Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 24 of 117
Found at i:3036211 original size:26 final size:28
Alignment explanation
Indices: 3036170--3036222 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
3036160 CATTAATTAA
*
3036170 ATTTAAATATTAA-TTTTAATAAAATTC
1 ATTTAAATATAAATTTTTAATAAAATTC
*
3036197 ATTT-AATATAAATTTTTAATTAAATT
1 ATTTAAATATAAATTTTTAATAAAATT
3036223 TTTTATTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTAAATATAAATTTTTAATAAAATTC
Found at i:3036216 original size:13 final size:13
Alignment explanation
Indices: 3036162--3036225 Score: 57
Period size: 12 Copynumber: 5.2 Consensus size: 13
3036152 TATCGTATCA
3036162 TTAAT-TAAA-TT
1 TTAATATAAATTT
* *
3036173 TAAATATTAA-TT
1 TTAATATAAATTT
3036185 TTAATA-AAATTCAT
1 TTAATATAAATT--T
3036199 TTAATATAAATTT
1 TTAATATAAATTT
3036212 TTAAT-TAAATTT
1 TTAATATAAATTT
3036224 TT
1 TT
3036226 TATTCACAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 6 0.14
12 20 0.45
13 6 0.14
14 7 0.16
15 5 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATATAAATTT
Found at i:3039758 original size:3 final size:3
Alignment explanation
Indices: 3039750--3039775 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3039740 ATTTACTAAA
3039750 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3039776 ATCCATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3040617 original size:2 final size:2
Alignment explanation
Indices: 3040610--3040637 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3040600 TTTGTAACCA
3040610 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
3040638 TTGAAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3054576 original size:19 final size:19
Alignment explanation
Indices: 3054549--3054588 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3054539 ACATGTCAGA
*
3054549 CTAAAATTCTTTCAAAGGG
1 CTAAAATTCTTTCAAAAGG
*
3054568 CTAAGATTCTTTCAAAAGG
1 CTAAAATTCTTTCAAAAGG
3054587 CT
1 CT
3054589 TAATCTACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (19 bp):
CTAAAATTCTTTCAAAAGG
Found at i:3057414 original size:259 final size:260
Alignment explanation
Indices: 3057020--3057488 Score: 628
Period size: 259 Copynumber: 1.8 Consensus size: 260
3057010 TCAGCAAGCA
* *
3057020 TTACAAAATAAAACAGTAACAAGAACTTGATGAAGAGGAAAACAGCTTCTCGCATAAAAGAAATT
1 TTACAAAATAAAACAGTAACAAGAACCTGATGAAGAGGAAAACAGCTTCTCACATAAAAGAAATT
* * * *
3057085 ATGTCGTTAACTCCTAAATCTCCTGCTATAATGAACCCTAAAACTCTTTCAAGTTAAAGTTCGAA
66 ATGCCGTTAACTCCGAAATCTCCTGCCATAATGAACCCTAAAACTCTTTCAAGTTAAAGTACGAA
* * * * *
3057150 AACTCAAAAGATTGTGTTGCCAACAGCT-CTT-TT-TCGTTGCAATAATACCTGATATAAATTAG
131 AACTCAAAAGATCGTATTGCCAACAGCTCCTTCTTCTCGTTGCAATAAAACCTAATATAAACTAG
* *
3057212 AAATTTAAACGTAATGGTCAAAGACAAGTATATAAAAGACGAAGCAAAATAAAAGTTTAGTAGGC
196 AAATTGAAACATAATGGTCAAAGACAAGTATATAAAAGACGAAGCAAAATAAAAGTTTAGTAGGC
* * * * *
3057277 TTACACAATAAAGCAGTAACAAGAACCTGATGATGAGGAAAA-AGGAACTTTTCACATAAAGGAA
1 TTACAAAATAAAACAGTAACAAGAACCTGATGAAGAGGAAAACA-G--CTTCTCACATAAAAGAA
* *
3057341 ATTCTGCCGTTAACTCCGAAATCTCCTGCCATAATGGACCCTAAAACT-TTTCCCAAGTTAAA-T
63 ATTATGCCGTTAACTCCGAAATCTCCTGCCATAATGAACCCTAAAACTCTTT--CAAGTTAAAGT
* * *
3057404 ACTG-AAACTCAGAAGATCGTATTGCCAACAGCTCCTTCTTCTGGTTGTAATAAAACCTAATATA
126 AC-GAAAACTCAAAAGATCGTATTGCCAACAGCTCCTTCTTCTCGTTGCAATAAAACCTAATATA
3057468 AACTAGAAATTGAAACATAAT
190 AACTAGAAATTGAAACATAAT
3057489 AGTTAGACAT
Statistics
Matches: 180, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
256 1 0.01
257 39 0.22
258 3 0.02
259 85 0.47
260 13 0.07
261 2 0.01
262 37 0.21
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (260 bp):
TTACAAAATAAAACAGTAACAAGAACCTGATGAAGAGGAAAACAGCTTCTCACATAAAAGAAATT
ATGCCGTTAACTCCGAAATCTCCTGCCATAATGAACCCTAAAACTCTTTCAAGTTAAAGTACGAA
AACTCAAAAGATCGTATTGCCAACAGCTCCTTCTTCTCGTTGCAATAAAACCTAATATAAACTAG
AAATTGAAACATAATGGTCAAAGACAAGTATATAAAAGACGAAGCAAAATAAAAGTTTAGTAGGC
Found at i:3057796 original size:22 final size:22
Alignment explanation
Indices: 3057766--3057807 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3057756 TATGGATGAA
* *
3057766 ATAAATATTCAAAAATAAATTT
1 ATAAATATTAAAAAACAAATTT
*
3057788 ATAAGTATTAAAAAACAAAT
1 ATAAATATTAAAAAACAAAT
3057808 AAATTTCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAATATTAAAAAACAAATTT
Found at i:3061547 original size:21 final size:21
Alignment explanation
Indices: 3061523--3061562 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3061513 CATATTTTTA
3061523 ATATAATTAATTAAATTTATC
1 ATATAATTAATTAAATTTATC
*
3061544 ATATCATTAATTAAATTTA
1 ATATAATTAATTAAATTTA
3061563 AATATTAATT
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:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAATTAATTAAATTTATC
Found at i:3061572 original size:17 final size:20
Alignment explanation
Indices: 3061519--3061567 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
3061509 TTATCATATT
*
3061519 TTTA-ATATAATTAATTAAA
1 TTTACATATCATTAATTAAA
3061538 TTTATCATATCATTAATTAAA
1 TTTA-CATATCATTAATTAAA
*
3061559 TTTAAATAT
1 TTTACATAT
3061568 TAATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 4 0.15
21 18 0.69
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTACATATCATTAATTAAA
Found at i:3061599 original size:26 final size:28
Alignment explanation
Indices: 3061558--3061610 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
3061548 CATTAATTAA
*
3061558 ATTTAAATATTAA-TTTTAATAAAATTC
1 ATTTAAATATAAATTTTTAATAAAATTC
*
3061585 ATTT-AATATAAATTTTTAATTAAATT
1 ATTTAAATATAAATTTTTAATAAAATT
3061611 TTTTATTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTAAATATAAATTTTTAATAAAATTC
Found at i:3061604 original size:13 final size:13
Alignment explanation
Indices: 3061550--3061613 Score: 57
Period size: 12 Copynumber: 5.2 Consensus size: 13
3061540 TATCATATCA
3061550 TTAAT-TAAA-TT
1 TTAATATAAATTT
* *
3061561 TAAATATTAA-TT
1 TTAATATAAATTT
3061573 TTAATA-AAATTCAT
1 TTAATATAAATT--T
3061587 TTAATATAAATTT
1 TTAATATAAATTT
3061600 TTAAT-TAAATTT
1 TTAATATAAATTT
3061612 TT
1 TT
3061614 TATTCACAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 6 0.14
12 20 0.45
13 6 0.14
14 7 0.16
15 5 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATATAAATTT
Found at i:3062617 original size:18 final size:18
Alignment explanation
Indices: 3062594--3062632 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3062584 GCTTGACATG
3062594 AAAAAGTACTTGTAAACT
1 AAAAAGTACTTGTAAACT
3062612 AAAAAGTACTTGTAAACT
1 AAAAAGTACTTGTAAACT
3062630 AAA
1 AAA
3062633 CTAGGGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAAAGTACTTGTAAACT
Found at i:3064137 original size:18 final size:17
Alignment explanation
Indices: 3064114--3064147 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3064104 TTAGGGCTGA
3064114 AAAATTAAAAATTAATTT
1 AAAATTAAAAA-TAATTT
*
3064132 AAAATTATAAATAATT
1 AAAATTAAAAATAATT
3064148 AAATTGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTAAAAATAATTT
Found at i:3065401 original size:3 final size:3
Alignment explanation
Indices: 3065393--3065440 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3065383 TCGCATTTAC
3065393 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3065441 ATCCATGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3080759 original size:21 final size:21
Alignment explanation
Indices: 3080733--3080774 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3080723 CTATCTAACC
3080733 ATATATAACTTCTTTCAAAGG
1 ATATATAACTTCTTTCAAAGG
3080754 ATATATAACTTCTTTCAAAGG
1 ATATATAACTTCTTTCAAAGG
3080775 CCTTATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATATAACTTCTTTCAAAGG
Found at i:3083296 original size:25 final size:25
Alignment explanation
Indices: 3083265--3083314 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3083255 AGTGGGGAAT
3083265 TTGACTGATTATGAAACTTTAAGAA
1 TTGACTGATTATGAAACTTTAAGAA
3083290 TTGACTGATTATGAAACTTTAAGAA
1 TTGACTGATTATGAAACTTTAAGAA
3083315 ATTTGTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (25 bp):
TTGACTGATTATGAAACTTTAAGAA
Found at i:3085051 original size:259 final size:257
Alignment explanation
Indices: 3084703--3085249 Score: 647
Period size: 258 Copynumber: 2.1 Consensus size: 257
3084693 AAAATATATA
* *
3084703 TTTAGCAAGCATTACAAAATAAAACAGTAACAAAAACATGATGAGGAGGAAAAAATCTTCTCACA
1 TTTAGCAAGCATTACAAAATAAAACAGTAACAAAAACATAATGAGGAGGAAAAAAACTTCTCACA
*** *
3084768 CAAAGGAAATTCTGTTGTTTAACTCCTAAATCTCCTGCTATAATGAACCCTAAAACTCTTT-CAA
66 CAAAGGAAATTCTGTCCATTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACT-TTTCCAA
* *
3084832 GTTAAAGTT-CAAAAACTCAAAAGAT-TGTGTTGCCAATAGCTCATCTTCGTTGCAATAATACCT
130 GTT-AA-TTCCAAAAACTCAAAAGATCT-TATTGCCAACAGCTCATCTTC-TTGCAATAATACCT
* * *
3084895 AATATAAATTAGAAATTTAAACGTAATGGTGAAAGACAGGTATATAAAAGATGAAGCAACATAAA
191 AATATAAACTAGAAATTGAAACATAATGGTGAAAGACAGGTATATAAAAGATGAAGCAACATAAA
3084960 AG
256 AG
* * * * * * *
3084962 TTTAGTAAGC-TTACACAATAAAGCAGTAACAAGAACCTAATGATGAGGAAAAAGGAACTTTTCA
1 TTTAGCAAGCATTACAAAATAAAACAGTAACAAAAACATAATGAGGAGGAAAAA--AACTTCTCA
*
3085026 CATAAAGGAAATTCTG-CCATTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACTTTTCCA
64 CACAAAGGAAATTCTGTCCATTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACTTTTCCA
* * * * *
3085090 AGTTAATTCCTAAAACTCAGAAGATCTTATTGCCAACAGCTCTTCTTCTTGTAATAATAGCTAAT
129 AGTTAATTCCAAAAACTCAAAAGATCTTATTGCCAACAGCTCATCTTCTTGCAATAATACCTAAT
** * * * * * * *
3085155 ATAAACTAGAAATTGAAACATAATAATCAGAGATAGGTAT-TCAAAGCATGAAGCAAAATATATG
194 ATAAACTAGAAATTGAAACATAATGGTGAAAGACAGGTATATAAAAG-ATGAAGCAACATAAAAG
* * * *
3085219 TTCAACAAGTATTACAAAATAAAACAATAAC
1 TTTAGCAAGCATTACAAAATAAAACAGTAAC
3085250 TAGACCTACC
Statistics
Matches: 241, Mismatches: 40, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
256 5 0.02
257 69 0.29
258 91 0.38
259 54 0.22
260 22 0.09
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.27
Consensus pattern (257 bp):
TTTAGCAAGCATTACAAAATAAAACAGTAACAAAAACATAATGAGGAGGAAAAAAACTTCTCACA
CAAAGGAAATTCTGTCCATTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACTTTTCCAAG
TTAATTCCAAAAACTCAAAAGATCTTATTGCCAACAGCTCATCTTCTTGCAATAATACCTAATAT
AAACTAGAAATTGAAACATAATGGTGAAAGACAGGTATATAAAAGATGAAGCAACATAAAAG
Found at i:3085656 original size:27 final size:27
Alignment explanation
Indices: 3085588--3085639 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
3085578 AGCTCAATTT
3085588 TTATTTAAAGAAATAAAAATGAATCCA
1 TTATTTAAAGAAATAAAAATGAATCCA
3085615 TTATTTAAAGAAATAAAAATGAATC
1 TTATTTAAAGAAATAAAAATGAATC
3085640 TATTGGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (27 bp):
TTATTTAAAGAAATAAAAATGAATCCA
Found at i:3086011 original size:3 final size:3
Alignment explanation
Indices: 3086003--3086037 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3085993 ATTTACTAAA
*
3086003 ATT ATT ATT ATT ATT ATT ATG ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3086038 ATCCATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3086869 original size:2 final size:2
Alignment explanation
Indices: 3086862--3086891 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3086852 TTTGTAACCA
3086862 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
3086892 GAGAAAGGAT
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:3101273 original size:16 final size:16
Alignment explanation
Indices: 3101252--3101285 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3101242 TAAGAAGAGT
3101252 ACTAGAGGTGAAACCC
1 ACTAGAGGTGAAACCC
3101268 ACTAGAGGTGAAACCC
1 ACTAGAGGTGAAACCC
3101284 AC
1 AC
3101286 ATCACTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (16 bp):
ACTAGAGGTGAAACCC
Found at i:3101653 original size:67 final size:67
Alignment explanation
Indices: 3101576--3101701 Score: 225
Period size: 67 Copynumber: 1.9 Consensus size: 67
3101566 TCAATATTAC
* *
3101576 GAATTTTCATTTATTTCTATAAATAAAAATGAAAAAAATTAATTTGATAGAAAAGTAATCAACAA
1 GAATTTTCATTTATTTCTAAAAATAAAAATGAAAAAAATTAAATTGATAGAAAAGTAATCAACAA
3101641 AA
66 AA
*
3101643 GAATTTTCATTTATTTCTAAAAATAAAAATGAAAAAAATTAAATTGATAGAAAATTAAT
1 GAATTTTCATTTATTTCTAAAAATAAAAATGAAAAAAATTAAATTGATAGAAAAGTAAT
3101702 TGTTAAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (67 bp):
GAATTTTCATTTATTTCTAAAAATAAAAATGAAAAAAATTAAATTGATAGAAAAGTAATCAACAA
AA
Found at i:3103098 original size:20 final size:19
Alignment explanation
Indices: 3103061--3103100 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3103051 ATTTAAATTC
* *
3103061 ATTTTTATTTCTTTTAACA
1 ATTTTTATTTATTATAACA
3103080 ATTTTTATTTAATTATAACA
1 ATTTTTATTT-ATTATAACA
3103100 A
1 A
3103101 ATATTAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTATTTATTATAACA
Found at i:3109551 original size:17 final size:15
Alignment explanation
Indices: 3109528--3109570 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
3109518 CAATTGAAAC
3109528 AAAAAAATAAATAAAT
1 AAAAAAATAAA-AAAT
*
3109544 ACAAAAAATTGAAAAAT
1 A-AAAAAA-TAAAAAAT
3109561 AAAAAAATAA
1 AAAAAAATAA
3109571 TTATGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 11 0.48
18 3 0.13
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:3109566 original size:8 final size:8
Alignment explanation
Indices: 3109528--3109570 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
3109518 CAATTGAAAC
3109528 AAAAAAAT
1 AAAAAAAT
*
3109536 AAATAAAT
1 AAAAAAAT
3109544 ACAAAAAAT
1 A-AAAAAAT
**
3109553 TGAAAAAT
1 AAAAAAAT
3109561 AAAAAAAT
1 AAAAAAAT
3109569 AA
1 AA
3109571 TTATGAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3113077 original size:258 final size:257
Alignment explanation
Indices: 3112699--3113164 Score: 629
Period size: 258 Copynumber: 1.8 Consensus size: 257
3112689 TCAGCAAGCA
* * *
3112699 TTACAAAATAAAACAGTAAGAAAACTTGATGAAGAGGAAAACAGGCTTCTCGCATAAAGAAATTA
1 TTACAAAATAAAACAGTAACAAAACCTGATGAAGAGGAAAACAGGCTTCTCACATAAAGAAATTA
* * *
3112764 TGTTCGTTAACTCCTAAATCTCCTGCTATAATGAACCCTAAAACTCTTTCAAGTTAAAGTTC-GA
66 TGTCCGTTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACTCTTTCAAGTTAAA-TACTG-
* * * * *
3112828 AAACTCAAAAGATTGTGTTGCCAACAGCTCTTCTTC-GTTGCAATAATACCTGATATAAATTAGA
129 AAACTCAAAAGATCGTATTGCCAACAGCTCTTCTTCGGTTGCAATAAAACCTAATATAAACTAGA
* *
3112892 AATTTAAACGTAATGGTCAAAGACAAGTATATAAAAGACGAAGCAAAATAAAAGTTTAGTAGGC
194 AATTGAAACATAATGGTCAAAGACAAGTATATAAAAGACGAAGCAAAATAAAAGTTTAGTAGGC
* * * *
3112956 TTACACAATAAAGCAGTAACAAGAACCTGATGATGAGG-AAA-AGGAACTTTTCACATAAAGGAA
1 TTACAAAATAAAACAGTAACAA-AACCTGATGAAGAGGAAAACAGG--CTTCTCACATAAA-GAA
* *
3113019 ATTCTG-CCGTTAACTCCTAAATCTCCTGCCATAATGGACCCTAAAACT-TTTCCAAGTTAAATA
62 ATTATGTCCGTTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACTCTTT-CAAGTTAAATA
* *
3113082 CTGAAACTCAGAAGATCGTATTGCCAACAGCTCTTCTTCTGGTTGTAATAAAACCTAATATAAAC
126 CTGAAACTCAAAAGATCGTATTGCCAACAGCTCTTCTTC-GGTTGCAATAAAACCTAATATAAAC
3113147 TAGAAATTGAAACATAAT
190 TAGAAATTGAAACATAAT
3113165 AGTTAGACAT
Statistics
Matches: 180, Mismatches: 21, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
256 3 0.02
257 60 0.33
258 73 0.41
259 44 0.24
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (257 bp):
TTACAAAATAAAACAGTAACAAAACCTGATGAAGAGGAAAACAGGCTTCTCACATAAAGAAATTA
TGTCCGTTAACTCCTAAATCTCCTGCCATAATGAACCCTAAAACTCTTTCAAGTTAAATACTGAA
ACTCAAAAGATCGTATTGCCAACAGCTCTTCTTCGGTTGCAATAAAACCTAATATAAACTAGAAA
TTGAAACATAATGGTCAAAGACAAGTATATAAAAGACGAAGCAAAATAAAAGTTTAGTAGGC
Found at i:3116652 original size:20 final size:19
Alignment explanation
Indices: 3116611--3116651 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
3116601 TCGAAATAAA
3116611 TTATATATTTTTATTAATTT
1 TTATATATTTTTA-TAATTT
3116631 TTATATATATTTTA-AATTT
1 TTATATAT-TTTTATAATTT
3116650 TT
1 TT
3116652 TTAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 8 0.40
21 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATATTTTTATAATTT
Found at i:3116719 original size:22 final size:21
Alignment explanation
Indices: 3116680--3116720 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3116670 TTTTATACAT
* *
3116680 AAATTTATTTAAATATATTAA
1 AAATTTATTAAAAAATATTAA
3116701 AAATTATATTAAAAAATATT
1 AAATT-TATTAAAAAATATT
3116721 TACACAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTATTAAAAAATATTAA
Found at i:3118042 original size:2 final size:2
Alignment explanation
Indices: 3118037--3118064 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3118027 CAGTAACCTC
3118037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3118065 CTGATGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3118283 original size:2 final size:2
Alignment explanation
Indices: 3118276--3118307 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3118266 AGCTCTTAAA
3118276 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
3118308 GATTAATTCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3119872 original size:27 final size:27
Alignment explanation
Indices: 3119813--3119866 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3119803 AACAGAATAC
3119813 TCAGATTATCAAAACACAGTAGCATAA
1 TCAGATTATCAAAACACAGTAGCATAA
*
3119840 TCAGATTATCAAAACACAGTAGTATAA
1 TCAGATTATCAAAACACAGTAGCATAA
3119867 GTAGATGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (27 bp):
TCAGATTATCAAAACACAGTAGCATAA
Found at i:3121590 original size:64 final size:64
Alignment explanation
Indices: 3121457--3121590 Score: 141
Period size: 64 Copynumber: 2.1 Consensus size: 64
3121447 CAATGCTTTG
* *
3121457 AATAATTCTCTCATAAAAAATAAAAGCGATTATTAAAGGTATTTTCTACAAAAAAAACGCTTTTC
1 AATAATTCTCT-ATAAAAAATAAAAGCGATTATTAAAGGTATTTTCTACAAAAAAAACACTATTC
* * ** *
3121522 -ATAATTCTCT-TAAAAAATTATAGAG-GATTATTAAAGGTATTTTTTTTATCAAAAAACAC-AT
1 AATAATTCTCTATAAAAAA-TA-AAAGCGATTATTAAAGGTATTTTCTACA-AAAAAAACACTAT
3121583 TC
63 TC
3121585 AATAAT
1 AATAAT
3121591 GCCTTTTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
62 7 0.12
63 25 0.43
64 26 0.45
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (64 bp):
AATAATTCTCTATAAAAAATAAAAGCGATTATTAAAGGTATTTTCTACAAAAAAAACACTATTC
Found at i:3122692 original size:14 final size:14
Alignment explanation
Indices: 3122675--3122717 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3122665 ACATATAAAA
3122675 TAAATTATATATAT
1 TAAATTATATATAT
*
3122689 TAAATTATAAATAT
1 TAAATTATATATAT
3122703 T--ATTATAT-TAT
1 TAAATTATATATAT
3122714 TAAA
1 TAAA
3122718 CTAATTTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.16
12 6 0.24
13 1 0.04
14 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATTATATATAT
Found at i:3122838 original size:23 final size:22
Alignment explanation
Indices: 3122804--3122846 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
3122794 GAATTTTAAT
3122804 AATTAAAGTTATCAGATATTATA
1 AATTAAAGTTATCAG-TATTATA
*
3122827 AATTAATA-TTATTAGTATTA
1 AATTAA-AGTTATCAGTATTA
3122847 GAATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 12 0.67
24 1 0.06
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
AATTAAAGTTATCAGTATTATA
Found at i:3122926 original size:21 final size:21
Alignment explanation
Indices: 3122886--3122926 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3122876 GTTAATGCAC
*
3122886 AAATTTTATTTTTTTATTTAA
1 AAATTTTATTATTTTATTTAA
3122907 AAATTTTATTAATTTT-TTTA
1 AAATTTTATT-ATTTTATTTA
3122927 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
AAATTTTATTATTTTATTTAA
Found at i:3123341 original size:62 final size:62
Alignment explanation
Indices: 3123219--3123392 Score: 158
Period size: 62 Copynumber: 2.8 Consensus size: 62
3123209 ACCTGAAATG
* * * * * *
3123219 CCTTCAATAATCCCCTCATAAAAAA-TAAAGGGGATTACTGAA-ACATTTTTTTG-CAGAAAACA
1 CCTTCAATAATCTCATTATAAAAAATTAAA-GGGATTATTGAAGGCA-TTTTTGGCCA-AAAACA
* * * *
3123281 CTTTCAATAATC-CATTCTAAAAAATTATAGGAGATTATTGAAGGCATTTTTGGCCAAAAACG
1 CCTTCAATAATCTCATTATAAAAAATTAAAGG-GATTATTGAAGGCATTTTTGGCCAAAAACA
* * * *
3123343 CCTTCAATAATCTCTTTATCAAAATTTAAAGGGATTATTGAAGGCGTTTT
1 CCTTCAATAATCTCATTATAAAAAATTAAAGGGATTATTGAAGGCATTTT
3123393 CTGCAATAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
61 11 0.12
62 62 0.68
63 18 0.20
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (62 bp):
CCTTCAATAATCTCATTATAAAAAATTAAAGGGATTATTGAAGGCATTTTTGGCCAAAAACA
Found at i:3127584 original size:34 final size:33
Alignment explanation
Indices: 3127511--3127586 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
3127501 CAAATACCGT
* * * *
3127511 TAAATTAACAGTATTTTTTTGCTACAAATGCCA
1 TAAATTAACAATATTTTTATGATAAAAATGCCA
* *
3127544 TCAAATTAACAATGTTTTTATGATAAAAATGTCA
1 T-AAATTAACAATATTTTTATGATAAAAATGCCA
3127578 CTAAATTAA
1 -TAAATTAA
3127587 TGACATCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
33 1 0.03
34 33 0.94
35 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (33 bp):
TAAATTAACAATATTTTTATGATAAAAATGCCA
Found at i:3131194 original size:7 final size:7
Alignment explanation
Indices: 3131182--3131207 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3131172 ACAAAGGATT
3131182 TTTAAAA
1 TTTAAAA
3131189 TTTAAAA
1 TTTAAAA
3131196 TTTAAAA
1 TTTAAAA
3131203 TTTAA
1 TTTAA
3131208 TTCATTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:3142025 original size:15 final size:16
Alignment explanation
Indices: 3142005--3142034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3141995 TGGAAATCGA
3142005 AAAG-AAAATAGAATT
1 AAAGAAAAATAGAATT
3142020 AAAGAAAAATAGAAT
1 AAAGAAAAATAGAAT
3142035 ATATTATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
AAAGAAAAATAGAATT
Found at i:3142572 original size:9 final size:9
Alignment explanation
Indices: 3142558--3142625 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
3142548 TTCTATCTGA
3142558 TATTATTTT
1 TATTATTTT
3142567 TATTATTTT
1 TATTATTTT
*
3142576 T-TTCTTTCT
1 TATTATTT-T
*
3142585 T-TTGTATTT
1 TATTAT-TTT
3142594 TATGTA-TTT
1 TAT-TATTTT
3142603 TATTATTTAT
1 TATTATTT-T
*
3142613 TATTATTAT
1 TATTATTTT
3142622 TATT
1 TATT
3142626 GTGTATTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
8 7 0.14
9 30 0.61
10 11 0.22
11 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
TATTATTTT
Found at i:3142611 original size:16 final size:16
Alignment explanation
Indices: 3142592--3142735 Score: 83
Period size: 16 Copynumber: 9.1 Consensus size: 16
3142582 TCTTTTGTAT
3142592 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
3142608 TTTATTATTATTATTA
1 TTTATTATTATTATTA
*
3142624 TTGT-GTATTAATATATATA
1 TT-TATTATT-AT-TAT-TA
* *
3142643 TTT-TTTTCTATTAATA
1 TTTATTAT-TATTATTA
3142659 TTTA-TATGTATT-TTA
1 TTTATTAT-TATTATTA
3142674 TTTA-TA-TAGTTA-TA
1 TTTATTATTA-TTATTA
3142688 TTTATTATTATTA-T-
1 TTTATTATTATTATTA
* *
3142702 GTTATCATTATTATTA
1 TTTATTATTATTATTA
*
3142718 TATTATTATTATCATTA
1 T-TTATTATTATTATTA
3142735 T
1 T
3142736 CATTTTTTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.02
14 19 0.19
15 19 0.19
16 30 0.29
17 19 0.19
18 8 0.08
19 5 0.05
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:3142615 original size:3 final size:3
Alignment explanation
Indices: 3142589--3142735 Score: 67
Period size: 3 Copynumber: 48.0 Consensus size: 3
3142579 CTTTCTTTTG
* *
3142589 TAT T-T TAT GTAT T-T TAT TATT TAT TAT TAT TAT TAT TGT GTAT TAA
1 TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT
* * *
3142635 TA- TAT ATAT TTT TTT CTAT TAA TAT T-T ATAT GTAT T-T TATT TAT
1 TAT TAT -TAT TAT TAT -TAT TAT TAT TAT -TAT -TAT TAT TA-T TAT
* *
3142679 ATAGT TA- TATT TAT TAT TAT TA- TGT TAT CAT TAT TAT TA- TAT TAT
1 -TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3142724 TAT TAT CAT TAT
1 TAT TAT TAT TAT
3142736 CATTTTTTTT
Statistics
Matches: 112, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
2 14 0.12
3 71 0.63
4 26 0.23
5 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3142701 original size:23 final size:22
Alignment explanation
Indices: 3142651--3142701 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3142641 TATTTTTTTC
*
3142651 TATTA-ATATTTATATGTATTT
1 TATTATATAGTTATATGTATTT
*
3142672 TATTTATATAGTTATATTTATTAT
1 TA-TTATATAGTTATATGTATT-T
3142696 TATTAT
1 TATTAT
3142702 GTTATCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 3 0.12
23 17 0.68
24 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TATTATATAGTTATATGTATTT
Found at i:3142706 original size:14 final size:13
Alignment explanation
Indices: 3142589--3142729 Score: 89
Period size: 14 Copynumber: 10.7 Consensus size: 13
3142579 CTTTCTTTTG
*
3142589 TATT-TTATGTAT
1 TATTATTATTTAT
3142601 T-TTATTATTTAT
1 TATTATTATTTAT
3142613 TATTATTA-TTAT
1 TATTATTATTTAT
* *
3142625 TGTGTATTAATATAT
1 TAT-TATT-ATTTAT
*
3142640 ATATT-TTTTTCTAT
1 -TATTATTATT-TAT
* *
3142654 TAATATT-TATAT
1 TATTATTATTTAT
3142666 GTATT-TTATTTAT
1 -TATTATTATTTAT
3142679 ATAGTTA-TATTTAT
1 -TA-TTATTATTTAT
3142693 TATTATTATGTTAT
1 TATTATTAT-TTAT
*
3142707 CATTATTATTATAT
1 TATTATTATT-TAT
3142721 TATTATTAT
1 TATTATTAT
3142730 CATTATCATT
Statistics
Matches: 101, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
11 2 0.02
12 23 0.23
13 30 0.30
14 40 0.40
15 4 0.04
16 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:3142711 original size:17 final size:17
Alignment explanation
Indices: 3142683--3142735 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
3142673 ATTTATATAG
3142683 TTATATT-T-ATTATTA
1 TTATATTATCATTATTA
*
3142698 TTATGTTATCATTATTA
1 TTATATTATCATTATTA
* *
3142715 TTATATTATTATTATCA
1 TTATATTATCATTATTA
3142732 TTAT
1 TTAT
3142736 CATTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 25 0.78
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATATTATCATTATTA
Found at i:3143233 original size:19 final size:19
Alignment explanation
Indices: 3143200--3143236 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3143190 CAGTTTTCGG
**
3143200 TTGAATTTTTTGACGAAAC
1 TTGAATTTTCCGACGAAAC
3143219 TTGAATTTTCCGACGAAA
1 TTGAATTTTCCGACGAAA
3143237 ATTCCGGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGAATTTTCCGACGAAAC
Found at i:3143322 original size:11 final size:11
Alignment explanation
Indices: 3143306--3143331 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3143296 CTGGTGATCA
3143306 TCCGGCCAACT
1 TCCGGCCAACT
3143317 TCCGGCCAACT
1 TCCGGCCAACT
3143328 TCCG
1 TCCG
3143332 ACTAAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.46, G:0.19, T:0.19
Consensus pattern (11 bp):
TCCGGCCAACT
Found at i:3143754 original size:10 final size:10
Alignment explanation
Indices: 3143720--3143860 Score: 76
Period size: 10 Copynumber: 13.8 Consensus size: 10
3143710 TTTTTTGAAT
3143720 TTTTTATTTA
1 TTTTTATTTA
*
3143730 TTTGT-TTTA
1 TTTTTATTTA
*
3143739 TCTTTATTTA
1 TTTTTATTTA
3143749 TTTTTATTTA
1 TTTTTATTTA
*
3143759 TTAGATTAGATTTA
1 TT---TT-TATTTA
* *
3143773 TTTAATATTTT
1 TTT-TTATTTA
3143784 TTCTTTATCTTA
1 TT-TTTAT-TTA
3143796 TTTTTA-TT-
1 TTTTTATTTA
*
3143804 TTTGT-TTTA
1 TTTTTATTTA
* *
3143813 CTTTTCTTTA
1 TTTTTATTTA
*
3143823 ATTTT-TTTA
1 TTTTTATTTA
3143832 TTTTTATTTA
1 TTTTTATTTA
* *
3143842 TTTTCACTTTT
1 TTTTTA-TTTA
3143853 TTTTTATT
1 TTTTTATT
3143861 ATTCTATTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 26
0.69 0.12 0.18
Matches are distributed among these distances:
8 6 0.06
9 20 0.20
10 38 0.38
11 22 0.22
12 5 0.05
13 2 0.02
14 7 0.07
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:3143812 original size:22 final size:21
Alignment explanation
Indices: 3143778--3143845 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 21
3143768 ATTTATTTAA
3143778 TATTTTTTCTTTATCTTATT-TT
1 TATTTTTTCTTTA-CTT-TTCTT
3143800 TATTTTTGT-TTTACTTTTCTT
1 TATTTTT-TCTTTACTTTTCTT
* * *
3143821 TA-ATTTT-TTTATTTTTATT
1 TATTTTTTCTTTACTTTTCTT
3143840 TATTTT
1 TATTTT
3143846 CACTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.33
20 7 0.18
21 7 0.18
22 11 0.28
23 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (21 bp):
TATTTTTTCTTTACTTTTCTT
Found at i:3143823 original size:46 final size:45
Alignment explanation
Indices: 3143734--3143858 Score: 119
Period size: 46 Copynumber: 2.7 Consensus size: 45
3143724 TATTTATTTG
* * *
3143734 TTTTATCTTTATTTATTTTTATTTATTAG-ATTAGATTTATTTAATA
1 TTTTTTCTTTATTTATTTTTATTT-TT-GTTTTACATTTATTTAATA
* * *
3143780 TTTTTTCTTTATCTTATTTTTATTTTTGTTTTACTTTTCTTTAATT
1 TTTTTTCTTTAT-TTATTTTTATTTTTGTTTTACATTTATTTAATA
* *
3143826 TTTTTATTTTTATTTATTTTCACTTTTT-TTTTA
1 TTTTT-TCTTTATTTATTTTTA-TTTTTGTTTTA
3143859 TTATTCTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 43 0.64
47 23 0.34
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (45 bp):
TTTTTTCTTTATTTATTTTTATTTTTGTTTTACATTTATTTAATA
Found at i:3143836 original size:19 final size:18
Alignment explanation
Indices: 3143797--3143845 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3143787 TTTATCTTAT
*
3143797 TTTTATTT-TTGTTTTAC
1 TTTTATTTATTTTTTTAC
* *
3143814 TTTTCTTTAATTTTTTTAT
1 TTTTATTT-ATTTTTTTAC
3143833 TTTTATTTATTTT
1 TTTTATTTATTTT
3143846 CACTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 14 0.54
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTATTTATTTTTTTAC
Found at i:3143852 original size:25 final size:25
Alignment explanation
Indices: 3143824--3143871 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3143814 TTTTCTTTAA
*
3143824 TTTTTTTATTTTTATT-TATTTTCAC
1 TTTTTTT-TTATTATTCTATTTTCAC
3143849 TTTTTTTTTATTATTCTATTTTC
1 TTTTTTTTTATTATTCTATTTTC
3143872 TTCAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTTTTATTATTCTATTTTCAC
Found at i:3143869 original size:35 final size:36
Alignment explanation
Indices: 3143794--3143870 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 36
3143784 TTCTTTATCT
* * * *
3143794 TATTTTTATTTTTGTTTTACTTTTCTTTAATTTTTT
1 TATTTTTATTTATGTTTCACTTTTCTTTAATTATTC
* *
3143830 TATTTTTATTTAT-TTTCACTTTTTTTTTATTATTC
1 TATTTTTATTTATGTTTCACTTTTCTTTAATTATTC
3143865 TATTTT
1 TATTTT
3143871 CTTCAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (36 bp):
TATTTTTATTTATGTTTCACTTTTCTTTAATTATTC
Found at i:3143870 original size:18 final size:17
Alignment explanation
Indices: 3143794--3143870 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
3143784 TTCTTTATCT
*
3143794 TATTTTTATTT-TTGTTT
1 TATTTTTATTTATT-TTC
* * *
3143811 TACTTTTCTTTAATTTTTT
1 TATTTTTATTT-A-TTTTC
3143830 TATTTTTATTTATTTTC
1 TATTTTTATTTATTTTC
*
3143847 -ACTTTTTTTTTATTATTC
1 TA-TTTTTATTTATT-TTC
3143865 TATTTT
1 TATTTT
3143871 CTTCAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.02
17 24 0.50
18 8 0.17
19 13 0.27
20 2 0.04
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (17 bp):
TATTTTTATTTATTTTC
Found at i:3143966 original size:58 final size:58
Alignment explanation
Indices: 3143897--3144228 Score: 490
Period size: 58 Copynumber: 5.7 Consensus size: 58
3143887 AATTTTCCAA
3143897 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * * *
3143955 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * * *
3144013 AAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAATCAAAATTTCA
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT--AAATTTCC
3144073 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA-AAATTTCC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
3144130 AAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTCC
1 -AAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * *
3144189 -AAAAAAGATTTTTGGGGAAAGGTTGAAAGTATCAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
3144229 TCTACACAAG
Statistics
Matches: 249, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
57 43 0.17
58 146 0.59
59 8 0.03
60 52 0.21
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:3144093 original size:176 final size:177
Alignment explanation
Indices: 3143881--3144227 Score: 610
Period size: 176 Copynumber: 2.0 Consensus size: 177
3143871 CTTCAAATAA
*
3143881 AAATCAAATTTTCCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
1 AAATCAAAATTTCCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
*
3143946 TAAATTTCC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATT
66 -AAATTTCCAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATT
*
3144010 TTCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGG
130 TCCAAAAAAG-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGG
3144059 AAATCAAAATTT-C-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
1 AAATCAAAATTTCCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
3144122 AAATTTCCAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
66 AAATTTCCAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
* *
3144187 CCAAAAAAGATTTTTGGGGAAAGGTTGAAAGTATCAATTTT
131 CCAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
3144228 CTCTACACAA
Statistics
Matches: 163, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
175 38 0.23
176 113 0.69
177 1 0.01
178 11 0.07
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (177 bp):
AAATCAAAATTTCCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
AAATTTCCAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
CCAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGG
Found at i:3144107 original size:118 final size:116
Alignment explanation
Indices: 3143878--3144228 Score: 510
Period size: 118 Copynumber: 3.0 Consensus size: 116
3143868 TTTCTTCAAA
*
3143878 TAAAAATCAAATTTTCCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 TAAAAAT-AAATTTT-C-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAG
*
3143943 AAATAAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCT
63 AAATAAATTT-CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* *
3143998 TAAAAATAAATTTTC-AAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAA
1 TAAAAATAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAA
*
3144062 TCAAAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
66 T--AAATTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
3144116 TAGAAA-AAATTTCCAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAA
1 TAAAAATAAATTTTCAAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAGAA
* * *
3144179 ATAAATTTCCAAAAAAGATTTTTGGGGAAAGGTTGAAAGTATCAATTTTC
65 ATAAATTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
3144229 TCTACACAAG
Statistics
Matches: 212, Mismatches: 14, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
115 37 0.17
116 54 0.25
117 10 0.05
118 97 0.46
119 7 0.03
120 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (116 bp):
TAAAAATAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAA
TAAATTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:3144280 original size:12 final size:12
Alignment explanation
Indices: 3144263--3144287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3144253 CCTACCTTTC
3144263 TATTTTGATTTT
1 TATTTTGATTTT
3144275 TATTTTGATTTT
1 TATTTTGATTTT
3144287 T
1 T
3144288 CTTTAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TATTTTGATTTT
Found at i:3146469 original size:16 final size:19
Alignment explanation
Indices: 3146448--3146496 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
3146438 TTTTATGTAT
3146448 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
3146465 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
3146483 TGTATATATTTATT
1 TGTAT-TATTTATT
3146497 TATTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:3146508 original size:16 final size:15
Alignment explanation
Indices: 3146439--3146509 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
3146429 TCCTTTGTAT
3146439 TTTATGTATTGTATTA
1 TTTATGTATT-TATTA
3146455 TTTAT-TA-TTATTA
1 TTTATGTATTTATTA
*
3146468 -TTATGTATTAATATA
1 TTTATGTATTTAT-TA
* *
3146483 TGTATATATTTATTTA
1 TTTATGTATTTA-TTA
*
3146499 TTTATTTATTT
1 TTTATGTATTT
3146510 TCTGTTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 4 0.09
15 4 0.09
16 24 0.55
17 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTATGTATTTATTA
Found at i:3146582 original size:83 final size:83
Alignment explanation
Indices: 3146436--3146594 Score: 193
Period size: 84 Copynumber: 1.9 Consensus size: 83
3146426 TCTTCCTTTG
3146436 TATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTTATTTA-T
1 TATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTTATTTATT
3146500 TTATTTATTTTCTGTTAA
66 TTATTTATTTTCTGTTAA
* * * * *
3146518 TATTTATATGTATTTTATTATTTGTGTATTATTACTAATATGTA-T-ATAT-TTTTTATCTTT-T
1 TATTT-TATGTATTGTATTATTTAT-TATTATTA-T--TATGTATTAATATATGTATATATTTAT
3146579 TTATTTTATTTATTTT
61 TTATTTTATTTATTTT
3146595 TGTATTTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
82 5 0.08
83 21 0.32
84 28 0.42
85 5 0.08
86 1 0.02
87 6 0.09
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (83 bp):
TATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTTATTTATT
TTATTTATTTTCTGTTAA
Found at i:3146603 original size:18 final size:18
Alignment explanation
Indices: 3146569--3146611 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3146559 GTATATATTT
*
3146569 TTTATCTTTTTTATTTTA
1 TTTATCTTTTGTATTTTA
3146587 TTTAT-TTTTGTATTTTTA
1 TTTATCTTTTGTA-TTTTA
3146605 TTTATCT
1 TTTATCT
3146612 AATTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 15 0.68
19 1 0.05
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTATCTTTTGTATTTTA
Found at i:3147534 original size:13 final size:13
Alignment explanation
Indices: 3147516--3147540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3147506 CTCCAGGTTT
3147516 TTTTTTTTATTTG
1 TTTTTTTTATTTG
3147529 TTTTTTTTATTT
1 TTTTTTTTATTT
3147541 ATTTATTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTATTTG
Found at i:3147590 original size:17 final size:17
Alignment explanation
Indices: 3147568--3147613 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
3147558 TATTTAATAT
3147568 TTTTTATCTTTATCTTA
1 TTTTTATCTTTATCTTA
* *
3147585 TTTTTATTTTTATTTTA
1 TTTTTATCTTTATCTTA
*
3147602 CTTTT-TCTTTAT
1 TTTTTATCTTTAT
3147614 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATCTTTATCTTA
Found at i:3147619 original size:25 final size:24
Alignment explanation
Indices: 3147567--3147662 Score: 78
Period size: 25 Copynumber: 4.0 Consensus size: 24
3147557 TTATTTAATA
*
3147567 TTTTTTATCTTTATCTTATT-TTTA-
1 TTTTTTAT-TTTA-CTTTTTCTTTAT
3147591 -TTTTTATTTTACTTTTTCTTTAT
1 TTTTTTATTTTACTTTTTCTTTAT
3147614 TTTTTTATTTTCACTTTTAT-TTT-T
1 TTTTTTATTTT-ACTTTT-TCTTTAT
3147638 TTATTTTATTATT-CTATTTTCTTTA
1 TT-TTTTATT-TTACT-TTTTCTTTA
3147663 AATAAAAATC
Statistics
Matches: 61, Mismatches: 1, Indels: 18
0.76 0.01 0.22
Matches are distributed among these distances:
21 5 0.08
22 8 0.13
23 7 0.11
24 16 0.26
25 22 0.36
26 3 0.05
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTATTTTACTTTTTCTTTAT
Found at i:3147624 original size:6 final size:6
Alignment explanation
Indices: 3147568--3147657 Score: 60
Period size: 6 Copynumber: 14.7 Consensus size: 6
3147558 TATTTAATAT
* * *
3147568 TTTTTA TCTTTA -TCTTA TTTTTA TTTTTA -TTTTA CTTTTTC TTTATT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTT-TTA
* * *
3147615 TTTTTA TTTTCA CTTTTA TTTTTT TATTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA TT-TT-TA TTTT
3147658 CTTTAAATAA
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
5 10 0.15
6 36 0.55
7 15 0.23
8 4 0.06
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:3147766 original size:59 final size:59
Alignment explanation
Indices: 3147668--3148083 Score: 554
Period size: 59 Copynumber: 6.9 Consensus size: 59
3147658 CTTTAAATAA
*
3147668 AAATCAAAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAATC-AAATTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
3147729 AAATCAAAATTTTC-GAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 AAATC-AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
3147788 AAAT-AAATTTTCAAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 AAATCAAATTTTC-----AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
3147851 AAAT-AAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-G
1 AAATCAAATTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * * * *
3147909 AAAATCAAAATTTCCAAAAAGTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAG
1 -AAATCAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
** * *
3147969 AAAT-AAATTTTCAAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 AAATCAAATTTTCAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
3148028 AAATCAAAGTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
1 AAATCAAATTTTC--AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
3148084 TCCACACAAG
Statistics
Matches: 322, Mismatches: 20, Indels: 26
0.88 0.05 0.07
Matches are distributed among these distances:
57 8 0.02
58 13 0.04
59 178 0.55
60 15 0.05
61 47 0.15
62 6 0.02
63 55 0.17
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (59 bp):
AAATCAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:3147871 original size:181 final size:178
Alignment explanation
Indices: 3147668--3148083 Score: 665
Period size: 181 Copynumber: 2.3 Consensus size: 178
3147658 CTTTAAATAA
3147668 AAATCAAAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATC-AAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* *
3147733 CAAAATTTTCGAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATT
65 CAAAA-TTTCCAAAAAGTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAGAAATAAATT
* *
3147797 TTCAAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
129 TTC----AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG
*
3147851 AAAT-AAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
1 AAATCAAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC
3147915 AAAATTTCCAAAAAGTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAGAAATAAATTTT
66 AAAATTTCCAAAAAGTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAGAAATAAATTTT
** *
3147980 CAAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
131 CAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
3148028 AAATCAAAGTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
1 AAATCAAATTTTC-AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
3148084 TCCACACAAG
Statistics
Matches: 220, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
177 46 0.21
178 7 0.03
179 41 0.19
180 9 0.04
181 113 0.51
183 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (178 bp):
AAATCAAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC
AAAATTTCCAAAAAGTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAGAAATAAATTTT
CAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:3149260 original size:52 final size:51
Alignment explanation
Indices: 3149192--3149337 Score: 184
Period size: 53 Copynumber: 2.8 Consensus size: 51
3149182 CTTGTAAAAA
* *
3149192 AAGAATTTTAAAAGAAAGAAGATTCTTAATAGGTAAGTTTGACTTGCAAGAG
1 AAGAATTTTAAGAGAAA-AAGATTCTTAATAGGCAAGTTTGACTTGCAAGAG
* **
3149244 AAGAATTCTAAGAGAAAAAGGGATTCTTAATAGGCAAGTTTGACTTTTAAGAG
1 AAGAATTTTAAGAGAAAAA--GATTCTTAATAGGCAAGTTTGACTTGCAAGAG
* * *
3149297 AAGAATTTTAAGGGAAAAAGAATTTTTAGTAGGCAAGTTTG
1 AAGAATTTTAAGAGAAAAAG-ATTCTTAATAGGCAAGTTTG
3149338 TATGGTTATA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
51 3 0.04
52 33 0.40
53 46 0.56
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.29
Consensus pattern (51 bp):
AAGAATTTTAAGAGAAAAAGATTCTTAATAGGCAAGTTTGACTTGCAAGAG
Found at i:3158872 original size:66 final size:67
Alignment explanation
Indices: 3158794--3158918 Score: 198
Period size: 66 Copynumber: 1.9 Consensus size: 67
3158784 TCAATATTAA
* * *
3158794 TAATTTTCATTTATTTCTATAAATAAAATTG-AAAAAATTAAAATGATAGAAAAGTAATCAACAA
1 TAATTTTAATTTATTTCTAAAAATAAAAATGAAAAAAATTAAAATGATAGAAAAGTAATCAACAA
3158858 AC
66 AC
* *
3158860 TAATTTTAATTTATTTCTAAAAATAAAAATGAAAAAAATTAAATTGATAGAAAATTAAT
1 TAATTTTAATTTATTTCTAAAAATAAAAATGAAAAAAATTAAAATGATAGAAAAGTAAT
3158919 TGATAAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
66 28 0.53
67 25 0.47
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (67 bp):
TAATTTTAATTTATTTCTAAAAATAAAAATGAAAAAAATTAAAATGATAGAAAAGTAATCAACAA
AC
Found at i:3158921 original size:15 final size:16
Alignment explanation
Indices: 3158894--3158923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3158884 AAAAATGAAA
3158894 AAAATTAAATTGATAG
1 AAAATTAAATTGATAG
3158910 AAAATT-AATTGATA
1 AAAATTAAATTGATA
3158924 AAATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (16 bp):
AAAATTAAATTGATAG
Found at i:3159175 original size:23 final size:25
Alignment explanation
Indices: 3159129--3159175 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
3159119 CTTTATTTCC
*
3159129 AAAATAACAAAATTAAAATGTTTTA
1 AAAATAACAAAATTAAAATATTTTA
*
3159154 AAAATAA-AAAA-TAAATTATTTT
1 AAAATAACAAAATTAAAATATTTT
3159176 TGTAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
AAAATAACAAAATTAAAATATTTTA
Found at i:3161817 original size:24 final size:23
Alignment explanation
Indices: 3161785--3161840 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
3161775 TCCCTTAATT
3161785 TTTCTTTTTTTTTTC-TTTCCATTC
1 TTTCTTTTTTTTTTCATTT-C-TTC
3161809 TTTC-TTTTTTTTTCATTTCTTC
1 TTTCTTTTTTTTTTCATTTCTTC
3161831 TTT-TTTTTTT
1 TTTCTTTTTTT
3161841 GTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 12 0.40
23 11 0.37
24 7 0.23
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTTTTTTTTCATTTCTTC
Found at i:3161819 original size:22 final size:21
Alignment explanation
Indices: 3161789--3161840 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
3161779 TTAATTTTTC
3161789 TTTTTTTTTTC-TTTCCATTCTT
1 TTTTTTTTTTCATTT-C-TTCTT
3161811 TCTTTTTTTTTCATTTCTTCTT
1 T-TTTTTTTTTCATTTCTTCTT
3161833 TTTTTTTT
1 TTTTTTTT
3161841 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.25
22 7 0.25
23 11 0.39
24 3 0.11
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTCATTTCTTCTT
Found at i:3161825 original size:18 final size:19
Alignment explanation
Indices: 3161786--3161839 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
3161776 CCCTTAATTT
*
3161786 TTCTTTTTTTTTTCTTTCCA
1 TTCTTTCTTTTTT-TTTCCA
3161806 TTCTTTCTTTTTTTTT-CA
1 TTCTTTCTTTTTTTTTCCA
3161824 TT-TCTTCTTTTTTTTT
1 TTCT-TTCTTTTTTTTT
3161840 TGTTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 1 0.03
18 16 0.50
19 3 0.09
20 12 0.38
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTCTTTCTTTTTTTTTCCA
Found at i:3161840 original size:19 final size:19
Alignment explanation
Indices: 3161785--3161840 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 19
3161775 TCCCTTAATT
3161785 TTTCTTTTTTTTTTCTTTCCA
1 TTTC-TTTTTTTTT-TTTCCA
3161806 -TTCTTTCTTTTTTTTT-CA
1 TTTCTTT-TTTTTTTTTCCA
3161824 TTTCTTCTTTTTTTTTT
1 TTTCTT-TTTTTTTTTT
3161841 GTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.06
19 20 0.62
20 10 0.31
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTTTTTTTTTTTTCCA
Found at i:3161845 original size:24 final size:24
Alignment explanation
Indices: 3161784--3161845 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
3161774 ATCCCTTAAT
3161784 TTTTCTTTTTTTTTTCTTTCCATTC
1 TTTT-TTTTTTTTTTCTTTCCATTC
*
3161809 -TTTCTTTTTTTTTCATTT-C-TTC
1 TTTTTTTTTTTTTTC-TTTCCATTC
3161831 TTTTTTTTTTGTTTT
1 TTTTTTTTTT-TTTT
3161846 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 3 0.09
23 19 0.59
24 10 0.31
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.81
Consensus pattern (24 bp):
TTTTTTTTTTTTTTCTTTCCATTC
Found at i:3164905 original size:19 final size:18
Alignment explanation
Indices: 3164883--3164923 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3164873 AATCGAATTA
**
3164883 TATATATTTATTATTTTTT
1 TATATATTT-TTAAGTTTT
3164902 TATATATTTTTAAGTTTT
1 TATATATTTTTAAGTTTT
3164920 TATA
1 TATA
3164924 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TATATATTTTTAAGTTTT
Found at i:3164976 original size:12 final size:12
Alignment explanation
Indices: 3164959--3164997 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3164949 TCTATTTAAA
3164959 TATATTAAAAAT
1 TATATTAAAAAT
*
3164971 TATATTAAAATAA
1 TATATTAAAA-AT
*
3164984 TATATAAAAAAT
1 TATATTAAAAAT
3164996 TA
1 TA
3164998 ACAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATTAAAAAT
Found at i:3166641 original size:20 final size:20
Alignment explanation
Indices: 3166618--3166714 Score: 56
Period size: 20 Copynumber: 4.5 Consensus size: 20
3166608 TTTATGCATT
3166618 TTATTATTTATTTATTATTA
1 TTATTATTTATTTATTATTA
* *
3166638 TTATTATGTATTAATATATGTACA
1 TTATTATTTATTTAT-TAT-T--A
*
3166662 TCT-TTATTTATCTATTTATTTA
1 T-TATTATTTATTTA-TTA-TTA
3166684 TT-TTATTTTATTTTATT-TTA
1 TTATTA-TTTA-TTTATTATTA
*
3166704 TTAATATTTAT
1 TTATTATTTAT
3166715 ATGTATTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 21
0.68 0.08 0.24
Matches are distributed among these distances:
19 1 0.02
20 22 0.37
21 9 0.15
22 9 0.15
23 3 0.05
24 13 0.22
25 3 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTATTTATTTATTATTA
Found at i:3166681 original size:4 final size:4
Alignment explanation
Indices: 3166664--3166766 Score: 55
Period size: 4 Copynumber: 23.2 Consensus size: 4
3166654 TATGTACATC
*
3166664 TTTA TTTA TCTA TTTA TTTA TTTTA TTTTA TTTTA TTTTA TTAATA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA -TTTA -TTTA TT--TA TTTA
* * * *
3166714 TATGTA TTTTA TTTA TATA GTTA TATA TTTA TATTA TATTA TTT- TTTT
1 T-T-TA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA T-TTA TTTA TTTA
3166762 TTTA T
1 TTTA T
3166767 CTTGTAATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
3 3 0.04
4 40 0.49
5 31 0.38
6 7 0.09
7 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:3166690 original size:5 final size:5
Alignment explanation
Indices: 3166676--3166727 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
3166666 TATTTATCTA
* *
3166676 TTTA- TTTAT TTTAT TTTAT TTTAT TTTA- TTAAT ATTTAT ATGTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT -TTTAT TTTAT
3166726 TT
1 TT
3166728 ATATAGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
4 7 0.17
5 25 0.61
6 9 0.22
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:3166711 original size:21 final size:22
Alignment explanation
Indices: 3166687--3166731 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3166677 TTATTTATTT
*
3166687 TATTTTAT-TTTATTTTATTAA
1 TATTTTATATGTATTTTATTAA
*
3166708 TA-TTTATATGTATTTTATTTA
1 TATTTTATATGTATTTTATTAA
3166729 TAT
1 TAT
3166732 AGTTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTTATATGTATTTTATTAA
Found at i:3166742 original size:21 final size:22
Alignment explanation
Indices: 3166697--3166752 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
3166687 TATTTTATTT
*
3166697 TATTTTA-TTA-ATATTTATATG
1 TATTTTATTTATATAGTTATA-G
3166718 TATTTTATTTATATAGTTATA-
1 TATTTTATTTATATAGTTATAG
3166739 TA-TTTATATTATAT
1 TATTTTAT-TTATAT
3166753 TATTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 5 0.16
21 15 0.48
22 3 0.10
23 8 0.26
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TATTTTATTTATATAGTTATAG
Found at i:3166765 original size:21 final size:21
Alignment explanation
Indices: 3166741--3166781 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3166731 TAGTTATATA
*
3166741 TTTATATTATATTATTTTTTT
1 TTTATATTATAATATTTTTTT
* *
3166762 TTTATCTTGTAATATTTTTT
1 TTTATATTATAATATTTTTT
3166782 GGGTTTATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTATATTATAATATTTTTTT
Found at i:3167385 original size:20 final size:20
Alignment explanation
Indices: 3167344--3167391 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3167334 TGAACTTCTT
*
3167344 ATGAAATTTTCCAAATTTCG
1 ATGAAATTTTCCAAATTCCG
*
3167364 ATGATATTTTCCAGAA-TCCG
1 ATGAAATTTTCCA-AATTCCG
3167384 ATGAAATT
1 ATGAAATT
3167392 CAACTGGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGAAATTTTCCAAATTCCG
Found at i:3167740 original size:13 final size:12
Alignment explanation
Indices: 3167720--3167845 Score: 58
Period size: 13 Copynumber: 9.4 Consensus size: 12
3167710 TTTTTTTGGA
3167720 ATTTTTTTATTT
1 ATTTTTTTATTT
3167732 ATTTGTTTTATTT
1 ATTT-TTTTATTT
*
3167745 ATTTATTTATTTT
1 ATTTTTTTA-TTT
3167758 ATTAGATTAGATTTATTT
1 ATT---TT---TTTATTT
3167776 AATATTTTTTATCTTT
1 -AT-TTTTTTA--TTT
* *
3167792 ATCTTATT-TTT
1 ATTTTTTTATTT
*
3167803 ATTTTTGT-TTT
1 ATTTTTTTATTT
3167814 ACTTTTCTTTATTT
1 A-TTTT-TTTATTT
*
3167828 TTTATTTTTATTT
1 ATT-TTTTTATTT
3167841 ATTTT
1 ATTTT
3167846 CACTTTTATT
Statistics
Matches: 88, Mismatches: 10, Indels: 32
0.68 0.08 0.25
Matches are distributed among these distances:
11 12 0.14
12 14 0.16
13 31 0.35
14 13 0.15
15 2 0.02
16 4 0.05
17 2 0.02
18 3 0.03
19 6 0.07
20 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:3167745 original size:17 final size:17
Alignment explanation
Indices: 3167720--3167760 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3167710 TTTTTTTGGA
3167720 ATTTT-TTTATTTATTT
1 ATTTTATTTATTTATTT
*
3167736 GTTTTATTTATTTATTT
1 ATTTTATTTATTTATTT
3167753 ATTTTATT
1 ATTTTATT
3167761 AGATTAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (17 bp):
ATTTTATTTATTTATTT
Found at i:3167803 original size:27 final size:25
Alignment explanation
Indices: 3167769--3167836 Score: 61
Period size: 27 Copynumber: 2.7 Consensus size: 25
3167759 TTAGATTAGA
*
3167769 TTTA-TTTAATATTTTTTATCTTTATC
1 TTTATTTTTATATTTTTTA-CTTT-TC
*
3167795 -TTATTTTTATTTTTGTTTTACTTTTC
1 TTTATTTTTA-TATT-TTTTACTTTTC
3167821 TTTATTTTT-TATTTTT
1 TTTATTTTTATATTTTT
3167837 ATTTATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
24 3 0.09
25 6 0.17
26 6 0.17
27 15 0.43
28 5 0.14
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTATTTTTATATTTTTTACTTTTC
Found at i:3167819 original size:17 final size:16
Alignment explanation
Indices: 3167799--3167857 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
3167789 TTTATCTTAT
3167799 TTTTATTTTTGTTTTAC
1 TTTTATTTTT-TTTTAC
* *
3167816 TTTTCTTTATTTTTTAT
1 TTTTATTT-TTTTTTAC
* *
3167833 TTTTATTTATTTTCAC
1 TTTTATTTTTTTTTAC
3167849 TTTTATTTT
1 TTTTATTTT
3167858 GTTCTATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 13 0.38
17 19 0.56
18 2 0.06
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTTTTTAC
Found at i:3167851 original size:28 final size:29
Alignment explanation
Indices: 3167798--3167857 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
3167788 CTTTATCTTA
*
3167798 TTTTTATTTTTGTTTTACTTTTC-TTTAT
1 TTTTTATTTTTGATTTACTTTTCTTTTAT
3167826 TTTTTATTTTT-ATTTA-TTTTCACTTTTAT
1 TTTTTATTTTTGATTTACTTTT--CTTTTAT
3167855 TTT
1 TTT
3167858 GTTCTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.14
27 4 0.14
28 12 0.43
29 8 0.29
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (29 bp):
TTTTTATTTTTGATTTACTTTTCTTTTAT
Found at i:3167865 original size:22 final size:22
Alignment explanation
Indices: 3167827--3167868 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3167817 TTTCTTTATT
*
3167827 TTTTATTTTTATTTATTTTCAC
1 TTTTATTTTTATCTATTTTCAC
3167849 TTTTATTTTGT-TCTATTTTC
1 TTTTATTTT-TATCTATTTTC
3167869 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTATCTATTTTCAC
Found at i:3167956 original size:61 final size:61
Alignment explanation
Indices: 3167883--3168100 Score: 318
Period size: 61 Copynumber: 3.6 Consensus size: 61
3167873 AATAAAAATC
* *
3167883 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAA
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
* *
3167944 AAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATCAAAGTTTCAAA
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
* * * * *
3168005 AAAAA-TATTTTTGACGAAAAGTTGCAAGTATCAATTTTTCTTAAAAAT-AAA-TTTC-CA
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
*
3168062 AAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
3168101 TCCTACACAA
Statistics
Matches: 142, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
57 6 0.04
58 34 0.24
59 3 0.02
60 37 0.26
61 62 0.44
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (61 bp):
AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAA
Found at i:3172301 original size:13 final size:11
Alignment explanation
Indices: 3172285--3172341 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 11
3172275 GATAAAAAAT
3172285 GAAAAAAAATGA
1 GAAAAAAAA-GA
3172297 TGAAAAAAAA-A
1 -GAAAAAAAAGA
3172308 GAAAAAAAAGAAA
1 GAAAAAAAAG--A
*
3172321 GAAAAAAATGA
1 GAAAAAAAAGA
3172332 GAAAATAAAA
1 GAAAA-AAAA
3172342 AAAAAGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 9 0.24
11 7 0.18
12 3 0.08
13 19 0.50
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (11 bp):
GAAAAAAAAGA
Found at i:3172334 original size:24 final size:23
Alignment explanation
Indices: 3172278--3172341 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
3172268 AACAATGGAT
* *
3172278 AAAAAATGA-AAAAAAATGATGA
1 AAAAAATGAGAAAAAAAAGAAGA
*
3172300 AAAAAA-AAGAAAAAAAAGAAAGA
1 AAAAAATGAGAAAAAAAAG-AAGA
3172323 AAAAAATGAGAAAATAAAA
1 AAAAAATGAGAAAA-AAAA
3172342 AAAAAGATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 9 0.26
24 6 0.18
25 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAAATGAGAAAAAAAAGAAGA
Found at i:3172336 original size:23 final size:23
Alignment explanation
Indices: 3172278--3172336 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
3172268 AACAATGGAT
3172278 AAAAAATGAAAAAAAATGATGAAA
1 AAAAAATGAAAAAAAATGA-GAAA
3172302 AAAAAA-GAAAAAAAA-GA-AAGA
1 AAAAAATGAAAAAAAATGAGAA-A
*
3172323 AAAAAATGAGAAAA
1 AAAAAATGAAAAAA
3172337 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 7 0.22
22 8 0.25
23 9 0.28
24 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (23 bp):
AAAAAATGAAAAAAAATGAGAAA
Found at i:3173637 original size:41 final size:40
Alignment explanation
Indices: 3173580--3174078 Score: 650
Period size: 41 Copynumber: 12.1 Consensus size: 40
3173570 GATTGTCAAT
3173580 GAGCAATTTATTTTCCAAAGTTTCGT-TGCCTCTGTTTAGAG
1 GAGCAATTTATTTTCCAAAG--TCGTGTGCCTCTGTTTAGAG
* *
3173621 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAA
1 GAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
* *
3173662 AAGCAATTTATTTTCCAAAGTCGTGGTGCCTCAGTTTAGAG
1 GAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
3173703 GAGCAATTTATTTTCCAAAGTTTCGT-TGCCTCTGTTTAGAG
1 GAGCAATTTATTTTCCAAAG--TCGTGTGCCTCTGTTTAGAG
*
3173744 GAGCAATTTATTTTCCAAAGTCGTAGTGCCTCTGTTTAGTG
1 GAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
* * * *
3173785 AAGCAATTTATTTTCTAAAGTTTCGT-TGCCTTTGTTTAGAA
1 GAGCAATTTATTTTCCAAAG--TCGTGTGCCTCTGTTTAGAG
3173826 GAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
3173867 GAGCAATTTATTTTCCAAAGTTTCGT-TGCCTCTGTTTAGAG
1 GAGCAATTTATTTTCCAAAG--TCGTGTGCCTCTGTTTAGAG
*
3173908 GAGCAATTTATTTTTCAAAGTCGTAGTGCCTCTGTTTAGAG
1 GAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
*
3173949 GAGCAATTTACTTTTCCAAGGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
*
3173991 GAGCAATTTACTTTT-CAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTCCAAAGTCGT-GTGCCTCTGTTTAGAG
*
3174032 GAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCAATTTAT-TTTC-CAAAGTCG-TGTGCCTCTGTTTAGAG
3174075 GAGC
1 GAGC
3174079 TTTGGTAAAA
Statistics
Matches: 411, Mismatches: 26, Indels: 40
0.86 0.05 0.08
Matches are distributed among these distances:
39 16 0.04
40 5 0.01
41 304 0.74
42 47 0.11
43 38 0.09
44 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (40 bp):
GAGCAATTTATTTTCCAAAGTCGTGTGCCTCTGTTTAGAG
Found at i:3174380 original size:5 final size:5
Alignment explanation
Indices: 3174370--3174458 Score: 56
Period size: 5 Copynumber: 16.6 Consensus size: 5
3174360 TTTATTTATC
* * *
3174370 TATTT TATTT TATTT TATTT TATTT T-GTT AATATT TATATG TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TAT-TT TATTT TATTT
*
3174421 ATATAGTT ATATATT TATTAT TATAT TATTT T-TTT TAT
1 -TAT--TT -TAT-TT TATT-T TATTT TATTT TATTT TAT
3174459 CTTGTAATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
4 6 0.09
5 35 0.51
6 19 0.28
7 2 0.03
8 6 0.09
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:3174415 original size:31 final size:32
Alignment explanation
Indices: 3174373--3174456 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 32
3174363 ATTTATCTAT
3174373 TTTATT-TTATTTTATTTTATTTTGTTA-ATA
1 TTTATTATTATTTTATTTTATTTTGTTATATA
* *
3174403 TTTA-TATGTATTTTA-TTTATATAGTTATATA
1 TTTATTAT-TATTTTATTTTATTTTGTTATATA
*
3174434 TTTATTATTATATTATTTT-TTTT
1 TTTATTATTATTTTATTTTATTTT
3174457 ATCTTGTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
29 1 0.02
30 15 0.34
31 22 0.50
32 6 0.14
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (32 bp):
TTTATTATTATTTTATTTTATTTTGTTATATA
Found at i:3174458 original size:14 final size:14
Alignment explanation
Indices: 3174317--3174451 Score: 51
Period size: 14 Copynumber: 9.9 Consensus size: 14
3174307 TTTATGTATT
*
3174317 TTATTATTTATTTA
1 TTATTATATATTTA
*
3174331 TTATTAT-TATGTA
1 TTATTATATATTTA
3174344 TTA--ATATATTTA
1 TTATTATATATTTA
*
3174356 -CATCT-T-TATTTA
1 TTAT-TATATATTTA
*
3174368 TCTATTTTAT-TTTA
1 T-TATTATATATTTA
*
3174382 TT-TTAT-T-TTATT
1 TTATTATATATT-TA
*
3174394 TTGTTA-ATATTTA
1 TTATTATATATTTA
*
3174407 -TATGTATTTTATTTA
1 TTAT-TA-TATATTTA
3174422 TATAGTTATATATTTA
1 T-TA-TTATATATTTA
3174438 TTATTATATTATTT
1 TTATTATA-TATTT
3174452 TTTTTATCTT
Statistics
Matches: 92, Mismatches: 10, Indels: 37
0.66 0.07 0.27
Matches are distributed among these distances:
11 6 0.07
12 19 0.21
13 18 0.20
14 22 0.24
15 14 0.15
16 8 0.09
17 4 0.04
18 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (14 bp):
TTATTATATATTTA
Found at i:3175437 original size:13 final size:13
Alignment explanation
Indices: 3175421--3175445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3175411 TTTTGGAATT
3175421 TTTTATTTATTTG
1 TTTTATTTATTTG
3175434 TTTTATTTATTT
1 TTTTATTTATTT
3175446 ATTTATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTG
Found at i:3175442 original size:17 final size:17
Alignment explanation
Indices: 3175422--3175457 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3175412 TTTGGAATTT
*
3175422 TTTATTTATTTGTTTTA
1 TTTATTTATTTATTTTA
3175439 TTTATTTATTTATTTTA
1 TTTATTTATTTATTTTA
3175456 TT
1 TT
3175458 AAATTAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTATTTATTTTA
Found at i:3175457 original size:5 final size:5
Alignment explanation
Indices: 3175421--3175566 Score: 51
Period size: 5 Copynumber: 29.8 Consensus size: 5
3175411 TTTTGGAATT
* ** **
3175421 TTTTA -TTTA -TTTG TTTTA -TTTA -TTTA -TTTA TTTTA TTAAA TTAGA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * *
3175466 -TTTA TTTAA TATT- TTTTA TCTTTA TCTTA TTTTTA TTTTTG TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA
* *
3175512 CTTTT- CTTTA TTTT- TTTTA TCTTTA -TTTA TTTTCA CTTTTA TTTTG
1 -TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTT-A -TTTTA TTTTA
*
3175558 TTCTA TTTT
1 TTTTA TTTT
3175567 CTTTAAATAA
Statistics
Matches: 107, Mismatches: 21, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
4 35 0.33
5 44 0.41
6 24 0.22
7 4 0.04
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:3175500 original size:27 final size:27
Alignment explanation
Indices: 3175470--3175526 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3175460 ATTAGATTTA
3175470 TTTAATATT-TTTTATCTTTATC-TTATT
1 TTTAATATTGTTTTA-CTTT-TCTTTATT
* *
3175497 TTTATTTTTGTTTTACTTTTCTTTATT
1 TTTAATATTGTTTTACTTTTCTTTATT
3175524 TTT
1 TTT
3175527 TTTATCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 19 0.73
28 5 0.19
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTAATATTGTTTTACTTTTCTTTATT
Found at i:3175534 original size:15 final size:15
Alignment explanation
Indices: 3175477--3175544 Score: 66
Period size: 15 Copynumber: 4.3 Consensus size: 15
3175467 TTATTTAATA
3175477 TTTTTTATCTTTATCT
1 TTTTTTATCTTTAT-T
* *
3175493 TATTTTTATTTTTGTT
1 T-TTTTTATCTTTATT
*
3175509 TTACTTT-TCTTTATT
1 TT-TTTTATCTTTATT
3175524 TTTTTTATCTTTATT
1 TTTTTTATCTTTATT
3175539 TATTTT
1 T-TTTT
3175545 CACTTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.07
15 18 0.43
16 10 0.24
17 11 0.26
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTTTATCTTTATT
Found at i:3175564 original size:22 final size:22
Alignment explanation
Indices: 3175526--3175567 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3175516 TCTTTATTTT
3175526 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
3175548 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
3175568 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:3175715 original size:122 final size:118
Alignment explanation
Indices: 3175582--3175861 Score: 416
Period size: 122 Copynumber: 2.3 Consensus size: 118
3175572 AATAAAAATC
*
3175582 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAA
1 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC-AAAAAA
* * *
3175647 ATATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAATTTTTTTAA
65 A-ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA--ATTTCAA
* * * *
3175704 AAAAAGGATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCAAAAAAA
1 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAA
* * * *
3175769 ATATTTTTGAGAAAAAGTTGGAAGTATCAATTTTTCTTAAAAATAAATTTCCA
66 ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAA
3175822 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
1 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
3175862 TCTACACAAG
Statistics
Matches: 142, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
118 40 0.28
120 42 0.30
121 7 0.05
122 53 0.37
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (118 bp):
AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAA
ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCAA
Found at i:3175735 original size:60 final size:59
Alignment explanation
Indices: 3175582--3175861 Score: 321
Period size: 60 Copynumber: 4.7 Consensus size: 59
3175572 AATAAAAATC
* ** *
3175582 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAA
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC-AATTTTC-AA
* * *
3175643 AAAAATATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AATTTTTTTAA
1 AAAAA-GTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAA--TTTTCAA
* * * * *
3175704 AAAAAGGATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATCAAAGTTTCAA
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC-AATTTTCAA
* * * * * *
3175764 AAAAAATATTTTTGAGAAAAAGTTGGAAGTATCAATTTTTCTTAAAAAT-AAATTTCCA
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAATTTTCAA
*
3175822 AAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
1 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
3175862 TCTACACAAG
Statistics
Matches: 186, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
58 42 0.23
60 88 0.47
61 12 0.06
62 44 0.24
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (59 bp):
AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAATTTTCAA
Found at i:3179198 original size:20 final size:19
Alignment explanation
Indices: 3179173--3179216 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3179163 TCAAATCAAA
3179173 TTATATAT-TTTTATTAATTT
1 TTATATATATTTTA--AATTT
3179193 TTATATATATTTTAAATTT
1 TTATATATATTTTAAATTT
3179212 TTATA
1 TTATA
3179217 AAACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
21 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATATATATTTTAAATTT
Found at i:3180592 original size:2 final size:2
Alignment explanation
Indices: 3180587--3180618 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3180577 GTCAGTAACC
3180587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3180619 CTGATATCAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3184540 original size:193 final size:191
Alignment explanation
Indices: 3184195--3184570 Score: 612
Period size: 192 Copynumber: 2.0 Consensus size: 191
3184185 ATTTATTTTT
*
3184195 AAAAAATTATTCTCGAGAAAAATAAATCAAAACTTTTTTATTGAAATAATTCTTAAAATATTCCA
1 AAAAAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATATTCCA
3184260 GTACGTTCGTAACATTAAAAGACTCTCTCTCACCTAGAGATTTCTTAAAGCATCTCTACTCGGAA
66 GTACGTTCGTAACATTAAAAGACTCTCTCTCACCTAGAGATTTCTTAAAGCATCTCTACTCGGAA
* * *
3184325 TACTTTTAGAATCTCATCTTT-GGAGG-CTCGAATTTATTTTTCGTAAGAAAATGTCGTTAA
131 TACTTTTAGAATCTCATCTTTGGGAGGTCT-AAATTTACTTTTCGTAAAAAAATGTCGTTAA
* * *
3184385 AAAAAATTTATTCTCGAGAAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATGTTT
1 AAAAAA-TTATTCTCGAG-AAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATATTC
* * *
3184450 CAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGTATCTCTACTCG
64 CAGTACGTTCGTAACATTAAAAG-ACTCTCTCTCACCTAGAGATTTCTTAAAGCATCTCTACTCG
3184515 GAATACTTTTAGAATCTCATCTTTGGGAGGTCTAAATTTACTTTTCGTAAAAAAAT
128 GAATACTTTTAGAATCTCATCTTTGGGAGGTCTAAATTTACTTTTCGTAAAAAAAT
3184571 TATGTCATGT
Statistics
Matches: 171, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
190 6 0.04
191 11 0.06
192 64 0.37
193 63 0.37
194 25 0.15
195 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (191 bp):
AAAAAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATATTCCA
GTACGTTCGTAACATTAAAAGACTCTCTCTCACCTAGAGATTTCTTAAAGCATCTCTACTCGGAA
TACTTTTAGAATCTCATCTTTGGGAGGTCTAAATTTACTTTTCGTAAAAAAATGTCGTTAA
Found at i:3185100 original size:207 final size:209
Alignment explanation
Indices: 3184702--3185096 Score: 466
Period size: 207 Copynumber: 1.9 Consensus size: 209
3184692 AATTTAATCA
* * * * *
3184702 TATTAAAGATTTTCTATAAATATTCCAATACGCTGGTAATATTTTACAAAAAATCTTCTCACTTA
1 TATTAAAGATTTTCTATAAATACTCCAATACACTGGTAATATCTTAAAAAAAATCTTCTCACCTA
* * * * * * *
3184767 GAGATTTCTTAAAGCATCTCTATTCGGAATACTTTTAGAATCCCATCATTGGATTAAATTTCTTT
66 GAGATTTCGTAAAGCATCACTACTCGAAATACCTTTAGAATCCCATCATCGGATAAAATTTCTTT
* *
3184832 TCTTCCTATTTTTATTACTTATATTTTTAATTTATTAATCAATTTTTATTTATTATTTTAAAAAA
131 TCTTCCTATTTTTATTACTTATAGTATTAATTTATTAATCAATTTTTATTTATTATTTTAAAAAA
3184897 GAAAATCTTTACTG
196 GAAAATCTTTACTG
*
3184911 TATTGAAA-ATTTT-TATAAATACTCCAATACACTGGTAGTA-CTTAAAAAAAATCTTCTCACCT
1 TATT-AAAGATTTTCTATAAATACTCCAATACACTGGTAATATCTTAAAAAAAATCTTCTCACCT
* * *
3184973 AGAGATTTCGTAGA-CATCACTACTCGAAATACCTTT-GAATCTCATCGTCGGATAAAAATTTCC
65 AGAGATTTCGTAAAGCATCACTACTCGAAATACCTTTAGAATCCCATCATCGGAT-AAAATTT-C
* * ** *
3185036 TTTTC-TCTTATTTTTTATTAGTT-TAGTATT-A-TTATTAAATTTATTTTTATATTATTGTTTT
128 TTTTCTTCCTA-TTTTTATTACTTATAGTATTAATTTATT-AATCAATTTTTAT-TTATTATTTT
3185097 TAAAGTTTAT
Statistics
Matches: 157, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
204 5 0.03
205 26 0.17
206 42 0.27
207 48 0.31
208 24 0.15
209 9 0.06
210 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.46
Consensus pattern (209 bp):
TATTAAAGATTTTCTATAAATACTCCAATACACTGGTAATATCTTAAAAAAAATCTTCTCACCTA
GAGATTTCGTAAAGCATCACTACTCGAAATACCTTTAGAATCCCATCATCGGATAAAATTTCTTT
TCTTCCTATTTTTATTACTTATAGTATTAATTTATTAATCAATTTTTATTTATTATTTTAAAAAA
GAAAATCTTTACTG
Found at i:3186171 original size:23 final size:23
Alignment explanation
Indices: 3186136--3186189 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3186126 CCCCTTGACT
*
3186136 TTTGTCTTATTTTTAT-TTCTTTTG
1 TTTGT-TTATTTTT-TGTTCTTTTA
*
3186160 TTTGTTTATTTTTTGTTTTTTTA
1 TTTGTTTATTTTTTGTTCTTTTA
3186183 TTTGTTT
1 TTTGTTT
3186190 TGTTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 21 0.78
24 5 0.19
ACGTcount: A:0.07, C:0.04, G:0.09, T:0.80
Consensus pattern (23 bp):
TTTGTTTATTTTTTGTTCTTTTA
Found at i:3186175 original size:15 final size:15
Alignment explanation
Indices: 3186155--3186185 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3186145 TTTTTATTTC
3186155 TTTTGTTTGTTTATT
1 TTTTGTTTGTTTATT
*
3186170 TTTTGTTTTTTTATT
1 TTTTGTTTGTTTATT
3186185 T
1 T
3186186 GTTTTGTTAA
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:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (15 bp):
TTTTGTTTGTTTATT
Found at i:3186894 original size:16 final size:17
Alignment explanation
Indices: 3186857--3186894 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
3186847 TCATTCCTTC
3186857 TTTTTTGCATTTCTTTT
1 TTTTTTGCATTTCTTTT
3186874 TTTTTTGC-TTT-TTTT
1 TTTTTTGCATTTCTTTT
*
3186889 TATTTT
1 TTTTTT
3186895 CCTGTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTGCATTTCTTTT
Found at i:3188099 original size:52 final size:52
Alignment explanation
Indices: 3187997--3188099 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
3187987 TAAAAATCTT
* *
3187997 TTTCCTTTTAAAATTCTTCTTTTGCAAGTCTAACTTGTTTATTAAGAATATC
1 TTTCCTTTTAAAATTCTTCTTTTGCAAGTCTAACTTGTCTATCAAGAATATC
* **
3188049 TTTCCTTTTAAAATTCTTCTTTTGTAAGTCT-TTTTGTCTATCAAGTAATAT
1 TTTCCTTTTAAAATTCTTCTTTTGCAAGTCTAACTTGTCTATCAAG-AATAT
3188100 TTAACAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 10 0.22
52 35 0.78
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (52 bp):
TTTCCTTTTAAAATTCTTCTTTTGCAAGTCTAACTTGTCTATCAAGAATATC
Found at i:3189111 original size:22 final size:22
Alignment explanation
Indices: 3189086--3189132 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3189076 TCAAGCAATA
*
3189086 TCTAACAAATTTTAAACAAATC
1 TCTAACAAATCTTAAACAAATC
3189108 TCTAACAAATCTTAAACAAATC
1 TCTAACAAATCTTAAACAAATC
3189130 TCT
1 TCT
3189133 TATGGGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (22 bp):
TCTAACAAATCTTAAACAAATC
Found at i:3189129 original size:11 final size:11
Alignment explanation
Indices: 3189089--3189130 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
3189079 AGCAATATCT
*
3189089 AACAAATTTTA
1 AACAAATCTTA
3189100 AACAAATCTCT-
1 AACAAATCT-TA
3189111 AACAAATCTTA
1 AACAAATCTTA
3189122 AACAAATCT
1 AACAAATCT
3189131 CTTATGGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 1 0.04
11 26 0.93
12 1 0.04
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (11 bp):
AACAAATCTTA
Found at i:3191457 original size:21 final size:21
Alignment explanation
Indices: 3191433--3191475 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3191423 AGATGAAGAT
*
3191433 ATTAATTTA-AAATTTAATTTA
1 ATTAATTTATAAAATT-ATTTA
3191454 ATTAATTTATAAAATTATTTA
1 ATTAATTTATAAAATTATTTA
3191475 A
1 A
3191476 AAAAAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAATTTATAAAATTATTTA
Found at i:3192232 original size:18 final size:18
Alignment explanation
Indices: 3192211--3192253 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3192201 AATGAATCAA
*
3192211 ATTAAATTATATATTTTT
1 ATTAAATTATATATATTT
*
3192229 ATTAATTTATATATATTT
1 ATTAAATTATATATATTT
3192247 -TTAAATT
1 ATTAAATT
3192254 TTTATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTAAATTATATATATTT
Done.