Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 158 of 182
Found at i:48413430 original size:332 final size:333
Alignment explanation
Indices: 48412823--48413469 Score: 1217
Period size: 332 Copynumber: 1.9 Consensus size: 333
48412813 GATGGGGTTA
* * * *
48412823 AAGTCCTGGATTTGTTGAAATTTGAGCTGAACGAGAGCTTGAACCCTACCGGATGTGAGGTTAGA
1 AAGTCCTGCATTTGCTGAAATTTGAGCAGAACGAGAGCTTGAACCCTACCGGATGTGAGGTGAGA
* *
48412888 TGCTTTTAAGGGCTGCTCTTGTACAGCTTATGCTAATATGAATGTAAGTGAGGGCTGCACCAGCT
66 TGCTTTTAAGGACTGCTCTTGTACAGCTTATGCTAATATGAATGTAAGTGAAGGCTGCACCAGCT
48412953 GTTTGATGTGGTTTGGTGACCTCTTTGATATTACTAAAGTTTCAGACATGTACCGAGGAGAAGAT
131 GTTTGATGTGGTTTGGTGACCTCTTTGATATTACTAAAGTTTCAGACATGTACCGAGGAGAAGAT
48413018 GTCTTTATAAGACTCTCAGCTTTAGGTCTAGGTATGCACACTTGCTATGCGTGTTATGCATTTTT
196 GTCTTTATAAGACTCTCAGCTTTAGGTCTAGGTATGCACACTTGCTATGCGTGTTATGCATTTTT
48413083 TCTTGAAGTACTCATGTTTGACAGATATTTGGAATCGAGTAATTCATTATCTTGTTATATTCATC
261 TCTTGAAGTACTCATGTTTGACAGATATTTGGAATCGAGTAATTCATTATCTTGTTATATTCATC
48413148 ATAATTGT
326 ATAATTGT
48413156 AAGTCCTGCATTTGCTGAAATTTGAGCAGAACGAGAGCTTGAACCCTACCGGATGTGAGGCTGA-
1 AAGTCCTGCATTTGCTGAAATTTGAGCAGAACGAGAGCTTGAACCCTACCGGATGTGAGG-TGAG
48413220 ATGC-TTTAAGGACTGCTCTTGTACAGCTTATGCTAATATGAATGTAAGTGAAGGCTGCACCAGC
65 ATGCTTTTAAGGACTGCTCTTGTACAGCTTATGCTAATATGAATGTAAGTGAAGGCTGCACCAGC
48413284 TGTTTGATGTGGTTTGGTGACCTCTTTGATATTACTAAAGTTTCAGACATGTACCGAGGAGAAGA
130 TGTTTGATGTGGTTTGGTGACCTCTTTGATATTACTAAAGTTTCAGACATGTACCGAGGAGAAGA
48413349 TGTCTTTATAAGACTCTCAGCTTTAGGTCTAGGTATGCACACTTGCTATGCGTGTTATGCATTTT
195 TGTCTTTATAAGACTCTCAGCTTTAGGTCTAGGTATGCACACTTGCTATGCGTGTTATGCATTTT
48413414 TTCTTGAAGTACTCATGTTTGACAGATATTTGGAATCGAGTAATTCATTATCTTGT
260 TTCTTGAAGTACTCATGTTTGACAGATATTTGGAATCGAGTAATTCATTATCTTGT
48413470 CTAGGATTAA
Statistics
Matches: 307, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
332 244 0.79
333 61 0.20
334 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (333 bp):
AAGTCCTGCATTTGCTGAAATTTGAGCAGAACGAGAGCTTGAACCCTACCGGATGTGAGGTGAGA
TGCTTTTAAGGACTGCTCTTGTACAGCTTATGCTAATATGAATGTAAGTGAAGGCTGCACCAGCT
GTTTGATGTGGTTTGGTGACCTCTTTGATATTACTAAAGTTTCAGACATGTACCGAGGAGAAGAT
GTCTTTATAAGACTCTCAGCTTTAGGTCTAGGTATGCACACTTGCTATGCGTGTTATGCATTTTT
TCTTGAAGTACTCATGTTTGACAGATATTTGGAATCGAGTAATTCATTATCTTGTTATATTCATC
ATAATTGT
Found at i:48419685 original size:8 final size:8
Alignment explanation
Indices: 48419672--48419700 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
48419662 AATTTCTCAA
48419672 ATCATTGC
1 ATCATTGC
48419680 ATCATTGC
1 ATCATTGC
48419688 ATCATTGC
1 ATCATTGC
48419696 ATCAT
1 ATCAT
48419701 ATCATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (8 bp):
ATCATTGC
Found at i:48420139 original size:20 final size:20
Alignment explanation
Indices: 48420114--48420157 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48420104 ACCATCAGGA
* *
48420114 GCACCGAAGTGCATATAGGG
1 GCACCGAAATGCAAATAGGG
*
48420134 GCACCGAAATGTAAATAGGG
1 GCACCGAAATGCAAATAGGG
48420154 GCAC
1 GCAC
48420158 GAATGTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.14
Consensus pattern (20 bp):
GCACCGAAATGCAAATAGGG
Found at i:48420166 original size:20 final size:19
Alignment explanation
Indices: 48420130--48420209 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 19
48420120 AAGTGCATAT
* *
48420130 AGGGGCACCGAAATGTAAAT
1 AGGGGCA-CGAAGTGTAAAC
48420150 AGGGGCACGAATGTGTAAAC
1 AGGGGCACGAA-GTGTAAAC
** *
48420170 AATGGCACTGTAA-TGCAAAC
1 AGGGGCAC-G-AAGTGTAAAC
48420190 AGGGGCACGAATGTGTAAAC
1 AGGGGCACGAA-GTGTAAAC
48420210 TGAGACACCG
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
18 2 0.04
19 5 0.11
20 37 0.79
21 1 0.02
22 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.16
Consensus pattern (19 bp):
AGGGGCACGAAGTGTAAAC
Found at i:48420194 original size:40 final size:40
Alignment explanation
Indices: 48420133--48420314 Score: 172
Period size: 40 Copynumber: 4.5 Consensus size: 40
48420123 TGCATATAGG
* * *
48420133 GGCACCGAAATGTAAATAGGGGCACGAATGTGTAAACAAT
1 GGCACCGTAATGCAAATAGGGGCACGAATGTGCAAACAAT
* * *
48420173 GGCACTGTAATGCAAACAGGGGCACGAATGTGTAAAC--T
1 GGCACCGTAATGCAAATAGGGGCACGAATGTGCAAACAAT
* * ** *
48420211 GAGACACCGTAATGTAAAGAGGGGCATAAATGTGCAAACAAA
1 G-G-CACCGTAATGCAAATAGGGGCACGAATGTGCAAACAAT
*
48420253 GGCACCGTAATGCAAATAGAAGGCACGAATGTGCAAACAGA-
1 GGCACCGTAATGCAAATAG-GGGCACGAATGTGCAAACA-AT
* * *
48420294 GACACCATAGTGCAAATAGGG
1 GGCACCGTAATGCAAATAGGG
48420315 TCACTTCATC
Statistics
Matches: 116, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 78 0.67
41 33 0.28
42 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.15
Consensus pattern (40 bp):
GGCACCGTAATGCAAATAGGGGCACGAATGTGCAAACAAT
Found at i:48420243 original size:80 final size:81
Alignment explanation
Indices: 48420135--48420299 Score: 224
Period size: 80 Copynumber: 2.0 Consensus size: 81
48420125 CATATAGGGG
* * * * * *
48420135 CACCGAAATGTAAATAGGGGCACGAATGTGTAAACAATGGCACTGTAATGCAAACAG-GGGCACG
1 CACCGAAATGTAAAGAGGGGCACAAATGTGCAAACAAAGGCACCGTAATGCAAACAGAAGGCACG
* *
48420199 AATGTGTAAACTGAGA
66 AATGTGCAAACAGAGA
* * *
48420215 CACCGTAATGTAAAGAGGGGCATAAATGTGCAAACAAAGGCACCGTAATGCAAATAGAAGGCACG
1 CACCGAAATGTAAAGAGGGGCACAAATGTGCAAACAAAGGCACCGTAATGCAAACAGAAGGCACG
48420280 AATGTGCAAACAGAGA
66 AATGTGCAAACAGAGA
48420296 CACC
1 CACC
48420300 ATAGTGCAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 49 0.67
81 24 0.33
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (81 bp):
CACCGAAATGTAAAGAGGGGCACAAATGTGCAAACAAAGGCACCGTAATGCAAACAGAAGGCACG
AATGTGCAAACAGAGA
Found at i:48420287 original size:21 final size:22
Alignment explanation
Indices: 48420239--48420291 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
48420229 GAGGGGCATA
48420239 AATGTGCAAACAAAGGCACCGT
1 AATGTGCAAACAAAGGCACCGT
*
48420261 AA--TGCAAATAGAAGGCA-CG-
1 AATGTGCAAACA-AAGGCACCGT
48420280 AATGTGCAAACA
1 AATGTGCAAACA
48420292 GAGACACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.08
20 9 0.35
21 13 0.50
22 2 0.08
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (22 bp):
AATGTGCAAACAAAGGCACCGT
Found at i:48425259 original size:19 final size:18
Alignment explanation
Indices: 48425213--48425260 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
48425203 TATATTTACT
48425213 ATTAAATTTAACTTTTAA
1 ATTAAATTTAACTTTTAA
* ** *
48425231 AATATTTTTAATTATTTAA
1 ATTAAATTTAACT-TTTAA
48425250 ATTAAATTTAA
1 ATTAAATTTAA
48425261 ACTAGCATGA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTAAATTTAACTTTTAA
Found at i:48438501 original size:20 final size:20
Alignment explanation
Indices: 48438467--48438506 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
48438457 GACAAAACTA
48438467 CTCCCATTGACTAAACAAATC
1 CTCCCATTGACTAAA-AAATC
48438488 CTCCCATT-ACTAAAAAATC
1 CTCCCATTGACTAAAAAATC
48438507 TAATACTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.25
Consensus pattern (20 bp):
CTCCCATTGACTAAAAAATC
Found at i:48442464 original size:23 final size:23
Alignment explanation
Indices: 48442438--48442485 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
48442428 ATTAAGCTAC
48442438 ATCGATAATCAAGATTAAAGCCT
1 ATCGATAATCAAGATTAAAGCCT
* *
48442461 ATCGATGATCAAGATTAAAGTCT
1 ATCGATAATCAAGATTAAAGCCT
48442484 AT
1 AT
48442486 TTACTATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (23 bp):
ATCGATAATCAAGATTAAAGCCT
Found at i:48449404 original size:2 final size:2
Alignment explanation
Indices: 48449386--48449436 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
48449376 AGTAAAATAC
*
48449386 AT AT CAT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48449429 AT AT AT AT
1 AT AT AT AT
48449437 CTAAAACCGT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48453386 original size:18 final size:16
Alignment explanation
Indices: 48453363--48453397 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
48453353 TCATATTATC
48453363 TTGAAATAAATTAAAAAA
1 TTGAAA-AAA-TAAAAAA
48453381 TTGAAAAAATAAAAAA
1 TTGAAAAAATAAAAAA
48453397 T
1 T
48453398 AGCAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
TTGAAAAAATAAAAAA
Found at i:48456264 original size:213 final size:213
Alignment explanation
Indices: 48455897--48457404 Score: 2219
Period size: 213 Copynumber: 7.1 Consensus size: 213
48455887 CAAGTCTCTG
* * * * *
48455897 AAGAGATTTCAATTCATAAAAGCTGTCAGGAAGGCAAATAAGGTTTTCACAATTGTTCAAT-TCC
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCT-C
*
48455961 AAAT-CATTAAGACCAATAAGATTGTCAATTGAGGATGGTAATGT-CTTCAAAGCCGTTCCGCTT
65 AAATAC-TCAAGACCAATAAGATTGTCAATTGAGGATGGTAAT-TCCTTCAAAGCCGTTCCGCTT
* * *
48456024 AAATCAAGATACCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAATCTCCAATCTCGAGCA
128 AAATCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCA
* *
48456089 ACCTTGAAGATTGAATATCTC
193 ACCTTGAAGGTCGAATATCTC
*
48456110 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCA
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
* *
48456175 AGTACTCAAGACCAATACGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
* *
48456240 TCAAGATCCCTCAACCTCTCCATGGTTTCCAAGATATCTGGGAAAGTCTCCAATCTTGAGCAACC
131 TCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAACC
* * *
48456305 -TGCAAGGTCGAATTTTTG
196 TTG-AAGGTCGAATATCTC
* *
48456323 AAGAGATTTCAATTTATAAAGACTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
* * *
48456388 AAAACTCAAGACCAATAAGATTGTCAATTGATGATGGTAATGT-CTTCAAAGCCGTTCTGCTTAA
66 AATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAAT-TCCTTCAAAGCCGTTCCGCTTAA
* * *
48456452 ATCAAGATCCCCCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAATCTCCAATCTCGAGCAAC
130 ATCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAAC
* * *
48456517 CTTGAAGATTGAATAGCTC
195 CTTGAAGGTCGAATATCTC
48456536 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
* *
48456601 AA-ACCTCAAGACCAATAAGATTGTCAATTGGGGATGGTAATTCCTTCAAAGCCGTTCCCCTTAA
66 AATA-CTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
* *
48456665 ATCAAGATACCTCAACCTCTCCATGGTGTCCAAGATATT-TGGGAAAGTCTCCAATCTCGAGCAA
130 ATCAAGATCCCTCAACCTCTCCATGGTGTCCAAGAT-TTCTGGGAAAGTCTCCAATCTTGAGCAA
*
48456729 CC-TGCAAGGTCGAATTTCTC
194 CCTTG-AAGGTCGAATATCTC
* *
48456749 AAGAGATTTCAATTTATAAAGGCTGCCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATGTCA
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
* * *
48456814 AATACTCAAGACCAATAAGATTGTCAATTGGGGATGGTAATTCTTTCAAAGCCGCTCCGCTTAAA
66 AATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
* *
48456879 CCAAGATCCCTCAACGTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAACC
131 TCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAACC
** * *
48456944 TCCAAGGTAGAATATTTC
196 TTGAAGGTCGAATATCTC
* * *
48456962 AAGAGATTTCAATTCATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
* * * *
48457027 AATCCTTAAGACCTATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTTCGCTTAAA
66 AATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
* * * * * *
48457092 TCCAGATCCCTCAACCTCTCCATGGTGTCCAAAATTTCTGGGAAAATCTCCAATTTTGTGCAATC
131 TCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAACC
*
48457157 -TGCAAGGTCGAATTTCTC
196 TTG-AAGGTCGAATATCTC
48457175 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
*
48457240 AA-ACCTCAAGACCAATAAGATTGTCAATTGGGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
66 AATA-CTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
* * *
48457304 ATCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTTTGGGAAAGTATCCAATCTTGAGCAAT
130 ATCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAAC
* ** * *
48457369 GTCCAAGAAT-GAATACCTC
195 CTTGAAG-GTCGAATATCTC
48457388 AAGAGATTTCAATTTAT
1 AAGAGATTTCAATTTAT
48457405 GAATACTTGT
Statistics
Matches: 1167, Mismatches: 111, Indels: 34
0.89 0.08 0.03
Matches are distributed among these distances:
212 9 0.01
213 1149 0.98
214 9 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (213 bp):
AAGAGATTTCAATTTATAAAGGCTGTCAGGGAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
AATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
TCAAGATCCCTCAACCTCTCCATGGTGTCCAAGATTTCTGGGAAAGTCTCCAATCTTGAGCAACC
TTGAAGGTCGAATATCTC
Found at i:48465130 original size:121 final size:119
Alignment explanation
Indices: 48464949--48465165 Score: 328
Period size: 121 Copynumber: 1.8 Consensus size: 119
48464939 TGCTTTAACC
* * *
48464949 GACACTAATATTTTTTATCAGATAAAAAATATTTGACATTGACCATTGCATGATCGACACCCCTT
1 GACACTAATATTTTTTATCAGATAAAAAAAATTTGACATTAACCATTGCATGAGCGACACCCCTT
* *
48465014 TTTGTCAGATAAAAAATTTAAATATTTTGGTATTGGCCATCGCATGGATTAATT
66 TTTGTCAAATAAAAAATTAAAATATTTTGGTATTGGCCATCGCATGGATTAATT
* *
48465068 GACACTAGTATTTTTTTATCAGATAAAAAAAATTTTA-ATGTTAACCATTGCATGAGCGACACCC
1 GACACTAATA-TTTTTTATCAGATAAAAAAAATTTGACA--TTAACCATTGCATGAGCGACACCC
*
48465132 CTTTTTGTCAAATAAAAAATTAAAATTTTTTGGT
63 CTTTTTGTCAAATAAAAAATTAAAATATTTTGGT
48465166 GTTAATCATT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
119 10 0.11
120 24 0.28
121 53 0.61
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (119 bp):
GACACTAATATTTTTTATCAGATAAAAAAAATTTGACATTAACCATTGCATGAGCGACACCCCTT
TTTGTCAAATAAAAAATTAAAATATTTTGGTATTGGCCATCGCATGGATTAATT
Found at i:48466420 original size:26 final size:25
Alignment explanation
Indices: 48466386--48466436 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
48466376 TGATTTTATA
*
48466386 TATTTTAAA-ATTTTATTAATTATTTT
1 TATTATAAATATTTT-TTAATT-TTTT
48466412 TATTATAAATATTTTTTAATTTTTT
1 TATTATAAATATTTTTTAATTTTTT
48466437 AGATTGCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 14 0.61
27 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTATAAATATTTTTTAATTTTTT
Found at i:48466581 original size:21 final size:19
Alignment explanation
Indices: 48466557--48466602 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
48466547 TAATATTTTC
*
48466557 TATTTTTGAAATGTTTTTATA
1 TATTTTTG-AAT-TTTTAATA
48466578 TATTTTTGAATTTTTAATA
1 TATTTTTGAATTTTTAATA
48466597 T-TTTTT
1 TATTTTT
48466603 ACAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 3 0.12
21 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TATTTTTGAATTTTTAATA
Found at i:48466602 original size:28 final size:29
Alignment explanation
Indices: 48466529--48466613 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
48466519 ATGTAAGATA
48466529 TATTTTTGAAT-TTTTTTATAATATTTTC
1 TATTTTTGAATATTTTTTATAATATTTTC
48466557 TATTTTTGAA-ATGTTTTTAT-ATATTTT-
1 TATTTTTGAATAT-TTTTTATAATATTTTC
*
48466584 TGAATTTTT-AATATTTTTTACAAATATTTT
1 T--ATTTTTGAATATTTTTTA-TAATATTTT
48466614 TTACATTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
27 1 0.02
28 26 0.53
29 15 0.31
30 7 0.14
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (29 bp):
TATTTTTGAATATTTTTTATAATATTTTC
Found at i:48466602 original size:29 final size:28
Alignment explanation
Indices: 48466529--48466602 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
48466519 ATGTAAGATA
*
48466529 TATTTTTGAATTTTTTTATAATATTTTC
1 TATTTTTAAATTTTTTTATAATATTTTC
*
48466557 TATTTTTGAAATGTTTTTAT-ATATTTT-
1 TATTTTT-AAATTTTTTTATAATATTTTC
48466584 TGAATTTTTAATATTTTTT
1 T--ATTTTTAA-ATTTTTT
48466603 ACAAATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 1 0.03
28 16 0.41
29 22 0.56
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (28 bp):
TATTTTTAAATTTTTTTATAATATTTTC
Found at i:48466611 original size:13 final size:13
Alignment explanation
Indices: 48466593--48466618 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48466583 TTGAATTTTT
48466593 AATATTTTTTACA
1 AATATTTTTTACA
48466606 AATATTTTTTACA
1 AATATTTTTTACA
48466619 TTTTCGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTTTTACA
Found at i:48466613 original size:29 final size:29
Alignment explanation
Indices: 48466530--48466613 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
48466520 TGTAAGATAT
* *
48466530 ATTTTTGAAT-TTTTTTATAATATTTTCT
1 ATTTTTGAATATTTTTTAAAATATTTTCA
* *
48466558 ATTTTTGAA-ATGTTTTT-ATATATTTTTGA
1 ATTTTTGAATAT-TTTTTAAAATA-TTTTCA
48466587 ATTTTT-AATATTTTTTACAAATATTTT
1 ATTTTTGAATATTTTTTA-AAATATTTT
48466614 TTACATTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 20 0.44
29 21 0.47
30 4 0.09
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (29 bp):
ATTTTTGAATATTTTTTAAAATATTTTCA
Found at i:48472827 original size:55 final size:53
Alignment explanation
Indices: 48472699--48472829 Score: 122
Period size: 55 Copynumber: 2.4 Consensus size: 53
48472689 AGCCAACACA
* *
48472699 AATTTTTTATCTAACAAAATATGTCAATCATGCTATAGCCAACACAAAAAAATT
1 AATTTTTTATCTAA-AAAAAATGTCAACCATGCTATAGCCAACACAAAAAAATT
* * * **
48472753 AATTTTTTACCAGATAAAAAAATGTCAACCATGC-A-ACGACTAACAACAAAAATTTT
1 AATTTTTTATC-TA-AAAAAAATGTCAACCATGCTATA-G-CCAAC-ACAAAAAAATT
48472809 GAATTTTTTATCTAAAAAAAA
1 -AATTTTTTATCTAAAAAAAA
48472830 ACATCGACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
53 1 0.02
54 12 0.19
55 28 0.45
56 11 0.18
57 10 0.16
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (53 bp):
AATTTTTTATCTAAAAAAAATGTCAACCATGCTATAGCCAACACAAAAAAATT
Found at i:48476705 original size:13 final size:13
Alignment explanation
Indices: 48476689--48476715 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48476679 AACATTAACG
48476689 GTTAATGGTTAAA
1 GTTAATGGTTAAA
48476702 GTTAATGGTTAAA
1 GTTAATGGTTAAA
48476715 G
1 G
48476716 GGTCTTTTTA
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:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (13 bp):
GTTAATGGTTAAA
Found at i:48476777 original size:41 final size:41
Alignment explanation
Indices: 48476730--48476833 Score: 124
Period size: 41 Copynumber: 2.5 Consensus size: 41
48476720 TTTTTATGTG
*
48476730 TTTTATGATTTTTATAGAA-TTTTAC-AATTTTTTATAATTTT
1 TTTTATGATTTTTATAAAATTTTTACTAA-TTTTTA-AATTTT
* *
48476771 TTTTATGATTTTTATAAAATTTTTTCTAATTTTTAATTTTT
1 TTTTATGATTTTTATAAAATTTTTACTAATTTTTAAATTTT
*
48476812 TTTTAT-ATTTTTAGTGAAATTT
1 TTTTATGATTTTTA-TAAAATTT
48476834 AATATTTGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
40 7 0.12
41 36 0.64
42 11 0.20
43 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (41 bp):
TTTTATGATTTTTATAAAATTTTTACTAATTTTTAAATTTT
Found at i:48476782 original size:10 final size:10
Alignment explanation
Indices: 48476749--48476823 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
48476739 TTTTATAGAA
*
48476749 TTTTACAATT
1 TTTTATAATT
48476759 TTTTATAATTTT
1 TTTTATAA--TT
*
48476771 TTTTATGATT
1 TTTTATAATT
*
48476781 TTTATAAAATT
1 TTT-TATAATT
*
48476792 TTTTCTAATT
1 TTTTATAATT
* **
48476802 TTTAATTTTT
1 TTTTATAATT
48476812 TTTTAT-ATT
1 TTTTATAATT
48476821 TTT
1 TTT
48476824 AGTGAAATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
9 5 0.10
10 28 0.56
11 8 0.16
12 9 0.18
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (10 bp):
TTTTATAATT
Found at i:48476782 original size:21 final size:20
Alignment explanation
Indices: 48476758--48476824 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
48476748 ATTTTACAAT
48476758 TTTTTATAATTTTTTTTATGA
1 TTTTTATAATTTTTTTTAT-A
*
48476779 TTTTTATAAAATTTTTTCTA-A
1 TTTTTAT--AATTTTTTTTATA
*
48476800 TTTTTA-ATTTTTTTTTATA
1 TTTTTATAATTTTTTTTATA
48476819 TTTTTA
1 TTTTTA
48476825 GTGAAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.22
19 7 0.17
21 14 0.35
23 10 0.25
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (20 bp):
TTTTTATAATTTTTTTTATA
Found at i:48477168 original size:90 final size:86
Alignment explanation
Indices: 48476959--48477219 Score: 282
Period size: 90 Copynumber: 3.0 Consensus size: 86
48476949 ATGGTCAAAT
* *
48476959 GGCCTTTTTGATGCATTT-AACAGTTCAAGTACCCAATTGAATG-AAAAAAATCAAGGGCTTAAT
1 GGCCTTTTTGATGCATTTGAA-AGTTCAAGTACCCAATTGAATGAAAAAAAAGCTAGGGCTTAAT
*
48477022 TGCTTTTTCTTAAAAAAGTTTGA
65 TGCTTTTT-TGAAAAAAGTTTGA
* * * *
48477045 GG-ATCTTTTCATGCATTTGAAAGTTCAAATACCCAATTGAGTGAAAAAGAAGAAGCTAGGGCTT
1 GGCCT-TTTTGATGCATTTGAAAGTTCAAGTACCCAATTGAATG-AAAA-AA-AAGCTAGGGCTT
48477109 AATTGCTTTTTTGAAAAAA-TTTGAA
62 AATTGCTTTTTTGAAAAAAGTTTG-A
* *
48477134 GGCCTTTTTGATGCATTGTGAATGTTTAAGTACCCAATTGAATGCAAAAAATAAG-TAGAGGCTT
1 GGCCTTTTTGATGCATT-TGAAAGTTCAAGTACCCAATTGAATG-AAAAAA-AAGCTAG-GGCTT
**
48477198 AATTTTTTTTTTG-AAAAAGTTT
62 AATTGCTTTTTTGAAAAAAGTTT
48477220 AAGAGTTTTG
Statistics
Matches: 147, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
85 1 0.01
86 34 0.23
87 2 0.01
88 15 0.10
89 47 0.32
90 48 0.33
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (86 bp):
GGCCTTTTTGATGCATTTGAAAGTTCAAGTACCCAATTGAATGAAAAAAAAGCTAGGGCTTAATT
GCTTTTTTGAAAAAAGTTTGA
Found at i:48477209 original size:89 final size:87
Alignment explanation
Indices: 48476959--48477219 Score: 284
Period size: 89 Copynumber: 3.0 Consensus size: 87
48476949 ATGGTCAAAT
*
48476959 GGCCTTTTTGATGCATTT-AACAGTTCAAGTACCCAATTGAATGAAAAAAATCA--AGGGCTTAA
1 GGCCTTTTTGATGCATTTGAA-AGTTCAAGTACCCAATTGAATGAAAAAAATAAGTAGGGCTTAA
*
48477021 TTGCTTTTTCTT-AAAAAAGTTTGA
65 TT--TTTTTTTTGAAAAAAGTTTGA
* * * * *
48477045 GG-ATCTTTTCATGCATTTGAAAGTTCAAATACCCAATTGAGTGAAAAAGAAGAAGCTAGGGCTT
1 GGCCT-TTTTGATGCATTTGAAAGTTCAAGTACCCAATTGAATGAAAAA-AATAAG-TAGGGCTT
**
48477109 AATTGCTTTTTTGAAAAAA-TTTGAA
63 AATTTTTTTTTTGAAAAAAGTTTG-A
* * *
48477134 GGCCTTTTTGATGCATTGTGAATGTTTAAGTACCCAATTGAATGCAAAAAATAAGTAGAGGCTTA
1 GGCCTTTTTGATGCATT-TGAAAGTTCAAGTACCCAATTGAATGAAAAAAATAAGTAG-GGCTTA
48477199 ATTTTTTTTTTG-AAAAAGTTT
64 ATTTTTTTTTTGAAAAAAGTTT
48477220 AAGAGTTTTG
Statistics
Matches: 144, Mismatches: 19, Indels: 21
0.78 0.10 0.11
Matches are distributed among these distances:
85 1 0.01
86 39 0.27
87 5 0.03
88 17 0.12
89 44 0.31
90 38 0.26
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (87 bp):
GGCCTTTTTGATGCATTTGAAAGTTCAAGTACCCAATTGAATGAAAAAAATAAGTAGGGCTTAAT
TTTTTTTTTGAAAAAAGTTTGA
Found at i:48478581 original size:103 final size:103
Alignment explanation
Indices: 48478401--48478607 Score: 254
Period size: 103 Copynumber: 2.0 Consensus size: 103
48478391 AGTTTGTGTG
** * *
48478401 AGTCGCACTGGCTGATACATGGGCGTGCTCCCAAACCGTGTAACTCACTGTTTTGAGGATAGGGT
1 AGTCGCACTGGCTGATACACAGGAGTGCTCCCAAACCGTGTAACTCACTGTTTTAAGGATAGGGT
* * * *
48478466 CGCATGACCAGGCACAT-AGGCGTGTGTCAGGCTATGTA
66 CGCACGACCAGGCACATGA-GCATGTGCCAGGCCATGTA
* ** * *
48478504 AGTCGCACTGGCTGATACACAGGAGTGCTCCCAGATTGTGTAACTCATTGTTTTAAGGATATGGT
1 AGTCGCACTGGCTGATACACAGGAGTGCTCCCAAACCGTGTAACTCACTGTTTTAAGGATAGGGT
* **
48478569 TGCACGGGCAGGCACATGAGCATGTGCCAGGCCATGTA
66 CGCACGACCAGGCACATGAGCATGTGCCAGGCCATGTA
48478607 A
1 A
48478608 AGCCATATGA
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
103 86 0.99
104 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (103 bp):
AGTCGCACTGGCTGATACACAGGAGTGCTCCCAAACCGTGTAACTCACTGTTTTAAGGATAGGGT
CGCACGACCAGGCACATGAGCATGTGCCAGGCCATGTA
Found at i:48485860 original size:3 final size:3
Alignment explanation
Indices: 48485852--48485877 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48485842 CTTCGATCAT
48485852 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
48485878 AAGAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:48486164 original size:105 final size:103
Alignment explanation
Indices: 48485984--48486183 Score: 328
Period size: 105 Copynumber: 1.9 Consensus size: 103
48485974 TAGCCTTGCA
* * * *
48485984 TTTGCTTCACTCTTAGAAACTTGTAGGCAGAGTAGTACTACTTTACAGTGCGAAAGCGTGTGGGA
1 TTTGCTTCACTCTTAGAAACTTGTAGGCAGAGTAGTACTACTTAACAGTGCAAAACCGAGTGGGA
48486049 CATTCACATTGAAAATAGTTGTACCACTTTTAAGAGCG
66 CATTCACATTGAAAATAGTTGTACCACTTTTAAGAGCG
* *
48486087 TTTGCTTCTCTCTTAGAAACTTGTAGGTAGAGAGTAGTACTACTTAACAGTGCAAAACCGAGTGG
1 TTTGCTTCACTCTTAGAAACTTGTAGG--CAGAGTAGTACTACTTAACAGTGCAAAACCGAGTGG
48486152 GACATTCACATTGAAAATAGTTGTACCACTTT
64 GACATTCACATTGAAAATAGTTGTACCACTTT
48486184 GCAAACCAAT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 26 0.29
105 63 0.71
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (103 bp):
TTTGCTTCACTCTTAGAAACTTGTAGGCAGAGTAGTACTACTTAACAGTGCAAAACCGAGTGGGA
CATTCACATTGAAAATAGTTGTACCACTTTTAAGAGCG
Found at i:48486727 original size:29 final size:30
Alignment explanation
Indices: 48486642--48486730 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
48486632 GATTAAATCA
* *
48486642 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGCACC
* ** *
48486672 ACAATTAAAGTTTCACGTGCATAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGCACC
*
48486703 AAATTAAAG-TTCATGTATACAATTGCAC
1 AAATTAAAGTTTCAAGTATACAATTGCAC
48486731 ATTAAATCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 15 0.31
30 9 0.19
31 24 0.50
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGCACC
Found at i:48490723 original size:24 final size:23
Alignment explanation
Indices: 48490688--48490735 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
48490678 TAATCTTTGT
* *
48490688 AAAAATTCTTAAAAATTATAAAA
1 AAAAATTATTAAAAAATATAAAA
48490711 AAAAATTAATTAAAAAATATAAAA
1 AAAAATT-ATTAAAAAATATAAAA
48490735 A
1 A
48490736 TTATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAATTATTAAAAAATATAAAA
Found at i:48494634 original size:6 final size:6
Alignment explanation
Indices: 48494586--48494663 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
48494576 CATTTTTGGG
* ***
48494586 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTTT TTTAAA GTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA
* *
48494635 -TTAAA GATTAAA TTTAAA TTTGAA TTTAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAA
48494664 TAAAAAGAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 10 0.18
6 32 0.57
7 14 0.25
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:48494663 original size:18 final size:18
Alignment explanation
Indices: 48494585--48494654 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
48494575 TCATTTTTGG
*
48494585 GTTTAAATTT-AATTTAA
1 GTTTAAATTTAAATTAAA
***
48494602 GTTTAAACTTTTTTTTTAAA
1 GTTTAAA--TTTAAATTAAA
48494622 GTTTAAATTTAAATTAAA
1 GTTTAAATTTAAATTAAA
*
48494640 GATTAAATTTAAATT
1 GTTTAAATTTAAATT
48494655 TGAATTTAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
17 7 0.16
18 22 0.51
19 3 0.07
20 11 0.26
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (18 bp):
GTTTAAATTTAAATTAAA
Found at i:48495449 original size:3 final size:3
Alignment explanation
Indices: 48495441--48495468 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48495431 TAACTGTTTT
48495441 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
48495469 GTTATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:48495502 original size:13 final size:13
Alignment explanation
Indices: 48495462--48495507 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
48495452 ATAATAATAA
48495462 TAAT-AATGTTAT
1 TAATAAATGTTAT
*
48495474 TAAAAAATGTTAT
1 TAATAAATGTTAT
48495487 TAATAAATGGTT-T
1 TAATAAAT-GTTAT
48495500 TAATAAAT
1 TAATAAAT
48495508 ATTAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (13 bp):
TAATAAATGTTAT
Found at i:48496651 original size:29 final size:29
Alignment explanation
Indices: 48496610--48496883 Score: 149
Period size: 28 Copynumber: 9.4 Consensus size: 29
48496600 GAAGGTCCCT
*
48496610 AAACTGTCCAAAAATTATATTTTGACC-CTG
1 AAACT-TCTAAAAATTATATTTTGACCTC-G
*
48496640 -AACTTCTAAAAATTACATTTTTGACCTCG
1 AAACTTCTAAAAATTATA-TTTTGACCTCG
* * * *
48496669 AAACTTCCAAAAATTACATTTTGACCCCCC
1 AAACTTCTAAAAATTATATTTTGA-CCTCG
48496699 AAACTTCTAAAAATTCCAT-TTTTGACCTCG
1 AAACTTCTAAAAATT--ATATTTTGACCTCG
* *
48496729 AAACTTCTAAAAAATATATTTT-ATCC-CC
1 AAACTTCTAAAAATTATATTTTGA-CCTCG
** *
48496757 AAACTT-TCAAAAATTCCATTTT-ACCCCCG
1 AAACTTCT-AAAAATTATATTTTGA-CCTCG
* **
48496786 -AACTTCCAAAAATTCCATTTT-ACCCTC-
1 AAACTTCTAAAAATTATATTTTGA-CCTCG
* * *
48496813 AAACTTCCAAAAATTCCAT-TTTTAACC-CTA
1 AAACTTCTAAAAATT--ATATTTTGACCTC-G
* * * * *
48496843 AAACTTCCAAAAATTACATTTTTACCCCC
1 AAACTTCTAAAAATTATATTTTGACCTCG
48496872 AAACTTCTAAAA
1 AAACTTCTAAAA
48496884 TTCCATTTTT
Statistics
Matches: 201, Mismatches: 24, Indels: 39
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.00
28 75 0.37
29 50 0.25
30 68 0.34
31 6 0.03
32 1 0.00
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCTAAAAATTATATTTTGACCTCG
Found at i:48496659 original size:28 final size:27
Alignment explanation
Indices: 48496606--48496943 Score: 205
Period size: 30 Copynumber: 11.6 Consensus size: 27
48496596 CTTCGAAGGT
* *
48496606 CCCTAAACTGTCCAAAAATTATATTTTGA
1 CCCTAAACT-TCTAAAAATTACATTTT-A
*
48496635 CCCTGAACTTCTAAAAATTACATTTTTGA
1 CCCTAAACTTCTAAAAATTACA-TTTT-A
* *
48496664 CCTCGAAACTTCCAAAAATTACATTTTGA
1 CC-CTAAACTTCTAAAAATTACATTTT-A
* *
48496693 CCCCCCAAACTTCTAAAAATTCCATTTTTGA
1 --CCCTAAACTTCTAAAAATTACA-TTTT-A
* * *
48496724 CCTCGAAACTTCTAAAAAATATATTTTA
1 CC-CTAAACTTCTAAAAATTACATTTTA
* *
48496752 TCCCCAAACTT-TCAAAAATTCCATTTTA
1 -CCCTAAACTTCT-AAAAATTACATTTTA
** * *
48496780 CCCCCGAACTTCCAAAAATTCCATTTTA
1 -CCCTAAACTTCTAAAAATTACATTTTA
* *
48496808 CCCTCAAACTTCCAAAAATTCCATTTTTAA
1 CCCT-AAACTTCTAAAAATTACA-TTTT-A
*
48496838 CCCTAAAACTTCCAAAAATTACATTTTTA
1 CCCT-AAACTTCTAAAAATTACA-TTTTA
* *
48496867 CCCCCAAACTTCT-AAAATTCCATTTTTTAAA
1 -CCCTAAACTTCTAAAAATTACA--TTTT--A
*
48496898 CCCTGAAACTTATAAAAATTACCATTTTA
1 CCCT-AAACTTCTAAAAATTA-CATTTTA
48496927 CCCCTAAA-TGTCTAAAA
1 -CCCTAAACT-TCTAAAA
48496944 TATCATTTTT
Statistics
Matches: 257, Mismatches: 31, Indels: 42
0.78 0.09 0.13
Matches are distributed among these distances:
27 4 0.02
28 81 0.32
29 57 0.22
30 87 0.34
31 20 0.08
32 6 0.02
33 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (27 bp):
CCCTAAACTTCTAAAAATTACATTTTA
Found at i:48496984 original size:59 final size:60
Alignment explanation
Indices: 48496668--48496956 Score: 230
Period size: 60 Copynumber: 4.9 Consensus size: 60
48496658 TTTTGACCTC
** *
48496668 GAAACTTCCAAAAATTA-CATTTTGACCCCCCAAACTTCTAAAAATTCCA-TTTTT-GA-CCT
1 GAAACTTATAAAAATTACCATTTT-A-CCCCCAAACTTCT-AAAATTCCATTTTTTAAACCCT
* * * * * * *
48496727 CGAAACTTCTAAAAAATA-TATTTTATCCCCAAACTTTCAAAAATTCCA--TTTT-ACCCCC
1 -GAAACTTATAAAAATTACCATTTTACCCCCAAAC-TTCTAAAATTCCATTTTTTAAACCCT
** * *
48496785 G-AACTTCCAAAAATT-CCATTTTACCCTCAAACTTCCAAAAATTCCA-TTTTT-AACCCT
1 GAAACTTATAAAAATTACCATTTTACCCCCAAACTT-CTAAAATTCCATTTTTTAAACCCT
* **
48496842 AAAACTTCCAAAAATTA-CATTTTTACCCCCAAACTTCTAAAATTCCATTTTTTAAACCCT
1 GAAACTTATAAAAATTACCA-TTTTACCCCCAAACTTCTAAAATTCCATTTTTTAAACCCT
*
48496902 GAAACTTATAAAAATTACCATTTTACCCCTAAA-TGTCTAAAATAT-CATTTTTTAA
1 GAAACTTATAAAAATTACCATTTTACCCCCAAACT-TCTAAAAT-TCCATTTTTTAA
48496957 CTCTAAATTT
Statistics
Matches: 194, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
55 2 0.01
56 36 0.19
57 13 0.07
58 45 0.23
59 25 0.13
60 70 0.36
61 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (60 bp):
GAAACTTATAAAAATTACCATTTTACCCCCAAACTTCTAAAATTCCATTTTTTAAACCCT
Found at i:48497003 original size:28 final size:28
Alignment explanation
Indices: 48496971--48497044 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
48496961 AAATTTTTTG
48496971 AAAATTACCATTTTGCCCTCAAAAGTCC
1 AAAATTACCATTTTGCCCTCAAAAGTCC
*
48496999 AAAATTACCATTTTGCACTCAAAAGTCC
1 AAAATTACCATTTTGCCCTCAAAAGTCC
48497027 AAAATTACCATTTTGCCC
1 AAAATTACCATTTTGCCC
48497045 CTGGGCATCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTCAAAAGTCC
Found at i:48498539 original size:24 final size:24
Alignment explanation
Indices: 48498490--48498552 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
48498480 AATTTTTGAC
* *
48498490 GTTTGCAATATTCTGGCGAACAAG
1 GTTTGCAATATTATGGAGAACAAG
**
48498514 GTTTGCAATATTATGGAGAATTAG
1 GTTTGCAATATTATGGAGAACAAG
* *
48498538 GTTCGCAACATTATG
1 GTTTGCAATATTATG
48498553 ACGAACCAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (24 bp):
GTTTGCAATATTATGGAGAACAAG
Found at i:48499642 original size:16 final size:17
Alignment explanation
Indices: 48499623--48499661 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
48499613 TAAATGATTT
48499623 TTTTATTAA-TTTTTAA
1 TTTTATTAACTTTTTAA
48499639 TTTT-TTAACTTTTTAA
1 TTTTATTAACTTTTTAA
48499655 TTTTATT
1 TTTTATT
48499662 TAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTAACTTTTTAA
Found at i:48499645 original size:8 final size:8
Alignment explanation
Indices: 48499623--48499674 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
48499613 TAAATGATTT
48499623 TTTTATTAA
1 TTTT-TTAA
48499632 -TTTTTAA
1 TTTTTTAA
48499639 TTTTTTAA
1 TTTTTTAA
*
48499647 CTTTTTAA
1 TTTTTTAA
48499655 TTTTATTTAA
1 -TTT-TTTAA
48499665 TATTTTTAA
1 T-TTTTTAA
48499674 T
1 T
48499675 AAATTGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 4 0.11
8 17 0.46
9 9 0.24
10 7 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTTTAA
Found at i:48501730 original size:213 final size:213
Alignment explanation
Indices: 48501363--48502815 Score: 1917
Period size: 213 Copynumber: 6.8 Consensus size: 213
48501353 TAAGATGCAA
* *
48501363 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
* * * * **
48501428 AATCCTCAAGACAAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGTTGCTCCACTTAAA
66 AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGTTCTGCTTAAA
* *
48501493 TAAAGATAT-TTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
131 TCAAGAT-TCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
*
48501557 CTTCAAGATCTAATCTCTT
195 CTTCAAGATCTAATCTCTC
48501576 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
* *
48501641 AATCCTCAAGACCAGTAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGCTCCT-CTTAA
66 AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCG-TTCTGCTTAA
* * *
48501705 ATTAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCAAACAAC
130 ATCAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
48501770 CTTCAAGATCTAATCTCTC
195 CTTCAAGATCTAATCTCTC
* * * * * *
48501789 AAGAGATTTCAATTTATAAAAGTTGTGAGGAAGGTAAATACGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
*
48501854 AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCCTCAAAG-CTGTTCTGCTTAA
66 AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTC-GTTCTGCTTAA
** *
48501918 ATCAAGAACCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTTGAGCAAC
130 ATCAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
* *
48501983 CATCAAGAT-TGAATATCTC
195 CTTCAAGATCT-AATCTCTC
* * * * *
48502002 AAGAGATTTCAATTTATAAAAGCTGTCAGGGAGGAAAACAAGGTCTTT-ACAGCTT-CTCATACT
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGT-TTTCACAG-TTGATCAAACT
*
48502065 CAAATCCTCAAGACCAATAAGATTCTCAATTGAGGATGGTAATTCCTTCAAAGTCGTT-TCGCTT
64 CAAATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGTTCT-GCTT
** *
48502129 AAATCAAGAAACCTCAACCTCTCCATGGTGTCCATGATTTCTGGGAAAATCTCCAATCTCGAGCA
128 AAATCAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCA
* *
48502194 ACCTTGAAGAT-TCAATATCTC
193 ACCTTCAAGATCT-AATCTCTC
* * * *
48502215 GAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGAACAATA-AC
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAA-ACTC
** * * *
48502279 AAAGACTTAAGACCAATAAGATTGTCAATTGAGGATGGTAACTCCTTCAAAGCCGTTCTGCTTAA
65 AAATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGTTCTGCTTAA
* * * * *
48502344 ATCAAGATACCACAACCTCTCCATGATGTCCATGACTTCTGGGAAAATCTCCAATCTCAAACAAC
130 ATCAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
* *
48502409 CTCCAAGTTCTAATCTCTC
195 CTTCAAGATCTAATCTCTC
* * * * *
48502428 AAGAGATTTCAATTTATAATAGTTGTGAGGAAGGCAAATAAGGTTTTCACAGTCGACCAAACTCA
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
* * *
48502493 AATTCTCAAGGCCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCTGCTTAAA
66 AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGTTCTGCTTAAA
* *
48502558 TCAAGA-TCACTCAATCTCTCCATCGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
131 TCAAGATTC-CTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
* *
48502622 CATCAAGATCGAATAC-CTC
195 CTTCAAGATCTAAT-CTCTC
* * * * *
48502641 GAGAGATTTCAATTTATAAAAGCTGTTAGGAAGGCAAACAAGGTTTTCACAGTTGCTCAATCTCA
1 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
* * * * * * *
48502706 AATGCTCAATACCAATAAGGTGGTCAATTGAGGATGTTAATTCTTTCAAAGCCGTAT-TG-TATA
66 AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGT-TCTGCT-TA
* ** * * * *
48502769 AAACAAGAACCCTTAACTTCTCCATGGTGTCCAAGATTTCT-GGAAAA
129 AATCAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAA
48502816 CTAAACAGAT
Statistics
Matches: 1101, Mismatches: 119, Indels: 41
0.87 0.09 0.03
Matches are distributed among these distances:
212 21 0.02
213 1067 0.97
214 13 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (213 bp):
AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGATCAAACTCA
AATCCTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGTCGTTCTGCTTAAA
TCAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAACC
TTCAAGATCTAATCTCTC
Found at i:48502588 original size:639 final size:639
Alignment explanation
Indices: 48501363--48502815 Score: 2159
Period size: 639 Copynumber: 2.3 Consensus size: 639
48501353 TAAGATGCAA
* *
48501363 AAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCTCA
1 AAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGCTCAATCTCA
* * * * *
48501428 AATCCTCAAGACAAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGTTGCTCCACTTAAA
66 AATCCTCAAGACCAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGTCGTTTCGCTTAAA
* * ** *
48501493 TAAAGATATTTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAACC
131 TCAAGAAACCTCAACCTCTCCATGGTGTCCATGATTTCTGGGAAAATCTCCAATCTCGAGCAACC
* * *
48501558 TTCAAGATCTAATCTCTTAAGAGATTTCAATTTATAAAAGTTGTCAGGAAGGCAAACAAGGTTTT
196 TTCAAGATCTAATATCTCAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTT
* * ** * *
48501623 CACAGTTGATCAAACTCAAATCCTCAAGACCAGTAAGATTGTCAATTGAGGATGGTAATTCCTTC
261 CACAGTTGAACAAACACAAAGACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAACTCCTTC
* * * * *
48501688 AAAGTCGCTCCTCTTAAATTAAGATTCCTCAACCTCTCCATGGTGTCCATGACTTCTGGGAAAAT
326 AAAGCCGCTCCTCTTAAATCAAGATACCACAACCTCTCCATGATGTCCATGACTTCTGGGAAAAT
*
48501753 CTCCAATCTCAAACAACCTTCAAGATCTAATCTCTCAAGAGATTTCAATTTATAAAAGTTGTGAG
391 CTCCAATCTCAAACAACCTCCAAGATCTAATCTCTCAAGAGATTTCAATTTATAAAAGTTGTGAG
* * * ** *
48501818 GAAGGTAAATACGGTTTTCACAGTTGTTCAATCTCAAATCCTCAAGACCAATAAGATTGTCAATT
456 GAAGGCAAATAAGGTTTTCACAGTCGACCAAACTCAAATCCTCAAGACCAATAAGATTGTCAATT
* * *
48501883 GAGGATGGTAATTCCCTCAAAGCTGTTCTGCTTAAATCAAGAACCCTCAACCTCTCCATGGTGTC
521 GAGGATGGTAATTCCCTCAAAGCCGTTCTGCTTAAATCAAGAACACTCAACCTCTCCATCGTGTC
* * *
48501948 CATGACTTCTGGGAAAATCTCCAATCTTGAGCAACCATCAAGATTGAATATCTC
586 CATGACTTCTGGGAAAATCTCCAATCTCGAGCAACCATCAAGATCGAATACCTC
* *
48502002 AAGAGATTTCAATTTATAAAAGCTGTCAGGGAGGAAAACAAGGTCTTT-ACAGCTT-CTC-ATAC
1 AAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGT-TTTCACAG-TTGCTCAAT-C
*
48502064 TCAAATCCTCAAGACCAATAAGATTCTCAATTGAGGATGGTAATTCCTTCAAAGTCGTTTCGCTT
63 TCAAATCCTCAAGACCAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGTCGTTTCGCTT
48502129 AAATCAAGAAACCTCAACCTCTCCATGGTGTCCATGATTTCTGGGAAAATCTCCAATCTCGAGCA
128 AAATCAAGAAACCTCAACCTCTCCATGGTGTCCATGATTTCTGGGAAAATCTCCAATCTCGAGCA
* *
48502194 ACCTTGAAGAT-TCAATATCTCGAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGG
193 ACCTTCAAGATCT-AATATCTCAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGG
*
48502258 TTTTCACAGTTGAACAATA-ACAAAGACTTAAGACCAATAAGATTGTCAATTGAGGATGGTAACT
257 TTTTCACAGTTGAACAA-ACACAAAGACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAACT
*
48502322 CCTTCAAAGCCG-TTCTGCTTAAATCAAGATACCACAACCTCTCCATGATGTCCATGACTTCTGG
321 CCTTCAAAGCCGCTCCT-CTTAAATCAAGATACCACAACCTCTCCATGATGTCCATGACTTCTGG
* *
48502386 GAAAATCTCCAATCTCAAACAACCTCCAAGTTCTAATCTCTCAAGAGATTTCAATTTATAATAGT
385 GAAAATCTCCAATCTCAAACAACCTCCAAGATCTAATCTCTCAAGAGATTTCAATTTATAAAAGT
* *
48502451 TGTGAGGAAGGCAAATAAGGTTTTCACAGTCGACCAAACTCAAATTCTCAAGGCCAATAAGATTG
450 TGTGAGGAAGGCAAATAAGGTTTTCACAGTCGACCAAACTCAAATCCTCAAGACCAATAAGATTG
* * *
48502516 TCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCTGCTTAAATCAAGATCACTCAATCTCTCCAT
515 TCAATTGAGGATGGTAATTCCCTCAAAGCCGTTCTGCTTAAATCAAGAACACTCAACCTCTCCAT
48502581 CGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAACCATCAAGATCGAATACCTC
580 CGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAACCATCAAGATCGAATACCTC
* *
48502641 GAGAGATTTCAATTTATAAAAGCTGTTAGGAAGGCAAACAAGGTTTTCACAGTTGCTCAATCTCA
1 AAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGCTCAATCTCA
* * * ** * * *
48502706 AATGCTCAATACCAATAAGGTGGTCAATTGAGGATGTTAATTCTTTCAAAGCCGTATT-G-TATA
66 AATCCTCAAGACCAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGTCGT-TTCGCT-TA
* * * * *
48502769 AAACAAGAACCCTTAACTTCTCCATGGTGTCCAAGATTTCT-GGAAAA
129 AATCAAGAAACCTCAACCTCTCCATGGTGTCCATGATTTCTGGGAAAA
48502816 CTAAACAGAT
Statistics
Matches: 733, Mismatches: 70, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
638 18 0.02
639 705 0.96
640 10 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (639 bp):
AAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTGCTCAATCTCA
AATCCTCAAGACCAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGTCGTTTCGCTTAAA
TCAAGAAACCTCAACCTCTCCATGGTGTCCATGATTTCTGGGAAAATCTCCAATCTCGAGCAACC
TTCAAGATCTAATATCTCAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTT
CACAGTTGAACAAACACAAAGACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAACTCCTTC
AAAGCCGCTCCTCTTAAATCAAGATACCACAACCTCTCCATGATGTCCATGACTTCTGGGAAAAT
CTCCAATCTCAAACAACCTCCAAGATCTAATCTCTCAAGAGATTTCAATTTATAAAAGTTGTGAG
GAAGGCAAATAAGGTTTTCACAGTCGACCAAACTCAAATCCTCAAGACCAATAAGATTGTCAATT
GAGGATGGTAATTCCCTCAAAGCCGTTCTGCTTAAATCAAGAACACTCAACCTCTCCATCGTGTC
CATGACTTCTGGGAAAATCTCCAATCTCGAGCAACCATCAAGATCGAATACCTC
Found at i:48504903 original size:23 final size:23
Alignment explanation
Indices: 48504859--48504904 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48504849 AAAAAAAATT
***
48504859 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCAAATAACTCGAA
*
48504882 TAACTCGATTCAAATAATTCGAA
1 TAACTCGATTCAAATAACTCGAA
48504905 ATTCGAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCAAATAACTCGAA
Found at i:48511380 original size:30 final size:29
Alignment explanation
Indices: 48511346--48511404 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
48511336 GAATTGAATC
48511346 AAATCAAAATTGCATGTATAAAATTGTACA
1 AAATCAAAATT-CATGTATAAAATTGTACA
* * * *
48511376 AAATCAACATTTATGTGTACAATTGTACA
1 AAATCAAAATTCATGTATAAAATTGTACA
48511405 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTCATGTATAAAATTGTACA
Found at i:48511503 original size:22 final size:21
Alignment explanation
Indices: 48511478--48511547 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
48511468 TGCATTTAAA
48511478 TTATAAATAATATATTATTATG
1 TTATAAAT-ATATATTATTATG
* * * *
48511500 TTATTTACTATATAGTATTATT
1 TTA-TAAATATATATTATTATG
48511522 TTATAAATCATAT-TT-TTA-G
1 TTATAAAT-ATATATTATTATG
48511541 TTATAAA
1 TTATAAA
48511548 GTTTATCGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 7 0.18
20 3 0.08
21 4 0.11
22 21 0.55
23 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATAAATATATATTATTATG
Found at i:48514265 original size:29 final size:31
Alignment explanation
Indices: 48514200--48514269 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
48514190 ACTATAAAAA
* **
48514200 TAGTCACTTTTGTTTGACTTAGATTACATTT
1 TAGTCACTTATGTTTGAAATAGATTACATTT
*
48514231 TAGTCACTTATGTTTGAAAT-G-TTACGTTT
1 TAGTCACTTATGTTTGAAATAGATTACATTT
48514260 TAGTCACTTA
1 TAGTCACTTA
48514270 CGTTATCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.49
30 1 0.03
31 17 0.49
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (31 bp):
TAGTCACTTATGTTTGAAATAGATTACATTT
Found at i:48514427 original size:18 final size:18
Alignment explanation
Indices: 48514404--48514446 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
48514394 TTTACCGTTG
48514404 TAATTAATTTAAATAT-TT
1 TAATTAA-TTAAATATATT
*
48514422 TAATTAATTAAATTTATT
1 TAATTAATTAAATATATT
48514440 TAATTAA
1 TAATTAA
48514447 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAATATATT
Found at i:48516555 original size:29 final size:28
Alignment explanation
Indices: 48516481--48516571 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
48516471 TCGATATTGT
* * *
48516481 TTTTAATTATATTTTAAATTTTTTTAAAAA
1 TTTTAATAATATTTT-AA-TATTTTATAAA
* *
48516511 TTTTAA-ATTTTATTTAATACTTTTATAAA
1 TTTTAATAATAT-TTTAATA-TTTTATAAA
48516540 TTTTAATAATATTTTACATA-TTTATAAA
1 TTTTAATAATATTTTA-ATATTTTATAAA
48516568 TTTT
1 TTTT
48516572 TTAAAGATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
28 13 0.26
29 22 0.44
30 15 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAATAATATTTTAATATTTTATAAA
Found at i:48521182 original size:15 final size:15
Alignment explanation
Indices: 48521162--48521195 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48521152 TTGCTTTCTT
48521162 TTTTCTTTTGTGAAA
1 TTTTCTTTTGTGAAA
* *
48521177 TTTTCTTTTTTGAAG
1 TTTTCTTTTGTGAAA
48521192 TTTT
1 TTTT
48521196 TTTAAGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (15 bp):
TTTTCTTTTGTGAAA
Found at i:48527380 original size:190 final size:189
Alignment explanation
Indices: 48527057--48527417 Score: 704
Period size: 190 Copynumber: 1.9 Consensus size: 189
48527047 CATAAAATAT
*
48527057 TGAATATCAGTGCTCCCACATCAAAAAATAACTATGGGACTATAGAATGAATAAAGGTCTAACAT
1 TGAATATCAGTGCTCCCACATCAAAAAATAACTATGGGACTATAGAATGAATAAAGCTCTAACAT
48527122 CTAAACCTTTATGGAATCAAAGTGATAACCCCAAGGAGAATGTAATTTTGGTGTAAATGTTTGTT
66 CTAAACCTTTATGGAATCAAAGTGATAACCCCAAGGAGAATGTAATTTTGGTGTAAATGTTTGTT
48527187 AATTTTTTTAAGGAATCAAATATGAACGGGGAGGAGATAAGAATTGATGAGCACCTTTAG
131 AATTTTTTTAAGGAATCAAATATGAAC-GGGAGGAGATAAGAATTGATGAGCACCTTTAG
48527247 TGAATATCAGTGCTCCCACATCAAAAAATAACTATGGGACTATAGAATGAATAAAGCTCTAACAT
1 TGAATATCAGTGCTCCCACATCAAAAAATAACTATGGGACTATAGAATGAATAAAGCTCTAACAT
48527312 CTAAACCTTTATGGAATCAAAGTGATAACCCCAAGGAGAATGTAATTTTGGTGTAAATGTTTGTT
66 CTAAACCTTTATGGAATCAAAGTGATAACCCCAAGGAGAATGTAATTTTGGTGTAAATGTTTGTT
48527377 AATTTTTTTAAGGAATCAAATATGAACGGGAGGAGATAAGA
131 AATTTTTTTAAGGAATCAAATATGAACGGGAGGAGATAAGA
48527418 GACTGTCAAG
Statistics
Matches: 170, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
189 14 0.08
190 156 0.92
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (189 bp):
TGAATATCAGTGCTCCCACATCAAAAAATAACTATGGGACTATAGAATGAATAAAGCTCTAACAT
CTAAACCTTTATGGAATCAAAGTGATAACCCCAAGGAGAATGTAATTTTGGTGTAAATGTTTGTT
AATTTTTTTAAGGAATCAAATATGAACGGGAGGAGATAAGAATTGATGAGCACCTTTAG
Found at i:48528267 original size:19 final size:19
Alignment explanation
Indices: 48528243--48528280 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48528233 CAACTAAGGA
48528243 AATAATATCTCTTAATTAG
1 AATAATATCTCTTAATTAG
48528262 AATAATATCTCTTAATTAG
1 AATAATATCTCTTAATTAG
48528281 CATCTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (19 bp):
AATAATATCTCTTAATTAG
Found at i:48529433 original size:22 final size:22
Alignment explanation
Indices: 48529403--48529446 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
48529393 GCTCTGATGC
*
48529403 CATGTTGAAATTAGAGAAGAAT
1 CATGATGAAATTAGAGAAGAAT
*
48529425 CATGATGAAATTAGAGATGAAT
1 CATGATGAAATTAGAGAAGAAT
48529447 ACTCTAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (22 bp):
CATGATGAAATTAGAGAAGAAT
Found at i:48540703 original size:3 final size:3
Alignment explanation
Indices: 48540697--48540731 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
48540687 ATTATTAGTC
48540697 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
48540732 CCCTTCCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:48553149 original size:18 final size:18
Alignment explanation
Indices: 48553128--48553191 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
48553118 TATTTTCATG
48553128 AAAATATATATTAAGTTA
1 AAAATATATATTAAGTTA
* * *
48553146 AAAATAT-TATCCAAACCCTTG
1 AAAATATATAT--TAA--GTTA
48553167 AAAATATATATTAAGTTA
1 AAAATATATATTAAGTTA
48553185 AAAATAT
1 AAAATAT
48553192 TATCCAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 3 0.09
18 16 0.46
19 2 0.06
20 2 0.06
21 9 0.26
22 3 0.09
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAATATATATTAAGTTA
Found at i:48553170 original size:39 final size:39
Alignment explanation
Indices: 48553126--48553205 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
48553116 CTTATTTTCA
48553126 TGAAAATATATATTAAGTTAAAAATATTATCCAAACCCT
1 TGAAAATATATATTAAGTTAAAAATATTATCCAAACCCT
*
48553165 TGAAAATATATATTAAGTTAAAAATATTATCCAAATCCT
1 TGAAAATATATATTAAGTTAAAAATATTATCCAAACCCT
48553204 TG
1 TG
48553206 TACTATTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.35
Consensus pattern (39 bp):
TGAAAATATATATTAAGTTAAAAATATTATCCAAACCCT
Found at i:48553657 original size:19 final size:18
Alignment explanation
Indices: 48553610--48553648 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
48553600 CCTACGATTC
48553610 ATTGAATTTCACCTTTTT
1 ATTGAATTTCACCTTTTT
48553628 ATTGAATTTCACCTTTTT
1 ATTGAATTTCACCTTTTT
48553646 ATT
1 ATT
48553649 ATTCTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTGAATTTCACCTTTTT
Found at i:48584008 original size:20 final size:20
Alignment explanation
Indices: 48583985--48584031 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
48583975 TTTCAGAGGT
48583985 ATCGATAATTTTCATTAAAA
1 ATCGATAATTTTCATTAAAA
* ** *
48584005 ATCGATACTTTTTTTTTAAA
1 ATCGATAATTTTCATTAAAA
48584025 ATCGATA
1 ATCGATA
48584032 GCACGAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (20 bp):
ATCGATAATTTTCATTAAAA
Found at i:48593149 original size:15 final size:13
Alignment explanation
Indices: 48593129--48593179 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 13
48593119 ATTGAATGAA
48593129 ATTTTTAATATATAT
1 ATTTTTAAT-TAT-T
*
48593144 ATTTTTATTTTATT
1 ATTTTTA-ATTATT
48593158 ATTTTTAATTATT
1 ATTTTTAATTATT
*
48593171 -TATTTAATT
1 ATTTTTAATT
48593180 GAGCTTGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 8 0.25
13 5 0.16
14 8 0.25
15 10 0.31
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTAATTATT
Found at i:48593160 original size:14 final size:15
Alignment explanation
Indices: 48593129--48593175 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
48593119 ATTGAATGAA
48593129 ATTTTTAATATATAT
1 ATTTTTAATATATAT
* *
48593144 ATTTTTATTTTAT-T
1 ATTTTTAATATATAT
*
48593158 ATTTTTAAT-TATTT
1 ATTTTTAATATATAT
48593172 ATTT
1 ATTT
48593176 AATTGAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 11 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTAATATATAT
Found at i:48608139 original size:18 final size:18
Alignment explanation
Indices: 48608103--48608141 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
48608093 TTTTCATAGT
* *
48608103 ATTAATTTTTATTTGAAA
1 ATTAATTTTTATATAAAA
48608121 ATTAATTTTTATATAAAA
1 ATTAATTTTTATATAAAA
48608139 ATT
1 ATT
48608142 TAAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTAATTTTTATATAAAA
Found at i:48608166 original size:25 final size:26
Alignment explanation
Indices: 48608102--48608173 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 26
48608092 TTTTTCATAG
*
48608102 TATTAATTTTTATTTGAAAATTAATTTT
1 TATT-ATTTTAATTT-AAAATTAATTTT
***
48608130 TA-TATAAAAATTTAAAATT-ATTTT
1 TATTATTTTAATTTAAAATTAATTTT
48608154 TATTATTTTAATTATAAAAT
1 TATTATTTTAATT-TAAAAT
48608174 ACTTATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
24 7 0.20
25 13 0.37
26 12 0.34
27 1 0.03
28 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TATTATTTTAATTTAAAATTAATTTT
Found at i:48610081 original size:266 final size:266
Alignment explanation
Indices: 48609606--48610132 Score: 860
Period size: 266 Copynumber: 2.0 Consensus size: 266
48609596 TGCCCAGCTT
*
48609606 AATTTACTATTTAATAATTAAAAATATATAATTGTTAATATTTTTTCATGGTTGTTTTGCCATTT
1 AATTTACTATTTAATAATTAAAAATATATAATTGTTAATATTTTTTCAGGGTTGTTTTGCCATTT
* * * *
48609671 TTTTCCCTTCACTAGCGAACAGAAGTATCAGTTAATTTTAATTTCTAAGTCTTTGTTTCTTTTAA
66 TTTTCCCTTCACTAGCAAACAGAAGTATCAGTTAAATTTAATTTCTAACTCTTTATTTCTTTTAA
* *
48609736 CTTTCACAAATGGTGAGAAAATTTTTACTTGTTCTCGAAATATTTCTTGTTATTGCTTCCTATTT
131 CTTTCACAAATGCTGAGAAAATTTTTACTTGTTCTCGAAATATTTCTTGTTATTGCTTCCTATCT
*
48609801 TTTCTCCTTTTCAACTTTTTCTTGAAAATTTATCCATATGCTTTTAATTTTCTTCATGATTAAGA
196 TTTCTCCGTTTCAACTTTTTCTTGAAAATTTATCCATATGCTTTTAATTTTCTTCATGATTAAGA
48609866 TAAACA
261 TAAACA
* *
48609872 AATTTACTATTTAATAATTAAAAATATATAATTGTTAATTTTTTTTCAGGGTTGTTTTGCGA-TT
1 AATTTACTATTTAATAATTAAAAATATATAATTGTTAATATTTTTTCAGGGTTGTTTTGCCATTT
* *
48609936 TTTTCCTTTCACTAGCAAACAGAAGTATCAAG-TAAATTTAATTTTTAACTCTTTATTTCTTTTA
66 TTTTCCCTTCACTAGCAAACAGAAGTATC-AGTTAAATTTAATTTCTAACTCTTTATTTCTTTTA
* ** *
48610000 ACTTTCACAAATGCTGAGAAAATTTTTGCTTTGTTCTTTAAATATTTTTTGTTATTGCTTCCTAT
130 ACTTTCACAAATGCTGAGAAAATTTTTAC-TTGTTCTCGAAATATTTCTTGTTATTGCTTCCTAT
* *
48610065 CTTTTCTCCGTTTCAACTTTTTCTTGAAAATTTATTCATATGCTTTTAATTTTTTTCATGATTAA
194 CTTTTCTCCGTTTCAACTTTTTCTTGAAAATTTATCCATATGCTTTTAATTTTCTTCATGATTAA
48610130 GAT
259 GAT
48610133 GCACAATAAA
Statistics
Matches: 241, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
265 84 0.35
266 157 0.65
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (266 bp):
AATTTACTATTTAATAATTAAAAATATATAATTGTTAATATTTTTTCAGGGTTGTTTTGCCATTT
TTTTCCCTTCACTAGCAAACAGAAGTATCAGTTAAATTTAATTTCTAACTCTTTATTTCTTTTAA
CTTTCACAAATGCTGAGAAAATTTTTACTTGTTCTCGAAATATTTCTTGTTATTGCTTCCTATCT
TTTCTCCGTTTCAACTTTTTCTTGAAAATTTATCCATATGCTTTTAATTTTCTTCATGATTAAGA
TAAACA
Found at i:48617153 original size:81 final size:82
Alignment explanation
Indices: 48617000--48617163 Score: 240
Period size: 81 Copynumber: 2.0 Consensus size: 82
48616990 ATTGAATGGA
* * * *
48617000 TTTAAAATATAATTTTTTTATCAATTGAGTATTAGTTTTGTTGGGTATTGAAATTATTGTCAGCG
1 TTTAAAATATAAGTTTCTTATCAATTGAGTATTAGTTTTGTTGGATATTGAAATTATTATCAGCG
**
48617065 T-TGAAAAAATATAAAT
66 TAAAAAAAAATATAAAT
* *
48617081 TTTAAATTATAAGTTTCTTATCAATTGAGTATTAGTTTTGTTGGATATTGAAATTATTATCAGTG
1 TTTAAAATATAAGTTTCTTATCAATTGAGTATTAGTTTTGTTGGATATTGAAATTATTATCAGCG
*
48617146 TAAAAAAAAATATGAAT
66 TAAAAAAAAATATAAAT
48617163 T
1 T
48617164 CGATCACGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 60 0.82
82 13 0.18
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (82 bp):
TTTAAAATATAAGTTTCTTATCAATTGAGTATTAGTTTTGTTGGATATTGAAATTATTATCAGCG
TAAAAAAAAATATAAAT
Found at i:48635024 original size:33 final size:30
Alignment explanation
Indices: 48634966--48635030 Score: 76
Period size: 33 Copynumber: 2.1 Consensus size: 30
48634956 ACAAATTAGT
* * *
48634966 CATCACTATCAGATAAACAACCATTTACTA
1 CATCACTATCAGAAAAACAAACATTTAATA
48634996 CATCACTATCAGACCAAGAACAAACATTTAATA
1 CATCACTATCAGA--AA-AACAAACATTTAATA
48635029 CA
1 CA
48635031 ACACATGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 13 0.45
32 1 0.03
33 15 0.52
ACGTcount: A:0.46, C:0.26, G:0.05, T:0.23
Consensus pattern (30 bp):
CATCACTATCAGAAAAACAAACATTTAATA
Found at i:48635254 original size:17 final size:18
Alignment explanation
Indices: 48635226--48635262 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
48635216 CATAAATATC
48635226 TATATAATGCATAAACAA
1 TATATAATGCATAAACAA
48635244 TATAT-ATGCATAAACAA
1 TATATAATGCATAAACAA
48635261 TA
1 TA
48635263 GGTAATGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (18 bp):
TATATAATGCATAAACAA
Found at i:48636905 original size:81 final size:80
Alignment explanation
Indices: 48636810--48636960 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 80
48636800 TTGATCCTCT
* * *
48636810 TAAAAATGATAAATTTTTATTTAATCTTTTAAAAATTAAATTTTTACTATCATAAAAATTACAAT
1 TAAAAATGATAAATTTTAATTTAATCATTTAAAAATTAAATTTTTACCATCATAAAAATTACAAT
48636875 TTAACATTGCCCGTC
66 TTAACATTGCCCGTC
*
48636890 TAAAAATGATAAAATTTTAATTTAATCATTTAAAAATTATATTTTTACCATCATAAAAATTACAA
1 TAAAAATGAT-AAATTTTAATTTAATCATTTAAAAATTAAATTTTTACCATCATAAAAATTACAA
48636955 TTTAAC
65 TTTAAC
48636961 TTCGGCCCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 10 0.15
81 56 0.85
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.42
Consensus pattern (80 bp):
TAAAAATGATAAATTTTAATTTAATCATTTAAAAATTAAATTTTTACCATCATAAAAATTACAAT
TTAACATTGCCCGTC
Found at i:48637757 original size:31 final size:31
Alignment explanation
Indices: 48637722--48637781 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
48637712 TTTTTGGTCC
*
48637722 AATTTGATA-CTCAAATTTGACACATTTTTCT
1 AATTTGATATCT-AAACTTGACACATTTTTCT
*
48637753 AATTTGATATCTAAACTTGACACTTTTTT
1 AATTTGATATCTAAACTTGACACATTTTT
48637782 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.47
Consensus pattern (31 bp):
AATTTGATATCTAAACTTGACACATTTTTCT
Found at i:48638100 original size:29 final size:29
Alignment explanation
Indices: 48638000--48638102 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
48637990 TTTATAAATA
*
48638000 TAGGTACCAAATT-GAATCTAAAAAAAGTT
1 TAGGTACCAAATTAG-ATCAAAAAAAAGTT
*
48638029 TAGGTACCAAATTAGGA--AAAAATGTCAAGTT
1 TAGGTACCAAATTA-GATCAAAAA---AAAGTT
*
48638060 TAGGTACGAAATTAGATCAAAAAAAAGTT
1 TAGGTACCAAATTAGATCAAAAAAAAGTT
*
48638089 TAGGTATCAAATTA
1 TAGGTACCAAATTA
48638103 AAAAAATGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
28 4 0.07
29 30 0.49
30 3 0.05
31 19 0.31
32 5 0.08
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.27
Consensus pattern (29 bp):
TAGGTACCAAATTAGATCAAAAAAAAGTT
Found at i:48638116 original size:60 final size:59
Alignment explanation
Indices: 48638000--48638111 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 59
48637990 TTTATAAATA
*
48638000 TAGGTACCAAATTGAATCTAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTT
1 TAGGTACCAAATTGAATCAAAAAAAAGTTTAGGTACCAAATTA-GAAAAAATGTCAAGTT
* *
48638060 TAGGTACGAAATT-AGATCAAAAAAAAGTTTAGGTATCAAATTA-AAAAAATGT
1 TAGGTACCAAATTGA-ATCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGT
48638112 GTCAAATTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
58 9 0.19
59 1 0.02
60 38 0.79
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (59 bp):
TAGGTACCAAATTGAATCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAGTT
Found at i:48645300 original size:13 final size:13
Alignment explanation
Indices: 48645282--48645309 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48645272 AAAACATGCC
48645282 TTTATAATTTTAA
1 TTTATAATTTTAA
48645295 TTTATAATTTTAA
1 TTTATAATTTTAA
48645308 TT
1 TT
48645310 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATAATTTTAA
Found at i:48646338 original size:56 final size:56
Alignment explanation
Indices: 48646274--48646399 Score: 191
Period size: 56 Copynumber: 2.2 Consensus size: 56
48646264 TTGATTTCTT
* * *
48646274 TATCCGTAAGGATATTATTGAAAAGGGATATCCACAAAT-ATATCAATGAAAAGGAA
1 TATCCGTAAGGATATTATTAAAAAAGGATATCCAC-AATGATATCAATGAAAAAGAA
* *
48646330 TATTCGTAAGGATATTATTAAAAAAGGATATCCGCAATGATATCAATGAAAAAGAA
1 TATCCGTAAGGATATTATTAAAAAAGGATATCCACAATGATATCAATGAAAAAGAA
48646386 TATCCGTAAGGATA
1 TATCCGTAAGGATA
48646400 CCATGAAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 3 0.05
56 60 0.95
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.26
Consensus pattern (56 bp):
TATCCGTAAGGATATTATTAAAAAAGGATATCCACAATGATATCAATGAAAAAGAA
Found at i:48646450 original size:29 final size:28
Alignment explanation
Indices: 48646274--48646529 Score: 157
Period size: 28 Copynumber: 9.1 Consensus size: 28
48646264 TTGATTTCTT
* * *
48646274 TATCCGTAAGGATATTATTGAAAAGGGA
1 TATCCGAAAGGATATCATTGAAAAGGTA
** * *
48646302 TATCC-ACAAATATATCAATGAAAAGGAA
1 TATCCGA-AAGGATATCATTGAAAAGGTA
* * * *
48646330 TATTCGTAAGGATATTATTAAAAAAGG-A
1 TATCCGAAAGGATATCATT-GAAAAGGTA
* * * * *
48646358 TATCCGCAATGATATCAATGAAAAAGAA
1 TATCCGAAAGGATATCATTGAAAAGGTA
* *
48646386 TATCCGTAAGGATACCA-TGAAAAGGGT-
1 TATCCGAAAGGATATCATTGAAAA-GGTA
*
48646413 CATCCGAAAGGATATCATTGAAAAGGTTA
1 TATCCGAAAGGATATCATTGAAAAGG-TA
*
48646442 TATCCGAAAGGATAT--TTGAAAATGTTA
1 TATCCGAAAGGATATCATTGAAAA-GGTA
* * ** *
48646469 TATTCGAATGGATATTTTTGAAAATGTTA
1 TATCCGAAAGGATATCATTGAAAA-GGTA
*
48646498 TATCCGGAAGGATATTC-TTGAAAAGGTTA
1 TATCCGAAAGGATA-TCATTGAAAAGG-TA
48646527 TAT
1 TAT
48646530 TCGGATGGAT
Statistics
Matches: 178, Mismatches: 37, Indels: 25
0.74 0.15 0.10
Matches are distributed among these distances:
27 49 0.28
28 73 0.41
29 55 0.31
30 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (28 bp):
TATCCGAAAGGATATCATTGAAAAGGTA
Found at i:48646468 original size:27 final size:29
Alignment explanation
Indices: 48646414--48646529 Score: 148
Period size: 29 Copynumber: 4.1 Consensus size: 29
48646404 GAAAAGGGTC
48646414 ATCCGAAAGGATA-TCATTGAAAAGGTTAT
1 ATCCGAAAGGATATTC-TTGAAAAGGTTAT
*
48646443 ATCCGAAAGGATA-T-TTGAAAATGTTAT
1 ATCCGAAAGGATATTCTTGAAAAGGTTAT
* * * *
48646470 ATTCGAATGGATATTTTTGAAAATGTTAT
1 ATCCGAAAGGATATTCTTGAAAAGGTTAT
*
48646499 ATCCGGAAGGATATTCTTGAAAAGGTTAT
1 ATCCGAAAGGATATTCTTGAAAAGGTTAT
48646528 AT
1 AT
48646530 TCGGATGGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
27 23 0.30
28 1 0.01
29 53 0.69
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (29 bp):
ATCCGAAAGGATATTCTTGAAAAGGTTAT
Found at i:48646482 original size:56 final size:58
Alignment explanation
Indices: 48646417--48646541 Score: 173
Period size: 56 Copynumber: 2.2 Consensus size: 58
48646407 AAGGGTCATC
* *
48646417 CGAAAGGATATCATTGAAAAGGTTATATCCGAAAGGATA-T-TTGAAAATGTTATATT
1 CGAATGGATATCATTGAAAAGGTTATATCCGAAAGGATATTCTTGAAAAGGTTATATT
** * *
48646473 CGAATGGATATTTTTGAAAATGTTATATCCGGAAGGATATTCTTGAAAAGGTTATATT
1 CGAATGGATATCATTGAAAAGGTTATATCCGAAAGGATATTCTTGAAAAGGTTATATT
*
48646531 CGGATGGATAT
1 CGAATGGATAT
48646542 ATCCGAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 34 0.57
57 1 0.02
58 25 0.42
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (58 bp):
CGAATGGATATCATTGAAAAGGTTATATCCGAAAGGATATTCTTGAAAAGGTTATATT
Found at i:48647146 original size:12 final size:13
Alignment explanation
Indices: 48647131--48647159 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
48647121 AATGATTACA
48647131 TGAATTGG-TATG
1 TGAATTGGTTATG
48647143 TGAATTGGTTATG
1 TGAATTGGTTATG
48647156 TGAA
1 TGAA
48647160 AATATATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (13 bp):
TGAATTGGTTATG
Found at i:48648829 original size:29 final size:30
Alignment explanation
Indices: 48648778--48648834 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
48648768 TTAATTCAAT
48648778 TTTTTCAAATTAAACACCTTTTATTTTTCA
1 TTTTTCAAATTAAACACCTTTTATTTTTCA
* *
48648808 TTTTTCAAATTAAA-TCTTTTTATTTTT
1 TTTTTCAAATTAAACACCTTTTATTTTT
48648835 ATTCTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTCAAATTAAACACCTTTTATTTTTCA
Found at i:48648919 original size:6 final size:6
Alignment explanation
Indices: 48648868--48648937 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
48648858 TATTCTGTTT
*
48648868 TTTAAA TTTAATA TTT-TA TTTACT- TTTAT- TATT-TA TTTAT- TTTATA
1 TTTATA TTT-ATA TTTATA TTTA-TA TTTATA T-TTATA TTTATA TTTATA
48648914 TTTATA TTTATA TTTATA TATTAT
1 TTTATA TTTATA TTTATA T-TTAT
48648938 CTATTGTCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
5 15 0.27
6 30 0.55
7 10 0.18
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:48648921 original size:17 final size:17
Alignment explanation
Indices: 48648873--48648935 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
48648863 TGTTTTTTAA
*
48648873 ATTTAATAT-TTTATTT
1 ATTTTATATATTTATTT
48648889 ACTTTTAT-TATTTATTT
1 A-TTTTATATATTTATTT
48648906 ATTTTATAT-TTATATTT
1 ATTTTATATATT-TATTT
48648923 ATATTTATATATT
1 AT-TTTATATATT
48648936 ATCTATTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 10 0.25
17 21 0.52
18 7 0.17
19 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATATATTTATTT
Found at i:48648950 original size:34 final size:34
Alignment explanation
Indices: 48648878--48648951 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
48648868 TTTAAATTTA
* *
48648878 ATATTT-TATTTACTTTTATTATTTATTTATTTT
1 ATATTTATATTTACTTTTATTATTTATCTATTGT
48648911 ATATTTATATTTA-TATTTA-TATATTATCTATTGT
1 ATATTTATATTTACT-TTTATTAT-TTATCTATTGT
*
48648945 CTATTTA
1 ATATTTA
48648952 ATTATTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 10 0.29
34 25 0.71
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (34 bp):
ATATTTATATTTACTTTTATTATTTATCTATTGT
Found at i:48649388 original size:13 final size:13
Alignment explanation
Indices: 48649370--48649395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48649360 CCCAACTTAG
48649370 TTTAAAGATAAAC
1 TTTAAAGATAAAC
48649383 TTTAAAGATAAAC
1 TTTAAAGATAAAC
48649396 AATCCTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTAAAGATAAAC
Found at i:48653315 original size:11 final size:11
Alignment explanation
Indices: 48653287--48653332 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
48653277 AACATCCATT
48653287 ATAAAGCCAAC
1 ATAAAGCCAAC
*
48653298 ATAAAAGCTAAC
1 AT-AAAGCCAAC
* *
48653310 ATAAAGTCATC
1 ATAAAGCCAAC
48653321 ATAAAGCCAAC
1 ATAAAGCCAAC
48653332 A
1 A
48653333 AAAAATAGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.54, C:0.22, G:0.09, T:0.15
Consensus pattern (11 bp):
ATAAAGCCAAC
Found at i:48655502 original size:22 final size:22
Alignment explanation
Indices: 48655477--48655536 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
48655467 ATTTTTATAA
48655477 AGAGAAATTGATAGAAAAATCT
1 AGAGAAATTGATAGAAAAATCT
*
48655499 AGAGAAATTGATAGAAAATTCT
1 AGAGAAATTGATAGAAAAATCT
48655521 AGAGAAA-TGA-AGAAAA
1 AGAGAAATTGATAGAAAA
48655537 GAAATGATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 6 0.16
21 3 0.08
22 28 0.76
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (22 bp):
AGAGAAATTGATAGAAAAATCT
Found at i:48658028 original size:32 final size:29
Alignment explanation
Indices: 48657971--48658029 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 29
48657961 GACAAATAGT
*
48657971 CATCACTATCAGATAAACAACCATTTACA
1 CATCACTATCAGATAAACAAACATTTACA
48658000 CATCACTATCAGACTAGGAACAAACATTTA
1 CATCACTATCAGA-TA--AACAAACATTTA
48658030 ATACAACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.50
30 2 0.08
32 11 0.42
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (29 bp):
CATCACTATCAGATAAACAAACATTTACA
Found at i:48659960 original size:80 final size:80
Alignment explanation
Indices: 48659867--48660017 Score: 266
Period size: 80 Copynumber: 1.9 Consensus size: 80
48659857 ATTGATCCTC
* *
48659867 CTAAAAATGATAAATTTTTATTTAATCCTTTAAAAATTAAATTTTTACTATAATAAAAATTACAA
1 CTAAAAATGATAAATTTTGATTTAATCATTTAAAAATTAAATTTTTACTATAATAAAAATTACAA
48659932 TTTAATATTGTCTCT
66 TTTAATATTGTCTCT
* *
48659947 CTAAAAATGATAAATTTTGATTTAATCATTTAAAAATTACATTTTTACTATCATAAAAATTACAA
1 CTAAAAATGATAAATTTTGATTTAATCATTTAAAAATTAAATTTTTACTATAATAAAAATTACAA
48660012 TTTAAT
66 TTTAAT
48660018 TTCGATCTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (80 bp):
CTAAAAATGATAAATTTTGATTTAATCATTTAAAAATTAAATTTTTACTATAATAAAAATTACAA
TTTAATATTGTCTCT
Found at i:48660702 original size:7 final size:7
Alignment explanation
Indices: 48660690--48660717 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
48660680 TTTATTTTAT
48660690 TTTAATA
1 TTTAATA
48660697 TTTAATA
1 TTTAATA
48660704 TTTAATA
1 TTTAATA
48660711 TTTAATA
1 TTTAATA
48660718 ATTTTATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTAATA
Found at i:48660887 original size:31 final size:30
Alignment explanation
Indices: 48660808--48660887 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
48660798 TTTTTGGTCC
*
48660808 AATTTGGTACTCAAATTTGACACTTTTTTCT
1 AATTTGGTACT-AAACTTGACACTTTTTTCT
* *
48660839 AATTTGATATCTAAACTTGACACTTTTTTTTT
1 AATTTGGTA-CTAAACTTGACAC-TTTTTTCT
*
48660871 AATTTGGTACTTAACTT
1 AATTTGGTACTAAACTT
48660888 TTTGGATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 25 0.60
32 17 0.40
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.50
Consensus pattern (30 bp):
AATTTGGTACTAAACTTGACACTTTTTTCT
Found at i:48660948 original size:59 final size:59
Alignment explanation
Indices: 48660837--48660949 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
48660827 ACACTTTTTT
* *** * *
48660837 CTAATTTGATATCTAAACTTGACACTTTTTTTTTAATTTGGTACTTAACTTTTTGGATC
1 CTAATTTGATACCTAAACTTGACACTTTTTTCCAAATTTGATACCTAACTTTTTGGATC
*
48660896 CTAATTTGATACCTAAACTTGACTC-TTTTTCCAAATTTGATACCTAATCTTTTT
1 CTAATTTGATACCTAAACTTGACACTTTTTTCCAAATTTGATACCTAA-CTTTTT
48660950 TAATATTAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 17 0.37
59 29 0.63
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.49
Consensus pattern (59 bp):
CTAATTTGATACCTAAACTTGACACTTTTTTCCAAATTTGATACCTAACTTTTTGGATC
Found at i:48661768 original size:168 final size:172
Alignment explanation
Indices: 48661558--48661868 Score: 495
Period size: 168 Copynumber: 1.8 Consensus size: 172
48661548 TATTTCTATG
* *
48661558 TTATCGCTTCCTATCTTTTCTAAGATCTTTCTTCCCCTCACTTTTGATTTGGGCTTTTGTTTCCT
1 TTATCGCTTCCTATCTTTTCTAAGATCTTCCTTCCACTCACTTTTGATTTGGGCTTTTGTTTCCT
* *
48661623 TTTCATCTTATTGTCG-AAA-ATTT-ATTCTTTTTC-TTATGACCTATTAAACTAAAGTAGGGAT
66 TTTCATCTAACTGTCGAAAATATTTAATTCTTTTTCTTTATGACCTATTAAACTAAAGTAGGGAT
48661684 AAATACCAATGCTATACTTGAACTGGTATTTTTCCCATCATA
131 AAATACCAATGCTATACTTGAACTGGTATTTTTCCCATCATA
* *
48661726 TTATCGCTTCCTATCTTTTCTAATATCTTCCTTCCACTCACTTTTGATTTGGGTTTTTGTTTCCT
1 TTATCGCTTCCTATCTTTTCTAAGATCTTCCTTCCACTCACTTTTGATTTGGGCTTTTGTTTCCT
* *
48661791 TTTCATCTAACTGTTGAAAATTTATTTAATTCTTTTTCTTTATGTCCTATTAAACTAAAGTAGGG
66 TTTCATCTAACTGTCGAAAA--TATTTAATTCTTTTTCTTTATGACCTATTAAACTAAAGTAGGG
*
48661856 ATGAATACCAATG
129 ATAAATACCAATG
48661869 AACTATGGTT
Statistics
Matches: 128, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
168 74 0.58
169 3 0.02
172 4 0.03
173 10 0.08
174 37 0.29
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (172 bp):
TTATCGCTTCCTATCTTTTCTAAGATCTTCCTTCCACTCACTTTTGATTTGGGCTTTTGTTTCCT
TTTCATCTAACTGTCGAAAATATTTAATTCTTTTTCTTTATGACCTATTAAACTAAAGTAGGGAT
AAATACCAATGCTATACTTGAACTGGTATTTTTCCCATCATA
Found at i:48663022 original size:47 final size:49
Alignment explanation
Indices: 48662947--48663039 Score: 172
Period size: 48 Copynumber: 1.9 Consensus size: 49
48662937 TTTATCATTA
48662947 GTTCATTCAAACTCTCAAATCAAAATCCCTACC-CCAAATCAAACTGGG
1 GTTCATTCAAACTCTCAAATCAAAATCCCTACCTCCAAATCAAACTGGG
48662995 GTTCATTCAAACTC-CAAATCAAAATCCCTACCTCCAAATCAAACT
1 GTTCATTCAAACTCTCAAATCAAAATCCCTACCTCCAAATCAAACT
48663040 AGAGGAGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 18 0.41
48 26 0.59
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (49 bp):
GTTCATTCAAACTCTCAAATCAAAATCCCTACCTCCAAATCAAACTGGG
Found at i:48667764 original size:48 final size:48
Alignment explanation
Indices: 48667679--48667771 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
48667669 TTCATCATTA
* * *
48667679 GTTCATTCAAACTCTCGAATCAAAATCCCTACCCCAAATCAAACTGGT
1 GTTCATTCAAACTCCCAAATCAAAATCACTACCCCAAATCAAACTGGT
*
48667727 GTTCATTCAAAC-CCCAAATCAAAATCACTATCTCCAAATCAAACT
1 GTTCATTCAAACTCCCAAATCAAAATCACTA-CCCCAAATCAAACT
48667772 AGAAAAGAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 15 0.38
48 25 0.62
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.25
Consensus pattern (48 bp):
GTTCATTCAAACTCCCAAATCAAAATCACTACCCCAAATCAAACTGGT
Found at i:48669749 original size:16 final size:16
Alignment explanation
Indices: 48669724--48669754 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48669714 TAAAGGAACA
*
48669724 ATTGATAAGAGATTAG
1 ATTGAAAAGAGATTAG
48669740 ATTGAAAAGAGATTA
1 ATTGAAAAGAGATTA
48669755 ATAGAGGAAA
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:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (16 bp):
ATTGAAAAGAGATTAG
Found at i:48671063 original size:24 final size:24
Alignment explanation
Indices: 48671036--48671091 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
48671026 ACAAATAAAC
*
48671036 TCGTTTAAAAGCTTATTTATTGAT
1 TCGTTTAAAAGCTCATTTATTGAT
* * *
48671060 TCGTTTATAAGCTCGTTTATTGGT
1 TCGTTTAAAAGCTCATTTATTGAT
48671084 TCGTTTAA
1 TCGTTTAA
48671092 TTCGTATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.50
Consensus pattern (24 bp):
TCGTTTAAAAGCTCATTTATTGAT
Found at i:48672843 original size:24 final size:24
Alignment explanation
Indices: 48672816--48672861 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
48672806 TCATTAACAT
48672816 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
*
48672840 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATGTTCAATTA
48672862 AGTTAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:48672890 original size:23 final size:23
Alignment explanation
Indices: 48672846--48672891 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
48672836 TATATGTTCG
* *
48672846 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
48672869 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
48672892 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:48673142 original size:55 final size:55
Alignment explanation
Indices: 48673073--48673183 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
48673063 CAAGTCCAAC
* *
48673073 ACTTAAAACTATCCTACATAAAATCCTCATCTATAAATATCTTAATGATGAAGAA
1 ACTTAAAACCATCCTACATAAAATCCTCACCTATAAATATCTTAATGATGAAGAA
* *
48673128 ACTTAAAACCATCCTACATGAGATCCTCACCTATAAATATCTTAATGATGAAGAA
1 ACTTAAAACCATCCTACATAAAATCCTCACCTATAAATATCTTAATGATGAAGAA
48673183 A
1 A
48673184 TGGTCGACTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (55 bp):
ACTTAAAACCATCCTACATAAAATCCTCACCTATAAATATCTTAATGATGAAGAA
Found at i:48676318 original size:20 final size:20
Alignment explanation
Indices: 48676282--48676319 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48676272 AAAATATCTT
**
48676282 TTGATCGTTAACTTTAACAG
1 TTGATCGTTAAAGTTAACAG
48676302 TTGATCGTTAAAGTTAAC
1 TTGATCGTTAAAGTTAAC
48676320 TGTTCTTAAT
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:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (20 bp):
TTGATCGTTAAAGTTAACAG
Found at i:48676498 original size:31 final size:31
Alignment explanation
Indices: 48676411--48676498 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
48676401 TAAAAGTTTT
* *
48676411 AAAAAATA-TT-AAATTTTAATAAAAAATATA
1 AAAAAATATTTAAAATTTT-ATAAAAATTAGA
* *
48676441 AAAAAATATTTAAAA-TGTATTCAAAATTAGA
1 AAAAAATATTTAAAATTTTA-TAAAAATTAGA
48676472 AAAAAA-ATTGTAAAATTTTATAAAAAT
1 AAAAAATATT-TAAAATTTTATAAAAAT
48676499 CATACAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
30 12 0.26
31 29 0.62
32 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAAAATATTTAAAATTTTATAAAAATTAGA
Found at i:48676511 original size:19 final size:19
Alignment explanation
Indices: 48676489--48676528 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
48676479 TTGTAAAATT
*
48676489 TTATAAAA-ATCATACAAAA
1 TTATAAAATA-CATAAAAAA
48676508 TTATAAAATACATAAAAAA
1 TTATAAAATACATAAAAAA
48676527 TT
1 TT
48676529 TCTTTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
TTATAAAATACATAAAAAA
Found at i:48687438 original size:23 final size:23
Alignment explanation
Indices: 48687408--48687615 Score: 139
Period size: 23 Copynumber: 9.2 Consensus size: 23
48687398 ACAAAGTACT
*
48687408 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAAACAGA
48687431 GAGCACACGAAA-TGCTAATAACAGA
1 GAGCACAC-AAAGTGCT-A-AACAGA
* * *
48687456 GAGCACGA-GATGTGCTAAACGGA
1 GAGCAC-ACAAAGTGCTAAACAGA
* *
48687479 GAGCACACACAGTGCTAAACGGA
1 GAGCACACAAAGTGCTAAACAGA
* *
48687502 GAGTACACAAA--G-T--AC-TA
1 GAGCACACAAAGTGCTAAACAGA
* *
48687519 -AGCACACAAAGTGCTAATCAAA
1 GAGCACACAAAGTGCTAAACAGA
* *
48687541 GAGCACACGACGTGCTAATAACAGA
1 GAGCACACAAAGTGCT-A-AACAGA
* * *
48687566 GAGCACGA-GATGTGCTAAACGGA
1 GAGCAC-ACAAAGTGCTAAACAGA
*
48687589 GAGCACACACAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAACAGA
48687612 GAGC
1 GAGC
48687616 GTGCTAGAAT
Statistics
Matches: 145, Mismatches: 23, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
16 9 0.06
17 1 0.01
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 3 0.02
23 83 0.57
24 8 0.06
25 32 0.22
26 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAAACAGA
Found at i:48687533 original size:110 final size:110
Alignment explanation
Indices: 48687367--48687614 Score: 442
Period size: 110 Copynumber: 2.3 Consensus size: 110
48687357 TTGGGCAATA
* * *
48687367 GAGAGAACACACAGTGCTAAACAGAGAGTACACAAAGTACTGAGCACACAAAGTGCTAATCAGAG
1 GAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAGCACACAAAGTGCTAATCAAAG
48687432 AGCACACGAAATGCTAATAACAGAGAGCACGAGATGTGCTAAACG
66 AGCACACGAAATGCTAATAACAGAGAGCACGAGATGTGCTAAACG
*
48687477 GAGAGCACACACAGTGCTAAACGGAGAGTACACAAAGTACTAAGCACACAAAGTGCTAATCAAAG
1 GAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAGCACACAAAGTGCTAATCAAAG
**
48687542 AGCACACGACGTGCTAATAACAGAGAGCACGAGATGTGCTAAACG
66 AGCACACGAAATGCTAATAACAGAGAGCACGAGATGTGCTAAACG
48687587 GAGAGCACACACAGTGCTAAACAGAGAG
1 GAGAGCACACACAGTGCTAAACAGAGAG
48687615 CGTGCTAGAA
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 131 1.00
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (110 bp):
GAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAGCACACAAAGTGCTAATCAAAG
AGCACACGAAATGCTAATAACAGAGAGCACGAGATGTGCTAAACG
Found at i:48692604 original size:18 final size:18
Alignment explanation
Indices: 48692583--48692646 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
48692573 TATTTTCATG
48692583 AAAATATATATTAAGTTA
1 AAAATATATATTAAGTTA
* * *
48692601 AAAATAT-TATCCAAATCCTTG
1 AAAATATATAT--TAA--GTTA
48692622 AAAATATATATTAAGTTA
1 AAAATATATATTAAGTTA
48692640 AAAATAT
1 AAAATAT
48692647 TATCCAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 3 0.09
18 16 0.46
19 2 0.06
20 2 0.06
21 9 0.26
22 3 0.09
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAATATATATTAAGTTA
Found at i:48692625 original size:39 final size:39
Alignment explanation
Indices: 48692581--48692659 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
48692571 CTTATTTTCA
48692581 TGAAAATATATATTAAGTTAAAAATATTATCCAAATCCT
1 TGAAAATATATATTAAGTTAAAAATATTATCCAAATCCT
48692620 TGAAAATATATATTAAGTTAAAAATATTATCCAAATCCT
1 TGAAAATATATATTAAGTTAAAAATATTATCCAAATCCT
48692659 T
1 T
48692660 ATATTATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (39 bp):
TGAAAATATATATTAAGTTAAAAATATTATCCAAATCCT
Found at i:48708083 original size:60 final size:60
Alignment explanation
Indices: 48707757--48708095 Score: 329
Period size: 60 Copynumber: 5.7 Consensus size: 60
48707747 TTGGTATGGT
* * ** * *
48707757 CGACATCACCTTTTTATCTGAT-AAAAAAT-ATTTTTTTTGGTGTCGACCATTGCA-TGGC
1 CGACATCACTTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCA-TGCATTGGC
* * * * *
48707815 CAATATCACCTTTTTTATCTGAT--AAAAATCAAATTTTTTTTGTGTTGGTCATGCATTGGC
1 CGACATCA-CTTTTTTATCTAATAAAAAAATCAAA-TTTTTTGGTGTTGATCATGCATTGGC
* *
48707875 CGACA-CTACCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGATCATTGCA-TGGC
1 CGACATC-ACTTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCA-TGCATTGGC
* * * *
48707935 CGACACCACATTTTTTATCTAATAGAAAATTTAAATTTTTTGGTGTTGA-CAATGCATTGGC
1 CGACATCAC-TTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATC-ATGCATTGGC
* * *
48707996 TGACA-CTA-TCTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGGTTATGCATTGGC
1 CGACATC-ACT-TTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCATGCATTGGC
* *
48708056 CGACATCACTTTTTTATCTAATAAAAAAATTAATTTTTTT
1 CGACATCACTTTTTTATCTAATAAAAAAATCAAATTTTTT
48708096 ATCTGATAAA
Statistics
Matches: 236, Mismatches: 28, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
58 12 0.05
59 33 0.14
60 130 0.55
61 61 0.26
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (60 bp):
CGACATCACTTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCATGCATTGGC
Found at i:48708085 original size:121 final size:119
Alignment explanation
Indices: 48707764--48708095 Score: 395
Period size: 121 Copynumber: 2.8 Consensus size: 119
48707754 GGTCGACATC
* ** * * * *
48707764 ACCTTTTTATCTGAT-AAAAAAT-ATTTTTTTTGGTGTCGACCATTGCATGGCCAATATCACCTT
1 ACCTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCATTGCATGGCCGACATCA-CTT
* * * *
48707827 TTTTATCTGAT-AAAAATCAAATTTTTTTTGTGTTGGTCATGCATTGGCCGACACT
65 TTTTATCTAATAAAAAATTAAA-TTTTTTGGTGTTGGACATGCATTGGCCGACACT
* *
48707882 ACCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGATCATTGCATGGCCGACACCACATT
1 ACCTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCATTGCATGGCCGACATCAC-TT
* *
48707947 TTTTATCTAATAGAAAATTTAAATTTTTTGGTGTT-GACAATGCATTGGCTGACACT
65 TTTTATCTAATA-AAAAATTAAATTTTTTGGTGTTGGAC-ATGCATTGGCCGACACT
* * *
48708003 ATCTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGGTTA-TGCATTGGCCGACATCACTT
1 ACCTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCATTGCA-TGGCCGACATCACTT
*
48708067 TTTTATCTAATAAAAAAATTAATTTTTTT
65 TTTTATCTAAT-AAAAAATTAAATTTTTT
48708096 ATCTGATAAA
Statistics
Matches: 186, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
118 15 0.08
119 8 0.04
120 75 0.40
121 80 0.43
122 8 0.04
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (119 bp):
ACCTTTTTATCTAATAAAAAAATCAAATTTTTTGGTGTTGATCATTGCATGGCCGACATCACTTT
TTTATCTAATAAAAAATTAAATTTTTTGGTGTTGGACATGCATTGGCCGACACT
Found at i:48711313 original size:22 final size:21
Alignment explanation
Indices: 48711291--48711361 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
48711281 TTATTTTTAT
48711291 TATTTAATTATAAAATACTTA
1 TATTTAATTATAAAATACTTA
48711312 T-TTTAATATCATAACAA-A-TTA
1 TATTTAAT-T-ATAA-AATACTTA
*
48711333 TATTTAATTATAAATTACATTA
1 TATTTAATTATAAAATAC-TTA
*
48711355 TAATTAA
1 TATTTAA
48711362 AAACTCGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
19 1 0.02
20 11 0.27
21 7 0.17
22 20 0.49
23 2 0.05
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAATTATAAAATACTTA
Found at i:48711349 original size:17 final size:18
Alignment explanation
Indices: 48711327--48711360 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48711317 ATATCATAAC
*
48711327 AAATTATATT-TAATTAT
1 AAATTACATTATAATTAT
48711344 AAATTACATTATAATTA
1 AAATTACATTATAATTA
48711361 AAAACTCGTT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTACATTATAATTAT
Found at i:48714611 original size:3 final size:3
Alignment explanation
Indices: 48714603--48714634 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48714593 ACACTCTGCT
48714603 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48714635 TCTTCAGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:48718002 original size:5 final size:6
Alignment explanation
Indices: 48717985--48718009 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48717975 ACAATTTATG
48717985 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
48718010 TGATAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:48718454 original size:43 final size:43
Alignment explanation
Indices: 48718407--48718575 Score: 178
Period size: 43 Copynumber: 3.9 Consensus size: 43
48718397 TTTTAACGGG
* * *
48718407 GTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTTTAGCTAC
1 GTTTGTGGGAAAAGCACCGCTAAAGACCATGGTCTTTAGCTAC
* * *
48718450 GTTTGTGGGATAAGCGCCGCTAAAGACCATGGTCTTTAGCGAC
1 GTTTGTGGGAAAAGCACCGCTAAAGACCATGGTCTTTAGCTAC
* * * * *
48718493 ATTTGTGAGATAAGCACCGTTAAAGACCATGGTCTTTAG-TGGC
1 GTTTGTGGGAAAAGCACCGCTAAAGACCATGGTCTTTAGCT-AC
* ** * *
48718536 GTTCGTGCAAAAAGCACCGTTAAAGACCATGTTCTTTAGC
1 GTTTGTGGGAAAAGCACCGCTAAAGACCATGGTCTTTAGC
48718576 GGCATTTTTG
Statistics
Matches: 108, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
43 108 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (43 bp):
GTTTGTGGGAAAAGCACCGCTAAAGACCATGGTCTTTAGCTAC
Found at i:48719266 original size:26 final size:27
Alignment explanation
Indices: 48719237--48719292 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
48719227 AGTCATTTTT
48719237 TTTGCCTCAAA-TTACATTTTAGTCAC
1 TTTGCCTCAAAGTTACATTTTAGTCAC
** *
48719263 TTTGTTTGAAATGTTACATTTTAGTCAC
1 TTTGCCTCAAA-GTTACATTTTAGTCAC
48719291 TT
1 TT
48719293 ACGTTATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.32
28 17 0.68
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (27 bp):
TTTGCCTCAAAGTTACATTTTAGTCAC
Found at i:48720331 original size:20 final size:22
Alignment explanation
Indices: 48720297--48720338 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
48720287 CTTTTTTCTA
48720297 ATTTTTTATATTTTAAA-ATTT
1 ATTTTTTATATTTTAAAGATTT
*
48720318 ATTTTTTGTA-TTTAAAGATTT
1 ATTTTTTATATTTTAAAGATTT
48720339 TTTATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
ATTTTTTATATTTTAAAGATTT
Found at i:48721372 original size:17 final size:18
Alignment explanation
Indices: 48721341--48721376 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
48721331 TGAGTATTTG
48721341 TGTGATATTGATATGATA
1 TGTGATATTGATATGATA
*
48721359 TGTG-TATTGGTATGATA
1 TGTGATATTGATATGATA
48721376 T
1 T
48721377 TGAGCTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (18 bp):
TGTGATATTGATATGATA
Found at i:48721399 original size:28 final size:28
Alignment explanation
Indices: 48721334--48721399 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
48721324 TCTTTGTTGA
* *
48721334 GTATTTGTGTGATATTGATATGATATGT
1 GTATTTGTATGATATTGAGATGATATGT
* *
48721362 GTATTGGTATGATATTGAGCTG-TATTGT
1 GTATTTGTATGATATTGAGATGATA-TGT
*
48721390 GTTTTTGTAT
1 GTATTTGTAT
48721400 CATAGTATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.52
Consensus pattern (28 bp):
GTATTTGTATGATATTGAGATGATATGT
Found at i:48726716 original size:12 final size:12
Alignment explanation
Indices: 48726699--48726724 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48726689 AGTTCAGGTA
48726699 TTAATTTTATAT
1 TTAATTTTATAT
48726711 TTAATTTTATAT
1 TTAATTTTATAT
48726723 TT
1 TT
48726725 TTTGACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTTTATAT
Found at i:48728224 original size:31 final size:30
Alignment explanation
Indices: 48728186--48728284 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
48728176 TTAATATAAT
48728186 ATTTGGTACTTGAACTTGACATTTTTTCTTA
1 ATTTGGTACTTGAACTTGA-ATTTTTTCTTA
* ** *
48728217 ATTTGGTACTTAAACTT---TTTTCGACTCA
1 ATTTGGTACTTGAACTTGAATTTT-TTCTTA
* * *
48728245 ATTTGGTACCTGAACTTGATACTTTTTCCTA
1 ATTTGGTACTTGAACTTGA-ATTTTTTCTTA
48728276 ATTTGGTAC
1 ATTTGGTAC
48728285 CTAAACTTTC
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
27 4 0.08
28 18 0.35
31 27 0.52
32 3 0.06
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.47
Consensus pattern (30 bp):
ATTTGGTACTTGAACTTGAATTTTTTCTTA
Found at i:48728278 original size:59 final size:60
Alignment explanation
Indices: 48728186--48728340 Score: 215
Period size: 59 Copynumber: 2.6 Consensus size: 60
48728176 TTAATATAAT
* * * * *
48728186 ATTTGGTACTTGAACTTGACATTTTTTCTTAATTTGGTACTTAAACTTT-TTTCG-ACTCA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACCTAAACTTTCTTT-GAACCCA
*
48728245 ATTTGGTACCTGAACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTCTTTGAACCCA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACCTAAACTTTCTTTGAACCCA
* *
48728305 ATTTGGCACCTGAACTTGGTATTTTTTCCTAATTTG
1 ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTG
48728341 ATGCCTAAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 45 0.53
60 40 0.47
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACCTAAACTTTCTTTGAACCCA
Found at i:48728285 original size:31 final size:30
Alignment explanation
Indices: 48728244--48728340 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
48728234 TTTTCGACTC
48728244 AATTTGGTACCTGAACTTGATACTTTTTCCT
1 AATTTGGTACCTGAACTTG-TACTTTTTCCT
* ** *
48728275 AATTTGGTACCTAAACTT-T-CTTTGAACCC
1 AATTTGGTACCTGAACTTGTACTTT-TTCCT
* *
48728304 AATTTGGCACCTGAACTTGGTATTTTTTCCT
1 AATTTGGTACCTGAACTT-GTACTTTTTCCT
48728335 AATTTG
1 AATTTG
48728341 ATGCCTAAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
28 4 0.08
29 19 0.37
31 26 0.50
32 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (30 bp):
AATTTGGTACCTGAACTTGTACTTTTTCCT
Done.