Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 180 of 310
Found at i:58527721 original size:14 final size:15
Alignment explanation
Indices: 58527702--58527734 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
58527692 AACTGCAACC
58527702 CTTTTCTTACGCT-A
1 CTTTTCTTACGCTAA
58527716 CTTTTCTTACGCTAA
1 CTTTTCTTACGCTAA
58527731 CTTT
1 CTTT
58527735 GATAGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.15, C:0.27, G:0.06, T:0.52
Consensus pattern (15 bp):
CTTTTCTTACGCTAA
Found at i:58531589 original size:23 final size:23
Alignment explanation
Indices: 58531563--58531624 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 23
58531553 AAATAATTTT
58531563 TTTTAAAAAAAATTCTATATAAA
1 TTTTAAAAAAAATTCTATATAAA
58531586 TTTTAATAAAAAAATTCTATATAAA
1 TTTT-A-AAAAAAATTCTATATAAA
*
58531611 TTTTAAAAAGAATT
1 TTTTAAAAAAAATT
58531625 TTAATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 12 0.33
24 2 0.06
25 22 0.61
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTTAAAAAAAATTCTATATAAA
Found at i:58531596 original size:25 final size:25
Alignment explanation
Indices: 58531568--58531616 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
58531558 ATTTTTTTTA
58531568 AAAAAAATTCTATATAAATTTTAAT
1 AAAAAAATTCTATATAAATTTTAAT
58531593 AAAAAAATTCTATATAAATTTTAA
1 AAAAAAATTCTATATAAATTTTAA
58531617 AAAGAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAAAATTCTATATAAATTTTAAT
Found at i:58533231 original size:2 final size:2
Alignment explanation
Indices: 58533224--58533252 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58533214 TTAAAGAGAA
58533224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58533253 AAAGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58533326 original size:13 final size:13
Alignment explanation
Indices: 58533308--58533339 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
58533298 TTGTTAAACT
58533308 AGAAACCTTTTAC
1 AGAAACCTTTTAC
58533321 AGAAACCTTTTAC
1 AGAAACCTTTTAC
58533334 AGAAAC
1 AGAAAC
58533340 AAAATAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (13 bp):
AGAAACCTTTTAC
Found at i:58535242 original size:16 final size:17
Alignment explanation
Indices: 58535210--58535244 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58535200 TAATACATGA
*
58535210 AATAATATATGAAAAGT
1 AATAATATATAAAAAGT
58535227 AATAATATA-AAAAAGT
1 AATAATATATAAAAAGT
58535243 AA
1 AA
58535245 AACAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AATAATATATAAAAAGT
Found at i:58536778 original size:13 final size:13
Alignment explanation
Indices: 58536760--58536784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58536750 TATTTGGGTC
58536760 TATAAATGGACTG
1 TATAAATGGACTG
58536773 TATAAATGGACT
1 TATAAATGGACT
58536785 TTTATTTATC
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:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (13 bp):
TATAAATGGACTG
Found at i:58537385 original size:206 final size:206
Alignment explanation
Indices: 58537020--58537988 Score: 1481
Period size: 206 Copynumber: 4.7 Consensus size: 206
58537010 AAATCTACTT
* * *
58537020 CTTCGATTTGTT-TCCGGACAATGCAGAGATGCCAAATCATCTTAGATTTGCTTCAGCATAAGCA
1 CTTCGATTTGTTCT-CTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCA
* *
58537084 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCATAAGGATACCAAACCATCT
65 CGTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCT
* * * * *
58537149 TGGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCCGCCCTCCGTCAAATAT
130 TGGATCTGCTTCAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTCCGTCGAATAT
* *
58537214 GGAGACACCAAA
195 AGAGACGCCAAA
* * *
58537226 CTTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGACTTGCTTCAGCGTAAGCAT
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
** *
58537291 GCAAAAACCAAATCAGCTATGTCTTAGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
* * * * * * * * * *
58537356 GGATCAGCTTCAGTATAAACATATGAAGGTTAGATCTGCTATGTGTCTGCTCTCTGTCGAATATG
131 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTCCGTCGAATATA
58537421 GAGACGCCAAA
196 GAGACGCCAAA
* * *
58537432 CTTCGATTTGTTATCTGACAATACAGAGATGCCAAATCACCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
58537497 GTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
* *
58537562 GGATCTGCTTTAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTTCGTCGAATATA
131 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTCCGTCGAATATA
58537627 GAGACGCCAAA
196 GAGACGCCAAA
* **
58537638 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCATTGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * *
58537703 GTGAAAGCCAAATCAGCTATGTCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAATCATCT
66 GTGAAAACCAAATCAGCTATGTCTTCGA-TTTGCTCCTTGTAAGCACAAGGATACCAAACCATCT
* *
58537768 TGGATCTGCTTTAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTTCGTCGAATAT
130 TGGATCTGCTTCAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTCCGTCGAATAT
58537833 AGAGACGCCAAA
195 AGAGACGCCAAA
*
58537845 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * *
58537910 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
58537975 GGATCTTGCTTCAG
131 GGATC-TGCTTCAG
58537989 CCAGATCTGC
Statistics
Matches: 707, Mismatches: 53, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
206 499 0.71
207 208 0.29
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GTGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
GGATCTGCTTCAGTCTAATCATCTGAAGGTTAAATCTACTATATGTCTGCCCTCCGTCGAATATA
GAGACGCCAAA
Found at i:58538886 original size:22 final size:23
Alignment explanation
Indices: 58538860--58538904 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
58538850 TTCACCATGG
58538860 CCTCTCCATT-TTTCTCTTTTTT
1 CCTCTCCATTCTTTCTCTTTTTT
* * *
58538882 CCTCTTCTTTCTTTCTTTTTTTT
1 CCTCTCCATTCTTTCTCTTTTTT
58538905 TTCTTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (23 bp):
CCTCTCCATTCTTTCTCTTTTTT
Found at i:58551642 original size:20 final size:20
Alignment explanation
Indices: 58551609--58551647 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58551599 AAAAACAATA
*
58551609 TATATATTAAATAAGATAAT
1 TATATAATAAATAAGATAAT
* *
58551629 TATATAATATATAATATAA
1 TATATAATAAATAAGATAA
58551648 AAGTATATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TATATAATAAATAAGATAAT
Found at i:58551808 original size:16 final size:17
Alignment explanation
Indices: 58551777--58551811 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
58551767 TAATACATGA
58551777 AATAATATATGAAAAGT
1 AATAATATATGAAAAGT
58551794 AATAATATA-GAAAAGT
1 AATAATATATGAAAAGT
58551810 AA
1 AA
58551812 AACAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
AATAATATATGAAAAGT
Found at i:58553422 original size:8 final size:8
Alignment explanation
Indices: 58553409--58553435 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
58553399 GGCTATTACA
58553409 ACATATAT
1 ACATATAT
58553417 ACATATAT
1 ACATATAT
58553425 ACATATAT
1 ACATATAT
58553433 ACA
1 ACA
58553436 ATAATGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (8 bp):
ACATATAT
Found at i:58554784 original size:28 final size:28
Alignment explanation
Indices: 58554744--58554801 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
58554734 GCTTGTAACA
58554744 GTTTCCTTCATTGGATTTTTGACACATT
1 GTTTCCTTCATTGGATTTTTGACACATT
**
58554772 GTTTCCTTCATTGGATTTTTGTTACATT
1 GTTTCCTTCATTGGATTTTTGACACATT
58554800 GT
1 GT
58554802 CCATTAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (28 bp):
GTTTCCTTCATTGGATTTTTGACACATT
Found at i:58556960 original size:174 final size:174
Alignment explanation
Indices: 58556670--58557018 Score: 689
Period size: 174 Copynumber: 2.0 Consensus size: 174
58556660 TAACCCATAG
58556670 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
1 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
58556735 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
66 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
*
58556800 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGGCTTATTAGGC
131 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
58556844 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
1 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
58556909 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
66 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
58556974 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
131 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
58557018 T
1 T
58557019 ATTAATGTAT
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (174 bp):
TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
Found at i:58572162 original size:26 final size:26
Alignment explanation
Indices: 58572131--58572238 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
58572121 TGAAATTCCC
*
58572131 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
58572157 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58572183 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58572209 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
58572235 ATCA
1 ATCA
58572239 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:58576117 original size:21 final size:22
Alignment explanation
Indices: 58576058--58576121 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
58576048 CAGAAGCAGT
* *
58576058 ATACGACACATAAAGTGCTTGA
1 ATACGACACATATAGTGCCTGA
** *
58576080 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
58576100 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
58576122 TCGGCAAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:58576231 original size:6 final size:6
Alignment explanation
Indices: 58576220--58576265 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
58576210 AAATAATTTC
* *
58576220 TCAATT TCAATT TCAATT TCACTT TCAATGT ACAA-T TCAA-T TCAAT
1 TCAATT TCAATT TCAATT TCAATT TCAAT-T TCAATT TCAATT TCAAT
58576266 GCAATTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 9 0.26
6 21 0.62
7 4 0.12
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (6 bp):
TCAATT
Found at i:58577092 original size:7 final size:7
Alignment explanation
Indices: 58577082--58577131 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
58577072 ACTATATATA
58577082 ATATAAT
1 ATATAAT
58577089 ATATAAT
1 ATATAAT
58577096 ATATAAT
1 ATATAAT
58577103 ATATAAT
1 ATATAAT
58577110 ATATAAT
1 ATATAAT
58577117 ATATAAT
1 ATATAAT
58577124 ATATAAT
1 ATATAAT
58577131 A
1 A
58577132 AAACATAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:58577100 original size:21 final size:21
Alignment explanation
Indices: 58577074--58577131 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
58577064 TTTACTTTAC
58577074 TATAT-ATAATATAATATATAA
1 TATATAAT-ATATAATATATAA
58577095 TATATAATATATAATATATAA
1 TATATAATATATAATATATAA
58577116 TATATAATATATAATA
1 TATATAATATATAATA
58577132 AAACATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAATATATAATATATAA
Found at i:58577472 original size:45 final size:45
Alignment explanation
Indices: 58577422--58577559 Score: 153
Period size: 45 Copynumber: 3.1 Consensus size: 45
58577412 TTTATTTCAT
58577422 AATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
1 AATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
* * * * * *
58577467 AATATACA-AATAGATT-ACAATTCTTTATTTA-TT-TTATTT--CAT
1 AATATA-ATAATA-ATTAATAAATATAT-TTTACTTATTATTTAAGAA
58577509 AATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
1 AATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
58577554 AATATA
1 AATATA
58577560 CAAATATATT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
41 8 0.11
42 19 0.26
43 6 0.08
44 6 0.08
45 25 0.35
46 8 0.11
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (45 bp):
AATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
Found at i:58577498 original size:87 final size:87
Alignment explanation
Indices: 58577401--58577573 Score: 337
Period size: 87 Copynumber: 2.0 Consensus size: 87
58577391 ATTGCACTTG
58577401 TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGA
1 TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGA
58577466 AAATATACAAATAGATTACAAT
66 AAATATACAAATAGATTACAAT
58577488 TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGA
1 TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGA
*
58577553 AAATATACAAATATATTACAA
66 AAATATACAAATAGATTACAA
58577574 GTGTATTTTC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (87 bp):
TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAATATATTTTACTTATTATTTAAGA
AAATATACAAATAGATTACAAT
Found at i:58577513 original size:42 final size:42
Alignment explanation
Indices: 58577401--58577530 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 42
58577391 ATTGCACTTG
*
58577401 TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAA
1 TCTTTATTTATTTTATTTCATAATATAATAATAATTAACAAA
* * * * *
58577443 TATAT-TTTACTTATTATTTAAGAAAATATACA-AATAGATT-ACAAT
1 TCTTTATTTA-TT-TTATTT--CATAATATA-ATAATA-ATTAACAAA
*
58577488 TCTTTATTTATTTTATTTCATAATATAATAATAATTAATAAA
1 TCTTTATTTATTTTATTTCATAATATAATAATAATTAACAAA
58577530 T
1 T
58577531 ATATTTTACT
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
41 8 0.12
42 20 0.30
43 6 0.09
44 6 0.09
45 19 0.28
46 8 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (42 bp):
TCTTTATTTATTTTATTTCATAATATAATAATAATTAACAAA
Found at i:58577581 original size:45 final size:44
Alignment explanation
Indices: 58577422--58577582 Score: 136
Period size: 45 Copynumber: 3.6 Consensus size: 44
58577412 TTTATTTCAT
*
58577422 AATATA-ATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
1 AATATACA-AATAATT-ACAAATATATTTTACTTATTATTTAAGAA
* * * * *
58577467 AATATACAAATAGATTACAATTCTTTATTTA-TT-TTATTT--CAT
1 AATATACAAATA-ATTACAAATATAT-TTTACTTATTATTTAAGAA
*
58577509 AATATA-ATAATAATTAATAAATATATTTTACTTATTATTTAAGAA
1 AATATACA-AATAATT-ACAAATATATTTTACTTATTATTTAAGAA
* *
58577554 AATATACAAATATATTACAAGTGTATTTT
1 AATATACAAATA-ATTACAAATATATTTT
58577583 CATGTATTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
41 8 0.09
42 19 0.21
43 6 0.07
44 6 0.07
45 39 0.43
46 12 0.13
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (44 bp):
AATATACAAATAATTACAAATATATTTTACTTATTATTTAAGAA
Found at i:58577675 original size:22 final size:23
Alignment explanation
Indices: 58577647--58577696 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
58577637 TTATTTAATA
58577647 ATAATAAT-TTTA-ATATAAAAT
1 ATAATAATATTTATATATAAAAT
*
58577668 CATAATAATATTTATATATAATAT
1 -ATAATAATATTTATATATAAAAT
58577692 ATAAT
1 ATAAT
58577697 CGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 9 0.36
24 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATAATATTTATATATAAAAT
Found at i:58577872 original size:20 final size:19
Alignment explanation
Indices: 58577826--58577872 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
58577816 AGTCTTTTTT
*
58577826 CCTAATTTCTCCTAATTAAG
1 CCTAA-TTCACCTAATTAAG
58577846 -CTAAATTCACCTAATTAAAG
1 CCT-AATTCACCTAATT-AAG
58577866 CCTAATT
1 CCTAATT
58577873 AAATATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (19 bp):
CCTAATTCACCTAATTAAG
Found at i:58579079 original size:21 final size:22
Alignment explanation
Indices: 58579053--58579098 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
58579043 CTATTTTAAT
58579053 TTTATTTATTTATTATTATT-A
1 TTTATTTATTTATTATTATTCA
*
58579074 TTTATTTTTTTATTATTATTCA
1 TTTATTTATTTATTATTATTCA
58579096 TTT
1 TTT
58579099 TCTGATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTATTTATTATTATTCA
Found at i:58579088 original size:18 final size:18
Alignment explanation
Indices: 58579054--58579099 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
58579044 TATTTTAATT
58579054 TTATTTA-TTTATTATTA
1 TTATTTATTTTATTATTA
*
58579071 TTATTTATTTTTTTATTA
1 TTATTTATTTTATTATTA
*
58579089 TTATTCATTTT
1 TTATTTATTTT
58579100 CTGATCTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTATTTTATTATTA
Found at i:58579240 original size:3 final size:3
Alignment explanation
Indices: 58579227--58579267 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
58579217 CTCTAGCTCT
*
58579227 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58579268 CTATACATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:58582256 original size:7 final size:7
Alignment explanation
Indices: 58582216--58582262 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
58582206 ACTTTACTAT
58582216 ATATATA
1 ATATATA
58582223 ATATAATA
1 ATAT-ATA
58582231 ATAATATA
1 AT-ATATA
* *
58582239 GTATCTA
1 ATATATA
58582246 ATATATA
1 ATATATA
58582253 ATATATA
1 ATATATA
58582260 ATA
1 ATA
58582263 AAACATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 23 0.68
8 9 0.26
9 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:58583479 original size:14 final size:15
Alignment explanation
Indices: 58583451--58583479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58583441 ACATTAAGCA
58583451 AACAAATGTGTTTTT
1 AACAAATGTGTTTTT
58583466 AACAAATG-GTTTTT
1 AACAAATGTGTTTTT
58583480 GGAAAACGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (15 bp):
AACAAATGTGTTTTT
Found at i:58597046 original size:33 final size:33
Alignment explanation
Indices: 58596892--58597048 Score: 111
Period size: 33 Copynumber: 4.8 Consensus size: 33
58596882 TGTATATATG
** * *
58596892 TAAGACCATAGTTGGGTTATGGCATAT-TGATGA
1 TAAGACCATAGCCGGGCTATGGCAT-TCTAATGA
** * * *
58596925 TAAGACTGTAG-CTGACTATAGCATTCTAATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTAATGA
* * * * *
58596957 TAAGACTATAGCGGGGCTATGTCATACTGATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTAATGA
* * *
58596990 TAAGAACATAGCTGGGCTCTGGCATTCTAATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTAATGA
* * *
58597023 TAAGGCCATAACCGGGTTATGGCATT
1 TAAGACCATAGCCGGGCTATGGCATT
58597049 ATGAACGTAA
Statistics
Matches: 93, Mismatches: 29, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
31 1 0.01
32 23 0.25
33 69 0.74
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (33 bp):
TAAGACCATAGCCGGGCTATGGCATTCTAATGA
Found at i:58600947 original size:31 final size:31
Alignment explanation
Indices: 58600909--58600971 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
58600899 AAAAAAAGAA
58600909 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
1 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
58600940 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
1 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
58600971 A
1 A
58600972 CAAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (31 bp):
AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
Found at i:58605827 original size:24 final size:24
Alignment explanation
Indices: 58605800--58605849 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
58605790 GTTGATGAAC
*
58605800 CTCTTTGGGTTCGTGTTCTCAGAT
1 CTCTTTAGGTTCGTGTTCTCAGAT
58605824 CTCTTTAGGTTCGTGTTCTCAGAT
1 CTCTTTAGGTTCGTGTTCTCAGAT
58605848 CT
1 CT
58605850 AAGTATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (24 bp):
CTCTTTAGGTTCGTGTTCTCAGAT
Found at i:58607183 original size:12 final size:12
Alignment explanation
Indices: 58607168--58607207 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
58607158 TATTTAAATA
58607168 TAATTAATTATC
1 TAATTAATTATC
*
58607180 TAATTAA--ATA
1 TAATTAATTATC
58607190 TAATTAATTATC
1 TAATTAATTATC
58607202 TAATTA
1 TAATTA
58607208 TTTGAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATTAATTATC
Found at i:58607186 original size:22 final size:22
Alignment explanation
Indices: 58607161--58607207 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
58607151 AAATGGATAT
58607161 TTAAATATAATTAATTATCTAA
1 TTAAATATAATTAATTATCTAA
58607183 TTAAATATAATTAATTATCTAA
1 TTAAATATAATTAATTATCTAA
58607205 TTA
1 TTA
58607208 TTTGAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATATAATTAATTATCTAA
Found at i:58613656 original size:18 final size:17
Alignment explanation
Indices: 58613638--58613670 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58613628 TATGATGATT
58613638 TTTTA-ATATAAAAATA
1 TTTTATATATAAAAATA
*
58613654 TTTTATATATTAAAATA
1 TTTTATATATAAAAATA
58613671 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTATATATAAAAATA
Found at i:58615852 original size:45 final size:45
Alignment explanation
Indices: 58615796--58615887 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
58615786 AACAAATCAC
58615796 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
1 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
*
58615841 TATATTCATCGTCCATGTATGTCACCTAAAAGCACACCAAATTTT
1 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
58615886 TA
1 TA
58615888 CATTGAGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (45 bp):
TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
Found at i:58617345 original size:21 final size:21
Alignment explanation
Indices: 58617320--58617364 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
58617310 CCAATCAATT
* * *
58617320 AACCTATTCAAAATATGATAA
1 AACCTACTAAAAACATGATAA
*
58617341 AACCTACTAAAAACATGCTAA
1 AACCTACTAAAAACATGATAA
58617362 AAC
1 AAC
58617365 AATCATCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.22
Consensus pattern (21 bp):
AACCTACTAAAAACATGATAA
Found at i:58619318 original size:13 final size:14
Alignment explanation
Indices: 58619295--58619323 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
58619285 ATGTCCACTC
58619295 TTCTCTTCTTTCTT
1 TTCTCTTCTTTCTT
58619309 TTCT-TTCTTTCTT
1 TTCTCTTCTTTCTT
58619322 TT
1 TT
58619324 ATTTTGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTCTTCTTTCTT
Found at i:58625866 original size:26 final size:26
Alignment explanation
Indices: 58625820--58625872 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
58625810 GAAATTTTTT
* *
58625820 TAAAAAATAAAATATTATAAAAGTCA
1 TAAAAAATAAAAAAATATAAAAGTCA
*
58625846 TAAAAATATAAAAAAAT-TAAAATTCA
1 TAAAAA-ATAAAAAAATATAAAAGTCA
58625872 T
1 T
58625873 TATCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (26 bp):
TAAAAAATAAAAAAATATAAAAGTCA
Found at i:58626007 original size:19 final size:21
Alignment explanation
Indices: 58625966--58626013 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
58625956 TTAAAATTTT
58625966 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
58625987 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
58626006 AACTAAAA
1 AACTAAAA
58626014 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:58626242 original size:102 final size:102
Alignment explanation
Indices: 58626066--58626270 Score: 392
Period size: 102 Copynumber: 2.0 Consensus size: 102
58626056 TAAGGACTTA
58626066 AATCATAACCATGTAAAATATAAGATATTATCATCAAGATTTACATCCTCATCTTGCTCAAATTT
1 AATCATAACCATGTAAAATATAAGATATTATCATCAAGATTTACATCCTCATCTTGCTCAAATTT
*
58626131 TGGTGGCTTGTACCCTTTATTGAACCATTCTTCTTGT
66 TGGTGGCTTGTACCCTTTATTGAACCATTCATCTTGT
58626168 AATCATAACCATGTAAAATATAAGATATTATCATCAAGATTTACATCCTCATCTTGCTCAAATTT
1 AATCATAACCATGTAAAATATAAGATATTATCATCAAGATTTACATCCTCATCTTGCTCAAATTT
*
58626233 TGGTGGCTTGTACCCTTTCTTGAACCATTCATCTTGT
66 TGGTGGCTTGTACCCTTTATTGAACCATTCATCTTGT
58626270 A
1 A
58626271 GAATTTCAGG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (102 bp):
AATCATAACCATGTAAAATATAAGATATTATCATCAAGATTTACATCCTCATCTTGCTCAAATTT
TGGTGGCTTGTACCCTTTATTGAACCATTCATCTTGT
Found at i:58626800 original size:39 final size:41
Alignment explanation
Indices: 58626646--58626815 Score: 233
Period size: 40 Copynumber: 4.3 Consensus size: 41
58626636 GCTACTCGTT
* * *
58626646 CAAATGCCTTCGGGACATAGCCC-GATTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTATAGTAACTCGCA
*
58626686 CAAATACCTTCGGGACTTAACCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTATAGTAACTCGCA
58626726 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTATAGTAACTCGCA
* * * *
58626766 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTATAGTAACTCGCA
58626805 CAAATGCCTTC
1 CAAATGCCTTC
58626816 AGATCTTAGT
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
39 32 0.27
40 83 0.70
41 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAACCCGGATTATAGTAACTCGCA
Found at i:58636843 original size:40 final size:40
Alignment explanation
Indices: 58636806--58636923 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
58636796 GCTACTCGTT
* *
58636806 CAAATACCTTCGGGACATAGCCCGGTTATAGTGACTCGCA
1 CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
58636846 CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
58636886 CAAATGCCTTCGAGACTTAACCCGGATT-TAGTAACTCG
1 CAAATACCTTCGGGACTTAGCCCGG-TTATAGTAACTCG
58636924 AATTTAGATC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 70 0.97
41 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:58641836 original size:6 final size:7
Alignment explanation
Indices: 58641822--58641881 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
58641812 GTTTTTTAGT
58641822 TTTTAAA
1 TTTTAAA
*
58641829 TTTTAAT
1 TTTTAAA
* *
58641836 TTTTTAT
1 TTTTAAA
58641843 TTTTAAA
1 TTTTAAA
58641850 TTTTAATA
1 TTTTAA-A
58641858 TTTTAATA
1 TTTTAA-A
58641866 TTTT-AA
1 TTTTAAA
58641872 TTTT-AA
1 TTTTAAA
58641878 TTTT
1 TTTT
58641882 TTGAGTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
6 11 0.23
7 24 0.50
8 13 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTAAA
Found at i:58641838 original size:22 final size:22
Alignment explanation
Indices: 58641807--58641889 Score: 107
Period size: 22 Copynumber: 3.8 Consensus size: 22
58641797 TTTTTAAGTT
*
58641807 TTTTAGTTTTTTAGTTTTTAAA
1 TTTTAATTTTTTAGTTTTTAAA
58641829 TTTTAATTTTTTA-TTTTTAAA
1 TTTTAATTTTTTAGTTTTTAAA
* *
58641850 TTTTAATATTTTAATATTTT-AA
1 TTTTAATTTTTTAGT-TTTTAAA
58641872 TTTTAATTTTTTGAGTTT
1 TTTTAATTTTTT-AGTTT
58641890 ATTTTTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
21 20 0.37
22 28 0.52
23 6 0.11
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTAATTTTTTAGTTTTTAAA
Found at i:58641860 original size:8 final size:8
Alignment explanation
Indices: 58641822--58641872 Score: 65
Period size: 7 Copynumber: 6.9 Consensus size: 8
58641812 GTTTTTTAGT
58641822 TTTTAA-A
1 TTTTAATA
58641829 TTTTAAT-
1 TTTTAATA
*
58641836 TTTTTAT-
1 TTTTAATA
58641843 TTTTAA-A
1 TTTTAATA
58641850 TTTTAATA
1 TTTTAATA
58641858 TTTTAATA
1 TTTTAATA
58641866 TTTTAAT
1 TTTTAAT
58641873 TTTAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 23 0.59
8 16 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTAATA
Found at i:58641883 original size:8 final size:8
Alignment explanation
Indices: 58641790--58641883 Score: 67
Period size: 8 Copynumber: 12.5 Consensus size: 8
58641780 TATTGATTAA
*
58641790 TTTTAAAT
1 TTTTAATT
58641798 TTTTAAGTT
1 TTTTAA-TT
*
58641807 TTTTAGTT
1 TTTTAATT
*
58641815 TTTT-AGT
1 TTTTAATT
*
58641822 TTTTAA-A
1 TTTTAATT
58641829 TTTTAATT
1 TTTTAATT
58641837 TTTT-A-T
1 TTTTAATT
*
58641843 TTTTAA-A
1 TTTTAATT
*
58641850 TTTTAATA
1 TTTTAATT
*
58641858 TTTTAATA
1 TTTTAATT
58641866 TTTTAA--
1 TTTTAATT
58641872 TTTTAATT
1 TTTTAATT
58641880 TTTT
1 TTTT
58641884 GAGTTTATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
6 11 0.15
7 19 0.26
8 36 0.50
9 6 0.08
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (8 bp):
TTTTAATT
Found at i:58641883 original size:14 final size:14
Alignment explanation
Indices: 58641815--58641883 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
58641805 TTTTTTAGTT
* *
58641815 TTTTAGTTTTTAAA
1 TTTTAATTTTTTAA
*
58641829 TTTTAATTTTTTAT
1 TTTTAATTTTTTAA
* *
58641843 TTTTAAATTTTAATA
1 TTTTAATTTTTTA-A
*
58641858 TTTTAATATTTTAA
1 TTTTAATTTTTTAA
58641872 TTTTAATTTTTT
1 TTTTAATTTTTT
58641884 GAGTTTATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
14 34 0.77
15 10 0.23
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (14 bp):
TTTTAATTTTTTAA
Found at i:58642837 original size:41 final size:41
Alignment explanation
Indices: 58642772--58642952 Score: 204
Period size: 41 Copynumber: 4.4 Consensus size: 41
58642762 GGGATTATAT
* *
58642772 GACTTTTAGCGGCATTGTACCAAAAGCGCCACTATTGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* ** * *
58642813 GACTTTTAGTGGTTTTTTAGCAAAAGCGCCGCTATTGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* *
58642854 GACTTTTAGCGGCGTTTTACCAAAA-CACCACTATTGCTCT
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* * * * *
58642894 GACTTTTAGCAGCGTTTTAACAAAAAACGCCGCTATTGCTCT
1 GACTTTTAGCGGCGTTTT-ACCAAAAGCGCCACTATTGCTCC
*
58642936 G-TTTTTAGCGGCGTTTT
1 GACTTTTAGCGGCGTTTT
58642953 TGGTAGAACA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 29 0.24
41 76 0.64
42 14 0.12
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (41 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
Found at i:58642912 original size:81 final size:83
Alignment explanation
Indices: 58642772--58642952 Score: 233
Period size: 81 Copynumber: 2.2 Consensus size: 83
58642762 GGGATTATAT
* * * ** ** *
58642772 GACTTTTAGCGGCATTGTACCAAAAGCGCCACTATTGCTCCGACTTTTAGTGGTTTTTTAGC-AA
1 GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
*
58642836 AAGCGCCGCTATTGCTCC
66 AAACGCCGCTATTGCTCC
*
58642854 GACTTTTAGCGGCGTTTTACCAAAA-CACCACTATTGCTCTGACTTTTAGCAGCGTTTTAACAAA
1 GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
*
58642918 AAACGCCGCTATTGCTCT
66 AAACGCCGCTATTGCTCC
*
58642936 G-TTTTTAGCGGCGTTTT
1 GACTTTTAGCGGCGTTTT
58642953 TGGTAGAACA
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 44 0.51
82 42 0.49
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (83 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
AAACGCCGCTATTGCTCC
Found at i:58643022 original size:12 final size:12
Alignment explanation
Indices: 58643007--58643033 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58642997 GTTTTTTGAT
58643007 AAAACGCCGCTA
1 AAAACGCCGCTA
58643019 AAAACGCCGCTA
1 AAAACGCCGCTA
58643031 AAA
1 AAA
58643034 CCCTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:58653417 original size:46 final size:47
Alignment explanation
Indices: 58653177--58653446 Score: 182
Period size: 46 Copynumber: 5.7 Consensus size: 47
58653167 GGGTAAGTTA
* * * * *
58653177 CCGATGCCATGTGCCAGACATGGTCTTACACT-GGATATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCA-CTCGTC-TC-ATG
* *
58653226 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATC-TG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG--TCTCATG
* * * * *
58653274 TTCCGATGTCACGTCCTAGACATGGTCTTACACT-G-ACACATCTCATAG
1 --CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCAT-G
* * * * *
58653322 CCGATG-CATGTCCCAAACAT-GTCTTACATTGGCTTA-T-GTGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC--ACTCGTCTC-ATG
*
58653368 CCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTC-ATG
* *
58653414 CCGATGCCATGTCCTAGACATGGCCTTACACTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA
58653447 AATTTCATAA
Statistics
Matches: 173, Mismatches: 32, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
44 10 0.06
45 13 0.08
46 54 0.31
47 14 0.08
48 15 0.09
49 34 0.20
50 32 0.18
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCATG
Found at i:58653482 original size:140 final size:141
Alignment explanation
Indices: 58653220--58653489 Score: 336
Period size: 140 Copynumber: 1.9 Consensus size: 141
58653210 GATATCATCA
* ** * *
58653220 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTTCCGATGTCA
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG-ATATCAATGCCGATGCCA
* *
58653285 CGTCCTAGACATGGTCTTACACTGACACATCTCATAGCCGATGCATGTCCCAAACATGTCTTACA
65 CGTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACA
58653350 TTGGCTTATGTG
130 TTGGCTTATGTG
* * *
58653362 TCGAGGCCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCG-TCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
* *
58653424 GTCCTAGACATGGCCTTACACT-A-A-ATTTCATAATGTGGCCAATGCATGTCCCAGACATGTCT
66 GTCCTAGACATGGCCTTACACTGACACATCTCAT-A----GCCAATGCATGTCCCAAACATGTCT
58653486 TACA
126 TACA
58653490 CTAGCCCACA
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
135 6 0.05
136 2 0.02
137 1 0.01
138 33 0.30
140 44 0.40
141 13 0.12
142 12 0.11
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (141 bp):
TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
GTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACAT
TGGCTTATGTG
Found at i:58658829 original size:16 final size:16
Alignment explanation
Indices: 58658774--58658830 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
58658764 TGTCATATTG
*
58658774 CCATGGTATCTTTCAA
1 CCATGGTATTTTTCAA
* * * *
58658790 CCATGGTCTTGTGCATTG
1 CCATGGTATTTTTCA--A
58658808 CCATGGTATTTTTCAA
1 CCATGGTATTTTTCAA
58658824 CCATGGT
1 CCATGGT
58658831 CTTATTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCATGGTATTTTTCAA
Found at i:58659018 original size:46 final size:46
Alignment explanation
Indices: 58658805--58659027 Score: 333
Period size: 46 Copynumber: 4.9 Consensus size: 46
58658795 GTCTTGTGCA
*
58658805 TTGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTC-TCGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT-GTCATG
* *
58658850 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
* *
58658896 TTGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
** *
58658942 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
**
58658988 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
58659028 TTCAGAAAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
45 32 0.19
46 133 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
Found at i:58660296 original size:46 final size:47
Alignment explanation
Indices: 58660056--58660325 Score: 198
Period size: 46 Copynumber: 5.7 Consensus size: 47
58660046 GGGTAAGTTA
* * * * *
58660056 CCGATGCCATGTGCCAGACATGGTCTTACACT-GGATATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCA-CTCGTC-TC-ATG
* * *
58660105 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG--TCTC-ATG
* * * *
58660155 CCGATGCCACGTCCTAGACATGGTCTTACACT-G-ACACATCTCATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCAT-G
* * * * *
58660201 CCGATG-CATGTCCCAAACAT-GTCTTACATTGGCTTA-T-GTGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC--ACTCGTCTC-ATG
*
58660247 CCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTC-ATG
* *
58660293 CCGATGCCATGTCCTAGACATGGCCTTACACTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA
58660326 AATTTCATAA
Statistics
Matches: 174, Mismatches: 34, Indels: 27
0.74 0.14 0.11
Matches are distributed among these distances:
44 10 0.06
45 14 0.08
46 55 0.32
47 13 0.07
48 13 0.07
49 34 0.20
50 34 0.20
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCATG
Found at i:58660363 original size:140 final size:141
Alignment explanation
Indices: 58660099--58660368 Score: 354
Period size: 140 Copynumber: 1.9 Consensus size: 141
58660089 GATATCATCA
* **
58660099 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCGATGCCA
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG-ATATCAATGCCGATGCCA
* *
58660164 CGTCCTAGACATGGTCTTACACTGACACATCTCATAGCCGATGCATGTCCCAAACATGTCTTACA
65 CGTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACA
58660229 TTGGCTTATGTG
130 TTGGCTTATGTG
* * *
58660241 TCGAGGCCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCG-TCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
* *
58660303 GTCCTAGACATGGCCTTACACT-A-A-ATTTCATAATGTGGCCAATGCATGTCCCAGACATGTCT
66 GTCCTAGACATGGCCTTACACTGACACATCTCAT-A----GCCAATGCATGTCCCAAACATGTCT
58660365 TACA
126 TACA
58660369 CTAGCCCACA
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
135 6 0.05
136 2 0.02
137 1 0.01
138 35 0.31
140 44 0.39
141 13 0.12
142 12 0.11
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (141 bp):
TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
GTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACAT
TGGCTTATGTG
Found at i:58665708 original size:16 final size:16
Alignment explanation
Indices: 58665653--58665709 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
58665643 TGTCATATTG
*
58665653 CCATGGTATCTTTCAA
1 CCATGGTATTTTTCAA
* * * *
58665669 CCATGGTCTTGTGCATTG
1 CCATGGTATTTTTCA--A
58665687 CCATGGTATTTTTCAA
1 CCATGGTATTTTTCAA
58665703 CCATGGT
1 CCATGGT
58665710 CTTATTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCATGGTATTTTTCAA
Found at i:58665897 original size:46 final size:46
Alignment explanation
Indices: 58665684--58665906 Score: 333
Period size: 46 Copynumber: 4.9 Consensus size: 46
58665674 GTCTTGTGCA
*
58665684 TTGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTC-TCGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT-GTCATG
* *
58665729 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
* *
58665775 TTGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
** *
58665821 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
**
58665867 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
58665907 TTCAGAAAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
45 32 0.19
46 133 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
Found at i:58666779 original size:51 final size:51
Alignment explanation
Indices: 58666714--58666829 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
58666704 CTCAAACTTA
* *
58666714 CTTCATACTTCATCTGAAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
58666765 CTTCATATTTCATCTGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
58666816 TTTCATATTTCATC
1 CTTCATATTTCATC
58666830 CAGATAACTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (51 bp):
CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
Found at i:58668056 original size:11 final size:11
Alignment explanation
Indices: 58668040--58668087 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
58668030 CTTTATATAC
58668040 TAATAAAATAA
1 TAATAAAATAA
*
58668051 TAATAAAATATCT
1 TAATAAAATA--A
* *
58668064 TATTAAAATAT
1 TAATAAAATAA
58668075 TAATAAAATAA
1 TAATAAAATAA
58668086 TA
1 TA
58668088 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:58672751 original size:46 final size:47
Alignment explanation
Indices: 58672511--58672780 Score: 198
Period size: 46 Copynumber: 5.7 Consensus size: 47
58672501 GGGTAAGTTA
* * * * *
58672511 CCGATGCCATGTGCCAGACATGGTCTTACACT-GGATATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCA-CTCGTC-TC-ATG
* * *
58672560 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG--TCTC-ATG
* * * *
58672610 CCGATGCCACGTCCTAGACATGGTCTTACACT-G-ACACATCTCATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCAT-G
* * * * *
58672656 CCGATG-CATGTCCCAAACAT-GTCTTACATTGGCTTA-T-GTGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC--ACTCGTCTC-ATG
*
58672702 CCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTC-ATG
* *
58672748 CCGATGCCATGTCCTAGACATGGCCTTACACTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA
58672781 AATTTCATAA
Statistics
Matches: 174, Mismatches: 34, Indels: 27
0.74 0.14 0.11
Matches are distributed among these distances:
44 10 0.06
45 14 0.08
46 55 0.32
47 13 0.07
48 13 0.07
49 34 0.20
50 34 0.20
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCATG
Found at i:58672818 original size:140 final size:141
Alignment explanation
Indices: 58672554--58672823 Score: 354
Period size: 140 Copynumber: 1.9 Consensus size: 141
58672544 GATATCATCA
* **
58672554 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCGATGCCA
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG-ATATCAATGCCGATGCCA
* *
58672619 CGTCCTAGACATGGTCTTACACTGACACATCTCATAGCCGATGCATGTCCCAAACATGTCTTACA
65 CGTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACA
58672684 TTGGCTTATGTG
130 TTGGCTTATGTG
* * *
58672696 TCGAGGCCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCG-TCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
* *
58672758 GTCCTAGACATGGCCTTACACT-A-A-ATTTCATAATGTGGCCAATGCATGTCCCAGACATGTCT
66 GTCCTAGACATGGCCTTACACTGACACATCTCAT-A----GCCAATGCATGTCCCAAACATGTCT
58672820 TACA
126 TACA
58672824 CTAGCCCACA
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
135 6 0.05
136 2 0.02
137 1 0.01
138 35 0.31
140 44 0.39
141 13 0.12
142 12 0.11
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (141 bp):
TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
GTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACAT
TGGCTTATGTG
Found at i:58678163 original size:16 final size:16
Alignment explanation
Indices: 58678108--58678164 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
58678098 TGTCATATTG
*
58678108 CCATGGTATCTTTCAA
1 CCATGGTATTTTTCAA
* * * *
58678124 CCATGGTCTTGTGCATTG
1 CCATGGTATTTTTCA--A
58678142 CCATGGTATTTTTCAA
1 CCATGGTATTTTTCAA
58678158 CCATGGT
1 CCATGGT
58678165 CTTATTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCATGGTATTTTTCAA
Found at i:58678352 original size:46 final size:46
Alignment explanation
Indices: 58678139--58678361 Score: 333
Period size: 46 Copynumber: 4.9 Consensus size: 46
58678129 GTCTTGTGCA
*
58678139 TTGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTC-TCGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT-GTCATG
* *
58678184 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
* *
58678230 TTGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
** *
58678276 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
**
58678322 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
58678362 TTCAGAAAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
45 32 0.19
46 133 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
Found at i:58679234 original size:51 final size:51
Alignment explanation
Indices: 58679169--58679284 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
58679159 CTCAAACTTA
* *
58679169 CTTCATACTTCATCTGAAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
58679220 CTTCATATTTCATCTGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
58679271 TTTCATATTTCATC
1 CTTCATATTTCATC
58679285 CAGATAACTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (51 bp):
CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
Found at i:58681488 original size:20 final size:20
Alignment explanation
Indices: 58681459--58681501 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
58681449 GGTTCTAGAA
* *
58681459 GTTGCGTTCTGTCTGTTCTT
1 GTTGCATTCTGTCGGTTCTT
58681479 GTTGCATTCTGTCGGTTCTT
1 GTTGCATTCTGTCGGTTCTT
58681499 GTT
1 GTT
58681502 CTATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.19, G:0.26, T:0.53
Consensus pattern (20 bp):
GTTGCATTCTGTCGGTTCTT
Found at i:58682234 original size:9 final size:9
Alignment explanation
Indices: 58682222--58682251 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
58682212 TGAGGAACAA
58682222 GAGGAGGTG
1 GAGGAGGTG
58682231 GAGGAGGTG
1 GAGGAGGTG
*
58682240 GGGGAGGTG
1 GAGGAGGTG
58682249 GAG
1 GAG
58682252 TGTTTGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.70, T:0.10
Consensus pattern (9 bp):
GAGGAGGTG
Found at i:58684267 original size:94 final size:92
Alignment explanation
Indices: 58684123--58684293 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 92
58684113 TCTCGTAGCT
* **
58684123 GATGCATGTCCCAGACATGACTTACACTGGCTTACGTCTTGAGGCAGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGACTTACACTGGCTTACATAATGAGGCAGATGCATGTCCCAGACATG
*
58684188 TCTTGCACTAGCACTCCTCTCAATGTC
66 TCTTACACTAGCACTCCTCTCAATGTC
* *
58684215 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATGCA-GCCGATGCATGTCCCAGA
1 GATG-CATGTCCCAGACAT-GACTTACACTGGCT-TACATAATG-AGGCAGATGCATGTCCCAGA
58684278 CATGTCTTACACTAGC
62 CATGTCTTACACTAGC
58684294 CCAAAATAGC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
92 4 0.06
93 14 0.20
94 49 0.71
95 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGACTTACACTGGCTTACATAATGAGGCAGATGCATGTCCCAGACATG
TCTTACACTAGCACTCCTCTCAATGTC
Found at i:58686694 original size:27 final size:27
Alignment explanation
Indices: 58686631--58686707 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
58686621 AGAACTACCA
* *
58686631 AAATAAAATAAAATAAAAACAAATAAAC
1 AAAT-AAATAAAAGAAAAAGAAATAAAC
* *
58686659 AAA-ATAATAAAAGATAAAGAAATAAAT
1 AAATA-AATAAAAGAAAAAGAAATAAAC
58686686 AAATAAAT-AAAGAAAAAGAAAT
1 AAATAAATAAAAGAAAAAGAAAT
58686708 GATAAAAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 14 0.33
27 24 0.57
28 4 0.10
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.16
Consensus pattern (27 bp):
AAATAAATAAAAGAAAAAGAAATAAAC
Found at i:58686697 original size:26 final size:27
Alignment explanation
Indices: 58686637--58686707 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
58686627 ACCAAAATAA
* *
58686637 AATAAAATAAAAACAAATAAACAAAAT
1 AATAAAAGAAAAAGAAATAAACAAAAT
* *
58686664 AATAAAAGATAAAGAAATAAA-TAAAT
1 AATAAAAGAAAAAGAAATAAACAAAAT
58686690 AA-ATAAAGAAAAAGAAAT
1 AATA-AAAGAAAAAGAAAT
58686708 GATAAAAGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 1 0.03
26 19 0.50
27 18 0.47
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (27 bp):
AATAAAAGAAAAAGAAATAAACAAAAT
Found at i:58711521 original size:23 final size:22
Alignment explanation
Indices: 58711494--58711545 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
58711484 ATATCCATTA
58711494 GTTTATTCGATCTATCTTCTATTT
1 GTTTATTCGATC-AT-TTCTATTT
* *
58711518 -TTTATTCTATCATTTTTATTT
1 GTTTATTCGATCATTTCTATTT
58711539 GTTTATT
1 GTTTATT
58711546 ATGTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (22 bp):
GTTTATTCGATCATTTCTATTT
Found at i:58711781 original size:17 final size:19
Alignment explanation
Indices: 58711753--58711789 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58711743 GAAAACAAGA
58711753 AAAATAAAGAAA-TTAAGT
1 AAAATAAAGAAATTTAAGT
58711771 AAAAT-AAGAAATTTAAGT
1 AAAATAAAGAAATTTAAGT
58711789 A
1 A
58711790 TAAAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
AAAATAAAGAAATTTAAGT
Found at i:58719584 original size:27 final size:27
Alignment explanation
Indices: 58719556--58719838 Score: 320
Period size: 27 Copynumber: 10.6 Consensus size: 27
58719546 ACATAGCGGT
* * * *
58719556 AAAACAGTCATCTTACCATAAAAGGGT
1 AAAACAGTCATTTTACCACATAAGGGC
*
58719583 AAAATAGTCATTTTACCACATAAGGG-
1 AAAACAGTCATTTTACCACATAAGGGC
* *
58719609 ATAAACAATCATTTTATCAC--AAGGGC
1 A-AAACAGTCATTTTACCACATAAGGGC
* **
58719635 AAAACAGTTATTTTACCTTATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* ** *
58719662 AAAATAGTCATTTTACCATGTAAGAGC
1 AAAACAGTCATTTTACCACATAAGGGC
* * *
58719689 AAAATAATCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
58719716 AAAACAGTCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* * **
58719743 AAAATAGTCATTTTACCATATAAGCAC
1 AAAACAGTCATTTTACCACATAAGGGC
*
58719770 AAAACAGTCATTTTACCACAAAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
58719797 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
58719824 AAAACAGTCATTTTA
1 AAAACAGTCATTTTA
58719839 TCAATTAGGG
Statistics
Matches: 217, Mismatches: 35, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.08
26 2 0.01
27 197 0.91
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
AAAACAGTCATTTTACCACATAAGGGC
Found at i:58719741 original size:81 final size:79
Alignment explanation
Indices: 58719556--58719838 Score: 354
Period size: 81 Copynumber: 3.5 Consensus size: 79
58719546 ACATAGCGGT
* * * * * *
58719556 AAAACAGTCATCTTACCATAAAAGGGTAAAATAGTCATTTTACCACATAAG-GGATAAACAATCA
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAGAGCA-AAACAATCA
*
58719620 TTTTATCACAAGGGC
65 TTTTACCACAAGGGC
* ** * *
58719635 AAAACAGTTATTTTACCTTATAAGGGCAAAATAGTCATTTTACCATGTAAGAGCAAAATAATCAT
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAGAGCAAAACAATCAT
58719700 TTTACCACGTAAGGGC
66 TTTACCAC--AAGGGC
* *
58719716 AAAACAGTCATTTTACCACGTAAGGGCAAAATAGTCATTTTACCATATAAGCA-CAAAACAGTCA
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAG-AGCAAAACAATCA
58719780 TTTTACCACAAAAGGGC
65 TTTTACCAC--AAGGGC
* *
58719797 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTA
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTA
58719839 TCAATTAGGG
Statistics
Matches: 178, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
79 60 0.34
80 2 0.01
81 115 0.65
82 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (79 bp):
AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAGAGCAAAACAATCAT
TTTACCACAAGGGC
Found at i:58721672 original size:16 final size:16
Alignment explanation
Indices: 58721651--58721684 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
58721641 CTTCTCAGAC
58721651 ACTCCTAGAACAAATA
1 ACTCCTAGAACAAATA
58721667 ACTCCTAGAACAAATA
1 ACTCCTAGAACAAATA
58721683 AC
1 AC
58721685 CACTGAAGCA
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:0.50, C:0.26, G:0.06, T:0.18
Consensus pattern (16 bp):
ACTCCTAGAACAAATA
Found at i:58722938 original size:17 final size:17
Alignment explanation
Indices: 58722916--58722965 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
58722906 TATCAAGATA
58722916 AATATTAGATTAAATTT
1 AATATTAGATTAAATTT
*
58722933 AATATTAAGATAATAACTTT
1 AATATT-AGAT--TAAATTT
*
58722953 AATATTAAATTAA
1 AATATTAGATTAA
58722966 TAAAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 3 0.11
20 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AATATTAGATTAAATTT
Found at i:58723025 original size:36 final size:35
Alignment explanation
Indices: 58722956--58723026 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
58722946 TAACTTTAAT
*
58722956 ATTAAATTAATAAAATACTATTAAGAAAGTATTAC
1 ATTAAATTAATAAAATACTATTAAGAAAATATTAC
*
58722991 ATTAAATTTAATATTAA-ACTATTAA-AATAATATTAC
1 ATTAAA-TTAATA-AAATACTATTAAGAA-AATATTAC
58723027 TTTTGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
36 21 0.68
37 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAGAAAATATTAC
Found at i:58726986 original size:13 final size:13
Alignment explanation
Indices: 58726953--58726996 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
58726943 TTTAATTGAA
*
58726953 AAATTAATGTAGTT
1 AAATTAAT-TAATT
*
58726967 AAGTTAATTAATT
1 AAATTAATTAATT
*
58726980 AAATTAATTATTT
1 AAATTAATTAATT
58726993 AAAT
1 AAAT
58726997 AAATAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:58729593 original size:33 final size:35
Alignment explanation
Indices: 58729556--58729632 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 35
58729546 TAAGGTAATA
*
58729556 TAATATTATACCTGTTTTTTATTTT-TTTC-AATT
1 TAATATTATAACTGTTTTTTATTTTATTTCAAATT
*
58729589 TAATATTATAACTTTTTTTTATTTTAGTTTCAAATT
1 TAATATTATAACTGTTTTTTATTTTA-TTTCAAATT
58729625 TATATATT
1 TA-ATATT
58729633 TAAATGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 23 0.61
35 4 0.11
36 6 0.16
37 5 0.13
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (35 bp):
TAATATTATAACTGTTTTTTATTTTATTTCAAATT
Found at i:58731342 original size:20 final size:21
Alignment explanation
Indices: 58731299--58731351 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
58731289 TAGATATTAA
58731299 TAAAAAA-ATAAA--AATCTT
1 TAAAAAATATAAATTAATCTT
*
58731317 TTAAAAATATAAATTAAT-TT
1 TAAAAAATATAAATTAATCTT
*
58731337 TAAAAAGTATAAATT
1 TAAAAAATATAAATT
58731352 TTTGGACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 15 0.52
21 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAATATAAATTAATCTT
Found at i:58733010 original size:16 final size:16
Alignment explanation
Indices: 58732991--58733024 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
58732981 AAGATGTATT
58732991 AAAAATAAATTTTATA
1 AAAAATAAATTTTATA
*
58733007 AAAAATGAATTTTATA
1 AAAAATAAATTTTATA
58733023 AA
1 AA
58733025 TTGTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAAATAAATTTTATA
Found at i:58734840 original size:5 final size:5
Alignment explanation
Indices: 58734830--58734885 Score: 105
Period size: 5 Copynumber: 11.4 Consensus size: 5
58734820 TTATGTTTTA
58734830 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
58734880 A-TAT AT
1 ATTAT AT
58734886 AAACTAAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.08
5 46 0.92
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:58736068 original size:47 final size:48
Alignment explanation
Indices: 58736017--58736120 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 48
58736007 TGTCGGATAT
* * * * * *
58736017 TGTTACTGTTTC-AGGTTCGTTCTAATGAGGTACTGTGTGTATCGTAC
1 TGTTACTGTTTCTAGATTCGTTCCAATGAAGTACTCTGTGTACCATAC
*
58736064 TGTTACTG-TTCTAGATTTGTTCCAATGAAGTACTCTGTGTACCATAC
1 TGTTACTGTTTCTAGATTCGTTCCAATGAAGTACTCTGTGTACCATAC
*
58736111 TGCTACTGTT
1 TGTTACTGTT
58736121 ACTGTTACTG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
46 3 0.06
47 43 0.91
48 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (48 bp):
TGTTACTGTTTCTAGATTCGTTCCAATGAAGTACTCTGTGTACCATAC
Found at i:58736403 original size:18 final size:18
Alignment explanation
Indices: 58736324--58736428 Score: 95
Period size: 18 Copynumber: 5.9 Consensus size: 18
58736314 ACCAATCAAT
*
58736324 TGATTGATACTGAATAAC
1 TGATTGTTACTGAATAAC
* * * *
58736342 TTATTATTATTGAATAAT
1 TGATTGTTACTGAATAAC
58736360 TGATTGTTACTGAATAAC
1 TGATTGTTACTGAATAAC
* *
58736378 TGACTGTTACTGAATAAA
1 TGATTGTTACTGAATAAC
* * * *
58736396 TAATTGTT-TTGATTGAC
1 TGATTGTTACTGAATAAC
*
58736413 TGATTGTTAATGAATA
1 TGATTGTTACTGAATA
58736429 TTACTGATTA
Statistics
Matches: 65, Mismatches: 21, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
17 12 0.18
18 53 0.82
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (18 bp):
TGATTGTTACTGAATAAC
Found at i:58741734 original size:23 final size:22
Alignment explanation
Indices: 58741700--58741773 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
58741690 AAAGTGAATG
58741700 GAATTATATTAAATTGAAAATAT
1 GAATTA-ATTAAATTGAAAATAT
58741723 -ATAGTTAATT-AATT-AAAATAT
1 GA-A-TTAATTAAATTGAAAATAT
*
58741744 GAATTAATTGAAAATTGAAAA-GT
1 GAATTAATT--AAATTGAAAATAT
58741767 GAATTAA
1 GAATTAA
58741774 ATACCCTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
20 6 0.14
21 8 0.19
22 6 0.14
23 16 0.37
24 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (22 bp):
GAATTAATTAAATTGAAAATAT
Found at i:58741750 original size:16 final size:16
Alignment explanation
Indices: 58741729--58741762 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
58741719 ATATATAGTT
58741729 AATTAATT-AAAATATG
1 AATTAATTGAAAAT-TG
58741745 AATTAATTGAAAATTG
1 AATTAATTGAAAATTG
58741761 AA
1 AA
58741763 AAGTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTAATTGAAAATTG
Found at i:58742018 original size:47 final size:47
Alignment explanation
Indices: 58741946--58742052 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 47
58741936 CTGTTACCGT
* * * * * *
58741946 TACTGTTACTATTTCAGATTCGTTCCGATGAGTTACTGTGTGTATCA
1 TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
* *
58741993 TACTGTTACTGTTCCGGATTTGTTCCCATGAGGTACTCTGTGTACCA
1 TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
*
58742040 TACTGCTACTGTT
1 TACTGTTACTGTT
58742053 ACTGTTACTG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (47 bp):
TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
Found at i:58742306 original size:18 final size:18
Alignment explanation
Indices: 58742256--58742361 Score: 81
Period size: 18 Copynumber: 5.9 Consensus size: 18
58742246 AACTGATCAG
* *
58742256 TTGATTGATACTGTATAA
1 TTGATTGTTACTGAATAA
* *
58742274 CTT-ATTATTATTGAATAA
1 -TTGATTGTTACTGAATAA
58742292 TTGATTGTTACTGAATAA
1 TTGATTGTTACTGAATAA
* *
58742310 CTGACTGTTACTGAATAA
1 TTGATTGTTACTGAATAA
* * * *
58742328 ATAATTGTT-CTGATTGA
1 TTGATTGTTACTGAATAA
* *
58742345 CTGATTGTTAATGAATA
1 TTGATTGTTACTGAATA
58742362 TTACTGATTG
Statistics
Matches: 67, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
17 15 0.22
18 50 0.75
19 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (18 bp):
TTGATTGTTACTGAATAA
Found at i:58742325 original size:36 final size:36
Alignment explanation
Indices: 58742256--58742361 Score: 106
Period size: 36 Copynumber: 3.0 Consensus size: 36
58742246 AACTGATCAG
* * * * *
58742256 TTGATTGATACTGTATAACTTATTATTATTGAATAA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
* *
58742292 TTGATTGTTACTGAATAACTGACTGTTACTGAATAA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
* * * *
58742328 ATAATTGTT-CTGATTGACTGATTGTTAATGAATA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATA
58742362 TTACTGATTG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 21 0.36
36 37 0.64
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (36 bp):
TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
Found at i:58742360 original size:35 final size:36
Alignment explanation
Indices: 58742285--58742361 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 36
58742275 TTATTATTAT
* * *
58742285 TGAATAATTGATTGTTACTGAATAACTGACTGTTAC
1 TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
* * *
58742321 TGAATAAATAATTGTT-CTGATTGACTGATTGTTAA
1 TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
58742356 TGAATA
1 TGAATA
58742362 TTACTGATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 21 0.60
36 14 0.40
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (36 bp):
TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
Found at i:58749053 original size:21 final size:21
Alignment explanation
Indices: 58749027--58749071 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
58749017 CGAGATGTGA
58749027 AACATATCATGGATACGATCT
1 AACATATCATGGATACGATCT
58749048 AACATATCATGGATACGATCT
1 AACATATCATGGATACGATCT
58749069 AAC
1 AAC
58749072 TCTGGACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (21 bp):
AACATATCATGGATACGATCT
Found at i:58751567 original size:43 final size:42
Alignment explanation
Indices: 58751466--58751572 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 42
58751456 ATGTGGTTAT
* * *
58751466 ATGTAAGACCATGTCTGGGACATCAACATCGTATTTGATTCG
1 ATGTAAGACCATGTCTGGGACATCAACATCGTATATGAATAG
* * *
58751508 -TGTAAGACCCTCTCTGGGACAGTC-GCATCG-ATATGAGATAG
1 ATGTAAGACCATGTCTGGGACA-TCAACATCGTATATGA-ATAG
58751549 AATGTAAGACCATGTCTGGGACAT
1 -ATGTAAGACCATGTCTGGGACAT
58751573 TGGCATTGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
40 5 0.09
41 26 0.49
42 3 0.06
43 19 0.36
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (42 bp):
ATGTAAGACCATGTCTGGGACATCAACATCGTATATGAATAG
Found at i:58755757 original size:27 final size:27
Alignment explanation
Indices: 58755592--58755775 Score: 122
Period size: 27 Copynumber: 6.9 Consensus size: 27
58755582 TTACCCTATA
* * *
58755592 AGGGTATTTCAGTAATTTTAC-ACTACA
1 AGGGTATTTCGGTAATTTTACAAAT-CG
* * * *
58755619 ATGGTATTTCGATAATTATACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
58755646 GGGGTATTTCAGTAATTTTACAAGTCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
58755673 -GGGTATTTTGGTAGTTTCACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
58755699 AGGATATTTCGATAATTTCACAAAT-T
1 AGGGTATTTCGGTAATTTTACAAATCG
**
58755725 AGGGGTATTTCGGTAATTTTACAACCCG
1 A-GGGTATTTCGGTAATTTTACAAATCG
***
58755753 AGGGTATTTTAATAATTTTACAA
1 AGGGTATTTCGGTAATTTTACAA
58755776 GTCAGGGGTC
Statistics
Matches: 119, Mismatches: 34, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
26 21 0.18
27 95 0.80
28 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAATCG
Found at i:58763317 original size:45 final size:45
Alignment explanation
Indices: 58763268--58763437 Score: 147
Period size: 45 Copynumber: 3.9 Consensus size: 45
58763258 AGGATTTTCG
* *
58763268 ATATGTGTTTTCGTGTAAGACCACGTCAGGGACATTGGCATCGAT
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
* * * * *
58763313 ATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGACATCG-T
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
* *
58763357 AT-T-TGATTT-GTGTAAGACC-CTGTCTGGGATAGTGGCATCG--
1 ATATGTGATTTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGAT
* * ** * *
58763397 ACATGAGATAGCATGTAAGACCATGTCTGGGACATTGGCAT
1 ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCAT
58763438 TGTATGATAT
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 26 0.26
42 7 0.07
43 25 0.25
44 3 0.03
45 37 0.37
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (45 bp):
ATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
Found at i:58775880 original size:15 final size:16
Alignment explanation
Indices: 58775846--58775885 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
58775836 TATATATTCT
58775846 TTTTATTTTAAATTAG
1 TTTTATTTTAAATTAG
*
58775862 TTTTATTTTAATTTA-
1 TTTTATTTTAAATTAG
*
58775877 TTTTCTTTT
1 TTTTATTTT
58775886 CCCAAATCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTATTTTAAATTAG
Found at i:58789179 original size:19 final size:17
Alignment explanation
Indices: 58789155--58789189 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
58789145 AATACTCAAA
58789155 TATTTATTATGGTATGAGG
1 TATTTATT-TGGT-TGAGG
58789174 TATTTATTTGGTTGAG
1 TATTTATTTGGTTGAG
58789190 ATATGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (17 bp):
TATTTATTTGGTTGAGG
Found at i:58791467 original size:29 final size:29
Alignment explanation
Indices: 58791404--58791471 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
58791394 TAATCAACCG
58791404 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
58791433 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
58791462 CGCACACTTA
1 CGCACACTTA
58791472 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:58791583 original size:174 final size:174
Alignment explanation
Indices: 58791293--58791620 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
58791283 AACTCAAGGT
* * *
58791293 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
58791358 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
58791423 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
58791467 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
*
58791532 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
58791597 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
58791621 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:58791612 original size:29 final size:28
Alignment explanation
Indices: 58791573--58791648 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
58791563 CTTAATAATC
58791573 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTG-C-TGTACATTTA
*
58791603 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCTGTAC-ATTTA
58791632 AACCCGCACACTTAGTG
1 AACCCGCACACTTAGTG
58791649 TCAATCTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.79
30 3 0.07
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCTGTACATTTA
Found at i:58797462 original size:13 final size:13
Alignment explanation
Indices: 58797444--58797470 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58797434 CTTAAGGTCT
58797444 ATTTTTTATATAA
1 ATTTTTTATATAA
58797457 ATTTTTTATATAA
1 ATTTTTTATATAA
58797470 A
1 A
58797471 ATATGAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTTATATAA
Found at i:58798472 original size:20 final size:20
Alignment explanation
Indices: 58798447--58798484 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58798437 TTATATATTT
* *
58798447 AATTTTTTTTAAGTTTTAAG
1 AATTTTTTATAAATTTTAAG
58798467 AATTTTTTATAAATTTTA
1 AATTTTTTATAAATTTTA
58798485 GTTATAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTTTTATAAATTTTAAG
Found at i:58806317 original size:13 final size:13
Alignment explanation
Indices: 58806299--58806325 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58806289 CTTAAGGTCT
58806299 ATTTTTTATATAA
1 ATTTTTTATATAA
58806312 ATTTTTTATATAA
1 ATTTTTTATATAA
58806325 A
1 A
58806326 ATATGAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTTATATAA
Found at i:58807327 original size:20 final size:20
Alignment explanation
Indices: 58807302--58807339 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58807292 TTATATATTT
* *
58807302 AATTTTTTTTAAGTTTTAAG
1 AATTTTTTATAAATTTTAAG
58807322 AATTTTTTATAAATTTTA
1 AATTTTTTATAAATTTTA
58807340 GTTATAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTTTTATAAATTTTAAG
Found at i:58817539 original size:24 final size:24
Alignment explanation
Indices: 58817507--58817561 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
58817497 AGAAACTGTA
*
58817507 AGAGTCATTGTCCTTTGCATCTTT
1 AGAGCCATTGTCCTTTGCATCTTT
58817531 AGAGCCATTGTCCTTTGCATCTTT
1 AGAGCCATTGTCCTTTGCATCTTT
58817555 AGAGCCA
1 AGAGCCA
58817562 CCTAAGCACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (24 bp):
AGAGCCATTGTCCTTTGCATCTTT
Found at i:58824996 original size:14 final size:15
Alignment explanation
Indices: 58824973--58825006 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
58824963 TCCAAACTTC
*
58824973 AATTATTTAATT-AT
1 AATTAATTAATTAAT
58824987 AATTAATTAATTAAT
1 AATTAATTAATTAAT
58825002 AATTA
1 AATTA
58825007 GAAAACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAATTAATTAAT
Found at i:58828399 original size:18 final size:18
Alignment explanation
Indices: 58828362--58828400 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
58828352 ATATATATAA
* * *
58828362 ATGTGTATGTGCATATTT
1 ATGTGTACGTGCAAAGTT
58828380 ATGTGTACGTGCAAAGTT
1 ATGTGTACGTGCAAAGTT
58828398 ATG
1 ATG
58828401 AAATATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (18 bp):
ATGTGTACGTGCAAAGTT
Found at i:58828506 original size:24 final size:23
Alignment explanation
Indices: 58828479--58828564 Score: 61
Period size: 24 Copynumber: 3.6 Consensus size: 23
58828469 TTATGTGCAT
58828479 GTATGTATTATAAAGTATATAAA
1 GTATGTATTATAAAGTATATAAA
*
58828502 GGTATATA-TATACAAGGGTATATAAA
1 -GTATGTATTATA-AA--GTATATAAA
* *
58828528 -TAAGTAAGATATAAAGTATAT-AA
1 GTATGT-A-TTATAAAGTATATAAA
*
58828551 GTATGTATTTTAAA
1 GTATGTATTATAAA
58828565 AATATATACA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
22 5 0.10
23 7 0.14
24 21 0.43
25 1 0.02
26 11 0.22
27 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36
Consensus pattern (23 bp):
GTATGTATTATAAAGTATATAAA
Found at i:58830317 original size:27 final size:28
Alignment explanation
Indices: 58830287--58830356 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
58830277 CGGATTTCAA
58830287 CCAAACACACCAGAAT-AAATAATCCTC
1 CCAAACACACCAGAATAAAATAATCCTC
*
58830314 CCAAACACACTAGAATAAAATAATCCTC
1 CCAAACACACCAGAATAAAATAATCCTC
58830342 CCAAACACACCAGAA
1 CCAAACACACCAGAA
58830357 AGACATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 15 0.38
28 25 0.62
ACGTcount: A:0.50, C:0.33, G:0.04, T:0.13
Consensus pattern (28 bp):
CCAAACACACCAGAATAAAATAATCCTC
Found at i:58830573 original size:15 final size:16
Alignment explanation
Indices: 58830541--58830573 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58830531 AAACACACCT
*
58830541 TTCAATTTAATCACAA
1 TTCAAGTTAATCACAA
58830557 TTCAAGTTAAT-ACAA
1 TTCAAGTTAATCACAA
58830572 TT
1 TT
58830574 TCCACTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (16 bp):
TTCAAGTTAATCACAA
Found at i:58831518 original size:18 final size:18
Alignment explanation
Indices: 58831489--58831534 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
58831479 TTGTCTTGAC
* *
58831489 TTAATTTAATTTATTTATT
1 TTAATATAATTTA-ATATT
58831508 TT-ATATAATTTAATATT
1 TTAATATAATTTAATATT
58831525 TTAATATAAT
1 TTAATATAAT
58831535 AAAAATCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATATAATTTAATATT
Found at i:58831686 original size:12 final size:12
Alignment explanation
Indices: 58831669--58831698 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58831659 TAATATCAAT
*
58831669 TTAATATTATTA
1 TTAATATTACTA
58831681 TTAATATTACTA
1 TTAATATTACTA
58831693 TTAATA
1 TTAATA
58831699 AATATCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATATTACTA
Found at i:58836230 original size:33 final size:33
Alignment explanation
Indices: 58836193--58836258 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
58836183 ATCTGACTGG
* *
58836193 CTGGTTGGCTAGATTTTACATTTCGCATCACTA
1 CTGGTTAGCTAGATTTTACATTTCACATCACTA
* * *
58836226 CTGGTTAGCTAGCTTTTGCATTTCACATGACTA
1 CTGGTTAGCTAGATTTTACATTTCACATCACTA
58836259 GGTCCTCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (33 bp):
CTGGTTAGCTAGATTTTACATTTCACATCACTA
Found at i:58839874 original size:28 final size:28
Alignment explanation
Indices: 58839842--58839897 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
58839832 AACTGCTAAG
58839842 CATTAAAGAACTTAATTGATACAATAAT
1 CATTAAAGAACTTAATTGATACAATAAT
*
58839870 CATTAAAGGACTTAATTGATACAATAAT
1 CATTAAAGAACTTAATTGATACAATAAT
58839898 GATATTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (28 bp):
CATTAAAGAACTTAATTGATACAATAAT
Found at i:58849887 original size:67 final size:67
Alignment explanation
Indices: 58849779--58849909 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
58849769 AGAAATTTTC
* *
58849779 AACTGATTCTATAGTACTTGTTGCATTATTAATAGGGTTGAGCTCATAAGCTCAGGACAATGGAG
1 AACTGATTCTATAGTACTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGAG
58849844 GG
66 GG
*
58849846 AACTGATTCTATAGTACTTGTTGCATTATTAGTAGGATTGAGCTCATAAGCTCACGACAATGGA
1 AACTGATTCTATAGTACTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGA
58849910 AGGATGAGTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (67 bp):
AACTGATTCTATAGTACTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGAG
GG
Found at i:58855476 original size:24 final size:24
Alignment explanation
Indices: 58855449--58855495 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
58855439 AAACCTAATT
58855449 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
*
58855473 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTCAAATATATTAT
58855496 AATCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:58855511 original size:24 final size:24
Alignment explanation
Indices: 58855461--58855512 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
58855451 AATCAAAGTC
** **
58855461 AAATATATTATGCTAATAAATGTT
1 AAATATATTATAATAATAAATACT
*
58855485 AAATATATTATAATCATAAATACT
1 AAATATATTATAATAATAAATACT
58855509 AAAT
1 AAAT
58855513 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATAATAATAAATACT
Found at i:58870208 original size:17 final size:17
Alignment explanation
Indices: 58870186--58870218 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
58870176 TTAATTCAAG
58870186 ATAAATCAATCAAAATC
1 ATAAATCAATCAAAATC
58870203 ATAAATCAATCAAAAT
1 ATAAATCAATCAAAAT
58870219 TTATCCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAATCAATCAAAATC
Found at i:58882141 original size:16 final size:16
Alignment explanation
Indices: 58882120--58882152 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58882110 ATATTAACAC
58882120 ATAATTTACTATTTTA
1 ATAATTTACTATTTTA
58882136 ATAATTTACTATTTTA
1 ATAATTTACTATTTTA
58882152 A
1 A
58882153 CACATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAATTTACTATTTTA
Done.