Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 198 of 204
Found at i:58588210 original size:247 final size:247
Alignment explanation
Indices: 58587716--58588308 Score: 857
Period size: 247 Copynumber: 2.4 Consensus size: 247
58587706 GGTCCGGGAC
* * * * * **
58587716 GAAATAATTTTGAGTTGACGTTTATGATCAAACAGTATAAAATCGCTTCAAATAGGATGCTATTT
1 GAAATAATTTT--TTTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTT
* * * * * *
58587781 GAGAAAAATTTGTGAAATTGCGGCCTCGTGGACGCGCTATTACTACAGTAGGTCATGGATGAAAT
64 GAGAAGAATTTGTAAAATCGCGCCCTCGTGGACACGCTATTACTACAGTAGGTCATAGATGAAAT
*
58587846 AATTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATCTCTTCTAGAAGGATGCTATTTGAGAAG
129 AATTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATATCTTCTAGAAGGATGCTATTTGAGAAG
* * *
58587911 AATTTGTGAAATCACGGCCTCATGGACGCGATATTGCTACAGTAGCTCATGGAT
194 AATTTGTAAAATCACGCCCTCATGGACACGATATTGCTACAGTAGCTCATGGAT
* * * *
58587965 GAAATATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCTCTTCTAGCACGATGCTATTTG
1 GAAATA-ATTTTTTTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTG
* *
58588030 AGAAGAATTTGTAAAATCGCGCCCTCGTGGACATGCTATTGCTACAGTAGGTCATAGATGAAATA
65 AGAAGAATTTGTAAAATCGCGCCCTCGTGGACACGCTATTACTACAGTAGGTCATAGATGAAATA
*
58588095 A-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAATATCTTCTAGCAA-GATGCTATTTGAGAAG
130 ATTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATATCTTCTAG-AAGGATGCTATTTGAGAAG
* * * * *
58588158 AATTTGTAAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGTAGGTCATGGAT
194 AATTTGTAAAATCACGCCCTCATGGACACGATATTGCTACAGTAGCTCATGGAT
58588212 GAAATAATTTTTTTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGA
1 GAAATAATTTTTTTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGA
*
58588277 AAAGAATTTGTGAAAATCGCGCCCTCGTGGAC
66 GAAGAATTTGT-AAAATCGCGCCCTCGTGGAC
58588309 GCGTTTTTGC
Statistics
Matches: 308, Mismatches: 33, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
246 65 0.21
247 129 0.42
248 104 0.34
249 6 0.02
250 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (247 bp):
GAAATAATTTTTTTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGA
GAAGAATTTGTAAAATCGCGCCCTCGTGGACACGCTATTACTACAGTAGGTCATAGATGAAATAA
TTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATATCTTCTAGAAGGATGCTATTTGAGAAGAA
TTTGTAAAATCACGCCCTCATGGACACGATATTGCTACAGTAGCTCATGGAT
Found at i:58593647 original size:28 final size:27
Alignment explanation
Indices: 58593602--58593672 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
58593592 AAAATAAAAA
* *
58593602 ATTTACTAAAATGT-TATAACTTTTTTT
1 ATTTACCAAAATATATATAA-TTTTTTT
58593629 ATTTACCAAAATATATATAATTTTTTT
1 ATTTACCAAAATATATATAATTTTTTT
58593656 ATTTACCAAAATATATA
1 ATTTACCAAAATATATA
58593673 AAAAAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 36 0.88
28 5 0.12
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATATATAATTTTTTT
Found at i:58594021 original size:17 final size:19
Alignment explanation
Indices: 58593999--58594037 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
58593989 TTGTTGTTGT
58593999 TGTTATT-A-GTATTAAGA
1 TGTTATTAATGTATTAAGA
58594016 TGTTATTAATGTATTAAGA
1 TGTTATTAATGTATTAAGA
58594035 TGT
1 TGT
58594038 AACTTAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (19 bp):
TGTTATTAATGTATTAAGA
Found at i:58599832 original size:29 final size:30
Alignment explanation
Indices: 58599794--58599862 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
58599784 TTGTTTTTTT
* *
58599794 TATATATTTTGAT-AATAAATAAAAATTTA
1 TATATATTTTGATAAATAAAAAAAAAGTTA
58599823 TATATATTTTGATAAATAAAAAAAAAGTTA
1 TATATATTTTGATAAATAAAAAAAAAGTTA
*
58599853 TA-ACATTTTG
1 TATATATTTTG
58599863 GTAGTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
TATATATTTTGATAAATAAAAAAAAAGTTA
Found at i:58611623 original size:21 final size:23
Alignment explanation
Indices: 58611588--58611630 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
58611578 TGATTAATGC
*
58611588 ATTAACAAAATTTATATTAATAA
1 ATTAACAAAATTTATATAAATAA
58611611 ATTAA-AAAA-TTATATAAATA
1 ATTAACAAAATTTATATAAATA
58611631 TAGAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 4 0.21
23 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTAACAAAATTTATATAAATAA
Found at i:58614356 original size:13 final size:13
Alignment explanation
Indices: 58614340--58614392 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
58614330 TTTAAATCAA
58614340 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
58614353 ACTTCTCAATAGC
1 ACTTTTCAAAAGC
*** *
58614366 ACTTTTCTTCAGT
1 ACTTTTCAAAAGC
58614379 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
58614392 A
1 A
58614393 ATGAAGAACC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:58619974 original size:3 final size:3
Alignment explanation
Indices: 58619968--58619996 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
58619958 TTCTTCCCTT
58619968 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
58619997 TTCCTCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:58627868 original size:17 final size:17
Alignment explanation
Indices: 58627846--58627899 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
58627836 GAATGGTGTA
58627846 ATTCTACACTAGAATTC
1 ATTCTACACTAGAATTC
58627863 ATTCTACACTAGAATTC
1 ATTCTACACTAGAATTC
58627880 ATTCTACACTAGAATTC
1 ATTCTACACTAGAATTC
58627897 ATT
1 ATT
58627900 TTTCGCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (17 bp):
ATTCTACACTAGAATTC
Found at i:58636161 original size:18 final size:19
Alignment explanation
Indices: 58636133--58636170 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
58636123 GGAAGAGGCT
58636133 AAAAATGAATTTTTTTTAA
1 AAAAATGAATTTTTTTTAA
58636152 AAAAAT-AATTTTTTTTAA
1 AAAAATGAATTTTTTTTAA
58636170 A
1 A
58636171 TTCCTAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAAAATGAATTTTTTTTAA
Found at i:58650252 original size:13 final size:13
Alignment explanation
Indices: 58650234--58650274 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
58650224 GGACTTAGAC
58650234 TTTTATTTTTGGT
1 TTTTATTTTTGGT
*
58650247 TTTTA-TTTTGTT
1 TTTTATTTTTGGT
58650259 TATTTATTTTTGGT
1 T-TTTATTTTTGGT
58650273 TT
1 TT
58650275 CTGTTTGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.29
13 10 0.42
14 7 0.29
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTGGT
Found at i:58655259 original size:2 final size:2
Alignment explanation
Indices: 58655252--58655278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58655242 TTTTATAGTC
58655252 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 T
58655279 GGGGTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58657646 original size:23 final size:23
Alignment explanation
Indices: 58657598--58657678 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 23
58657588 GTTTAATTTA
*
58657598 TAAAAATATTTAATATATCATA-AT
1 TAAAAATA-TTAATATA-AATATAT
58657622 TAAAAATATTAATATAAATATAT
1 TAAAAATATTAATATAAATATAT
*
58657645 T--ACATATTAA-AT-AATATTAT
1 TAAAAATATTAATATAAATA-TAT
58657665 TAATAAATTATTAA
1 TAA-AAA-TATTAA
58657679 AAGTTATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
19 4 0.08
20 6 0.12
21 8 0.17
22 3 0.06
23 13 0.27
24 14 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAAATATTAATATAAATATAT
Found at i:58657669 original size:28 final size:29
Alignment explanation
Indices: 58657607--58657674 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
58657597 ATAAAAATAT
58657607 TTAATATA-T-CATAATTAAAAATATTAA
1 TTAATATATTACATAATTAAAAATATTAA
58657634 TATAAATATATTACAT-ATTAAATAATATT-A
1 T-T-AATATATTACATAATTAAA-AATATTAA
*
58657664 TTAATAAATTA
1 TTAATATATTA
58657675 TTAAAAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 1 0.03
28 9 0.26
29 7 0.20
30 9 0.26
31 9 0.26
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAATATATTACATAATTAAAAATATTAA
Found at i:58657677 original size:31 final size:30
Alignment explanation
Indices: 58657620--58657677 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
58657610 ATATATCATA
58657620 ATTAAAAATATTAATATAAATATATTACAT
1 ATTAAAAATATTAATATAAATATATTACAT
*
58657650 ATTAAATAATATTATTAATAAAT-TATTA
1 ATTAAA-AATATTAAT-ATAAATATATTA
58657678 AAAGTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 6 0.24
31 13 0.52
32 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTAAAAATATTAATATAAATATATTACAT
Found at i:58657690 original size:28 final size:26
Alignment explanation
Indices: 58657659--58657722 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
58657649 TATTAAATAA
58657659 TATTATTAATAAATTATTAAAAGTT-ATT
1 TATT-TTAATAAATTATT-AAA-TTAATT
* *
58657687 TATTTTATATATATTGTTAAATTAATT
1 TATTTTA-ATAAATTATTAAATTAATT
58657714 TATTTTAAT
1 TATTTTAAT
58657723 GTCAAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.12
27 16 0.50
28 12 0.38
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TATTTTAATAAATTATTAAATTAATT
Found at i:58667688 original size:13 final size:15
Alignment explanation
Indices: 58667658--58667694 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
58667648 ATTTATTTTG
*
58667658 AAAAAAAAACAAATT
1 AAAAATAAACAAATT
58667673 AAAAATAAA-AAA-T
1 AAAAATAAACAAATT
58667686 AAAAATAAA
1 AAAAATAAA
58667695 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 3 0.14
15 8 0.38
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATAAACAAATT
Found at i:58669444 original size:19 final size:19
Alignment explanation
Indices: 58669398--58669460 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
58669388 CGAACAAAAA
*
58669398 TTATAAAATAAACAAAATAAT
1 TTATAAAA-AATCAAAAT-AT
* *
58669419 TTTTAAAAATTCAAAATAT
1 TTATAAAAAATCAAAATAT
58669438 TTATAAAAAATCAAAA-AT
1 TTATAAAAAATCAAAATAT
58669456 TTATA
1 TTATA
58669461 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.19
19 16 0.43
20 7 0.19
21 7 0.19
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATAAAAAATCAAAATAT
Found at i:58669501 original size:12 final size:12
Alignment explanation
Indices: 58669482--58669511 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
58669472 ATTCAAAAAA
58669482 AAAT-TATAAAG
1 AAATATATAAAG
58669493 AAATATATAAAG
1 AAATATATAAAG
58669505 AAATATA
1 AAATATA
58669512 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (12 bp):
AAATATATAAAG
Found at i:58670947 original size:145 final size:145
Alignment explanation
Indices: 58670684--58670954 Score: 402
Period size: 145 Copynumber: 1.9 Consensus size: 145
58670674 CATCAATGAT
* ** * * * * *
58670684 TCAATTGTTGAATTTGAGCTGCAAAATGTTACTACAGTTATCGGAGCAAACCACGTACAATTCAT
1 TCAATTATTGAACCTGAGCTACAAAACGTTACTACAGTTACCAGAGCAAACCACATACAATTCAT
*
58670749 AATAATCAATTCATTCTATTCTGATTCTTGACAAAATTGTATAGAAAATATAAAGTTAAATTGTA
66 AATAATCAATGCATTCTATTCTGATTCTTGACAAAATTGTATAGAAAATATAAAGTTAAATTGTA
58670814 ACATCCCTCGCCCAA
131 ACATCCCTCGCCCAA
* *
58670829 TCAATTATTGAACCTGAGCTACGAAACGTTACTACAGTTACCAGAGCAAACCACATCCAATTCAT
1 TCAATTATTGAACCTGAGCTACAAAACGTTACTACAGTTACCAGAGCAAACCACATACAATTCAT
*
58670894 AATAATCGATGCATTCTATTGC-GATTCTTGACAAAATTGTATA-AAAAGTATAAAGTTAAAT
66 AATAATCAATGCATTCTATT-CTGATTCTTGACAAAATTGTATAGAAAA-TATAAAGTTAAAT
58670955 GGTATAAAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
144 4 0.04
145 107 0.96
146 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (145 bp):
TCAATTATTGAACCTGAGCTACAAAACGTTACTACAGTTACCAGAGCAAACCACATACAATTCAT
AATAATCAATGCATTCTATTCTGATTCTTGACAAAATTGTATAGAAAATATAAAGTTAAATTGTA
ACATCCCTCGCCCAA
Found at i:58671319 original size:25 final size:22
Alignment explanation
Indices: 58671266--58671310 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
58671256 ATTGCAATTG
* *
58671266 AAATTAAACTATAATTTTTATT
1 AAATAAAAATATAATTTTTATT
58671288 ATAATAAAAATATAA-TTTTATT
1 A-AATAAAAATATAATTTTTATT
58671310 A
1 A
58671311 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAAAAATATAATTTTTATT
Found at i:58672235 original size:11 final size:11
Alignment explanation
Indices: 58672219--58672243 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58672209 TAAAAAATTA
58672219 AAAAATATTTT
1 AAAAATATTTT
58672230 AAAAATATTTT
1 AAAAATATTTT
58672241 AAA
1 AAA
58672244 TTTAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:58672262 original size:24 final size:23
Alignment explanation
Indices: 58672230--58672274 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
58672220 AAAATATTTT
*
58672230 AAAAATATTTTAAATTTAAAATA
1 AAAAATATTTTAAAATTAAAATA
58672253 AAAAAGTATTTTAAAATTAAAA
1 AAAAA-TATTTTAAAATTAAAA
58672275 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAATATTTTAAAATTAAAATA
Found at i:58672263 original size:17 final size:15
Alignment explanation
Indices: 58672241--58672289 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 15
58672231 AAAATATTTT
58672241 AAATTTAAAATAAAA
1 AAATTTAAAATAAAA
58672256 AAGTATTTTAAAATTAAAA
1 AA--A-TTTAAAA-TAAAA
58672275 AAATTTAAAAATAAA
1 AAATTT-AAAATAAA
58672290 TATATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 7 0.24
17 6 0.21
18 7 0.24
19 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATTTAAAATAAAA
Found at i:58672265 original size:18 final size:16
Alignment explanation
Indices: 58672244--58672289 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
58672234 ATATTTTAAA
58672244 TTTAAAATAAAAAAGTAT
1 TTTAAAATAAAAAA--AT
58672262 TTTAAAATTAAAAAAAT
1 TTTAAAA-TAAAAAAAT
*
58672279 TTAAAAATAAA
1 TTTAAAATAAA
58672290 TATATTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.15
17 8 0.31
18 7 0.27
19 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
TTTAAAATAAAAAAAT
Found at i:58672286 original size:35 final size:35
Alignment explanation
Indices: 58672203--58672289 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
58672193 ATTTTATTTT
* *
58672203 AAAAATTAAAAAATTAAAAAATATTTTAAAAATATT
1 AAAAATTTAAAAA-TAAAAAATATTTTAAAAATATA
** *
58672239 TTAAATTT-AAAATAAAAAAGTATTTTAAAATTA-A
1 AAAAATTTAAAAATAAAAAA-TATTTTAAAAATATA
58672273 AAAAATTTAAAAATAAA
1 AAAAATTTAAAAATAAA
58672290 TATATTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
34 13 0.31
35 24 0.57
36 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (35 bp):
AAAAATTTAAAAATAAAAAATATTTTAAAAATATA
Found at i:58672297 original size:16 final size:16
Alignment explanation
Indices: 58672203--58672289 Score: 59
Period size: 19 Copynumber: 5.1 Consensus size: 16
58672193 ATTTTATTTT
*
58672203 AAAAATTAAAAAATTAA
1 AAAAATTTAAAAA-TAA
*
58672220 AAAATATTTTAAAAATATT
1 AAAA-A-TTTAAAAATA-A
**
58672239 TTAAATTT-AAAATAA
1 AAAAATTTAAAAATAA
*
58672254 AAAAGTATTTTAAAATTAA
1 AAAA--A-TTTAAAAATAA
58672273 AAAAATTTAAAAATAA
1 AAAAATTTAAAAATAA
58672289 A
1 A
58672290 TATATTTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
15 2 0.04
16 17 0.31
17 9 0.17
18 7 0.13
19 19 0.35
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (16 bp):
AAAAATTTAAAAATAA
Found at i:58686667 original size:2 final size:2
Alignment explanation
Indices: 58686660--58686684 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58686650 TAAAGTAAGT
58686660 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
58686685 GAAAGAAGGT
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:58687689 original size:29 final size:29
Alignment explanation
Indices: 58687647--58687705 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
58687637 CCATACACAT
58687647 TCTTTATTCATCTTGAATCAGCATTGTGA
1 TCTTTATTCATCTTGAATCAGCATTGTGA
58687676 TCTTTATTCATCTTGAATCAGCATTGTGA
1 TCTTTATTCATCTTGAATCAGCATTGTGA
58687705 T
1 T
58687706 AGAATATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.46
Consensus pattern (29 bp):
TCTTTATTCATCTTGAATCAGCATTGTGA
Found at i:58696373 original size:30 final size:30
Alignment explanation
Indices: 58696337--58696400 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
58696327 AGTATGCCGA
58696337 GGCTGATCTAGTTGCTTATGCTTTAAATGT
1 GGCTGATCTAGTTGCTTATGCTTTAAATGT
58696367 GGCTGATCTAGTTGCTTATGCTTTAAATGT
1 GGCTGATCTAGTTGCTTATGCTTTAAATGT
58696397 GGCT
1 GGCT
58696401 TAAGATATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (30 bp):
GGCTGATCTAGTTGCTTATGCTTTAAATGT
Found at i:58704070 original size:18 final size:18
Alignment explanation
Indices: 58704047--58704083 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
58704037 TGTTTAAACA
58704047 ATCAACTACCTTAATTTC
1 ATCAACTACCTTAATTTC
58704065 ATCAACTACCTTAATTTC
1 ATCAACTACCTTAATTTC
58704083 A
1 A
58704084 ACTACGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCAACTACCTTAATTTC
Found at i:58713478 original size:18 final size:18
Alignment explanation
Indices: 58713455--58713491 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
58713445 TGTTTAAACA
58713455 ATCAACTACCTTAATTTC
1 ATCAACTACCTTAATTTC
58713473 ATCAACTACCTTAATTTC
1 ATCAACTACCTTAATTTC
58713491 A
1 A
58713492 ACTACGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCAACTACCTTAATTTC
Found at i:58720592 original size:27 final size:27
Alignment explanation
Indices: 58720573--58720624 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
58720563 AAAAAACAGG
* *
58720573 AAAGTTTAAAGAATATAAAAGAAAATA
1 AAAGTTTAAAGAACATAAAAGAAAAGA
58720600 AAAGTTTAAAGAACATAAAAGAAAA
1 AAAGTTTAAAGAACATAAAAGAAAA
58720625 AAATTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.19
Consensus pattern (27 bp):
AAAGTTTAAAGAACATAAAAGAAAAGA
Found at i:58723841 original size:42 final size:42
Alignment explanation
Indices: 58723782--58723861 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
58723772 TATTTGAAGC
58723782 AATCAAAGTTTTTGGTGTTGATTTATATTTTAGTATTAACTT
1 AATCAAAGTTTTTGGTGTTGATTTATATTTTAGTATTAACTT
58723824 AATCAAAGTTTTTGGTGTTGATTTATATTTTAGTATTA
1 AATCAAAGTTTTTGGTGTTGATTTATATTTTAGTATTA
58723862 GTTAATAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.53
Consensus pattern (42 bp):
AATCAAAGTTTTTGGTGTTGATTTATATTTTAGTATTAACTT
Found at i:58726159 original size:15 final size:16
Alignment explanation
Indices: 58726133--58726162 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58726123 ATGTCGAATT
58726133 TATTTTTATTAAAATA
1 TATTTTTATTAAAATA
58726149 TATTTTT-TTAAAAT
1 TATTTTTATTAAAAT
58726163 TTATCGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTATTAAAATA
Found at i:58737934 original size:22 final size:22
Alignment explanation
Indices: 58737904--58737945 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
58737894 TATTAATGTT
*
58737904 AATATTAATA-TATTACAATTTA
1 AATAATAATATTATTA-AATTTA
58737926 AATAATAATATTATTAAATT
1 AATAATAATATTATTAAATT
58737946 CTTACAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATAATATTATTAAATTTA
Found at i:58745014 original size:43 final size:42
Alignment explanation
Indices: 58744966--58745122 Score: 251
Period size: 43 Copynumber: 3.6 Consensus size: 42
58744956 GCGTCGCTAA
58744966 CTTTAGCGGCGCTTTACTCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTAC-CACAAACGCCGCTAAAGACCATGAC
*
58745009 CTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTAC-CACAAACGCCGCTAAAGACCATGAC
* *
58745052 CTTTAGCGACGCTTTTACCACAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGC-TTTACCACAAACGCCGCTAAAGACCATGAC
58745095 CTTTAGCGGCGCTTCTACCACAAACGCC
1 CTTTAGCGGCGCTT-TACCACAAACGCC
58745123 ACTATAGGTC
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
42 2 0.02
43 101 0.94
44 4 0.04
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTACCACAAACGCCGCTAAAGACCATGAC
Found at i:58746261 original size:14 final size:14
Alignment explanation
Indices: 58746242--58746270 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58746232 ATCAAGAAAA
58746242 AAATTATGTATAAG
1 AAATTATGTATAAG
58746256 AAATTATGTATAAG
1 AAATTATGTATAAG
58746270 A
1 A
58746271 CTTACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
AAATTATGTATAAG
Found at i:58749397 original size:19 final size:17
Alignment explanation
Indices: 58749342--58749399 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
58749332 TATTAATTTT
*
58749342 AAATAAATAATTTTTGAA
1 AAATTAATAATTTTT-AA
58749360 AAATTAAGTAATATTTTAA
1 AAATTAA-TAAT-TTTTAA
58749379 AGAATTAGATAATTTTTAA
1 A-AATTA-ATAATTTTTAA
58749398 AA
1 AA
58749400 TTTTTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 13 0.37
21 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AAATTAATAATTTTTAA
Found at i:58749702 original size:10 final size:10
Alignment explanation
Indices: 58749654--58749714 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
58749644 AAAATAAAAG
58749654 TTTAAAATCTT
1 TTTAAAATC-T
* *
58749665 TTTTAAATTT
1 TTTAAAATCT
**
58749675 TTTAAAAAAT
1 TTTAAAATCT
58749685 TTTAAAATCT
1 TTTAAAATCT
58749695 TTTAAAATTCAT
1 TTTAAAA-TC-T
58749707 TTTAAAAT
1 TTTAAAAT
58749715 TTTAAATCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 23 0.56
11 10 0.24
12 8 0.20
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:58749711 original size:12 final size:12
Alignment explanation
Indices: 58749683--58749715 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
58749673 TTTTTAAAAA
58749683 ATTTTAAAA-TC
1 ATTTTAAAATTC
58749694 -TTTTAAAATTC
1 ATTTTAAAATTC
58749705 ATTTTAAAATT
1 ATTTTAAAATT
58749716 TTAAATCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:58749714 original size:30 final size:29
Alignment explanation
Indices: 58749648--58749720 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
58749638 ATTATAAAAA
* *
58749648 TAAAAGTTTAAAATCTTTTTTAAATTTTT
1 TAAAATTTTAAAATCTTTTTAAAATTTTT
58749677 TAAAAAATTTTAAAATC-TTTTAAAATTCATTT
1 T--AAAATTTTAAAATCTTTTTAAAATT--TTT
58749709 TAAAATTTTAAA
1 TAAAATTTTAAA
58749721 TCACATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 1 0.03
30 20 0.53
31 13 0.34
32 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTTTAAAATCTTTTTAAAATTTTT
Found at i:58750705 original size:8 final size:7
Alignment explanation
Indices: 58750639--58750685 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
58750629 GACCCTTAAC
58750639 CCCTAAA
1 CCCTAAA
58750646 CCCTAAA
1 CCCTAAA
*
58750653 TCCTAAA
1 CCCTAAA
*
58750660 CCTTAAAA
1 CCCT-AAA
58750668 CCCTAAA
1 CCCTAAA
58750675 CTCCT-AA
1 C-CCTAAA
58750682 CCCT
1 CCCT
58750686 CGGCCCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
6 3 0.09
7 22 0.65
8 9 0.26
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:58751353 original size:41 final size:40
Alignment explanation
Indices: 58751308--58751501 Score: 244
Period size: 41 Copynumber: 4.7 Consensus size: 40
58751298 ATATGTTTTT
58751308 GCGGCGCTTTACAAAAAACGCCGCTAAAGGTCTGCGCATTA
1 GCGGCGCTTT-CAAAAAACGCCGCTAAAGGTCTGCGCATTA
* * *
58751349 GCGGCGCTTCATGAAAAAACGCCGCTAAAGGTCAGTGCATTA
1 GCGGCGCTT--TCAAAAAACGCCGCTAAAGGTCTGCGCATTA
* * * *
58751391 GCGGCGCTTCCTGAAAATCGCCGCTAAAGGTATGCGCATTA
1 GCGGCGCTTTC-AAAAAACGCCGCTAAAGGTCTGCGCATTA
* *
58751432 GCGGCGCTTCTTAAAACACGCCGCTAAAGGTCTGCGCATTA
1 GCGGCGCTT-TCAAAAAACGCCGCTAAAGGTCTGCGCATTA
*
58751473 GCGGCGCTTCTCGAAAAACGCCGCTAAAG
1 GCGGCGCTT-TCAAAAAACGCCGCTAAAG
58751502 ACCCACAAGG
Statistics
Matches: 130, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 93 0.72
42 36 0.28
43 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
GCGGCGCTTTCAAAAAACGCCGCTAAAGGTCTGCGCATTA
Found at i:58751489 original size:82 final size:83
Alignment explanation
Indices: 58751308--58751501 Score: 286
Period size: 82 Copynumber: 2.3 Consensus size: 83
58751298 ATATGTTTTT
* *
58751308 GCGGCGCTT-TACAAAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCATGAAAAAACGCC
1 GCGGCGCTTCT-CGAAAAACGCCGCTAAAGGTATGCGCATTAGCGGCGCTTCATGAAAAAACGCC
*
58751372 GCTAAAGGTCAGTGCATTA
65 GCTAAAGGTCAGCGCATTA
* * *
58751391 GCGGCGCTTC-CTGAAAATCGCCGCTAAAGGTATGCGCATTAGCGGCGCTTC-TTAAAACACGCC
1 GCGGCGCTTCTC-GAAAAACGCCGCTAAAGGTATGCGCATTAGCGGCGCTTCATGAAAAAACGCC
*
58751454 GCTAAAGGTCTGCGCATTA
65 GCTAAAGGTCAGCGCATTA
58751473 GCGGCGCTTCTCGAAAAACGCCGCTAAAG
1 GCGGCGCTTCTCGAAAAACGCCGCTAAAG
58751502 ACCCACAAGG
Statistics
Matches: 100, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
82 54 0.54
83 46 0.46
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (83 bp):
GCGGCGCTTCTCGAAAAACGCCGCTAAAGGTATGCGCATTAGCGGCGCTTCATGAAAAAACGCCG
CTAAAGGTCAGCGCATTA
Found at i:58751674 original size:40 final size:40
Alignment explanation
Indices: 58751539--58751677 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
58751529 GGAGTTTAGG
* ** *
58751539 TTTTTTGCGGCGTTTTTTAGAAAAATGCCGCTAATGATC-A
1 TTTTTAGCGGCGTTTTTT-GAAAAGCGCCGCTAATGCTCGA
** **
58751579 TTTTTAGCGGCGCTTTCCT-AAAAGCGCCGCTAACACTCGA
1 TTTTTAGCGGCG-TTTTTTGAAAAGCGCCGCTAATGCTCGA
* **
58751619 TCTTTAGCGGCGTTTTTTGGGAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCGA
58751659 TTTTTAGCGGCGTTTTTTG
1 TTTTTAGCGGCGTTTTTTG
58751678 TACAAACGCC
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 18 0.22
40 58 0.73
41 4 0.05
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCGA
Found at i:58759214 original size:22 final size:22
Alignment explanation
Indices: 58759189--58759230 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
58759179 TTTGAATATT
*
58759189 AATATTAATA-TATTATAATTTA
1 AATAATAATATTATTA-AATTTA
58759211 AATAATAATATTATTAAATT
1 AATAATAATATTATTAAATT
58759231 ATTACAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATAATATTATTAAATTTA
Found at i:58763154 original size:16 final size:16
Alignment explanation
Indices: 58763116--58763163 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
58763106 ATTTTTTATG
58763116 AATTTTTTAAT-TTGTT
1 AATTTTTTAATATT-TT
*
58763132 AAATTTTTAATATTTT
1 AATTTTTTAATATTTT
* *
58763148 CATTTTTTTATATTTT
1 AATTTTTTAATATTTT
58763164 TTGAATCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
AATTTTTTAATATTTT
Found at i:58773971 original size:18 final size:18
Alignment explanation
Indices: 58773945--58773979 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58773935 AAATAATTTT
*
58773945 AATATTAAATAAATAATA
1 AATAGTAAATAAATAATA
*
58773963 AATAGTAAATAATTAAT
1 AATAGTAAATAAATAAT
58773980 GAAAAATACA
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:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAGTAAATAAATAATA
Found at i:58774128 original size:29 final size:28
Alignment explanation
Indices: 58774074--58774132 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
58774064 CTGTATCCAT
* **
58774074 ATTTTTCTTATTTCATACTTTTTAATCA
1 ATTTTTCTTATTTCATACATCATAATCA
*
58774102 ATTTTTCTTCATTTTATACATCATAATCA
1 ATTTTTCTT-ATTTCATACATCATAATCA
58774131 AT
1 AT
58774133 CAAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTTCTTATTTCATACATCATAATCA
Found at i:58775486 original size:41 final size:41
Alignment explanation
Indices: 58775429--58775511 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
58775419 ATGCGTTAGG
58775429 ACACAACGTATCGAATTCCCGATACGAGAATACATGCCAAA
1 ACACAACGTATCGAATTCCCGATACGAGAATACATGCCAAA
58775470 ACACAACGTATCGAATTCCCGATACGAGAATACATGCCAAA
1 ACACAACGTATCGAATTCCCGATACGAGAATACATGCCAAA
58775511 A
1 A
58775512 ACTTACTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.17
Consensus pattern (41 bp):
ACACAACGTATCGAATTCCCGATACGAGAATACATGCCAAA
Found at i:58776046 original size:20 final size:20
Alignment explanation
Indices: 58776023--58776061 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
58776013 GTATGTACAT
*
58776023 ATATATATATAAAT-TATAAG
1 ATATA-ATAAAAATATATAAG
58776043 ATATAATAAAAATATATAA
1 ATATAATAAAAATATATAA
58776062 TTATGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATATAATAAAAATATATAAG
Found at i:58776067 original size:49 final size:47
Alignment explanation
Indices: 58775986--58776095 Score: 134
Period size: 49 Copynumber: 2.3 Consensus size: 47
58775976 AAAATGAATA
58775986 AAATTATAAAAATATAAAAAGATATATGTATGTACATATATATATAT
1 AAATTATAAAAATATAAAAAGATATATGTATGTACATATATATATAT
* * ***
58776033 AAATTATAAGATATAATAAAAATATATAAT-TATGTGTGTATATATATAT
1 AAATTATAA-AAAT-ATAAAAAGATAT-ATGTATGTACATATATATATAT
58776082 AAATTA-AAAAATAT
1 AAATTATAAAAATAT
58776096 GTACGTATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
46 2 0.04
47 12 0.22
48 5 0.09
49 33 0.61
50 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.37
Consensus pattern (47 bp):
AAATTATAAAAATATAAAAAGATATATGTATGTACATATATATATAT
Found at i:58776194 original size:16 final size:16
Alignment explanation
Indices: 58776144--58776194 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
58776134 TATATATTTG
* *
58776144 AAAT-TATAAAATAAA
1 AAATATATAAAACATA
*
58776159 AAATATAT-ATACATA
1 AAATATATAAAACATA
58776174 TAAATATATAAAACATA
1 -AAATATATAAAACATA
58776191 AAAT
1 AAAT
58776195 GTACGTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 8 0.28
16 15 0.52
17 6 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATATAAAACATA
Found at i:58777070 original size:15 final size:15
Alignment explanation
Indices: 58777052--58777081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58777042 CGAAAGGAAG
58777052 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
*
58777067 AAAAGAAAAAGAAAA
1 AAAAAAAAAAGAAAA
58777082 TAGATCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:58777462 original size:20 final size:18
Alignment explanation
Indices: 58777437--58777481 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
58777427 TTGGGCTTAA
58777437 GTTTTGGTCTGGGTAGTTGG
1 GTTTTGGT-T-GGTAGTTGG
* *
58777457 GTTTTGGTTTGTAGTTTG
1 GTTTTGGTTGGTAGTTGG
58777475 GTTTTGG
1 GTTTTGG
58777482 GTTTAATTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 1 0.04
20 8 0.35
ACGTcount: A:0.04, C:0.02, G:0.40, T:0.53
Consensus pattern (18 bp):
GTTTTGGTTGGTAGTTGG
Found at i:58779105 original size:21 final size:21
Alignment explanation
Indices: 58779081--58779195 Score: 131
Period size: 21 Copynumber: 5.5 Consensus size: 21
58779071 TAAAAAAAAA
*
58779081 CTCATAAGGGTTGAACAGAAG
1 CTCATAAGAGTTGAACAGAAG
* * *
58779102 CTCATAAGAGCTGAACGGAAA
1 CTCATAAGAGTTGAACAGAAG
* *
58779123 CTCATATGAGTTAAACAGAAG
1 CTCATAAGAGTTGAACAGAAG
* * *
58779144 CTCATAAGAGCTGAACGGAAA
1 CTCATAAGAGTTGAACAGAAG
*
58779165 CTCATAAAAGTTGAACAGAAG
1 CTCATAAGAGTTGAACAGAAG
*
58779186 CTCAAAAGAG
1 CTCATAAGAG
58779196 CTAAACGAAG
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
CTCATAAGAGTTGAACAGAAG
Found at i:58779110 original size:42 final size:42
Alignment explanation
Indices: 58779064--58779202 Score: 188
Period size: 42 Copynumber: 3.3 Consensus size: 42
58779054 CAGTTGATAG
*** *
58779064 TAAGAGCTAAAAAAAAACTCATAAGGGTTGAACAGAAGCTCA
1 TAAGAGCTAAACGGAAACTCATAAGAGTTGAACAGAAGCTCA
* * *
58779106 TAAGAGCTGAACGGAAACTCATATGAGTTAAACAGAAGCTCA
1 TAAGAGCTAAACGGAAACTCATAAGAGTTGAACAGAAGCTCA
* *
58779148 TAAGAGCTGAACGGAAACTCATAAAAGTTGAACAGAAGCTCA
1 TAAGAGCTAAACGGAAACTCATAAGAGTTGAACAGAAGCTCA
*
58779190 AAAGAGCTAAACG
1 TAAGAGCTAAACG
58779203 AAGAGTAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (42 bp):
TAAGAGCTAAACGGAAACTCATAAGAGTTGAACAGAAGCTCA
Found at i:58788089 original size:17 final size:18
Alignment explanation
Indices: 58788069--58788102 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58788059 TATCGTAAAA
58788069 AATAAAAATA-AAAAGAC
1 AATAAAAATATAAAAGAC
*
58788086 AATAAATATATAAAAGA
1 AATAAAAATATAAAAGA
58788103 AGTGAGATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAAAAATATAAAAGAC
Found at i:58796611 original size:2 final size:2
Alignment explanation
Indices: 58796606--58796639 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58796596 CCTTTTTTCA
58796606 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
58796640 TATTTGTCTT
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:58801316 original size:3 final size:3
Alignment explanation
Indices: 58801310--58801339 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
58801300 GAACAACAAC
58801310 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58801340 GAAAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58801549 original size:23 final size:22
Alignment explanation
Indices: 58801509--58801552 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
58801499 AAATTATAAA
*
58801509 ATATAAGAATATATATATGTAC
1 ATATAAGAAAATATATATGTAC
58801531 ATATAAGAAAAATATATATGTA
1 ATATAAG-AAAATATATATGTA
58801553 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (22 bp):
ATATAAGAAAATATATATGTAC
Found at i:58802304 original size:23 final size:22
Alignment explanation
Indices: 58802261--58802318 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
58802251 AAAGGGTATC
* *
58802261 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
58802282 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
58802305 TGCATATCATATCT
1 TACAAATCATATCT
58802319 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:58803128 original size:88 final size:88
Alignment explanation
Indices: 58803019--58803304 Score: 246
Period size: 88 Copynumber: 3.2 Consensus size: 88
58803009 TTTCAACTTA
58803019 CTCCACTACTG-TTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACATTGGGAAG
1 CTCCACTACTGCTT-AGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACATTGGGAAG
*
58803083 ATAAGATTCGCTGTCATCGATCTG
65 ATAAGATTCGCTGTCTTCGATCTG
* * *** * * * * * *
58803107 CTCCACTATTGCTTAGGGAGATAAGATCT-GTAATTTTTAACCTACTCTACTGCTGCT-CA--AG
1 CTCCACTACTGCTTAGGGAGATAAG-GCTAGT-GGCTTAAATCTGCT-T-C-CCTACTACATTGG
* * ** * * *
58803168 G-AGATAAG-GTCTACAATCTTCAACCTA
61 GAAGATAAGATTC-GCTGTCTTCGATCTG
* * *
58803195 TTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGA
1 CTCCACTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACATTGGGAAGA
58803260 TAAGATTCG-TCGTCTTCGATCTG
66 TAAGATTCGCT-GTCTTCGATCTG
58803283 CTCCACTACTGCTTAGGGAGAT
1 CTCCACTACTGCTTAGGGAGAT
58803305 CAGATCTGTA
Statistics
Matches: 142, Mismatches: 42, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
84 4 0.03
85 2 0.01
86 1 0.01
87 14 0.10
88 97 0.68
89 16 0.11
90 1 0.01
91 3 0.02
92 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (88 bp):
CTCCACTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACATTGGGAAGA
TAAGATTCGCTGTCTTCGATCTG
Found at i:58803171 original size:44 final size:44
Alignment explanation
Indices: 58803107--58803219 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 44
58803097 CATCGATCTG
* * * ** * *
58803107 CTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTA
1 CTCCACTACTGCTCAAGGAGATAAGATCTACAATCTTCAACCTA
* * *
58803151 CTCTACTGCTGCTCAAGGAGATAAGGTCTACAATCTTCAACCTA
1 CTCCACTACTGCTCAAGGAGATAAGATCTACAATCTTCAACCTA
* *
58803195 TTCCACTACTGCTCAGGGAGATAAG
1 CTCCACTACTGCTCAAGGAGATAAG
58803220 GCTAGTGGCT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTCAAGGAGATAAGATCTACAATCTTCAACCTA
Found at i:58803202 original size:176 final size:176
Alignment explanation
Indices: 58803010--58803377 Score: 596
Period size: 176 Copynumber: 2.1 Consensus size: 176
58803000 ATCTGTAATT
* * *
58803010 TTCAACTTACTCCACTACTGTTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACA
1 TTCAACCTATTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACA
*
58803075 TTGGGAAGATAAGATTCG-CTGTCATCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTA
66 TTGGGAAGATAAGATTCGTC-GTCATCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * *
58803139 ATTTTTAACCTACTCTACTGCTGCTCAAGGAGATAAG-GTCTACAATC
130 ATTTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGATTC-ACAATC
*
58803186 TTCAACCTATTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACC
1 TTCAACCTATTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACA
* *
58803251 TTGGGAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATCAGATCTGTAA
66 TTGGGAAGATAAGATTCGTCGTCATCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
* *
58803316 TTTTCAACCTACTCCACTGCTGCTCAGGGAGATATGATTCACAATC
131 TTTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGATTCACAATC
58803362 TTCAACCTATTCCACT
1 TTCAACCTATTCCACT
58803378 GCTAACCAGG
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
176 175 0.98
177 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (176 bp):
TTCAACCTATTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACA
TTGGGAAGATAAGATTCGTCGTCATCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
TTTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGATTCACAATC
Found at i:58803331 original size:44 final size:44
Alignment explanation
Indices: 58803283--58803377 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
58803273 CTTCGATCTG
* * *
58803283 CTCCACTACTGCTTAGGGAGATCAGATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAACCTA
* * **
58803327 CTCCACTGCTGCTCAGGGAGATATGAT-TCACAATCTTCAACCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCT-GTAATCTTCAACCTA
*
58803371 TTCCACT
1 CTCCACT
58803378 GCTAACCAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (44 bp):
CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAACCTA
Found at i:58803376 original size:88 final size:89
Alignment explanation
Indices: 58803108--58803377 Score: 230
Period size: 88 Copynumber: 3.1 Consensus size: 89
58803098 ATCGATCTGC
* * * *
58803108 TCCACTATTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACTCTACTGCTGCTCAAGGAGAT
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTAAACCTACTCCACTGCTGCTCAGGGAGAT
* *
58803173 AAG-GTCTACAATCTTCAACCTAT
66 AAGATTCGACAATCTTCAACCTAT
* * *** * * * * *
58803196 TCCACTACTGCTCAGGGAGATAAG-GCTAGT-GGCTTAAATCTGCTTCC-CTACTAC-CTTGGGA
1 TCCACTACTGCTTAGGGAGATAAGATCT-GTAATTTTAAACCTAC-TCCACTGCTGCTC-AGGG-
* * * * **
58803257 AGATAAGATTCGTC-GTCTTCGATCTGC
62 AGATAAGATTCGACAATCTTCAACCTAT
* *
58803284 TCCACTACTGCTTAGGGAGATCAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGAT
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTAAACCTACTCCACTGCTGCTCAGGGAGAT
*
58803349 ATGATTC-ACAATCTTCAACCTAT
66 AAGATTCGACAATCTTCAACCTAT
58803372 TCCACT
1 TCCACT
58803378 GCTAACCAGG
Statistics
Matches: 131, Mismatches: 41, Indels: 20
0.68 0.21 0.10
Matches are distributed among these distances:
86 1 0.01
87 17 0.13
88 92 0.70
89 20 0.15
90 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (89 bp):
TCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTAAACCTACTCCACTGCTGCTCAGGGAGAT
AAGATTCGACAATCTTCAACCTAT
Found at i:58803378 original size:44 final size:44
Alignment explanation
Indices: 58803318--58804147 Score: 630
Period size: 44 Copynumber: 19.8 Consensus size: 44
58803308 ATCTGTAATT
* *
58803318 TTCAACCTACTCCACTGCTG-CTCAGGGAGATATGATTCACAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
*
58803362 TTCAACCTATTCCACTGCTAACCAGGGAGATAGG-------A--
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
58803397 TTC-ACCTATTCCACTGCTGACCAGGGAGATAGAACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
** *
58803440 TTCAACCTATTCCACTATTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
58803484 TTCAACCTATTCCACTACTGACTAGGGAGATAGG-------A--
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
58803519 TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* * * * *
58803562 TTTAACCTATTCCACTGCTAACCAGAGAGATAAGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* ** *
58803606 TTCAACCTATGCCACTATTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
58803650 TTCAACCTATTCCACTGCTGACTAGGGAGATAGG-------A--
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * * *****
58803685 TTC-ACCTATTCCACTGCTGACTAGGAAGATAGGACT-AGTGGA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * * * * * * **
58803727 TTAAATCTGCTTCC-CTACT-ACCTTAGGAAGATAAGATTCGCTGTC
1 TTCAACCT-ATTCCACTGCTGACC--AGGGAGATAGGATTCACAATC
* * ** ** * * * ** *
58803772 TTCGATCTGCTCCACTATTG-CTTAGGGAAATAAGA-TCTGTAATT
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTC-ACAATC
* * *
58803816 TTTAACCTACTCCACTACTG-CTCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
*
58803860 TTCAACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
58803904 TTTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 -TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* * **
58803948 TTCAACCTATTCCACTACTGACCAAGGAGATAGGACGCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
58803992 TTCAACCTATTCCACTGCTGATCAGGGAGATAGG-------A--
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
58804027 TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* * * *
58804070 TTCAACCTATTCCACTACTGACTAGGGAGATATGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
58804114 TTTAACCTATTCCACTGCTGACCAGGGAGATAGG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGG
58804148 GCTTTGTGAT
Statistics
Matches: 643, Mismatches: 86, Indels: 114
0.76 0.10 0.14
Matches are distributed among these distances:
34 114 0.18
35 12 0.02
37 4 0.01
41 3 0.00
42 4 0.01
43 23 0.04
44 461 0.72
45 22 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:58803451 original size:78 final size:78
Alignment explanation
Indices: 58803322--58803479 Score: 223
Period size: 78 Copynumber: 2.0 Consensus size: 78
58803312 GTAATTTTCA
*
58803322 ACCTACTCCACTGCTGCTCAGGGAGATATGATTCACAATCTTCAACCTATTCCACTGCTAACCAG
1 ACCTACTCCACTGCTGCTCAGGGAGATATGATTCACAATCTTCAACCTATTCCACTACTAACCAG
*
58803387 GGAGATAGGATTC
66 GGAGATAGGACTC
* * *
58803400 ACCTATTCCACTGCTGAC-CAGGGAGATA-GAACTT-ACAATCTTCAACCTATTCCACTATTGAC
1 ACCTACTCCACTGCTG-CTCAGGGAGATATG-A-TTCACAATCTTCAACCTATTCCACTACTAAC
58803462 CAGGGAGATAGGACTC
63 CAGGGAGATAGGACTC
58803478 AC
1 AC
58803480 AATCTTCAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
77 1 0.01
78 68 0.94
79 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (78 bp):
ACCTACTCCACTGCTGCTCAGGGAGATATGATTCACAATCTTCAACCTATTCCACTACTAACCAG
GGAGATAGGACTC
Found at i:58803511 original size:122 final size:122
Alignment explanation
Indices: 58803318--58804147 Score: 758
Period size: 122 Copynumber: 6.6 Consensus size: 122
58803308 ATCTGTAATT
* * * * *
58803318 TTCAACCTACTCCACTGCTG-CTCAGGGAGATATGATTCACAATCTTCAACCTATTCCACTGCTA
1 TTCAACCTATTCCACTACTGAC-CAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTG
*
58803382 ACCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATC
65 ACCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
* *
58803440 TTCAACCTATTCCACTATTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGA
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGA
*
58803505 CTAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
66 CCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
* * * * * * **
58803562 TTTAACCTATTCCACTGCTAACCAGAGAGATAAGACTCACAATCTTCAACCTATGCCACTATTGA
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGA
*
58803627 CCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATAGG-------A
66 CCAGGGAGATAGG-------A--TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAA
58803685 --
121 TC
* * * ***** * * * *
58803685 TTC-ACCTATTCCACTGCTGACTAGGAAGATAGGACT-AGTGGATTAAATCTGCTTCC-CTACT-
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCT-ATTCCACTGCTG
* * * * * * * * *
58803746 ACCTTAGGAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTATTGCTTAGGGAAATAAGATCTG
65 ACC--AGGGAGATAGGATTCAC-CTATTCCA-CTGCT-GAC-----C--AGGGAGATAGGA-CT-
*
58803811 T--AATT
116 TACAATC
* * *
58803816 TTTAACCTACTCCACTACTG-CTCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTG
1 TTCAACCTATTCCACTACTGAC-CAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTG
*
58803880 ACCAAGGAGATAGGATTCACAATCTTTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACA
65 ACCAGGGAGATAGG-------A---TTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACA
58803945 ATC
120 ATC
* *
58803948 TTCAACCTATTCCACTACTGACCAAGGAGATAGGACGCACAATCTTCAACCTATTCCACTGCTGA
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGA
*
58804013 TCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
66 CCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
* * *
58804070 TTCAACCTATTCCACTACTGACTAGGGAGATATGACTCACAATCTTTAACCTATTCCACTGCTGA
1 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGA
58804135 CCAGGGAGATAGG
66 CCAGGGAGATAGG
58804148 GCTTTGTGAT
Statistics
Matches: 573, Mismatches: 84, Indels: 102
0.75 0.11 0.13
Matches are distributed among these distances:
112 1 0.00
113 8 0.01
114 5 0.01
115 3 0.01
120 3 0.01
121 11 0.02
122 344 0.60
123 3 0.01
125 2 0.00
129 2 0.00
130 1 0.00
131 8 0.01
132 149 0.26
133 12 0.02
134 4 0.01
139 3 0.01
140 5 0.01
141 5 0.01
142 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (122 bp):
TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGA
CCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
Found at i:58803526 original size:34 final size:34
Alignment explanation
Indices: 58803488--58803552 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
58803478 ACAATCTTCA
*
58803488 ACCTATTCCACTACTGACTAGGGAGATAGGATTC
1 ACCTATTCCACTACTGACCAGGGAGATAGGATTC
*
58803522 ACCTATTCCACTGCTGACCAGGGAGATAGGA
1 ACCTATTCCACTACTGACCAGGGAGATAGGA
58803553 CTTACAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (34 bp):
ACCTATTCCACTACTGACCAGGGAGATAGGATTC
Found at i:58803572 original size:166 final size:167
Alignment explanation
Indices: 58803400--58804147 Score: 804
Period size: 166 Copynumber: 4.4 Consensus size: 167
58803390 GATAGGATTC
58803400 ACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATCTTCAACCTATTCCACTATTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATCTTCAACCTATTCCACTATTGACCAG
58803465 GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACT-AGGGAGATAGGATTCACCTATT
66 GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACTCAGGGAGATAGGATTCACCTATT
58803529 CCACTGCTGACCAGGGAGATAGGACTTACAATCTTTA
131 CCACTGCTGACCAGGGAGATAGGACTTACAATCTTTA
* * * *
58803566 ACCTATTCCACTGCTAACCAGAGAGATA-AGACTCACAATCTTCAACCTATGCCACTATTGACCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGA-ACTTACAATCTTCAACCTATTCCACTATTGACCA
*
58803630 GGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACT-AGGGAGATAGGATTCACCTAT
65 GGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACTCAGGGAGATAGGATTCACCTAT
* * ***** *
58803694 TCCACTGCTGACTAGGAAGATAGGAC-TAGTGGATTAA
130 TCCACTGCTGACCAGGGAGATAGGACTTACAATCTTTA
* * * * * ** * * **
58803731 ATCTGCTTCC-CTACT-ACCTTAGGAAGATA-AGA-TTCGCTGTCTTCGATCTGCTCCACTATTG
1 ACCT-ATTCCACTGCTGACC--AGGGAGATAGA-ACTT-ACAATCTTCAACCTATTCCACTATTG
* * * ** * * *
58803792 -CTTAGGGAAATAAGA-TCTGTAATTTTTAACCTACTCCACTACTG-CTCAGGGAGATAGGATTC
61 AC-CAGGGAGATAGGACTC-ACAATCTTCAACCTATTCCACTACTGACTCAGGGAGATAGG----
* *
58803854 ACAATCTTCAACCTATTCCACTGCTGACCAAGGAGATAGGA-TTCACAATCTTTC
120 ---A--TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTTA
* * *
58803908 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGACCAA
1 ACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATCTTCAACCTATTCCACTATTGACCAG
* *
58803973 GGAGATAGGACGCACAATCTTCAACCTATTCCACTGCTGA-TCAGGGAGATAGGATTCACCTATT
66 GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACTCAGGGAGATAGGATTCACCTATT
*
58804037 CCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
131 CCACTGCTGACCAGGGAGATAGGACTTACAATCTTTA
* * * * **
58804074 ACCTATTCCACTACTGACTAGGGAGATATG-ACTCACAATCTTTAACCTATTCCACTGCTGACCA
1 ACCTATTCCACTGCTGACCAGGGAGATA-GAACTTACAATCTTCAACCTATTCCACTATTGACCA
58804138 GGGAGATAGG
65 GGGAGATAGG
58804148 GCTTTGTGAT
Statistics
Matches: 474, Mismatches: 79, Indels: 58
0.78 0.13 0.09
Matches are distributed among these distances:
164 3 0.01
165 19 0.04
166 322 0.68
167 6 0.01
169 1 0.00
173 1 0.00
175 3 0.01
176 102 0.22
177 14 0.03
178 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (167 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGAACTTACAATCTTCAACCTATTCCACTATTGACCAG
GGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACTCAGGGAGATAGGATTCACCTATT
CCACTGCTGACCAGGGAGATAGGACTTACAATCTTTA
Found at i:58803692 original size:34 final size:34
Alignment explanation
Indices: 58803654--58803718 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
58803644 ACAATCTTCA
*
58803654 ACCTATTCCACTGCTGACTAGGGAGATAGGATTC
1 ACCTATTCCACTGCTGACTAGGAAGATAGGATTC
58803688 ACCTATTCCACTGCTGACTAGGAAGATAGGA
1 ACCTATTCCACTGCTGACTAGGAAGATAGGA
58803719 CTAGTGGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACTAGGAAGATAGGATTC
Found at i:58804039 original size:34 final size:34
Alignment explanation
Indices: 58803996--58804060 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
58803986 ACAATCTTCA
*
58803996 ACCTATTCCACTGCTGATCAGGGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
58804030 ACCTATTCCACTGCTGACCAGGGAGATAGGA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA
58804061 CTTACAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
Found at i:58806401 original size:25 final size:25
Alignment explanation
Indices: 58806348--58806413 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
58806338 AAGAAAATCC
* *
58806348 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
58806373 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
58806398 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
58806414 TGTATTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:58808303 original size:2 final size:2
Alignment explanation
Indices: 58808296--58808382 Score: 147
Period size: 2 Copynumber: 43.5 Consensus size: 2
58808286 NNNNNNNNNN
58808296 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
58808338 CT CT CT CT CT CT CT CT CT CT CT CC CT CT CC CT CT CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
58808380 CT C
1 CT C
58808383 GTAATAAATA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:58809312 original size:21 final size:21
Alignment explanation
Indices: 58809286--58809340 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
58809276 TGTATATATA
*
58809286 TATATCTATATGTTTTTT-TT
1 TATATCTATATATTTTTTCTT
58809306 TCATATCTATATATTTTTTCTT
1 T-ATATCTATATATTTTTTCTT
*
58809328 TTTATCTATATAT
1 TATATCTATATAT
58809341 CTATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.87
22 3 0.10
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (21 bp):
TATATCTATATATTTTTTCTT
Found at i:58809339 original size:2 final size:2
Alignment explanation
Indices: 58809334--58809366 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
58809324 TCTTTTTATC
*
58809334 TA TA TA TC 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 T
58809367 TACCTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58813441 original size:3 final size:3
Alignment explanation
Indices: 58813433--58813468 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
58813423 GATCAAGAAC
58813433 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
58813469 GAAAAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58814441 original size:23 final size:22
Alignment explanation
Indices: 58814398--58814455 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
58814388 AAAGGGTATC
* *
58814398 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
58814419 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
58814442 TGCATATCATATCT
1 TACAAATCATATCT
58814456 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:58815085 original size:13 final size:13
Alignment explanation
Indices: 58815066--58815116 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
58815056 TAAACCAAAT
58815066 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
58815079 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* * *
58815092 TTTTCCACAGTAC
1 TTTTCAAAAGCAC
58815105 TTTTCAAAAGCA
1 TTTTCAAAAGCA
58815117 ATAAAGAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:58821382 original size:12 final size:13
Alignment explanation
Indices: 58821358--58821389 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
58821348 TATTAAAAAA
58821358 TTATTTCAATTAT
1 TTATTTCAATTAT
58821371 TTATTT-AATTAT
1 TTATTTCAATTAT
58821383 TTATTTC
1 TTATTTC
58821390 TTTTTACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTCAATTAT
Found at i:58823056 original size:23 final size:23
Alignment explanation
Indices: 58823030--58823086 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
58823020 GTTGTTTGAA
*
58823030 TTATTCGAGTTAACTCGAATTAT
1 TTATTCGAGTTAACTCGAATTAC
* *
58823053 TTATTCGAGTCAACTTGAATTAC
1 TTATTCGAGTTAACTCGAATTAC
58823076 TTATTCGAGTT
1 TTATTCGAGTT
58823087 TCGAGTTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (23 bp):
TTATTCGAGTTAACTCGAATTAC
Found at i:58823273 original size:26 final size:26
Alignment explanation
Indices: 58823240--58823301 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
58823230 CAAAATAATT
*
58823240 TTCAAAAATTTAAAATATTTATAAAAA
1 TTCAAAAATTT-AAATATTTAAAAAAA
* *
58823267 TTCAAAAATTTATATTTTTAAAAAAA
1 TTCAAAAATTTAAATATTTAAAAAAA
58823293 TTCTAAAAA
1 TTC-AAAAA
58823302 ATTCTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (26 bp):
TTCAAAAATTTAAATATTTAAAAAAA
Found at i:58823277 original size:18 final size:19
Alignment explanation
Indices: 58823230--58823280 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
58823220 ATAAAATAAA
58823230 CAAAATAATTT-TCAAAAATT
1 CAAAAT-ATTTAT-AAAAATT
*
58823250 TAAAATATTTATAAAAATT
1 CAAAATATTTATAAAAATT
58823269 CAAAA-ATTTATA
1 CAAAATATTTATA
58823281 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.25
19 15 0.54
20 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAATATTTATAAAAATT
Found at i:58823302 original size:10 final size:10
Alignment explanation
Indices: 58823287--58823313 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
58823277 TATATTTTTA
58823287 AAAAAATTCT
1 AAAAAATTCT
58823297 AAAAAATTCT
1 AAAAAATTCT
58823307 AAAAAAT
1 AAAAAAT
58823314 ATATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:58825570 original size:2 final size:2
Alignment explanation
Indices: 58825553--58825590 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
58825543 GAGGAGGAAA
* *
58825553 AT AT AT AC AT AC 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
58825591 GAATGAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:58836505 original size:5 final size:5
Alignment explanation
Indices: 58836495--58836520 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58836485 TGAGCATTCG
58836495 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
58836521 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:58837572 original size:9 final size:9
Alignment explanation
Indices: 58837554--58837590 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
58837544 TATAGTTTGA
*
58837554 TATTCAAAT
1 TATTCGAAT
58837563 TATTCGAAT
1 TATTCGAAT
*
58837572 TATTCGAGT
1 TATTCGAAT
58837581 TATTCGAAT
1 TATTCGAAT
58837590 T
1 T
58837591 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:58839481 original size:28 final size:29
Alignment explanation
Indices: 58839440--58839496 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
58839430 TCATTGAATA
58839440 CAAAGGGGGTTGCTAAGTGCTGATTCCCC
1 CAAAGGGGGTTGCTAAGTGCTGATTCCCC
58839469 CAAA-GGGGTTGCTAAGTGCTGATTCCCC
1 CAAAGGGGGTTGCTAAGTGCTGATTCCCC
58839497 GACTCATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.25
Consensus pattern (29 bp):
CAAAGGGGGTTGCTAAGTGCTGATTCCCC
Found at i:58839517 original size:33 final size:34
Alignment explanation
Indices: 58839475--58839602 Score: 143
Period size: 33 Copynumber: 3.6 Consensus size: 34
58839465 CCCCCAAAGG
58839475 GGTTGCTAAGTGCTGATTCCCCGACTCA-TTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTTGGT
* * *
58839508 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATTTGAATGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--CT-CATTTG---GT
58839550 GGTTGCTAAGTGCTGATTCCCCGACT-ATTTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTTGGT
58839583 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
58839603 ACCATATCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 41 0.51
34 3 0.04
35 1 0.01
36 5 0.06
37 1 0.01
38 2 0.02
39 3 0.04
40 1 0.01
41 3 0.04
42 21 0.26
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTTGGT
Found at i:58839596 original size:75 final size:76
Alignment explanation
Indices: 58839470--58839682 Score: 313
Period size: 75 Copynumber: 2.8 Consensus size: 76
58839460 TGATTCCCCC
58839470 AAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
* *
58839535 -TTTAAATTTG
66 CCTTAAATGTG
* *
58839545 AATGGGGTTGCTAAGTGCTGATTCCCCGACT-ATTTGGTGGTTGCTAAGTGCTGATTCCACCATA
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGACTCA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTA
*
58839609 TCCTTGAATGTG
65 TCCTTAAATGTG
* * * * *
58839621 AAAGGGGTTGCTAAATGCTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGAATCCACCG
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
58839683 ATAACGGTTA
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
74 1 0.01
75 61 0.50
76 60 0.49
77 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (76 bp):
AAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
CCTTAAATGTG
Found at i:58847255 original size:16 final size:16
Alignment explanation
Indices: 58847234--58847264 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58847224 CTATGCATGT
*
58847234 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
58847250 AAAATACAAAAGACA
1 AAAATACAAAAGACA
58847265 TAATAGTGAA
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:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:58849104 original size:24 final size:23
Alignment explanation
Indices: 58849061--58849113 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
58849051 CTCCTCCCTC
58849061 TCTTTTCTCCATTTTCTTCTTCT
1 TCTTTTCTCCATTTTCTTCTTCT
58849084 TCTTTTCTCTC-TTTT-TT-TTCT
1 TCTTTTCTC-CATTTTCTTCTTCT
58849105 TC-TTTCTCC
1 TCTTTTCTCC
58849114 TCCTCCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 6 0.21
21 6 0.21
22 2 0.07
23 13 0.45
24 1 0.03
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (23 bp):
TCTTTTCTCCATTTTCTTCTTCT
Found at i:58850073 original size:27 final size:28
Alignment explanation
Indices: 58850043--58850114 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
58850033 GGGTTTAGGG
58850043 TTTAAGG-TTAGGGTTTTGTTAAAATAA
1 TTTAAGGTTTAGGGTTTTGTTAAAATAA
* *
58850070 TTTAAGGTTTATGGTTGTGTTAAAATAA
1 TTTAAGGTTTAGGGTTTTGTTAAAATAA
58850098 TTT-AGGTTTAGGGTTTT
1 TTTAAGGTTTAGGGTTTT
58850115 AGGTTTAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 19 0.47
28 21 0.52
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.49
Consensus pattern (28 bp):
TTTAAGGTTTAGGGTTTTGTTAAAATAA
Found at i:58850241 original size:35 final size:33
Alignment explanation
Indices: 58850136--58850252 Score: 126
Period size: 35 Copynumber: 3.5 Consensus size: 33
58850126 TTTTAAAAAA
* * *
58850136 TAAATCAGGGTTTAAAGTTTTAAAAAAAATAAT
1 TAAATTAGGGTTTAGAGTTTTAAAAAAATTAAT
* * * * *
58850169 TAAATTAAGTTTTAGGGGTTTTAAATAAATAAAT
1 TAAATTAGGGTTTA-GAGTTTTAAAAAAATTAAT
*
58850203 TAAATTAGGGTTTAGAGTTTTTTAAAAAAATTATT
1 TAAATTAGGGTTTAGAG--TTTTAAAAAAATTAAT
58850238 TAAATTAGGGTTTAG
1 TAAATTAGGGTTTAG
58850253 TTTTTTTTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
33 13 0.19
34 26 0.39
35 28 0.42
ACGTcount: A:0.44, C:0.01, G:0.15, T:0.40
Consensus pattern (33 bp):
TAAATTAGGGTTTAGAGTTTTAAAAAAATTAAT
Found at i:58850548 original size:125 final size:126
Alignment explanation
Indices: 58850317--58850709 Score: 517
Period size: 126 Copynumber: 3.1 Consensus size: 126
58850307 CAATAATATT
* * * *
58850317 TTTTTCTACAGTATTTTC-AGAAAAATTAATTTTGAA-AAGACGGTTCTGAA-AAGAAAATGTCA
1 TTTTTCTACAGTAGTTTCTA-AAAAAATAATTTT-AAGAAGACGGTTCTGAACAA-ATAGTGTCA
* * *
58850379 AAAACACTTCAAGCAGGATGCACTGTCAGCAAAATTACT-CAAAAAGCTCCCACGTGGATGCTC
63 AAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGCTC
*
58850442 TTTTTCTACAGTAGTTTCTAAAAAAATAATTTTAAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTTCTAAAAAAATAATTTTAAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * * * * * *
58850507 ATGCTTTAAGCAGAATGCACTGTCAACAAAAATACTAAAAAAAGCTCCCACGTGGGCACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGCTC
* * * * *
58850568 TTTTTCTACAATAGTTCCTAAAAAAATAATTTTAAGAAGACGGTTCTGAACAAGTGGTGTTAAAA
1 TTTTTCTACAGTAGTTTCTAAAAAAATAATTTTAAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* *
58850633 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTAATGAAAAAAA-CTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAAGCTCCCACGTGGACGCTC
58850694 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
58850710 CTTGTTTGGC
Statistics
Matches: 232, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
124 2 0.01
125 82 0.35
126 141 0.61
127 7 0.03
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTTCTAAAAAAATAATTTTAAGAAGACGGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGCTC
Found at i:58854193 original size:41 final size:41
Alignment explanation
Indices: 58854136--58854216 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
58854126 AACGAGAAAG
*
58854136 GGTAAGTGGGGACTAGTTCTATCAAACACAAATATTTTTTA
1 GGTAAGTGGGGACTAGTTCTATCAAAAACAAATATTTTTTA
58854177 GGTAAGTGGGGACTAGTTCTATCAAAAACAAATATTTTTT
1 GGTAAGTGGGGACTAGTTCTATCAAAAACAAATATTTTTT
58854217 CTTTGTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (41 bp):
GGTAAGTGGGGACTAGTTCTATCAAAAACAAATATTTTTTA
Found at i:58857211 original size:14 final size:14
Alignment explanation
Indices: 58857192--58857218 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58857182 TATCACGTCA
58857192 ATAATTTTAACAGG
1 ATAATTTTAACAGG
58857206 ATAATTTTAACAG
1 ATAATTTTAACAG
58857219 TCTTAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (14 bp):
ATAATTTTAACAGG
Found at i:58859918 original size:18 final size:18
Alignment explanation
Indices: 58859895--58859934 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
58859885 GTTGAATTTT
*
58859895 ATAATTTGAATAACTCAA
1 ATAATTCGAATAACTCAA
58859913 ATAATTCGAATAACTCAA
1 ATAATTCGAATAACTCAA
58859931 ATAA
1 ATAA
58859935 CATATTGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAATTCGAATAACTCAA
Found at i:58866445 original size:120 final size:120
Alignment explanation
Indices: 58866309--58866785 Score: 807
Period size: 120 Copynumber: 4.0 Consensus size: 120
58866299 TATATATAAT
58866309 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-TTAATTATTAAGAATTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAA-TATTAAGAATTT
*
58866373 TATTAAATTATATATTTTTATTAAATTATATTTAATAACAATTATTTTAAATTATA
65 TATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATA
* * *
58866429 TTTTATATTATCATATATTATGATTTTAGTAAATTCATTAAAAGAATATTTAATATTAAGAATTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCA-TATAAGAATATTTAATATTAAGAATTT
*
58866494 TATATAAATTATATA-TTTTATTAAATTATATTTTAATATTAATTATTTTAAATTATA
65 TAT-TAAATTATATATTTTTATTAAATTATA-TTTAATAATAATTATTTTAAATTATA
58866551 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
**
58866616 ATTAAATTATATATATTTT-TTAAATTATATTTAATAATTGTTATTTTAAATTATA
66 ATTAAATTATATAT-TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATA
*
58866671 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGACTATTTAATATTAAGAATTTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
*
58866736 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
66 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
58866786 ATATGATTAA
Statistics
Matches: 335, Mismatches: 15, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
119 4 0.01
120 175 0.52
121 78 0.23
122 78 0.23
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATA
Found at i:58866520 original size:17 final size:18
Alignment explanation
Indices: 58866490--58866539 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
58866480 AATATTAAGA
58866490 ATTTTATATAAATTATAT
1 ATTTTATATAAATTATAT
58866508 ATTTTAT-TAAATTATAT
1 ATTTTATATAAATTATAT
* *
58866525 -TTTAATATTAATTAT
1 ATTTTATATAAATTAT
58866540 TTTAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTATATAAATTATAT
Found at i:58866529 original size:12 final size:12
Alignment explanation
Indices: 58866514--58866555 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
58866504 ATATATTTTA
58866514 TTAAATTATATT
1 TTAAATTATATT
58866526 TTAATATTAATTATT
1 TTAA-ATT-A-TATT
58866541 TTAAATTATATT
1 TTAAATTATATT
58866553 TTA
1 TTA
58866556 TAGTATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.41
13 4 0.15
14 4 0.15
15 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAAATTATATT
Found at i:58866535 original size:66 final size:63
Alignment explanation
Indices: 58866348--58866771 Score: 238
Period size: 59 Copynumber: 7.0 Consensus size: 63
58866338 TAAATTCATA
*
58866348 TAAGAATA-TTAATTATTAAGAATTTTAT-TAAATTATATATTTTTATTAAATTATATTTAATAA
1 TAAGAATATTTAA-TATTAAGAATTTTATATAAATTATATA-TTTTATTAAATTATATTTAATAT
* ** * * * * ** * * * *
58866411 CAATTAT-TTTAA-ATT-A-TATTTTATAT-TATCATATATTATGATTTTAGTAAATTCATTA-
1 TAAGAATATTTAATATTAAGAATTTTATATAAATTATATATT-TTATTAAATTATATTTAATAT
*
58866469 AAAGAATATTTAATATTAAGAATTTTATATAAATTATATATTTTATTAAATTATATTTTAATAT
1 TAAGAATATTTAATATTAAGAATTTTATATAAATTATATATTTTATTAAATTATA-TTTAATAT
** * * ** * * *
58866533 TAATTAT-TTTAA-ATT-A-TATTTTATAGT--ATTATATATTATGATTTTAGTA-AATTCATA-
1 TAAGAATATTTAATATTAAGAATTTTATA-TAAATTATATATT-TTATTAAATTATATTTAATAT
*
58866590 TAAGAATATTTAATATTAAGAATTTTAT-TAAATTATATATATTTTTTAAATTATATTTAATAAT
1 TAAGAATATTTAATATTAAGAATTTTATATAAATTATATAT-TTTATTAAATTATATTTAAT-AT
* * * ** * * *
58866654 T--G-TTATTTTAA-ATT-A-TATTTTATAGT--ATTATATATTATGATTTTAGTA-AATTCATA
1 TAAGAATA-TTTAATATTAAGAATTTTATA-TAAATTATATATT-TTATTAAATTATATTTAATA
58866710 -
63 T
*
58866710 TAAGACTATTTAATATTAAGAATTTTAT-TAAATTATATATTTTTATTAAATTATATTTAATA
1 TAAGAATATTTAATATTAAGAATTTTATATAAATTATATA-TTTTATTAAATTATATTTAATA
58866772 ATAATTATGT
Statistics
Matches: 262, Mismatches: 63, Indels: 73
0.66 0.16 0.18
Matches are distributed among these distances:
56 1 0.00
57 6 0.02
58 28 0.11
59 75 0.29
60 23 0.09
61 56 0.21
62 40 0.15
63 28 0.11
64 5 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (63 bp):
TAAGAATATTTAATATTAAGAATTTTATATAAATTATATATTTTATTAAATTATATTTAATAT
Found at i:58866563 original size:15 final size:14
Alignment explanation
Indices: 58866505--58866571 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 14
58866495 ATATAAATTA
*
58866505 TATATTTTATTAAAT
1 TATATTTTA-TATAT
58866520 TATATTTTA-ATAT
1 TATATTTTATATAT
58866533 TAATTATTTTA-A-AT
1 T-A-TATTTTATATAT
58866547 TATATTTTATAGTAT
1 TATATTTTATA-TAT
*
58866562 TATATATTAT
1 TATATTTTAT
58866572 GATTTTAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 7 0.16
13 6 0.13
14 4 0.09
15 28 0.62
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (14 bp):
TATATTTTATATAT
Found at i:58866667 original size:13 final size:12
Alignment explanation
Indices: 58866633--58866675 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
58866623 TATATATATT
58866633 TTTTAAATTATA
1 TTTTAAATTATA
* *
58866645 TTTAATAATTGTTA
1 TTTTA-AATT-ATA
58866659 TTTTAAATTATA
1 TTTTAAATTATA
58866671 TTTTA
1 TTTTA
58866676 TAGTATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 11 0.44
13 8 0.32
14 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTTAAATTATA
Found at i:58867009 original size:45 final size:44
Alignment explanation
Indices: 58866923--58867015 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
58866913 ATTATAGCAT
*
58866923 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
* *
58866967 CATTTCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTC
58867012 CATT
1 CATT
58867016 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 20 0.47
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:58867023 original size:16 final size:16
Alignment explanation
Indices: 58867004--58867064 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
58866994 ACTATTACGC
58867004 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
* * *
58867020 CTCTATTTCATTATAC
1 CTCTATTCCATTACAG
58867036 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
58867052 CTCTATTCCATTA
1 CTCTATTCCATTA
58867065 TAGCGAACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.25, C:0.30, G:0.03, T:0.43
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:58867044 original size:32 final size:32
Alignment explanation
Indices: 58867003--58867066 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
58866993 TACTATTACG
*
58867003 CCTCTATTCCATTACAGCTCTATTTCATTATA
1 CCTCTATTCCATTACAGCTCTATTCCATTATA
58867035 CCTCTATTCCATTACAGCTCTATTCCATTATA
1 CCTCTATTCCATTACAGCTCTATTCCATTATA
58867067 GCGAACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.03, T:0.42
Consensus pattern (32 bp):
CCTCTATTCCATTACAGCTCTATTCCATTATA
Found at i:58870105 original size:18 final size:17
Alignment explanation
Indices: 58870078--58870129 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 17
58870068 AAGTAGTGAT
58870078 AATT-TATTTTTAGAATA
1 AATTCTATTTTTAGAA-A
58870095 AATTCTATTTTCTGAGAAA
1 AATTCTATTTT-T-AGAAA
58870114 AATTCATAGTTTTTAG
1 AATTC-TA-TTTTTAG
58870130 TCATATAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
18 6 0.20
19 9 0.30
20 7 0.23
21 4 0.13
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (17 bp):
AATTCTATTTTTAGAAA
Found at i:58871028 original size:17 final size:16
Alignment explanation
Indices: 58871006--58871040 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
58870996 TATATATTTT
58871006 TTTAATCAAATATACTA
1 TTTAATCAAATATA-TA
58871023 TTTAATCAAATATATA
1 TTTAATCAAATATATA
58871039 TT
1 TT
58871041 AAATATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAATCAAATATATA
Found at i:58877770 original size:38 final size:38
Alignment explanation
Indices: 58877719--58877796 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
58877709 GCATTTTAAC
58877719 AATTGAAAGATGATGGTATTTTGTGTTATTAACATGTA
1 AATTGAAAGATGATGGTATTTTGTGTTATTAACATGTA
58877757 AATTGAAAGATGATGGTATTTTGTGTTATTAACATGTA
1 AATTGAAAGATGATGGTATTTTGTGTTATTAACATGTA
58877795 AA
1 AA
58877797 AGGGTATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (38 bp):
AATTGAAAGATGATGGTATTTTGTGTTATTAACATGTA
Found at i:58878585 original size:61 final size:57
Alignment explanation
Indices: 58878468--58878605 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 57
58878458 TTTAATTCAT
* * * *
58878468 ATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTGTATTTA
1 ATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAAATATATTTA
*
58878526 ATAATAATTATATTAAAATATGATTAAATTATTTATTTTTATTTTTATTAAAATATATTTA
1 ATAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TTTTATTAAAATATATTTA
* *
58878587 AAAATAATTTTATTAAAAT
1 ATAATAATTATATTAAAAT
58878606 TTAATAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 13 0.19
58 16 0.23
59 2 0.03
60 4 0.06
61 34 0.49
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTA
Found at i:58878794 original size:16 final size:16
Alignment explanation
Indices: 58878773--58878827 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
58878763 GGAATTATTA
58878773 ATTACAGCTTTATTCC
1 ATTACAGCTTTATTCC
* *
58878789 ATTACAACTCTATTCC
1 ATTACAGCTTTATTCC
*
58878805 ATTACAG-TTCTATTCA
1 ATTACAGCTT-TATTCC
58878821 ATTACAG
1 ATTACAG
58878828 TGAATCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGCTTTATTCC
Found at i:58879141 original size:17 final size:17
Alignment explanation
Indices: 58879119--58879158 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
58879109 AGATGGATCC
58879119 TCGAGACCCTTCTCGAA
1 TCGAGACCCTTCTCGAA
**
58879136 TCGAGATGCTTCTCGAA
1 TCGAGACCCTTCTCGAA
58879153 TCGAGA
1 TCGAGA
58879159 TGAGTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (17 bp):
TCGAGACCCTTCTCGAA
Found at i:58879159 original size:17 final size:17
Alignment explanation
Indices: 58879127--58879160 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
58879117 CCTCGAGACC
58879127 CTTCTCGAATCGAGATG
1 CTTCTCGAATCGAGATG
58879144 CTTCTCGAATCGAGATG
1 CTTCTCGAATCGAGATG
58879161 AGTGATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
CTTCTCGAATCGAGATG
Found at i:58882306 original size:33 final size:33
Alignment explanation
Indices: 58882264--58882521 Score: 153
Period size: 33 Copynumber: 7.6 Consensus size: 33
58882254 AATATGAAGG
58882264 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
58882297 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CAT-T---GGT
*
58882340 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
58882367 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
58882400 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--CT-CAT-T---GGT
* * *
58882442 GGTTGTTAAGTGCTGATT-CCC--C-CA--AGA
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
58882469 GGTTGCTAAGTGCTGATTCTCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
58882502 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
58882522 ACCATATCTT
Statistics
Matches: 175, Mismatches: 19, Indels: 62
0.68 0.07 0.24
Matches are distributed among these distances:
27 36 0.21
28 7 0.04
31 4 0.02
32 2 0.01
33 62 0.35
34 6 0.03
35 2 0.01
36 1 0.01
37 3 0.02
38 3 0.02
39 3 0.02
40 3 0.02
41 3 0.02
42 20 0.11
43 20 0.11
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:58882402 original size:103 final size:103
Alignment explanation
Indices: 58882260--58882565 Score: 483
Period size: 102 Copynumber: 3.0 Consensus size: 103
58882250 ATTGAATATG
*
58882260 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
58882325 TTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
58882363 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT-
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * *
58882427 TTTAAATGTGAAGGGGGTTGTTAAGTGCTGATTCCCCC
66 TTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
58882465 AAGAGGTTGCTAAGTGCTGATTCTCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
58882530 TTTGAATTTGAAA-GGGGTTGCTAAGTGTTGA-TCCCC
66 TTTGAATAT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
58882566 GGATCACTGG
Statistics
Matches: 187, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
102 99 0.53
103 86 0.46
104 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:58884386 original size:16 final size:13
Alignment explanation
Indices: 58884373--58884401 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
58884363 TCAAACGATC
58884373 AAATTTTCACACG
1 AAATTTTCACACG
58884386 AAATTTTCACAC-
1 AAATTTTCACACG
58884398 AAAT
1 AAAT
58884402 AACTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:58884661 original size:17 final size:16
Alignment explanation
Indices: 58884639--58884673 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
58884629 TTTTTTTATT
58884639 TTTAATCAAATATACTA
1 TTTAATCAAATATA-TA
58884656 TTTAATCAAATATATA
1 TTTAATCAAATATATA
58884672 TT
1 TT
58884674 AAATACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAATCAAATATATA
Done.