCCC
131 AAATCTTT-CTAGTAAGTTACGTTCTCGATAGATTGGTCCATTTATTATAACTAATGTGTTT-CC
641127 CATGGTGCAGTTGAAATCAAAAGTTCTAA-TACTAGAAAATTTTTTAAGGTGAATGGACATTGTT
194 CATGGTGCAGTTGAAATCAAAAGTTC-AAGTACTAGAAAATTTTTTAAGGTGAATGGACATTGTT
641191 TCAAGCCTTTTTACGAAGGTTTCCAAGCATTTAAGGTGGAA
258 TCAAGCCTTTTTACGAAGGTTTCCAAGCATTTAAGGTGGAA
641232 GAAAT
1 GAAAT
641237 CACCTTAGAA
Statistics
Matches: 290, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
297 79 0.27
298 103 0.36
299 106 0.37
300 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (298 bp):
GAAATTCACAATGAGACCTATGAAAATTCAAGGATTTACAAGGAAAGAATTAAGGACTTCCATGA
CCAGATGATTGCAAGAAAAACATTTACCATTAGTAAAAAAGTTCTACTTTTCCATGCAAAACTTA
AAATCTTTCTAGTAAGTTACGTTCTCGATAGATTGGTCCATTTATTATAACTAATGTGTTTCCCA
TGGTGCAGTTGAAATCAAAAGTTCAAGTACTAGAAAATTTTTTAAGGTGAATGGACATTGTTTCA
AGCCTTTTTACGAAGGTTTCCAAGCATTTAAGGTGGAA
Found at i:641819 original size:3 final size:3
Alignment explanation
Indices: 641811--641837 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
641801 AGTTAAAATT
641811 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
641838 GCATGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:642624 original size:16 final size:17
Alignment explanation
Indices: 642603--642639 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
642593 AAAACAAAAG
642603 AAAAAAA-AATAAAAT-T
1 AAAAAAAGAA-AAAATGT
642619 AAAAAAAGAAAAAATGT
1 AAAAAAAGAAAAAATGT
642636 AAAA
1 AAAA
642640 TGATAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAAAAGAAAAAATGT
Found at i:646535 original size:51 final size:51
Alignment explanation
Indices: 646477--646604 Score: 193
Period size: 51 Copynumber: 2.5 Consensus size: 51
646467 TTTTAACTAG
* * *
646477 ATGTATCGATACGTTGAAAAATGTATCGATACATTTGGGAAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGACAAA
* *
646528 ATGTATCGATACATTGAAAAATGCATCGATACATCTGGGTAAAAAGACAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGACAAA
* *
646579 ATGTATCCATACATTGAAGAATGTAT
1 ATGTATCGATACATTGAAAAATGTAT
646605 ATGTATCGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGAAAAAAGACAAA
Found at i:646684 original size:20 final size:20
Alignment explanation
Indices: 646659--646709 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
646649 AGACATAATA
* * *
646659 TATCGATACATTTATACATG
1 TATCGATACATTGAAAAATG
646679 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
646699 TATCGATACAT
1 TATCGATACAT
646710 CTGGGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:646717 original size:71 final size:72
Alignment explanation
Indices: 646528--646720 Score: 253
Period size: 77 Copynumber: 2.6 Consensus size: 72
646518 AAAAGACAGA
* *
646528 ATGTATCGATACATTGAAAAATGCATCGATACATCTGGGTAAAAAGACAAAATGTATCCATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATATATCCATACAT
* *
646593 TGAAGAATGTAT
66 T-----ATATAC
* * * * *
646605 ATGTATCGATACATTAAAAAATATATCGATACATCTAGGTAAAAAGACATAATATATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATATATCCATACAT
646670 T-TATAC
66 TATATAC
646676 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
646721 TGTGATCTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 45 0.43
77 59 0.57
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (72 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATATATCCATACAT
TATATAC
Found at i:648181 original size:24 final size:24
Alignment explanation
Indices: 648154--648202 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
648144 TAATTTATCA
*
648154 TTACAT-TTTTATTTTATTTTTAGT
1 TTACATATTTTA-TTTAATTTTAGT
*
648178 TTACTTATTTTATTTAATTTTAGT
1 TTACATATTTTATTTAATTTTAGT
648202 T
1 T
648203 GAATTGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (24 bp):
TTACATATTTTATTTAATTTTAGT
Found at i:649053 original size:16 final size:16
Alignment explanation
Indices: 649032--649062 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
649022 TTCGTGCCAT
649032 TAAAATTTATATATAA
1 TAAAATTTATATATAA
*
649048 TAAAATTTTTATATA
1 TAAAATTTATATATA
649063 TTTGTGAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATTTATATATAA
Found at i:649104 original size:27 final size:27
Alignment explanation
Indices: 649074--649131 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
649064 TTGTGAGATT
649074 AATAAATAATTAAAAT-TAAAATAAATA
1 AATAAAT-ATTAAAATATAAAATAAATA
* * *
649101 AATATATTTTAAAATATAAAATATATA
1 AATAAATATTAAAATATAAAATAAATA
649128 AATA
1 AATA
649132 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AATAAATATTAAAATATAAAATAAATA
Found at i:649114 original size:20 final size:20
Alignment explanation
Indices: 649074--649149 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 20
649064 TTGTGAGATT
* *
649074 AATAAATAATTA-AAATTAA
1 AATAAATAAATATAATTTAA
*
649093 AATAAATAAATATATTTTAA
1 AATAAATAAATATAATTTAA
*
649113 AATATAA-AATATATAAATATAA
1 AATA-AATAA-ATAT-AATTTAA
649135 AATAAATTAAATATA
1 AATAAA-TAAATATA
649150 CATGTGAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 11 0.24
20 11 0.24
21 9 0.20
22 13 0.28
23 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAAATAAATATAATTTAA
Found at i:649130 original size:15 final size:16
Alignment explanation
Indices: 649112--649149 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
649102 ATATATTTTA
*
649112 AAATATAAAATATA-T
1 AAATATAAAATAAATT
649127 AAATATAAAATAAATT
1 AAATATAAAATAAATT
649143 AAATATA
1 AAATATA
649150 CATGTGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAAAATAAATT
Found at i:649132 original size:27 final size:26
Alignment explanation
Indices: 649083--649133 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
649073 TAATAAATAA
649083 TTAAAATTAAAATAAATAAATATATT
1 TTAAAATTAAAATAAATAAATATATT
*
649109 TTAAAATATAAAATATATAAATATA
1 TTAAAAT-TAAAATAAATAAATATA
649134 AAATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAAAATTAAAATAAATAAATATATT
Found at i:649140 original size:27 final size:26
Alignment explanation
Indices: 649084--649145 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
649074 AATAAATAAT
***
649084 TAAAATTAAAATAAATAAATATATTT
1 TAAAATTAAAATAAATAAATATAAAA
*
649110 TAAAATATAAAATATATAAATATAAAA
1 TAAAAT-TAAAATAAATAAATATAAAA
649137 T-AAATTAAA
1 TAAAATTAAA
649146 TATACATGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 4 0.13
26 10 0.32
27 17 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAAATTAAAATAAATAAATATAAAA
Found at i:649391 original size:19 final size:19
Alignment explanation
Indices: 649348--649392 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
649338 TAATATTATG
649348 AAATTTAAATTTTTAATAAA
1 AAATTTAAATTTTT-ATAAA
649368 AAATTTAAATTTTT-TAAA
1 AAATTTAAATTTTTATAAA
649386 ATAATTT
1 A-AATTT
649393 TTTAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 5 0.21
20 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAAATTTTTATAAA
Found at i:650009 original size:25 final size:24
Alignment explanation
Indices: 649981--650036 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
649971 AATTCAAAAT
649981 ATTATTT-TTATTAAAAAATATTTAA
1 ATTATTTATT-TT-AAAAATATTTAA
*
650006 ATTAATTTATTTTAAATATATTTAA
1 ATT-ATTTATTTTAAAAATATTTAA
*
650031 AATATT
1 ATTATT
650037 AATATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.11
25 16 0.59
26 6 0.22
27 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATTTATTTTAAAAATATTTAA
Found at i:650374 original size:16 final size:16
Alignment explanation
Indices: 650343--650375 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
650333 TTTACTTGCG
650343 AATATATAAATAATCA
1 AATATATAAATAATCA
650359 AATATGATAAAT-ATCA
1 AATAT-ATAAATAATCA
650375 A
1 A
650376 TCAATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (16 bp):
AATATATAAATAATCA
Found at i:650513 original size:19 final size:18
Alignment explanation
Indices: 650491--650530 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
650481 AAATTATATA
650491 TATTTCACTAAAAATATTT
1 TATTTCA-TAAAAATATTT
* *
650510 TATTTCATAATATTATTT
1 TATTTCATAAAAATATTT
650528 TAT
1 TAT
650531 AATGTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTCATAAAAATATTT
Found at i:650526 original size:18 final size:17
Alignment explanation
Indices: 650471--650530 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
650461 TGCTTATGTG
650471 TTATTTCAATAAATTATAT
1 TTATTTC-ATAAATTAT-T
* *
650490 ATATTTCACTAAAAATATT
1 TTATTTCA-T-AAATTATT
650509 TTATTTCATAATATTATT
1 TTATTTCATAA-ATTATT
650527 TTAT
1 TTAT
650531 AATGTTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 2 0.06
18 11 0.32
19 15 0.44
20 6 0.18
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTCATAAATTATT
Found at i:651274 original size:24 final size:23
Alignment explanation
Indices: 651203--651292 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 23
651193 AATAAGTATA
* *
651203 AAAAAGATTAGTAGTTTTTTAAAT
1 AAAAAGATGAGTAG-TTTTTAAGT
*
651227 AAAAA-AT-AGGAAGTTTTCTCAAGT
1 AAAAAGATGA-GTAGTTTT-T-AAGT
*
651251 AAAAAGATGGGTAGTTATTTAAGT
1 AAAAAGATGAGTAGTT-TTTAAGT
651275 AAAAAG-TGAGTAGTTTTT
1 AAAAAGATGAGTAGTTTTT
651293 TTCAAATCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
22 8 0.15
23 14 0.25
24 23 0.42
25 8 0.15
26 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (23 bp):
AAAAAGATGAGTAGTTTTTAAGT
Found at i:651746 original size:16 final size:17
Alignment explanation
Indices: 651715--651752 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
651705 ATTTCTATTT
651715 AAAAACTATCTATTTAA
1 AAAAACTATCTATTTAA
*
651732 AAAAACTAT-TTTTTAA
1 AAAAACTATCTATTTAA
651748 AAAAA
1 AAAAA
651753 GATACCCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAACTATCTATTTAA
Found at i:651923 original size:23 final size:24
Alignment explanation
Indices: 651882--651932 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
651872 TTTACCTATC
651882 TTTTTAATATATTAATCT-AATAATT
1 TTTTTAATATATT-ATCTAAAT-ATT
*
651907 TTTTTAATTTATT-TCTAAATATT
1 TTTTTAATATATTATCTAAATATT
651930 TTT
1 TTT
651933 CACTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.38
24 3 0.12
25 12 0.50
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTAATATATTATCTAAATATT
Found at i:653124 original size:22 final size:23
Alignment explanation
Indices: 653082--653126 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
653072 TAATATTTAT
*
653082 TTTTTCTTATCATATTTTAATTA
1 TTTTTCTTATCATATTATAATTA
653105 TTTTTCTTAT-AT-TGTATAATTA
1 TTTTTCTTATCATAT-TATAATTA
653127 AGTTATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 9 0.45
23 10 0.50
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTTCTTATCATATTATAATTA
Found at i:653492 original size:17 final size:19
Alignment explanation
Indices: 653470--653507 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
653460 TGTCTAAATT
653470 ACATTTA-A-TAATTTTAA
1 ACATTTATACTAATTTTAA
653487 ACATTTATACTTAATTTTAA
1 ACATTTATAC-TAATTTTAA
653507 A
1 A
653508 AATTATCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
20 10 0.56
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
ACATTTATACTAATTTTAA
Found at i:654515 original size:12 final size:13
Alignment explanation
Indices: 654488--654520 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
654478 AAATTCTTTA
654488 AAATAATATTTATT
1 AAAT-ATATTTATT
654502 AAATATATTT-TT
1 AAATATATTTATT
654514 AAATATA
1 AAATATA
654521 ATATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 6 0.32
14 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATATTTATT
Found at i:654524 original size:15 final size:14
Alignment explanation
Indices: 654484--654526 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
654474 TTTTAAATTC
654484 TTTAAAATAATATT
1 TTTAAAATAATATT
654498 TATT-AAAT-ATATT
1 T-TTAAAATAATATT
654511 TTTAAATATAATATT
1 TTTAAA-ATAATATT
654526 T
1 T
654527 ATAATATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.08
13 8 0.32
14 7 0.28
15 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAATAATATT
Found at i:655301 original size:20 final size:19
Alignment explanation
Indices: 655277--655315 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
655267 TAAAATATGG
*
655277 AAAAAAAAAATAAATTATTTT
1 AAAAATAAAA-AAA-TATTTT
655298 AAAAATAAAAAAATATTT
1 AAAAATAAAAAAATATTT
655316 AAATATGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATAAAAAAATATTTT
Found at i:655685 original size:24 final size:24
Alignment explanation
Indices: 655651--655732 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
655641 TTAATTCAAT
655651 TTAT-AACTTTTGTATAGATAAAA
1 TTATAAACTTTTGTATAGATAAAA
* *
655674 TTATAAATTTTTCTCATA-A-AATAA
1 TTATAAACTTTTGT-ATAGATAA-AA
*
655698 TT-TATAACTTTTGTACAGATAAAA
1 TTATA-AACTTTTGTATAGATAAAA
655722 TTATAAACTTT
1 TTATAAACTTT
655733 CCTCACAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
23 10 0.21
24 30 0.64
25 7 0.15
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (24 bp):
TTATAAACTTTTGTATAGATAAAA
Found at i:655749 original size:24 final size:24
Alignment explanation
Indices: 655674--655756 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
655664 ATAGATAAAA
* * *
655674 TTATAAATTTTTCTCATAAAATAAT
1 TTATAAACTTTCCTCA-CAAATAAT
** * *
655699 TTAT-AACTTTTGT-ACAGATAAAA
1 TTATAAACTTTCCTCACAAAT-AAT
655722 TTATAAACTTTCCTCACAAATAAT
1 TTATAAACTTTCCTCACAAATAAT
655746 TTATAAA-TTTC
1 TTATAAACTTTC
655757 ACATGAATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 3 0.07
23 11 0.24
24 23 0.50
25 9 0.20
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATAAACTTTCCTCACAAATAAT
Found at i:655767 original size:47 final size:48
Alignment explanation
Indices: 655648--655759 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 48
655638 TTATTAATTC
* * * * *
655648 AATTTATAACTTTTGTATAGATAAAATTATAAATTTTTCTCATAAAAT
1 AATTTATAACATTTGCACAGATAAAATTATAAACTTTCCTCATAAAAT
* * *
655696 AATTTATAACTTTTGTACAGATAAAATTATAAACTTTCCTCA-CAAAT
1 AATTTATAACATTTGCACAGATAAAATTATAAACTTTCCTCATAAAAT
655743 AATTTATAA-ATTT-CACA
1 AATTTATAACATTTGCACA
655760 TGAATAAAGT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
45 3 0.05
46 3 0.05
47 13 0.22
48 39 0.67
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (48 bp):
AATTTATAACATTTGCACAGATAAAATTATAAACTTTCCTCATAAAAT
Found at i:655993 original size:24 final size:23
Alignment explanation
Indices: 655966--656050 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 23
655956 TGCTATCAAG
655966 TAATTATAAATTTTTCTCACAAAA
1 TAATTATAAATTTTT-TCACAAAA
*
655990 TAATT-TATAATTTTTGCACAGATAA
1 TAATTATA-AATTTTTTCACA-A-AA
*
656015 -AATTATAAACTTTTTTCA-TAAA
1 TAATTATAAA-TTTTTTCACAAAA
656037 TAACTTATAAATTT
1 TAA-TTATAAATTT
656051 CGCATGGATA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
22 2 0.04
23 12 0.24
24 26 0.51
25 11 0.22
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTATAAATTTTTTCACAAAA
Found at i:656181 original size:295 final size:295
Alignment explanation
Indices: 655672--656221 Score: 886
Period size: 295 Copynumber: 1.9 Consensus size: 295
655662 GTATAGATAA
* *
655672 AATTATAAATTTTTCTCATAAAATAATTTATAACTTTTGTACAGATAAAATTATAAACTTTCCTC
1 AATTATAAATTTTTCTCACAAAATAATTTATAACTTTTGCACAGATAAAATTATAAACTTTCCTC
* * * *
655737 ACAAATAATTTATAAATTTCACATGAATAAAGTTACTAATATTCTAATAAACAACTTTAGCTTTT
66 ACAAATAACTTATAAATTTCACATGAATAAAGTTACTAATATTCTAACAAACAACTGTAACTTTT
* *
655802 TTATAAAAAAAACTATAAATCCTTTAGATCTCACAAGGTTTAATCTCTCTCACTTTATTTTAAAG
131 TTATAAAAAAAACTATAAATCCTCTAGATCTCACAAGGTTTAATCTCTCTCACTTTATTTTAAAA
*
655867 GTAAAAACCCTCTATATTTATAAAGAAAATTACTTATTAAATAAACTTTGCTATCAAGTAATTCA
196 GTAAAAACCCTCTATATTTATAAAAAAAATTACTTATTAAATAAACTTTGCTATCAAGTAATTCA
655932 CAAACAACTATAGCTTTATAATTTTGCTATCAAGT
261 CAAACAACTATAGCTTTATAATTTTGCTATCAAGT
* **
655967 AATTATAAATTTTTCTCACAAAATAATTTATAATTTTTGCACAGATAAAATTATAAACTTTTTTC
1 AATTATAAATTTTTCTCACAAAATAATTTATAACTTTTGCACAGATAAAATTATAAACTTTCCTC
* * *
656032 ATAAATAACTTATAAATTTCGCATGGATAAAGTTACTAATATTCTAACAAACAACTGTAACTTTT
66 ACAAATAACTTATAAATTTCACATGAATAAAGTTACTAATATTCTAACAAACAACTGTAAC-TTT
** * **
656097 TTTATGGAAAAAACTATAAATTCTCTAGATCTCACAAGGTTTAAT-TCTCTCGGTTTATTTTAAA
130 TTTATAAAAAAAACTATAAATCCTCTAGATCTCACAAGGTTTAATCTCTCTCACTTTATTTTAAA
* *
656161 AGTCAAGACCCTCTATATTTATAAAAAAAATTACTTATTAAATAAACTTTGCTATCAAGTA
195 AGTAAAAACCCTCTATATTTATAAAAAAAATTACTTATTAAATAAACTTTGCTATCAAGTA
656222 CTTTATAACT
Statistics
Matches: 232, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
295 188 0.81
296 44 0.19
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (295 bp):
AATTATAAATTTTTCTCACAAAATAATTTATAACTTTTGCACAGATAAAATTATAAACTTTCCTC
ACAAATAACTTATAAATTTCACATGAATAAAGTTACTAATATTCTAACAAACAACTGTAACTTTT
TTATAAAAAAAACTATAAATCCTCTAGATCTCACAAGGTTTAATCTCTCTCACTTTATTTTAAAA
GTAAAAACCCTCTATATTTATAAAAAAAATTACTTATTAAATAAACTTTGCTATCAAGTAATTCA
CAAACAACTATAGCTTTATAATTTTGCTATCAAGT
Found at i:660065 original size:33 final size:32
Alignment explanation
Indices: 660027--660114 Score: 79
Period size: 33 Copynumber: 2.7 Consensus size: 32
660017 AAGTTCGAGG
*
660027 AAGCAAAAGGAAAAGAAAGAAGGAAATATAAAA
1 AAGCAAAAGGAAAA-AAAGAAAGAAATATAAAA
* * *
660060 AAGCAAGAGAAGAAAAAAA-AAAGAGATATGAAA
1 AAGCAA-A-AGGAAAAAAAGAAAGAAATATAAAA
* *
660093 AAGAAAAAGAAAAAAAAAGAAA
1 AAGCAAAAG-GAAAAAAAGAAA
660115 ATATGAGCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
31 1 0.02
32 8 0.18
33 25 0.57
34 4 0.09
35 6 0.14
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (32 bp):
AAGCAAAAGGAAAAAAAGAAAGAAATATAAAA
Found at i:660083 original size:16 final size:16
Alignment explanation
Indices: 660064--660115 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 16
660054 ATAAAAAAGC
660064 AAGAGAAGAAAAAAAA
1 AAGAGAAGAAAAAAAA
660080 AAGAGATATGAAAAAGAAA
1 AAGAGA-A-GAAAAA-AAA
660099 AAGA-AA-AAAAAAGAA
1 AAGAGAAGAAAAAA-AA
660114 AA
1 AA
660116 TATGAGCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 1 0.03
15 9 0.28
16 6 0.19
17 2 0.06
18 7 0.22
19 7 0.22
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (16 bp):
AAGAGAAGAAAAAAAA
Found at i:665511 original size:16 final size:16
Alignment explanation
Indices: 665487--665539 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
665477 ACATATTTTT
* *
665487 TAATGTTTATATTATA
1 TAATTTTTATATAATA
665503 T-ATCTTTTATATAATA
1 TAAT-TTTTATATAATA
665519 TAATTTTTATAATACATA
1 TAATTTTTAT-ATA-ATA
665537 TAA
1 TAA
665540 ATATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 18 0.58
17 5 0.16
18 6 0.19
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
TAATTTTTATATAATA
Found at i:666258 original size:14 final size:15
Alignment explanation
Indices: 666239--666268 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
666229 CATACATACA
666239 TATATAAA-TTAAAT
1 TATATAAATTTAAAT
666253 TATATAAATTTAAAT
1 TATATAAATTTAAAT
666268 T
1 T
666269 TAATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATAAATTTAAAT
Found at i:666500 original size:3 final size:3
Alignment explanation
Indices: 666492--666523 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
666482 ATTTAGCTGA
666492 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
666524 AAACGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:668959 original size:2 final size:2
Alignment explanation
Indices: 668954--668992 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
668944 TATATGTGTG
668954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
668993 CCTTACCCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:669482 original size:6 final size:6
Alignment explanation
Indices: 669473--669509 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
669463 TAAAGTGAAA
669473 GTGTTG GTGTTG GTGTTG GTGTTG GTGTTG GTGTTG G
1 GTGTTG GTGTTG GTGTTG GTGTTG GTGTTG GTGTTG G
669510 ACTCAAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (6 bp):
GTGTTG
Found at i:670220 original size:28 final size:28
Alignment explanation
Indices: 670189--670267 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
670179 AAATTTAATG
670189 ATATTATATATTATAAAATATAAAATTT
1 ATATTATATATTATAAAATATAAAATTT
* * * * *
670217 ATATT-TATTTTTTAAATTTTTTAAATTT
1 ATATTATATATTATAAA-ATATAAAATTT
*
670245 ATATTTATTTATTAATAAAATAT
1 ATA-TTATATATT-ATAAAATAT
670268 TATTATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
27 9 0.24
28 16 0.43
29 2 0.05
30 6 0.16
31 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTATATATTATAAAATATAAAATTT
Found at i:670838 original size:17 final size:17
Alignment explanation
Indices: 670816--670848 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
670806 GTATGGGTAC
670816 TTTTTATAATTGATTAG
1 TTTTTATAATTGATTAG
670833 TTTTTATAATTGATTA
1 TTTTTATAATTGATTA
670849 AATCTGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
TTTTTATAATTGATTAG
Found at i:671420 original size:16 final size:16
Alignment explanation
Indices: 671384--671418 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
671374 TTAGGTTTTA
671384 ATTTAATTTTTAAATT
1 ATTTAATTTTTAAATT
*
671400 ATTTACTTTTT-AATT
1 ATTTAATTTTTAAATT
671415 ATTT
1 ATTT
671419 TAAAATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTAATTTTTAAATT
Found at i:671463 original size:47 final size:47
Alignment explanation
Indices: 671412--671501 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
671402 TTACTTTTTA
* *
671412 ATTATTTTAAAATGTTA-TATATATTAATATATTCTTATCTTATTAAT
1 ATTATTTTAAAATGATATTATATATTAAT-TATTCTTATATTATTAAT
* * * *
671459 ATTATTTTTATATGATATTATATTTTAATTATTTTTATATTAT
1 ATTATTTTAAAATGATATTATATATTAATTATTCTTATATTAT
671502 ATTTTTATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 26 0.72
48 10 0.28
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (47 bp):
ATTATTTTAAAATGATATTATATATTAATTATTCTTATATTATTAAT
Found at i:672655 original size:14 final size:14
Alignment explanation
Indices: 672638--672683 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
672628 TTAATTTTTT
672638 AAAATTATTGAATA
1 AAAATTATTGAATA
*
672652 AAAATTATTGCATTA
1 AAAATTATTG-AATA
672667 ATAAATTATTG-ATA
1 A-AAATTATTGAATA
672681 AAA
1 AAA
672684 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 13 0.46
15 4 0.14
16 9 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATTATTGAATA
Found at i:673345 original size:21 final size:22
Alignment explanation
Indices: 673306--673347 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
673296 TTATTTGATT
*
673306 TTTAAATTAATTTTTATTTTTG
1 TTTAAATTAATTTTCATTTTTG
*
673328 TTTATATT-ATTTTCATTTTT
1 TTTAAATTAATTTTCATTTTT
673348 TTAATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTAAATTAATTTTCATTTTTG
Found at i:673357 original size:21 final size:22
Alignment explanation
Indices: 673310--673357 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
673300 TTGATTTTTA
* *
673310 AATTAATTTTTATTTTTGTTTAT
1 AATT-ATTTTCATTTTTGTTAAT
673333 -ATTATTTTCATTTTT-TTAAT
1 AATTATTTTCATTTTTGTTAAT
673353 AATTA
1 AATTA
673358 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
AATTATTTTCATTTTTGTTAAT
Found at i:673438 original size:16 final size:16
Alignment explanation
Indices: 673419--673477 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
673409 AATAATTAAC
673419 TATATATTTAATTTTT
1 TATATATTTAATTTTT
*
673435 TATATTTAATTAATTTATT
1 TATA--TATTTAATTT-TT
673454 TA-ATATTTAAATTTTT
1 TATATATTT-AATTTTT
*
673470 TAAATATT
1 TATATATT
673478 AAAATTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 12 0.33
17 10 0.28
18 10 0.28
19 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATATTTAATTTTT
Found at i:673461 original size:20 final size:18
Alignment explanation
Indices: 673426--673463 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
673416 AACTATATAT
673426 TTAATTTTTTATATTTAA
1 TTAATTTTTTATATTTAA
673444 TTAATTTATTTAATATTTAA
1 TTAATTT-TTT-ATATTTAA
673464 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAATTTTTTATATTTAA
Found at i:673479 original size:16 final size:17
Alignment explanation
Indices: 673446--673491 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
673436 ATATTTAATT
673446 AATTTATTTAATATTTA
1 AATTTATTTAATATTTA
*
673463 AATTT-TTTAAATATTAA
1 AATTTATTT-AATATTTA
673480 AATTTATATTAA
1 AATTTAT-TTAA
673492 CTTATAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 17 0.68
18 3 0.12
19 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:673484 original size:34 final size:34
Alignment explanation
Indices: 673422--673491 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 34
673412 AATTAACTAT
*
673422 ATATTTAATTTTTTATATTTAATTAATTTAT-TTA
1 ATATTTAATTTTTTAAATTTAA-TAATTTATATTA
673456 ATATTTAAATTTTTTAAATATTAA-AATTTATATTA
1 ATATTT-AATTTTTTAAAT-TTAATAATTTATATTA
673491 A
1 A
673492 CTTATAAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 13 0.41
35 15 0.47
36 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
ATATTTAATTTTTTAAATTTAATAATTTATATTA
Found at i:673508 original size:2 final size:2
Alignment explanation
Indices: 673501--673530 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
673491 ACTTATAAGC
673501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
673531 CTTATTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:674145 original size:18 final size:19
Alignment explanation
Indices: 674106--674145 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
674096 GGAAGATATA
* *
674106 ATTTAAACTATTTAATTTT
1 ATTTAAACTATATAATTAT
674125 ATTTAAA-TATATAATTAT
1 ATTTAAACTATATAATTAT
674143 ATT
1 ATT
674146 AATATGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAACTATATAATTAT
Found at i:675096 original size:24 final size:24
Alignment explanation
Indices: 675064--675110 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
675054 TATAAGTATA
675064 ATTTTTATAATTTATAAAGTAATG
1 ATTTTTATAATTTATAAAGTAATG
*
675088 ATTTTTATAATTTATGAAGTAAT
1 ATTTTTATAATTTATAAAGTAAT
675111 CCTACACACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTTTATAATTTATAAAGTAATG
Found at i:676258 original size:4 final size:4
Alignment explanation
Indices: 676251--676281 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
676241 TATATATATA
*
676251 TATG TATG TATG TATG TACG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
676282 TTGGTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:678854 original size:19 final size:18
Alignment explanation
Indices: 678832--678881 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
678822 TATATAAAAA
678832 TAAATATAATATAAATTAT
1 TAAATATAATATAAATT-T
*
678851 TAAATATATTA-AAATTT
1 TAAATATAATATAAATTT
678868 TAAATATAA-ATAAA
1 TAAATATAATATAAA
678882 AAATCTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 5 0.18
19 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATAATATAAATTT
Found at i:678863 original size:17 final size:18
Alignment explanation
Indices: 678832--678882 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
678822 TATATAAAAA
678832 TAAATATA-ATATAAATTAT
1 TAAATATATATA-AAATT-T
678851 TAAATATAT-TAAAATTT
1 TAAATATATATAAAATTT
*
678868 TAAATATAAATAAAA
1 TAAATATATATAAAA
678883 AATCTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.31
18 10 0.34
19 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATATATATAAAATTT
Found at i:678913 original size:18 final size:19
Alignment explanation
Indices: 678887--678967 Score: 96
Period size: 18 Copynumber: 4.4 Consensus size: 19
678877 ATAAAAAATC
*
678887 TATTAATTA-AATAATTTA
1 TATTTATTATAATAATTTA
678905 TATTTATTATAATAA-TTA
1 TATTTATTATAATAATTTA
* * *
678923 TATTAAAATATATTAATTTA
1 TATT-TATTATAATAATTTA
678943 TATTTATTA-AATAATTTA
1 TATTTATTATAATAATTTA
678961 TATTTAT
1 TATTTAT
678968 ATTTTATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
18 30 0.57
19 16 0.30
20 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTATTATAATAATTTA
Found at i:679460 original size:14 final size:14
Alignment explanation
Indices: 679420--679466 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
679410 GTGAAAAATA
679420 AAAAAATAATATTTT
1 AAAAAAT-ATATTTT
** *
679435 AAAATTTTTATTTT
1 AAAAAATATATTTT
679449 AAAAAATATA-TTT
1 AAAAAATATATTTT
679462 AAAAA
1 AAAAA
679467 TAAATTAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:680995 original size:17 final size:17
Alignment explanation
Indices: 680962--680994 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
680952 CACACACATA
680962 GGTTTCAATTTTATTTT
1 GGTTTCAATTTTATTTT
*
680979 GGTTTTAATTTT-TTTT
1 GGTTTCAATTTTATTTT
680995 TATTATTATT
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:0.15, C:0.03, G:0.12, T:0.70
Consensus pattern (17 bp):
GGTTTCAATTTTATTTT
Found at i:681674 original size:20 final size:20
Alignment explanation
Indices: 681651--681697 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
681641 CACCATTTAA
681651 CTTTTTAAGTTTTCCATAGT
1 CTTTTTAAGTTTTCCATAGT
*
681671 CTTTTTAAGTTTTCCATTGT
1 CTTTTTAAGTTTTCCATAGT
681691 CTTTTTA
1 CTTTTTA
681698 GCAGCTCGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.60
Consensus pattern (20 bp):
CTTTTTAAGTTTTCCATAGT
Found at i:681821 original size:21 final size:22
Alignment explanation
Indices: 681757--681821 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 22
681747 GCACTTTACC
*
681757 TTTTCAGG-TTTATCATT-ACT
1 TTTTCAGGCTTTACCATTGACT
* * *
681777 TTTTCA-GCTTTGCCATAG-CC
1 TTTTCAGGCTTTACCATTGACT
681797 TTTTCAGGCTTT-CCATTGACT
1 TTTTCAGGCTTTACCATTGACT
681818 TTTT
1 TTTT
681822 AAGCATATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 24 0.69
21 10 0.29
ACGTcount: A:0.15, C:0.22, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTTCAGGCTTTACCATTGACT
Found at i:681956 original size:21 final size:20
Alignment explanation
Indices: 681903--681950 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
681893 GGCATTTGAC
* * *
681903 CTTTTTAGATTCATCATTAT
1 CTTTTTAAATTTATCATAAT
*
681923 TTTTTTAAATTTATCATAAT
1 CTTTTTAAATTTATCATAAT
681943 CTTTTTAA
1 CTTTTTAA
681951 GCTTTACATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.58
Consensus pattern (20 bp):
CTTTTTAAATTTATCATAAT
Found at i:681999 original size:20 final size:21
Alignment explanation
Indices: 681976--682015 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
681966 TTTAGGATTA
681976 TCAT-TAGCTTTTCAAGCTCG
1 TCATATAGCTTTTCAAGCTCG
* *
681996 TCATATATCTTTTTAAGCTC
1 TCATATAGCTTTTCAAGCTC
682016 ACCAAAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (21 bp):
TCATATAGCTTTTCAAGCTCG
Found at i:682854 original size:74 final size:74
Alignment explanation
Indices: 682644--682843 Score: 242
Period size: 73 Copynumber: 2.7 Consensus size: 74
682634 CATTCGACTC
* * * * **
682644 ACATGGTCTAATCAATCTACCAAGCATATAAACAGATAATACCAAGTTATCATATAGACATGCTT
1 ACATGGTCTAATCAATCTACTAATCATATAAACAGATAATGCCAAGTTATCATATAAACATTTTT
* *
682709 ATTTGACCT
66 ATTTAAACT
* * *
682718 ACATGATCT-ATTAATCTACTTAGT-ATATAAACAGATAATGCCAAGTTATCATATAAACATTTT
1 ACATGGTCTAATCAATCTAC-TAATCATATAAACAGATAATGCCAAGTTATCATATAAACATTTT
682781 TATTTAAACT
65 TATTTAAACT
* * * *
682791 ACATGGTCTAATCAATCTACTAATCATATAAACGGAAAATGCTAACTTATCAT
1 ACATGGTCTAATCAATCTACTAATCATATAAACAGATAATGCCAAGTTATCAT
682844 GTCCACATTT
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
73 63 0.60
74 42 0.40
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (74 bp):
ACATGGTCTAATCAATCTACTAATCATATAAACAGATAATGCCAAGTTATCATATAAACATTTTT
ATTTAAACT
Found at i:684638 original size:30 final size:30
Alignment explanation
Indices: 684587--684661 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 30
684577 CATCACATAA
*
684587 TCAAAAAACTA-TAAAAA--ATCTAAAAACT
1 TCAAAAAACAATTAAAAAGTATCT-AAAACT
*
684615 TCAAAAAA-AATTAAAAAGTATCTAAAATT
1 TCAAAAAACAATTAAAAAGTATCTAAAACT
684644 TCAAAAAACAATTAAAAA
1 TCAAAAAACAATTAAAAA
684662 TATGAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 1 0.02
28 14 0.34
29 13 0.32
30 13 0.32
ACGTcount: A:0.65, C:0.11, G:0.01, T:0.23
Consensus pattern (30 bp):
TCAAAAAACAATTAAAAAGTATCTAAAACT
Found at i:684788 original size:18 final size:18
Alignment explanation
Indices: 684767--684801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
684757 TTTCCTCGCC
*
684767 CTTTCCTTCCTTTCCCTA
1 CTTTCCTTACTTTCCCTA
*
684785 CTTTCTTTACTTTCCCT
1 CTTTCCTTACTTTCCCT
684802 TTCTCTCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.40, G:0.00, T:0.54
Consensus pattern (18 bp):
CTTTCCTTACTTTCCCTA
Found at i:684900 original size:25 final size:25
Alignment explanation
Indices: 684819--684919 Score: 66
Period size: 25 Copynumber: 3.9 Consensus size: 25
684809 TCTTCCTCTC
*
684819 TTTTTTT--AATTTTCAA-TTTTTA
1 TTTTTTTAAAATTTTAAATTTTTTA
** *
684841 TTTTTTTCCTAATTTTAAATTTATATTT
1 TTTTTTT-AAAATTTTAAATTT-T-TTA
684869 TCATTTTTTAAAATTTTAAATTTTTTA
1 T--TTTTTTAAAATTTTAAATTTTTTA
*
684896 -TTTTTTATATATTTTATAATTTTT
1 TTTTTTTA-AAATTTTA-AATTTTT
684920 ATCATGTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
22 7 0.11
24 7 0.11
25 15 0.24
26 9 0.14
27 3 0.05
28 4 0.06
29 12 0.19
30 6 0.10
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTTAAAATTTTAAATTTTTTA
Found at i:685260 original size:23 final size:23
Alignment explanation
Indices: 685234--685279 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
685224 TCCTATGTTA
685234 AAATATCATAAATTTATATAAAT
1 AAATATCATAAATTTATATAAAT
*
685257 AAATATCTTAAATTTATATAAAT
1 AAATATCATAAATTTATATAAAT
685280 TTTTTACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATCATAAATTTATATAAAT
Found at i:686424 original size:20 final size:20
Alignment explanation
Indices: 686388--686425 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
686378 AGGTGTATAA
*
686388 TTTTTTAAGAAGTTATTAAT
1 TTTTTTAAAAAGTTATTAAT
686408 TTTTTTCAAAAAG-TATTA
1 TTTTTT-AAAAAGTTATTA
686426 CAATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTTTAAAAAGTTATTAAT
Found at i:690384 original size:13 final size:14
Alignment explanation
Indices: 690345--690404 Score: 61
Period size: 15 Copynumber: 4.2 Consensus size: 14
690335 TTATTACATA
690345 ATACAAATAAAATAT
1 ATACAAAT-AAATAT
*
690360 ATAAAAAT-AATAT
1 ATACAAATAAATAT
690373 -TACAAATAAATAT
1 ATACAAATAAATAT
*
690386 AATATAATATAAATAT
1 -ATACAA-ATAAATAT
690402 ATA
1 ATA
690405 AATATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.16
13 10 0.26
15 14 0.37
16 8 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
ATACAAATAAATAT
Found at i:690503 original size:16 final size:16
Alignment explanation
Indices: 690471--690504 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
690461 TAATTATAAC
690471 ATATAAAATAATACAA
1 ATATAAAATAATACAA
690487 ATATATAAATAAT-CAA
1 ATATA-AAATAATACAA
690503 AT
1 AT
690505 TTATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAAAATAATACAA
Found at i:691626 original size:44 final size:44
Alignment explanation
Indices: 691528--691626 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
691518 GTTTTTGTGA
* *
691528 TAATTAT-TTAGATATAAATATAATATAAATTGTTAAATAAATT
1 TAATTATATTAAATATAAATATAATATAAATTGTAAAATAAATT
** * *
691571 TAAAAAAATTAAATATAAATATAATATATA-T-TAAATATATAATT
1 TAATTATATTAAATATAAATATAATATAAATTGTAAA-ATA-AATT
691615 TAATTATATTAA
1 TAATTATATTAA
691627 TCTTTAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
42 3 0.07
43 8 0.18
44 33 0.75
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (44 bp):
TAATTATATTAAATATAAATATAATATAAATTGTAAAATAAATT
Found at i:692459 original size:25 final size:24
Alignment explanation
Indices: 692431--692505 Score: 57
Period size: 25 Copynumber: 3.0 Consensus size: 24
692421 ACGATTATAT
692431 AAATTTAATATGTATAAAATTATTA
1 AAATTTAATAT-TATAAAATTATTA
* *
692456 AAATATTATATAAATATATAA-T-TTA
1 AAAT-TTA-AT-ATTATAAAATTATTA
*
692481 AAATTT-ATATAATATAAATTATTA
1 AAATTTAATATTATA-AAATTATTA
692505 A
1 A
692506 TATCTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
23 1 0.03
24 6 0.15
25 11 0.28
26 4 0.10
27 8 0.21
28 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
AAATTTAATATTATAAAATTATTA
Found at i:692491 original size:16 final size:16
Alignment explanation
Indices: 692470--692524 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
692460 ATTATATAAA
692470 TATATAATTTAAAATT
1 TATATAATTTAAAATT
* *
692486 TATATAATATAAATTAT
1 TATATAATTTAAAAT-T
692503 TA-AT-ATCTTAAAATT
1 TATATAAT-TTAAAATT
*
692518 GATATAA
1 TATATAA
692525 ATATAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
15 4 0.13
16 22 0.73
17 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TATATAATTTAAAATT
Found at i:692492 original size:24 final size:23
Alignment explanation
Indices: 692453--692500 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
692443 TATAAAATTA
692453 TTAAAATATTATATAAATATATAAT
1 TTAAAATATTATAT-AATATA-AAT
692478 TTAAAAT-TTATATAATATAAAT
1 TTAAAATATTATATAATATAAAT
692500 T
1 T
692501 ATTAATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 6 0.26
24 6 0.26
25 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAAATATTATATAATATAAAT
Found at i:692505 original size:24 final size:26
Alignment explanation
Indices: 692447--692505 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
692437 AATATGTATA
692447 AAATTATTAAAATATTATATAAATAT
1 AAATTATTAAAATATTATATAAATAT
692473 ATAA-T-TTAAAAT-TTATAT-AATAT
1 A-AATTATTAAAATATTATATAAATAT
692496 AAATTATTAA
1 AAATTATTAA
692506 TATCTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 2 0.07
23 7 0.23
24 10 0.33
25 7 0.23
26 2 0.07
27 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATTATTAAAATATTATATAAATAT
Found at i:694328 original size:26 final size:26
Alignment explanation
Indices: 694299--694349 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
694289 ATTTTTATTT
* *
694299 AAATTTAATTATAAATATTAATATAA
1 AAATATAATTATAAATAGTAATATAA
*
694325 AAATATAATTTTAAATAGTAATATA
1 AAATATAATTATAAATAGTAATATA
694350 GATTTTAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AAATATAATTATAAATAGTAATATAA
Found at i:694338 original size:19 final size:19
Alignment explanation
Indices: 694316--694357 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
694306 ATTATAAATA
694316 TTAATATAAAAATATA-ATT
1 TTAA-ATAAAAATATAGATT
**
694335 TTAAATAGTAATATAGATT
1 TTAAATAAAAATATAGATT
694354 TTAA
1 TTAA
694358 GCCCACCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TTAAATAAAAATATAGATT
Found at i:695210 original size:20 final size:20
Alignment explanation
Indices: 695187--695228 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
695177 AAAGTAGTTA
695187 AAAATAAAATGGATAG-TTTT
1 AAAA-AAAATGGATAGATTTT
* *
695207 AAAAAGAGTGGATAGATTTT
1 AAAAAAAATGGATAGATTTT
695227 AA
1 AA
695229 GAAGTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (20 bp):
AAAAAAAATGGATAGATTTT
Found at i:697639 original size:21 final size:21
Alignment explanation
Indices: 697609--697701 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 21
697599 TAATTAGTGT
697609 TTTAAT-ATTTAATATTATAA
1 TTTAATAATTTAATATTATAA
*
697629 TTTAATAATTTAATATTATGA
1 TTTAATAATTTAATATTATAA
* * * *
697650 -TTAAAAAATTAATATACAAAAA
1 TTTAATAATTTAATAT--TATAA
* *
697672 ATTAATATTTTAATAATTAATAA
1 TTTAATAATTTAAT-ATT-ATAA
697695 TTTAATA
1 TTTAATA
697702 TACATGTCAA
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
20 19 0.35
21 13 0.24
22 2 0.04
23 19 0.35
24 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
TTTAATAATTTAATATTATAA
Found at i:697689 original size:15 final size:15
Alignment explanation
Indices: 697589--697701 Score: 58
Period size: 15 Copynumber: 7.8 Consensus size: 15
697579 TTAAATTTAA
697589 AATA-TTTATATAATT
1 AATATTTTA-ATAATT
* * *
697604 AGTGTTTTAATATTT
1 AATATTTTAATAATT
*
697619 AATATTATAAT--TT
1 AATATTTTAATAATT
*
697632 AATAATTTAAT-ATT
1 AATATTTTAATAATT
* *
697646 -ATGA-TTAAAAAATT
1 AAT-ATTTTAATAATT
*** *
697660 AATATACAAAAAATT
1 AATATTTTAATAATT
697675 AATATTTTAATAATT
1 AATATTTTAATAATT
*
697690 AATAATTTAATA
1 AATATTTTAATA
697702 TACATGTCAA
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
13 17 0.23
14 7 0.09
15 47 0.63
16 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATT
Found at i:699326 original size:2 final size:2
Alignment explanation
Indices: 699319--699352 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
699309 GAAAAGAGCC
699319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699353 CCAAACAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:700475 original size:19 final size:18
Alignment explanation
Indices: 700448--700497 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
700438 ATCGATATAT
*
700448 TTTAATATATTATTTTAAA
1 TTTATTATATT-TTTTAAA
700467 TTTATTATA-TTTTTAAA
1 TTTATTATATTTTTTAAA
700484 TATTATATATATTT
1 T-TTAT-TATATTT
700498 ATAATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.30
18 5 0.19
19 12 0.44
20 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATTATATTTTTTAAA
Found at i:700482 original size:17 final size:17
Alignment explanation
Indices: 700460--700520 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
700450 TAATATATTA
700460 TTTTAAATTTATTATAT
1 TTTTAAATTTATTATAT
700477 TTTTAAATATTA-TATAT
1 TTTTAAAT-TTATTATAT
* *
700494 ATTT--A--TAATATAT
1 TTTTAAATTTATTATAT
700507 TTTTAAATTTATTA
1 TTTTAAATTTATTA
700521 ATAAGATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
12 2 0.06
13 8 0.23
15 2 0.06
17 20 0.57
18 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAATTTATTATAT
Found at i:700489 original size:15 final size:15
Alignment explanation
Indices: 700469--700518 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
700459 ATTTTAAATT
700469 TATTATATTTTTAAA
1 TATTATATTTTTAAA
700484 TATTATATATATTT--A
1 TATTATAT-T-TTTAAA
*
700499 TAATATATTTTTAAA
1 TATTATATTTTTAAA
700514 T-TTAT
1 TATTAT
700519 TAATAAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.10
14 4 0.14
15 18 0.62
16 1 0.03
17 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATATTTTTAAA
Found at i:700509 original size:29 final size:29
Alignment explanation
Indices: 700442--700518 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
700432 ATTAATATCG
* *
700442 ATATATTTTAATATATTATTTTAAATTTATT
1 ATATATTTTAA-ATATTA-TATAAATTTATA
*
700473 ATAT-TTTTAAATATTATATATATTTATA
1 ATATATTTTAAATATTATATAAATTTATA
700501 ATATATTTTTAAAT-TTAT
1 ATATA-TTTTAAATATTAT
700519 TAATAAGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.32
29 10 0.24
30 14 0.34
31 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATATTTTAAATATTATATAAATTTATA
Found at i:700534 original size:47 final size:48
Alignment explanation
Indices: 700442--700539 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 48
700432 ATTAATATCG
***
700442 ATATATTTTAATATATTATTTTAAATTTATTATATTTTTAAATATTAT
1 ATATATTTTAATATATTATTTTAAATTTATTATATAGATAAATATTAT
*
700490 ATATATTTATAATATA-T-TTTTAAATTTATTA-ATAAGATATATATTAT
1 ATATATTT-TAATATATTATTTTAAATTTATTATAT-AGATAAATATTAT
700537 ATA
1 ATA
700540 AACATATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
46 2 0.05
47 26 0.59
48 9 0.20
49 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (48 bp):
ATATATTTTAATATATTATTTTAAATTTATTATATAGATAAATATTAT
Found at i:713887 original size:14 final size:15
Alignment explanation
Indices: 713865--713902 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
713855 AATTCTATAA
*
713865 TATAATATATTATT-
1 TATATTATATTATTG
713879 TATATTATA-TATTG
1 TATATTATATTATTG
713893 TATATTATAT
1 TATATTATAT
713903 AGTACATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TATATTATATTATTG
Found at i:716954 original size:40 final size:40
Alignment explanation
Indices: 716899--716974 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
716889 GAAAGAAATG
716899 GTTAATATGTGCATTTAAAGAAAGAAACAGTTAATAAACC
1 GTTAATATGTGCATTTAAAGAAAGAAACAGTTAATAAACC
* *
716939 GTTAATATGTGCATTTAAAGAAATAAACGGTTAATA
1 GTTAATATGTGCATTTAAAGAAAGAAACAGTTAATA
716975 TGTGCATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (40 bp):
GTTAATATGTGCATTTAAAGAAAGAAACAGTTAATAAACC
Found at i:716964 original size:29 final size:29
Alignment explanation
Indices: 716931--716986 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
716921 AGAAACAGTT
716931 AATAAACCGTTAATATGTGCATTTAAAGA
1 AATAAACCGTTAATATGTGCATTTAAAGA
*
716960 AATAAACGGTTAATATGTGCATTTAAA
1 AATAAACCGTTAATATGTGCATTTAAA
716987 CAATGTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (29 bp):
AATAAACCGTTAATATGTGCATTTAAAGA
Found at i:720418 original size:8 final size:8
Alignment explanation
Indices: 720405--720435 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
720395 TTGGATTAAC
720405 TTTAAAAA
1 TTTAAAAA
720413 TTTAAAAA
1 TTTAAAAA
*
720421 TTTAATAA
1 TTTAAAAA
720429 TTTAAAA
1 TTTAAAA
720436 TTCTAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTAAAAA
Found at i:721764 original size:15 final size:17
Alignment explanation
Indices: 721742--721780 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
721732 AATTATTACA
* *
721742 TAAAAAAAAT-ATATTT
1 TAAAAAAATTAATATGT
721758 TAAAAAAATTAATATGT
1 TAAAAAAATTAATATGT
721775 TAAAAA
1 TAAAAA
721781 GCACACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAAAATTAATATGT
Found at i:722163 original size:24 final size:23
Alignment explanation
Indices: 722136--722195 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
722126 TTTTAAATAC
*
722136 AATACATAAATATTATATAAAAAT
1 AATACATAAATATAATA-AAAAAT
722160 AATA-ATTAAAATATAATAAAAAAT
1 AATACA-T-AAATATAATAAAAAAT
722184 ACATACA-AAATA
1 A-ATACATAAATA
722196 AAAAATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
23 6 0.19
24 12 0.39
25 12 0.39
26 1 0.03
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
AATACATAAATATAATAAAAAAT
Found at i:722245 original size:20 final size:21
Alignment explanation
Indices: 722193--722248 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
722183 TACATACAAA
*
722193 ATAAAAAATTATATAAATATG
1 ATAAAAATTTATATAAATATG
* *
722214 AT-AAAATATATATTAATAT-
1 ATAAAAATTTATATAAATATG
722233 ATAAAAATTTATATAA
1 ATAAAAATTTATATAA
722249 CATAAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAAAATTTATATAAATATG
Found at i:722289 original size:18 final size:18
Alignment explanation
Indices: 722143--722291 Score: 60
Period size: 18 Copynumber: 8.3 Consensus size: 18
722133 TACAATACAT
*
722143 AAATATTATATAAAAATAA
1 AAAT-TTATATAAAATTAA
* * * * *
722162 TAATTAAAATATAATAAA
1 AAATTTATATAAAATTAA
** *
722180 AAATACATACAAAA-TAA
1 AAATTTATATAAAATTAA
* *
722197 AAAATTATATAAATATGATA
1 AAATTTATATAAA-ATTA-A
* *
722217 AAATATATATTAATATATAA
1 AAATTTATA-TAAAAT-TAA
*
722237 AAATTTATATAACA-T--
1 AAATTTATATAAAATTAA
722252 AAA-TTAT-TAATATATT-A
1 AAATTTATATAA-A-ATTAA
722269 AAATTTATATAAAATTAA
1 AAATTTATATAAAATTAA
722287 AAATT
1 AAATT
722292 AAATATAATT
Statistics
Matches: 93, Mismatches: 25, Indels: 25
0.65 0.17 0.17
Matches are distributed among these distances:
13 3 0.03
14 4 0.04
15 4 0.04
16 1 0.01
17 18 0.19
18 29 0.31
19 11 0.12
20 19 0.20
21 4 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (18 bp):
AAATTTATATAAAATTAA
Found at i:722293 original size:32 final size:32
Alignment explanation
Indices: 722214--722299 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
722204 TATAAATATG
*
722214 ATAAAATATAT-ATTAATATATAAAAATTTAT
1 ATAAAATAAATAATTAATATATAAAAATTTAT
* * *
722245 ATAACATAAATTATTAATATATTAAAATTTAT
1 ATAAAATAAATAATTAATATATAAAAATTTAT
722277 ATAAAATTAAA-AATTAA-ATATAA
1 ATAAAA-TAAATAATTAATATATAA
722300 TTATAATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 14 0.30
32 29 0.62
33 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAAATAAATAATTAATATATAAAAATTTAT
Found at i:722603 original size:2 final size:2
Alignment explanation
Indices: 722596--722621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
722586 ACAACCATTT
722596 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
722622 GCAATGCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:726991 original size:98 final size:99
Alignment explanation
Indices: 726822--727020 Score: 258
Period size: 98 Copynumber: 2.0 Consensus size: 99
726812 CATGCTGCAA
* *** ** * **
726822 TTCTATCTACATATTTAAGTAAACTTGTGATAGATTTTGCAAGGATCTGTGTTCAGCATTTTTGG
1 TTCTATCTACATATTTAAATAAACTTACAATAGATTTTGCAAGGATCTCAGTTCAGCACTTTCAG
**
726887 TGCTTACATT-TATAGAGCTAGGGG-CTTTAACTT
66 CCCTTACATTCTATAGAGCT-GGGGTCTTTAACTT
*
726920 TTCTATCTACATGTTTAAATAAACTTACAATAGATTTTGCAAGGATCTCAGTTCAGCACTTTCAG
1 TTCTATCTACATATTTAAATAAACTTACAATAGATTTTGCAAGGATCTCAGTTCAGCACTTTCAG
*
726985 CCCTTACATTCTATAGAGCTGGGGTTTTTAACTT
66 CCCTTACATTCTATAGAGCTGGGGTCTTTAACTT
727019 TT
1 TT
727021 GATGTATGCC
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
98 67 0.78
99 19 0.22
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (99 bp):
TTCTATCTACATATTTAAATAAACTTACAATAGATTTTGCAAGGATCTCAGTTCAGCACTTTCAG
CCCTTACATTCTATAGAGCTGGGGTCTTTAACTT
Found at i:730341 original size:2 final size:2
Alignment explanation
Indices: 730334--730364 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
730324 CCGAACCTCA
730334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
730365 AATAAAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:730920 original size:12 final size:12
Alignment explanation
Indices: 730903--730928 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
730893 GTTTGCTAAG
730903 AAGAAAGAAAAA
1 AAGAAAGAAAAA
730915 AAGAAAGAAAAA
1 AAGAAAGAAAAA
730927 AA
1 AA
730929 TTGGGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAAAA
Done.