Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 133 of 204
Found at i:40572183 original size:15 final size:15
Alignment explanation
Indices: 40572163--40572194 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40572153 CATCCCTAAC
40572163 AAAGTAGGATTTTAT
1 AAAGTAGGATTTTAT
40572178 AAAGTAGGATTTTAT
1 AAAGTAGGATTTTAT
40572193 AA
1 AA
40572195 TTCAACAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (15 bp):
AAAGTAGGATTTTAT
Found at i:40574257 original size:58 final size:58
Alignment explanation
Indices: 40574186--40574346 Score: 313
Period size: 58 Copynumber: 2.8 Consensus size: 58
40574176 TCCTTTTTAC
40574186 TTAATTAACTATTGAAACGATAAAATTTTCCAACAAAACTTTAATACCACATGATAGT
1 TTAATTAACTATTGAAACGATAAAATTTTCCAACAAAACTTTAATACCACATGATAGT
*
40574244 TTAATTAATTATTGAAACGATAAAATTTTCCAACAAAACTTTAATACCACATGATAGT
1 TTAATTAACTATTGAAACGATAAAATTTTCCAACAAAACTTTAATACCACATGATAGT
40574302 TTAATTAACTATTGAAACGATAAAATTTTCCAACAAAACTTTAAT
1 TTAATTAACTATTGAAACGATAAAATTTTCCAACAAAACTTTAAT
40574347 TAAACTCCGT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 101 1.00
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.34
Consensus pattern (58 bp):
TTAATTAACTATTGAAACGATAAAATTTTCCAACAAAACTTTAATACCACATGATAGT
Found at i:40594598 original size:5 final size:5
Alignment explanation
Indices: 40594588--40594638 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
40594578 ATATTCTTTT
40594588 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
40594638 T
1 T
40594639 GAGTTAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:40596660 original size:2 final size:2
Alignment explanation
Indices: 40596653--40596679 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40596643 AGAAAACGCA
40596653 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
40596680 AGTTAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40597771 original size:2 final size:2
Alignment explanation
Indices: 40597764--40597791 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40597754 ACAACATTTA
40597764 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
40597792 GAGTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40601255 original size:143 final size:142
Alignment explanation
Indices: 40601079--40601362 Score: 478
Period size: 143 Copynumber: 2.0 Consensus size: 142
40601069 CGGCGAGGTG
** *
40601079 GTAAGTCTTCAATTTTGTTTAATCATTTGGGTGCTTCTAATTGTTGGTTCTGCAGTCGGGTTTTT
1 GTAAGTCTTCAATTTTGTTTAATCATTCAGGTGCTTCTAATTGTTGGTACTGCAGTCGGGTTTTT
* *
40601144 CGTAAGTACCCTTTCTTTTTCGTTACGCATTAGGGTTTTTTCTGTTGTGAGTTTTAGGTTGCAAT
66 CGTAAGTACCCTTTCTTTTTCGTTACGCATTAGGG-TTTTTCTGCTGTGAATTTTAGGTTGCAAT
40601209 TTTCATGAATGTT
130 TTTCATGAATGTT
*
40601222 GTAAGTCTTCGATTTTGTTTAATCATTCAGGTGCTTCTAATTGTTGGTACTGCAGTCGGGTTTTT
1 GTAAGTCTTCAATTTTGTTTAATCATTCAGGTGCTTCTAATTGTTGGTACTGCAGTCGGGTTTTT
* * *
40601287 CGTAAGTACCCTTTTTTTTTCGTTACGCGTTAGGGTTTTTCTGCTGTGAATTTTAGTTTGCAATT
66 CGTAAGTACCCTTTCTTTTTCGTTACGCATTAGGGTTTTTCTGCTGTGAATTTTAGGTTGCAATT
40601352 TTCATGAATGT
131 TTCATGAATGT
40601363 AAAGTTAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
142 38 0.29
143 94 0.71
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (142 bp):
GTAAGTCTTCAATTTTGTTTAATCATTCAGGTGCTTCTAATTGTTGGTACTGCAGTCGGGTTTTT
CGTAAGTACCCTTTCTTTTTCGTTACGCATTAGGGTTTTTCTGCTGTGAATTTTAGGTTGCAATT
TTCATGAATGTT
Found at i:40605755 original size:16 final size:16
Alignment explanation
Indices: 40605714--40605758 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
40605704 TTTATTTTAT
40605714 TTTAA-ATTAAATA-A
1 TTTAATATTAAATATA
**
40605728 -TTAATAAGAAATATA
1 TTTAATATTAAATATA
40605743 TTTAATATTAAATATA
1 TTTAATATTAAATATA
40605759 ATTAGCCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 4 0.17
14 6 0.25
15 1 0.04
16 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAATATTAAATATA
Found at i:40606248 original size:25 final size:25
Alignment explanation
Indices: 40606192--40606248 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
40606182 ATATCTTGAT
*
40606192 TTGATTTGATTTGATTTAATTCCAA
1 TTGATTTGATTTGATTTAATTCAAA
** *
40606217 TCAATTTGATTTGATTCT-ATTTAAA
1 TTGATTTGATTTGATT-TAATTCAAA
40606242 TTGATTT
1 TTGATTT
40606249 ATTAATGTAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (25 bp):
TTGATTTGATTTGATTTAATTCAAA
Found at i:40607015 original size:82 final size:81
Alignment explanation
Indices: 40606887--40607244 Score: 375
Period size: 82 Copynumber: 4.4 Consensus size: 81
40606877 TGAGAATAAA
* * * ** *
40606887 AATTAAATTGAATAAAATCTGTTTCGCGATTTATTCCTGCCATTCAACAAATTTTATTCATTTTT
1 AATT-AATTGAAT-AATTCTATTTCGGGATTTATTCCCACCATTCAACAGATTTTATTCA-TTTT
* * **
40606952 TATTTTGTTTCCGAATGAG
63 GATTTTGTTTCCAAACAAG
* * * *
40606971 AATTAATTGAATAATTCTATTTCGGGATTTATTCCCACCGTTCAATAGGTTTTATTTATTTTGAT
1 AATTAATTGAATAATTCTATTTCGGGATTTATTCCCACCATTCAACAGATTTTATTCATTTTGAT
* *
40607036 TTTGTTTCCTAACGAG
66 TTTGTTTCCAAACAAG
* * * *
40607052 AATTAATTGAATAATTCTATTTCGGGATTTATTCCCGCCGTTTAACCGATTTTATTCGATTTTGA
1 AATTAATTGAATAATTCTATTTCGGGATTTATTCCCACCATTCAACAGATTTTATTC-ATTTTGA
*
40607117 TTTTGTTTCTAAACAAG
65 TTTTGTTTCCAAACAAG
* * * * * *
40607134 ATTTAATTAAATAATTTTGTTTCGAGATTTATTCCCACCATTTAACAGATTTTATTC-----GAT
1 AATTAATTGAATAATTCTATTTCGGGATTTATTCCCACCATTCAACAGATTTTATTCATTTTGAT
40607194 TTTGTTTCCAAACAAAG
66 TTTGTTTCCAAAC-AAG
* *
40607211 ATTTAATTAAATAATTCTATTTCGGGATTTATTC
1 AATTAATTGAATAATTCTATTTCGGGATTTATTC
40607245 TTGTCGTTTA
Statistics
Matches: 238, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
76 15 0.06
77 34 0.14
81 71 0.30
82 106 0.45
83 8 0.03
84 4 0.02
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (81 bp):
AATTAATTGAATAATTCTATTTCGGGATTTATTCCCACCATTCAACAGATTTTATTCATTTTGAT
TTTGTTTCCAAACAAG
Found at i:40607189 original size:163 final size:159
Alignment explanation
Indices: 40606887--40607281 Score: 407
Period size: 163 Copynumber: 2.4 Consensus size: 159
40606877 TGAGAATAAA
* * * * * *
40606887 AATTAAATTGAATAAAATCTGTTTCGCGATTTATTCCTGCCATTCAACAAATTTTATTC-ATTTT
1 AATT-AATTGAAT-AATTCTATTTCGGGATTTATTCCTGCCGTTTAACAGATTTTATTCGA-TTT
* * ** * * *
40606951 TTATTTTGTTTCCGAATGAGAATTAATTGAATAATTCTATTTCGGGATTTATTCCCACCGTTCAA
63 TGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTCGAGATTTATTCCCACCATTCAA
* * * * *
40607016 TAGGTTTTATTTATTTTGATTTTGTTTCCTAAC-GAG
128 CA-G--AT-TTTA-TTCGATTTTGTTTCCAAACAAAG
* *
40607052 AATTAATTGAATAATTCTATTTCGGGATTTATTCCCGCCGTTTAACCGATTTTATTCGATTTTGA
1 AATTAATTGAATAATTCTATTTCGGGATTTATTCCTGCCGTTTAACAGATTTTATTCGATTTTGA
* * * * *
40607117 TTTTGTTTCTAAACAAGATTTAATTAAATAATTTTGTTTCGAGATTTATTCCCACCATTTAACAG
66 TTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTCGAGATTTATTCCCACCATTCAACAG
40607182 ATTTTATTCGATTTTGTTTCCAAACAAAG
131 ATTTTATTCGATTTTGTTTCCAAACAAAG
* * * * * * *
40607211 ATTTAATTAAATAATTCTATTTCGGGATTTATTCTTGTCGTTTAATAGATTTGATTTTGATTTTG
1 AATTAATTGAATAATTCTATTTCGGGATTTATTCCTGCCGTTTAACAGATTTTA-TTCGATTTTG
40607276 ATTTTG
65 ATTTTG
40607282 ATTTTGATTT
Statistics
Matches: 193, Mismatches: 34, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
158 17 0.09
159 52 0.27
160 16 0.08
162 1 0.01
163 94 0.49
164 9 0.05
165 4 0.02
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (159 bp):
AATTAATTGAATAATTCTATTTCGGGATTTATTCCTGCCGTTTAACAGATTTTATTCGATTTTGA
TTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTCGAGATTTATTCCCACCATTCAACAG
ATTTTATTCGATTTTGTTTCCAAACAAAG
Found at i:40607271 original size:6 final size:6
Alignment explanation
Indices: 40607260--40607327 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
40607250 GTTTAATAGA
40607260 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT
40607308 TTTGAT TTTGAT TTT-AT TTT
1 TTTGAT TTTGAT TTTGAT TTT
40607328 CAAACAAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.16, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTGAT
Found at i:40607408 original size:76 final size:75
Alignment explanation
Indices: 40607305--40607525 Score: 230
Period size: 76 Copynumber: 2.8 Consensus size: 75
40607295 TTTTGATTTT
40607305 GATTTTGATTTTGATTTTATTTT-CAAACAAGATTTAATTAAATAATTTAGTTTCTGGATTTATT
1 GATTTT-ATTTTGATTTT-TTTTCCAAACAAGATTTAATTAAATAATTT-GTTTC-GGATTTATT
**
40607369 CTTG-CATTTAAAA
62 CCCGCCATTTAAAA
*
40607382 GATTTTATTTTGATTTTTTTTCCAAACAAGATTTAATCAAATAAATTCTGTTTCGGAATTTATTC
1 GATTTTATTTTGATTTTTTTTCCAAACAAGATTTAATTAAAT-AATT-TGTTTCGG-ATTTATTC
* *
40607447 CCGCCGTTTAATA
63 CCGCCATTTAAAA
* * *
40607460 GATTTTATTCGATTTCGATTTTGTTGCTAAACAAGATTTAATTAAATAATTTTGTTTCGGGATTT
1 GATTTTA-T---TTT-GATTTTTTTTCCAAACAAGATTTAATTAAATAA-TTTGTTTC-GGATTT
40607525 A
59 A
40607526 ATCCTACTGT
Statistics
Matches: 123, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
75 4 0.03
76 32 0.26
77 24 0.20
78 15 0.12
79 1 0.01
82 16 0.13
83 31 0.25
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (75 bp):
GATTTTATTTTGATTTTTTTTCCAAACAAGATTTAATTAAATAATTTGTTTCGGATTTATTCCCG
CCATTTAAAA
Found at i:40607457 original size:202 final size:201
Alignment explanation
Indices: 40607109--40607482 Score: 522
Period size: 202 Copynumber: 1.9 Consensus size: 201
40607099 GATTTTATTC
*
40607109 GATTTTGATTTTGTTTCTAAACAAGATTTAATTAAATAATTTTGTTTCGAGATTTATTCCCACCA
1 GATTTTGATTTTGTTTCTAAACAAGATTTAATTAAATAATTTAGTTTCGAGATTTATTCCCACCA
* * *
40607174 TTTAACAGATTTTATTCGATTTTGTTTCCAAACAAAGATTTAATTAAATAATTCTATTTCGGGAT
66 TTTAAAAGATTTTATTCGATTTTGTTTCCAAACAAAGATTTAATCAAATAATTCTATTTCGGAAT
** * * *
40607239 TTATTCTTGTCGTTTAATAGATTTGATTTTGATTTTGATTTTGATTTTGATTTTGATTTTGATTT
131 TTATTCCCGCCGTTTAATAGATTTGA-TTCGATTTCGATTTTGATTTTGATTTTGATTTTGATTT
40607304 TGATTTT
195 TGATTTT
* ***
40607311 GATTTTGATTTTATTT-TCAAACAAGATTTAATTAAATAATTTAGTTTCTG-GATTTATT-CTTG
1 GATTTTGATTTTGTTTCT-AAACAAGATTTAATTAAATAATTTAGTTTC-GAGATTTATTCCCAC
* * *
40607373 CATTTAAAAGATTTTATTTTGATTTTTTTTCCAAAC-AAGATTTAATCAAATAAATTCTGTTTCG
64 CATTTAAAAGATTTTA-TTCGATTTTGTTTCCAAACAAAGATTTAATCAAAT-AATTCTATTTCG
*
40607437 GAATTTATTCCCGCCGTTTAATAGATTTTATTCGATTTCGATTTTG
127 GAATTTATTCCCGCCGTTTAATAGATTTGATTCGATTTCGATTTTG
40607483 TTGCTAAACA
Statistics
Matches: 151, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
201 45 0.30
202 105 0.70
203 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (201 bp):
GATTTTGATTTTGTTTCTAAACAAGATTTAATTAAATAATTTAGTTTCGAGATTTATTCCCACCA
TTTAAAAGATTTTATTCGATTTTGTTTCCAAACAAAGATTTAATCAAATAATTCTATTTCGGAAT
TTATTCCCGCCGTTTAATAGATTTGATTCGATTTCGATTTTGATTTTGATTTTGATTTTGATTTT
GATTTT
Found at i:40607557 original size:83 final size:80
Alignment explanation
Indices: 40607303--40607562 Score: 221
Period size: 82 Copynumber: 3.2 Consensus size: 80
40607293 GATTTTGATT
* * *
40607303 TTGATTTTGATTTTGATTTTATTTTCAAACAAGATTTAATTAAATAATTTAGTTTCTGGATTTAT
1 TTGATTTTGATTTTGATTTTATTCT-AAACAAGATTTAATTAAATAATTTTGTTTCGGGATTTAT
*
40607368 TCTTGCAT-TT-AA-AA
65 TCCTGC-TGTTAAAGAA
* * * * *
40607382 --GATTTT-ATTTTGATTTTTTTTCCAAACAAGATTTAATCAAATAAATTCTGTTTCGGAATTTA
1 TTGATTTTGATTTTGA-TTTTATTCTAAACAAGATTTAATTAAAT-AATTTTGTTTCGGGATTTA
* * *
40607444 TTCCCGCCGTTTAATAGAT
64 TTCCTGCTG-TTAA-AGAA
* * * * *
40607463 TTTA-TTCGATTTCGATTTTGTTGCTAAACAAGATTTAATTAAATAATTTTGTTTCGGGATTTAA
1 TTGATTTTGATTTTGATTTTATT-CTAAACAAGATTTAATTAAATAATTTTGTTTCGGGATTTAT
*
40607527 TCCTACTGTTCAACAGAA
65 TCCTGCTGTT-AA-AGAA
40607545 TTGATTTTGATTTT-ATTT
1 TTGATTTTGATTTTGATTT
40607563 CGGAATTTTA
Statistics
Matches: 139, Mismatches: 29, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
76 25 0.18
77 32 0.23
78 2 0.01
79 1 0.01
80 1 0.01
81 3 0.02
82 42 0.30
83 33 0.24
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.49
Consensus pattern (80 bp):
TTGATTTTGATTTTGATTTTATTCTAAACAAGATTTAATTAAATAATTTTGTTTCGGGATTTATT
CCTGCTGTTAAAGAA
Found at i:40613944 original size:523 final size:528
Alignment explanation
Indices: 40613059--40614112 Score: 1466
Period size: 523 Copynumber: 2.0 Consensus size: 528
40613049 AAAAGAAAAA
*
40613059 CTTAGATCCCATATTGGTTAAATACCAAGTGTGAGATATGTATATATATGATAACCCACTTGAGG
1 CTTAGATCCCATATTGGTTAAATACCAAATGTGAGATATGTATATATATGATAACCCACTTGAGG
* * *
40613124 ATTATTAAATGACTAAACCTGAAACCCTGTCTCATGCGCAAAGGAGGGTACAGATCCAAACCCGC
66 ATTATTAAATGACTAAACCTGAAACCCTGCCTCACGCACAAAGGAGGGTACAGATCCAAACCCGC
* ** ** * * *
40613189 CGGGGTTGGGGGCGCACCCGCACGACGTGGGTGATGCAAAATGCCCAGATCGGTCAAGCCCAAAA
131 CAGGGTTGGGCACGCACCCGCACGACGTGGGCAACGCAAAATGCCCAGACCGATCAAGCCCAAAA
* *
40613254 AGGGCCTACGGATATTTTAACTCAATACAAAATTTATTTTTTTCCTCAACAGATATTATACATAG
196 AGGGCCTACGGATATTTTAACTCAATACAAAATTTATTTTTTTCCTCAACAGATATTATACAGAA
* * * *
40613319 TCTATTTTAAAAGGTCAAATATGTTGATTTGATTTGATCTAATCAATTTGATTTTATTTTATTTA
261 TCTATTTTAAAAGGTCAAATATCTTGATTTGATTTGATCCAATCAATTTGATTTGATTTTATTCA
* *
40613384 AATTGATTTATTAATGCATATTTGTATCTTTATTCATGGAAATTTCCAAAATTCCTCCATATTAA
326 AATTGATTTATTAATGCAGATTTGTATCTTTATTCATGGAAATTTCCAAAATTCCCCCATATTAA
* * * * *
40613449 AT-TCCTATAAAAGCCTAAAGAATACTGCATAGTTCTTTACAGCCATAGAGAATTAACGAATTTT
391 ATGT-CTATAAAAGCCTAAAGAATACTGCAGAATTCTTTACAGCCAAAAAGAAATAACGAATTTT
*
40613513 TTCACTCTAAAAAATTCTT-TTC-T-TTTT-CCTC-CCTAAATTTTCAAACTTTTCGGTGATAGA
455 TTCACTCTAAAAAATTCTTATTCTTCTTTTCCCTCTCC-AAATTTTCAAACTTTTCAGTGATAGA
40613573 AGAAGGCAAG
519 AGAAGGCAAG
40613583 CTTAGATCCCACT-TTGGTTTAAATACCAAATGTGAGATATGTATATATATGATAACCCACTTGA
1 CTTAGATCCCA-TATTGG-TTAAATACCAAATGTGAGATATGTATATATATGATAACCCACTTGA
* * * * * * *
40613647 GGGTTATTGAATGACTAAGCTTGAAACCCTGCCTCACGCACAAAGG-GGGTGCAGGTTCAAACCC
64 GGATTATTAAATGACTAAACCTGAAACCCTGCCTCACGCACAAAGGAGGGTACAGATCCAAACCC
* ** * * * *
40613711 GCCAGGGTTGGGCACGCACCTGCACGACGTGGGCAACGTGAAATGCCCGGACCGATTAGGCCCGA
129 GCCAGGGTTGGGCACGCACCCGCACGACGTGGGCAACGCAAAATGCCCAGACCGATCAAGCCCAA
* **
40613776 AAA-GGCCTACGGATATTTTAGC-CTAATACAAAATTTATTTTTTT-CTCAGTAGATATTATACA
194 AAAGGGCCTACGGATATTTTAACTC-AATACAAAATTTATTTTTTTCCTCAACAGATATTATACA
* * *
40613838 GAATTTTTTTTAAAAGGTCAAAGT-TCTTGATTTGATTTTATTCCAATCAATTTGATTTGATTTT
258 GAATCTATTTTAAAAGGTCAAA-TATCTTGATTTGATTTGA-TCCAATCAATTTGATTTGATTTT
*
40613902 ATTCAAATTGATTTATTAATGCAGATTTGTATCTTTATTCATGGAAATTTCTAAAATTCCCCCAT
321 ATTCAAATTGATTTATTAATGCAGATTTGTATCTTTATTCATGGAAATTTCCAAAATTCCCCCAT
* *
40613967 ATTGAATGTCTATAAAAGCCTAAAGAATACTGTAGAATTCTTTACAGCCAAAAAGAAATAACGAA
386 ATTAAATGTCTATAAAAGCCTAAAGAATACTGCAGAATTCTTTACAGCCAAAAAGAAATAACGAA
*
40614032 TTTTTTCACTCTAAAAAATTCTTAAATTCTTTTCTTTTCCCTCTCCAAATTTTCGAACTTTTCAG
451 TTTTTTCACTCTAAAAAATTCTT--ATTC--TTCTTTTCCCTCTCCAAATTTTCAAACTTTTCAG
*
40614097 TGATAGAAGAATGCAA
512 TGATAGAAGAAGGCAA
40614113 AGTTTGCCTG
Statistics
Matches: 464, Mismatches: 51, Indels: 23
0.86 0.09 0.04
Matches are distributed among these distances:
522 49 0.11
523 200 0.43
524 84 0.18
525 85 0.18
526 3 0.01
529 1 0.00
530 4 0.01
531 36 0.08
532 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (528 bp):
CTTAGATCCCATATTGGTTAAATACCAAATGTGAGATATGTATATATATGATAACCCACTTGAGG
ATTATTAAATGACTAAACCTGAAACCCTGCCTCACGCACAAAGGAGGGTACAGATCCAAACCCGC
CAGGGTTGGGCACGCACCCGCACGACGTGGGCAACGCAAAATGCCCAGACCGATCAAGCCCAAAA
AGGGCCTACGGATATTTTAACTCAATACAAAATTTATTTTTTTCCTCAACAGATATTATACAGAA
TCTATTTTAAAAGGTCAAATATCTTGATTTGATTTGATCCAATCAATTTGATTTGATTTTATTCA
AATTGATTTATTAATGCAGATTTGTATCTTTATTCATGGAAATTTCCAAAATTCCCCCATATTAA
ATGTCTATAAAAGCCTAAAGAATACTGCAGAATTCTTTACAGCCAAAAAGAAATAACGAATTTTT
TCACTCTAAAAAATTCTTATTCTTCTTTTCCCTCTCCAAATTTTCAAACTTTTCAGTGATAGAAG
AAGGCAAG
Found at i:40619628 original size:21 final size:21
Alignment explanation
Indices: 40619602--40619646 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
40619592 ATTCAAGTTG
40619602 GCTAGCATGTGATTTTGTATC
1 GCTAGCATGTGATTTTGTATC
40619623 GCTAGCATGTGATTTTGTATC
1 GCTAGCATGTGATTTTGTATC
40619644 GCT
1 GCT
40619647 CCCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (21 bp):
GCTAGCATGTGATTTTGTATC
Found at i:40625292 original size:20 final size:20
Alignment explanation
Indices: 40625254--40625303 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
40625244 CACATGTACT
*
40625254 TTATTTTTTTAAGGATTTATA
1 TTATTTTTTTAA-GATTTAAA
*
40625275 TATATTTTTTTAA-TTTTAAA
1 T-TATTTTTTTAAGATTTAAA
40625295 TTATTTTTT
1 TTATTTTTT
40625304 GATGTAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.31
20 6 0.23
21 1 0.04
22 11 0.42
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
TTATTTTTTTAAGATTTAAA
Found at i:40629489 original size:29 final size:31
Alignment explanation
Indices: 40629448--40629509 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
40629438 AGTCTCTATA
* *
40629448 TTTATAATCTTT-AAAGGATTAAATTAAAAT
1 TTTATAATCTTTAAAAGAATTAAAGTAAAAT
* *
40629478 TTTATCAT-TTTAAAAGAATTAAAGTACAAT
1 TTTATAATCTTTAAAAGAATTAAAGTAAAAT
40629508 TT
1 TT
40629510 CATCTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (31 bp):
TTTATAATCTTTAAAAGAATTAAAGTAAAAT
Found at i:40632771 original size:24 final size:24
Alignment explanation
Indices: 40632679--40632778 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 24
40632669 TACTGTGAAT
* *
40632679 TGTATTTTTAGAAATGCTACGAAC
1 TGTATTTATAGAAATACTACGAAC
* *
40632703 TATATTTATAGAAATACCACGAAC
1 TGTATTTATAGAAATACTACGAAC
* * *
40632727 TATA-TCATAG-AATATTACGAAC
1 TGTATTTATAGAAATACTACGAAC
* *
40632749 TGTATTTACAGAAATACTGCGAAC
1 TGTATTTATAGAAATACTACGAAC
40632773 TGTATT
1 TGTATT
40632779 GTAATCCATA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
22 13 0.21
23 9 0.15
24 40 0.65
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (24 bp):
TGTATTTATAGAAATACTACGAAC
Found at i:40632912 original size:54 final size:54
Alignment explanation
Indices: 40632854--40632956 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
40632844 AAATCAACGA
** *
40632854 ACCGCGAGATTTGTAAAAGTCC-ATAAGTAGAAGGTCATGATCGTAAATCGGTAG
1 ACCGCGAGATTCATAAAA-TCCTATAAGTAAAAGGTCATGATCGTAAATCGGTAG
*
40632908 ACCGCGAGATTCATAAAATCCTATAAGTAAAAGGTCGTGATCGTAAATC
1 ACCGCGAGATTCATAAAATCCTATAAGTAAAAGGTCATGATCGTAAATC
40632957 AACGGACCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 3 0.07
54 41 0.93
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (54 bp):
ACCGCGAGATTCATAAAATCCTATAAGTAAAAGGTCATGATCGTAAATCGGTAG
Found at i:40632988 original size:39 final size:39
Alignment explanation
Indices: 40632937--40633136 Score: 175
Period size: 39 Copynumber: 5.1 Consensus size: 39
40632927 CCTATAAGTA
* *
40632937 AAAGGTCGTGATCGTAAATCAACGGACCATAAGAAAGCC
1 AAAGGTCATGATCGTAAATCAACGGACCGTAAGAAAGCC
* * * * * * *
40632976 GAAGGCCATGATCGTAAATTAGCGAACCGTAAGAAAACT
1 AAAGGTCATGATCGTAAATCAACGGACCGTAAGAAAGCC
* * *
40633015 AAAGGTCATGATCGTAAATCCATGGACTGTAAGAAAGCC
1 AAAGGTCATGATCGTAAATCAACGGACCGTAAGAAAGCC
* * * * *
40633054 AAAAGTCGTGATCGTAAATCAGCGGACCCCTAAGAAAGCT
1 AAAGGTCATGATCGTAAATCAACGGA-CCGTAAGAAAGCC
* * * * ** *
40633094 GAATGTCATAACCGTAAATCAGTGGACCGTAAGTAAGCC
1 AAAGGTCATGATCGTAAATCAACGGACCGTAAGAAAGCC
40633133 AAAG
1 AAAG
40633137 ATCGCAATTG
Statistics
Matches: 122, Mismatches: 38, Indels: 2
0.75 0.23 0.01
Matches are distributed among these distances:
39 92 0.75
40 30 0.25
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (39 bp):
AAAGGTCATGATCGTAAATCAACGGACCGTAAGAAAGCC
Found at i:40633066 original size:78 final size:79
Alignment explanation
Indices: 40632937--40633135 Score: 213
Period size: 78 Copynumber: 2.5 Consensus size: 79
40632927 CCTATAAGTA
* * * * * * *
40632937 AAAGGTCGTGATCGTAAATCAACGGACCATAAGAAAGCCGAAGGCCATGATCGTAAATTAGC-GA
1 AAAGGTCATGATCGTAAATCCATGGACCGTAAGAAAGCCAAAAGCCATGATCGTAAATCAGCGGA
*
40633001 ACCGTAAGAAAACT
66 ACCCTAAGAAAACT
* * *
40633015 AAAGGTCATGATCGTAAATCCATGGACTGTAAGAAAGCCAAAAGTCGTGATCGTAAATCAGCGGA
1 AAAGGTCATGATCGTAAATCCATGGACCGTAAGAAAGCCAAAAGCCATGATCGTAAATCAGCGGA
* *
40633080 CCCCTAAGAAAGCT
66 ACCCTAAGAAAACT
* * * * *
40633094 GAATGTCATAACCGTAAAT-CAGTGGACCGTAAGTAAGCCAAA
1 AAAGGTCATGATCGTAAATCCA-TGGACCGTAAGAAAGCCAAA
40633136 GATCGCAATT
Statistics
Matches: 100, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
78 54 0.54
79 46 0.46
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (79 bp):
AAAGGTCATGATCGTAAATCCATGGACCGTAAGAAAGCCAAAAGCCATGATCGTAAATCAGCGGA
ACCCTAAGAAAACT
Found at i:40633120 original size:79 final size:78
Alignment explanation
Indices: 40632949--40633135 Score: 196
Period size: 79 Copynumber: 2.4 Consensus size: 78
40632939 AGGTCGTGAT
* * * * * * *
40632949 CGTAAATCAACGGACCATAAGAAAGCCGAAGGCCATGATCGTAAATTAGCGAACCGTAAGAAAAC
1 CGTAAATCCATGGACCGTAAGAAAGCCAAAAGCCATGATCGTAAATCAGCGAACCCTAAGAAAAC
* *
40633014 TAAAGGTCATGAT
66 TAAAGGTCATAAC
* * * * *
40633027 CGTAAATCCATGGACTGTAAGAAAGCCAAAAGTCGTGATCGTAAATCAGCGGACCCCTAAGAAAG
1 CGTAAATCCATGGACCGTAAGAAAGCCAAAAGCCATGATCGTAAATCAGC-GAACCCTAAGAAAA
* *
40633092 CTGAATGTCATAAC
65 CTAAAGGTCATAAC
*
40633106 CGTAAAT-CAGTGGACCGTAAGTAAGCCAAA
1 CGTAAATCCA-TGGACCGTAAGAAAGCCAAA
40633136 GATCGCAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
78 43 0.48
79 46 0.52
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (78 bp):
CGTAAATCCATGGACCGTAAGAAAGCCAAAAGCCATGATCGTAAATCAGCGAACCCTAAGAAAAC
TAAAGGTCATAAC
Found at i:40633229 original size:54 final size:54
Alignment explanation
Indices: 40633171--40633375 Score: 270
Period size: 54 Copynumber: 3.8 Consensus size: 54
40633161 GCGAGGTTCA
* *
40633171 TAAAATCTCATAAGTAAAAGGTTGTGATCATAAATCACTGGACCT-CAAGATTTG
1 TAAAATCTCATAAGTAAAAGGTCGTGATCATAAATCAGTGGA-CTGCAAGATTTG
*
40633225 TAAAATC-CTATAAGTAAAAGGTCGTGATCGTAAATCAGTGGACTGCAAGATTTG
1 TAAAATCTC-ATAAGTAAAAGGTCGTGATCATAAATCAGTGGACTGCAAGATTTG
* * * ** *
40633279 TAAAATCTCGTAAGTAAAAGGTCATGATCGTAAATCAGTGGACTGTGAGATTCG
1 TAAAATCTCATAAGTAAAAGGTCGTGATCATAAATCAGTGGACTGCAAGATTTG
* * *
40633333 TAAAATCTCGTAAGTAAAAGGTTGTGATCATAAATCAGCGGAC
1 TAAAATCTCATAAGTAAAAGGTCGTGATCATAAATCAGTGGAC
40633376 CGTAAGAAGG
Statistics
Matches: 136, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
53 3 0.02
54 132 0.97
55 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (54 bp):
TAAAATCTCATAAGTAAAAGGTCGTGATCATAAATCAGTGGACTGCAAGATTTG
Found at i:40633406 original size:39 final size:38
Alignment explanation
Indices: 40633363--40633486 Score: 140
Period size: 39 Copynumber: 3.2 Consensus size: 38
40633353 GTTGTGATCA
* * *
40633363 TAAATCAGCGGACCGTAAGAAGGCCGAAGGTCATGATTG
1 TAAATCAG-GGACCATAAGAAAGCCGAAGGTCATGATAG
* * * **
40633402 TAAATCAAGGGACCATAAGAAAACCAAAGGTAATGACCG
1 TAAATC-AGGGACCATAAGAAAGCCGAAGGTCATGATAG
*
40633441 TAAATCAGTGGATCATAAGAAAGCCGAAGGTCATGATAG
1 TAAATCAG-GGACCATAAGAAAGCCGAAGGTCATGATAG
40633480 TAAATCA
1 TAAATCA
40633487 ACGGGCCGCG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 2 0.03
39 66 0.94
40 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (38 bp):
TAAATCAGGGACCATAAGAAAGCCGAAGGTCATGATAG
Found at i:40634156 original size:14 final size:14
Alignment explanation
Indices: 40634137--40634163 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40634127 TTCATCTCTC
40634137 TTTGTTTATTCTTA
1 TTTGTTTATTCTTA
40634151 TTTGTTTATTCTT
1 TTTGTTTATTCTT
40634164 GAATTGCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTGTTTATTCTTA
Found at i:40637957 original size:30 final size:30
Alignment explanation
Indices: 40637921--40637978 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40637911 ATGTTTGTGT
40637921 TGGATAATTAACAAACCCCAAATTAATTAA
1 TGGATAATTAACAAACCCCAAATTAATTAA
* * *
40637951 TGGATAATTAATAGACTCCAAATTAATT
1 TGGATAATTAACAAACCCCAAATTAATT
40637979 GATAATGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (30 bp):
TGGATAATTAACAAACCCCAAATTAATTAA
Found at i:40638253 original size:25 final size:25
Alignment explanation
Indices: 40638225--40638280 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
40638215 ATATTAATTA
40638225 TGAATTATAGATTTAGTTTTGAAGG
1 TGAATTATAGATTTAGTTTTGAAGG
40638250 TGAATTATAGATTTAGTTTTGAAGG
1 TGAATTATAGATTTAGTTTTGAAGG
40638275 TGAATT
1 TGAATT
40638281 TTCAAAGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (25 bp):
TGAATTATAGATTTAGTTTTGAAGG
Found at i:40643571 original size:42 final size:42
Alignment explanation
Indices: 40643483--40643733 Score: 340
Period size: 42 Copynumber: 6.0 Consensus size: 42
40643473 GCGTTTACAG
* * * * *
40643483 AAAAAAATGCCGCTAAAGGTCATCTTCTTTAGAGGCGCTTCGA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AA
*
40643526 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* **
40643568 AAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
*
40643610 AAAAAAACCCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* * **
40643652 AGAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTTGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
* * *
40643694 TAAAAAACGCCGCTATAGATCATGTTCTTTAGCGGTGCTT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
40643734 TTGTAAAAAA
Statistics
Matches: 184, Mismatches: 24, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
42 149 0.81
43 35 0.19
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAA
Found at i:40644159 original size:21 final size:20
Alignment explanation
Indices: 40644135--40644220 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 20
40644125 GCTTCTCTCG
*
40644135 CTGCTTCTTATGCTGCAGCCT
1 CTGCTTCTT-CGCTGCAGCCT
*
40644156 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCT-TCGCTGCAGCCT
*
40644177 CTGCTTCCCTCGCTGCAGCCT
1 CTGCTT-CTTCGCTGCAGCCT
* *
40644198 CTGCTTCTCTCGTTGCCGCCT
1 CTGCTTCT-TCGCTGCAGCCT
40644219 CT
1 CT
40644221 ACTTTAAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 1 0.02
21 52 0.95
22 2 0.04
ACGTcount: A:0.05, C:0.41, G:0.19, T:0.36
Consensus pattern (20 bp):
CTGCTTCTTCGCTGCAGCCT
Found at i:40646207 original size:9 final size:9
Alignment explanation
Indices: 40646193--40646612 Score: 346
Period size: 9 Copynumber: 48.2 Consensus size: 9
40646183 GATAAATAAA
40646193 TTATGTAAG
1 TTATGTAAG
*
40646202 TTATGTACG
1 TTATGTAAG
40646211 TGTA--TAAG
1 T-TATGTAAG
40646219 TTATGTAAG
1 TTATGTAAG
40646228 TTATGT-A-
1 TTATGTAAG
*
40646235 TTAAGTAAG
1 TTATGTAAG
*
40646244 CTATGTAAG
1 TTATGTAAG
*
40646253 TTGTGT-A-
1 TTATGTAAG
40646260 TTATGTAAG
1 TTATGTAAG
40646269 TTATGTAAG
1 TTATGTAAG
**
40646278 TTATCAAAG
1 TTATGTAAG
* *
40646287 TAATGTATG
1 TTATGTAAG
40646296 TTATGTAAG
1 TTATGTAAG
40646305 -T-TGTAAG
1 TTATGTAAG
*
40646312 TTAT-TATG
1 TTATGTAAG
40646320 TATTATGTAAG
1 --TTATGTAAG
40646331 TTATGTAAG
1 TTATGTAAG
40646340 TTAAATGT-A-
1 TT--ATGTAAG
*
40646349 TTATGTAGG
1 TTATGTAAG
40646358 TTATGTAAG
1 TTATGTAAG
*
40646367 TTGTGTAAG
1 TTATGTAAG
* *
40646376 ATATTTAAG
1 TTATGTAAG
40646385 TTATGTAAG
1 TTATGTAAG
*
40646394 TTTTGT-A-
1 TTATGTAAG
40646401 TTATGTAAG
1 TTATGTAAG
40646410 TTATGTAAG
1 TTATGTAAG
40646419 TTATGTAAG
1 TTATGTAAG
40646428 TTAAATGT-A-
1 TT--ATGTAAG
*
40646437 TTATGTAGG
1 TTATGTAAG
40646446 TTATGTAAG
1 TTATGTAAG
*
40646455 TTGTGTAAG
1 TTATGTAAG
* *
40646464 ATATTTAAG
1 TTATGTAAG
40646473 TTATGTAAG
1 TTATGTAAG
*
40646482 TTTTGT-A-
1 TTATGTAAG
40646489 TTATGTAAG
1 TTATGTAAG
*
40646498 TTATGTATG
1 TTATGTAAG
*
40646507 CTATGTAAG
1 TTATGTAAG
40646516 TTAAATGT-A-
1 TT--ATGTAAG
*
40646525 TTATGTAGG
1 TTATGTAAG
40646534 TTATGTAAG
1 TTATGTAAG
*
40646543 TTGTGTAAG
1 TTATGTAAG
* *
40646552 ATATTTAAG
1 TTATGTAAG
40646561 TTATGTAAG
1 TTATGTAAG
*
40646570 TTTTGT-A-
1 TTATGTAAG
40646577 TTATGTAAG
1 TTATGTAAG
*
40646586 TTATGTATG
1 TTATGTAAG
*
40646595 CTATGT-A-
1 TTATGTAAG
40646602 TTATGTAAG
1 TTATGTAAG
40646611 TT
1 TT
40646613 GTTATGTTAT
Statistics
Matches: 323, Mismatches: 56, Indels: 64
0.73 0.13 0.14
Matches are distributed among these distances:
7 50 0.15
8 20 0.06
9 229 0.71
10 9 0.03
11 15 0.05
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40646320 original size:19 final size:19
Alignment explanation
Indices: 40646296--40646334 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40646286 GTAATGTATG
40646296 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
40646315 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
40646334 T
1 T
40646335 GTAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:40646444 original size:88 final size:88
Alignment explanation
Indices: 40646239--40646601 Score: 547
Period size: 88 Copynumber: 4.1 Consensus size: 88
40646229 TATGTATTAA
* * * ** * *
40646239 GTAAGCTATGTAAGTT--GTGTATTATGTAAGTTATGTAAGTTATCAAAG-TAATGTATGTTATG
1 GTAAGCTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGAT-ATTTAAGTTATG
*
40646301 TAAGTTGTAAGTTATTATGT-A-TTAT
65 TAAGTT-T-TG-TATTATGTAAGTTAT
*
40646326 GTAAGTTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
1 GTAAGCTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
40646391 AAGTTTTGTATTATGTAAGTTAT
66 AAGTTTTGTATTATGTAAGTTAT
*
40646414 GTAAGTTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
1 GTAAGCTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
40646479 AAGTTTTGTATTATGTAAGTTAT
66 AAGTTTTGTATTATGTAAGTTAT
*
40646502 GTATGCTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
1 GTAAGCTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
40646567 AAGTTTTGTATTATGTAAGTTAT
66 AAGTTTTGTATTATGTAAGTTAT
*
40646590 GTATGCTATGTA
1 GTAAGCTATGTA
40646602 TTATGTAAGT
Statistics
Matches: 260, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
86 8 0.03
87 17 0.07
88 191 0.73
89 43 0.17
90 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.46
Consensus pattern (88 bp):
GTAAGCTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
AAGTTTTGTATTATGTAAGTTAT
Found at i:40646748 original size:23 final size:23
Alignment explanation
Indices: 40646722--40646765 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
40646712 TTTTTTTTAT
*
40646722 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
40646745 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
40646766 TACATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:40649191 original size:366 final size:366
Alignment explanation
Indices: 40648555--40649269 Score: 1110
Period size: 366 Copynumber: 2.0 Consensus size: 366
40648545 TGCATCGACA
* *
40648555 TTTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCGTTTTA
1 TTTGCAGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTA
* * * * **
40648620 TAAAAATATAAGGAAACATTCTGGCGTTTTCCCAAACACGTCACAATTAATATATTGTTGAACCG
66 TAAAAATATAAGGAAACATTCTAGCGTTTTCCCAAAAACGCCACAATTAATATATTATCAAACCG
* * * *
40648685 ACGTCGTTTTCAGTAAATTTTATACATCATTGCAGCGTTTTTAATAAAACGCCACTAAAAGATTT
131 ACGCCGTTTTCAGAAAATTTTATACATCATTGCAGCGTTTATAATAAAACGCCACTAAAAGATTC
*
40648750 CATCCTTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCACTTTTAGGAA
196 CATCCTTCAACTGAAACGGCGCCGTTTTCGAAAAGTTCAAATATTATTTACAGCACTTTTAGGAA
* * *
40648815 AAACGCCACAACTAAAATTTATTCCCTAAGCCGAAACGACGTCGTATCGATAAATGCAATAAATA
261 AAACGCCACAACTAAAACTTATTCCCTAAACCGAAACGACGCCGTATCGATAAATGCAATAAATA
* ** *
40648880 TTTGTGGTGTTTTTTTATGAAAACACCGGTAATGTCTACAT
326 TTTATGGCATTTTTTTATCAAAACACCGGTAATGTCTACAT
*
40648921 TTTGCAGCGTTTTAATTAAAAATGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTA
1 TTTGCAGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTA
*
40648986 TAAAAATATAAGGAAACATTCTAGCGTTTTCCCAAAAATGCCACAATTAATATATTATCAAACC-
66 TAAAAATATAAGGAAACATTCTAGCGTTTTCCCAAAAACGCCACAATTAATATATTATCAAACCG
* * *
40649050 AGCGCCGTTTTCAGAAAATTTTATACATCCTTGC-GACGTTTATAATAAAACGGCACTAAAATAT
131 A-CGCCGTTTTCAGAAAATTTTATACATCATTGCAG-CGTTTATAATAAAACGCCACTAAAAGAT
* * * * *
40649114 TCCATCCTTCAACTGAAACGGCGCCGTTTTGGAAAAGTTTAAATATTATTTACGGCGCTTTTTGG
194 TCCATCCTTCAACTGAAACGGCGCCGTTTTCGAAAAGTTCAAATATTATTTACAGCACTTTTAGG
*
40649179 AAAAACGCCACAACTAAAACTTATTCCCTAAACCGAAACGACGCCGTATCGGTAAATGCAATAAA
259 AAAAACGCCACAACTAAAACTTATTCCCTAAACCGAAACGACGCCGTATCGATAAATGCAATAAA
*
40649244 TTTTTATGGCATTTTTTTATCAAAAC
324 TATTTATGGCATTTTTTTATCAAAAC
40649270 GCTGCTAAAT
Statistics
Matches: 315, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
365 2 0.01
366 313 0.99
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (366 bp):
TTTGCAGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTA
TAAAAATATAAGGAAACATTCTAGCGTTTTCCCAAAAACGCCACAATTAATATATTATCAAACCG
ACGCCGTTTTCAGAAAATTTTATACATCATTGCAGCGTTTATAATAAAACGCCACTAAAAGATTC
CATCCTTCAACTGAAACGGCGCCGTTTTCGAAAAGTTCAAATATTATTTACAGCACTTTTAGGAA
AAACGCCACAACTAAAACTTATTCCCTAAACCGAAACGACGCCGTATCGATAAATGCAATAAATA
TTTATGGCATTTTTTTATCAAAACACCGGTAATGTCTACAT
Found at i:40649343 original size:24 final size:23
Alignment explanation
Indices: 40649316--40649396 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 23
40649306 TGTATCATTC
40649316 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTAT-T
* *
40649340 ATTTAAACAAGTAATTACCTAAAAATT
1 ATTTAAATAATTAATTACCT----ATT
40649367 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTA-TT
40649392 ATTTA
1 ATTTA
40649397 TTATTTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 24 0.51
25 2 0.04
27 1 0.02
28 20 0.43
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (23 bp):
ATTTAAATAATTAATTACCTATT
Found at i:40649918 original size:7 final size:7
Alignment explanation
Indices: 40649908--40649940 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40649898 CTCTTAACAT
40649908 CTAACCC
1 CTAACCC
40649915 CTAA--C
1 CTAACCC
40649920 CTAACCC
1 CTAACCC
40649927 CTAACCC
1 CTAACCC
40649934 CTAACCC
1 CTAACCC
40649941 ATAAACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.21
7 19 0.79
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:40649925 original size:12 final size:12
Alignment explanation
Indices: 40649908--40649932 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40649898 CTCTTAACAT
40649908 CTAACCCCTAAC
1 CTAACCCCTAAC
40649920 CTAACCCCTAAC
1 CTAACCCCTAAC
40649932 C
1 C
40649933 CCTAACCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:40649997 original size:14 final size:14
Alignment explanation
Indices: 40649939--40650006 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
40649929 AACCCCTAAC
*
40649939 CCATAAACCTTAAAT
1 CCATAATCCTT-AAT
* *
40649954 CACATTAACCCTTAAA
1 C-CA-TAATCCTTAAT
* *
40649970 CCAGAATCCCTAAT
1 CCATAATCCTTAAT
40649984 CCATAATCCTTAATT
1 CCATAATCCTTAA-T
40649999 CCATAATC
1 CCATAATC
40650007 TATAAAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 18 0.43
15 12 0.29
16 5 0.12
17 7 0.17
ACGTcount: A:0.40, C:0.31, G:0.01, T:0.28
Consensus pattern (14 bp):
CCATAATCCTTAAT
Found at i:40650638 original size:41 final size:41
Alignment explanation
Indices: 40650570--40650648 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
40650560 TTTTAAATCC
* *
40650570 CTGAGCATTAGCGGCGCATCCTCAAAAACGCCGCTAAAGCA
1 CTGAGCATTAGCGGCGCATCATCAAAAACGCCACTAAAGCA
* * * *
40650611 CTGAGCATTAGCGGTGCTTTATTAAAAACGCCACTAAA
1 CTGAGCATTAGCGGCGCATCATCAAAAACGCCACTAAA
40650649 TCCACGAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCATCATCAAAAACGCCACTAAAGCA
Found at i:40651009 original size:114 final size:114
Alignment explanation
Indices: 40650592--40651065 Score: 581
Period size: 115 Copynumber: 4.1 Consensus size: 114
40650582 GGCGCATCCT
* * * * *
40650592 CAAAAACGCCGCTAAAGCACTGAGCATTAGCGGTGCTTTATTAAAAACGCCACTAAATCCACGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCATAAAAAACGCCACTAAATCCCCGAA
* * * * * **
40650657 AGCTAAGAAAACGGCGTCGTTGGGCTTAGGTTTCTTTGCGGCGCCTTCC
66 AGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAG
* * * * *
40650706 CAAAAACGCTGCTAAAAG-CCTGAGCATTAGCGGCGATTACTTAAAAAACGCCGCTAAGTCCCCG
1 CAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTT-CATAAAAAACGCCACTAAATCCCCG
* *
40650770 AAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAG
64 AAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAG
* * *
40650821 CAAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTAATTAAAAACGCCGCTAAATCCCCGA
1 CAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCATAAAAAACGCCACTAAATCCCCGA
* * *
40650886 AAGCTCAGAAAACAACGTCGTTGGGCTTAGGTTTTTTTGTTGCACTTTAG
65 AAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAG
* * * * *** *
40650936 CAAAAACGCCGCTAAAGCCCTGGGTATAAGCGTCGCTTCCCGAAAAACGCCACTAAATCCTCGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCATAAAAAACGCCACTAAATCCCCGAA
* * * *
40651001 AGCTCAGAAAACGATGTCGTTGGGATTAGGTTTTTTTGTGGCTCTTTAT
66 AGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAG
40651050 CAAAAACGCCGCTAAA
1 CAAAAACGCCGCTAAA
40651066 TCCCCGAAAG
Statistics
Matches: 312, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
114 130 0.42
115 163 0.52
116 19 0.06
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (114 bp):
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCATAAAAAACGCCACTAAATCCCCGAA
AGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAG
Found at i:40651094 original size:187 final size:188
Alignment explanation
Indices: 40650864--40651256 Score: 596
Period size: 187 Copynumber: 2.1 Consensus size: 188
40650854 GCGCTTAATT
*
40650864 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACGTCGTTGGGCTTAGGTTTTTTTGTTGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACGTCGTTGGGCTTAGGTTTTTTTGTGGC
* * *
40650929 ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGTATAAGC-GTCGCTTCCCGAAAAACGCCA-CTAA
66 ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGCATAAGCAG-CGCTTCCCCAAAAAAG-CAGCTAA
* * *
40650992 ATCCTCGAAAGCTCAGAAAACGATGTCGTTGGGATTAGG-TTTTTTTGTGGCTCTTTATC
129 ATCCTCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTTGTGGCGCTTTAGC
**
40651051 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACGTCGTTGGGCTTAGGTTTTTTTGTGGC
* * * *
40651116 ACTTTCGCAAAATCGCCGCTAAAGCCTTGGGCATTAGCAGCGCTTCCCCAAAAAAGCAGCTAAAT
66 ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGCATAAGCAGCGCTTCCCCAAAAAAGCAGCTAAAT
* *
40651181 CCTCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTTGTGGCGCTTTCGC
131 CCTCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTTGTGGCGCTTTAGC
*
40651239 AAAAACG-CACTAAATCCC
1 AAAAACGCCGCTAAATCCC
40651257 TGAGCATTAG
Statistics
Matches: 187, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
186 2 0.01
187 160 0.86
188 25 0.13
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (188 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACGTCGTTGGGCTTAGGTTTTTTTGTGGC
ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGCATAAGCAGCGCTTCCCCAAAAAAGCAGCTAAAT
CCTCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTTGTGGCGCTTTAGC
Found at i:40651097 original size:73 final size:73
Alignment explanation
Indices: 40650978--40651138 Score: 241
Period size: 73 Copynumber: 2.2 Consensus size: 73
40650968 TCGCTTCCCG
* * *
40650978 AAAAACGCCACTAAATCCTCGAAAGCTCAGAAAACGATGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
* *
40651043 TCTTTATC
66 ACTTTAGC
* *
40651051 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
*
40651116 ACTTTCGC
66 ACTTTAGC
*
40651124 AAAATCGCCGCTAAA
1 AAAAACGCCGCTAAA
40651139 GCCTTGGGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
ACTTTAGC
Found at i:40651324 original size:115 final size:113
Alignment explanation
Indices: 40651050--40651359 Score: 417
Period size: 114 Copynumber: 2.7 Consensus size: 113
40651040 GGCTCTTTAT
*
40651050 CAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGG
1 CAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGG
* * * * * *
40651115 CACTTTCGCAAAATCGCCGCTAAAGCCTTGGGCATTAGCAGCGCTTCCC
66 CGCTTTCGCAAAAACG-CACTAAAGCCCTGAGCATTAGCAGCACTTCCC
* * *
40651164 CAAAAAAGCAGCTAAATCCTCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTTGTG
1 CAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGG-TTTTTTTGTG
* * *
40651229 GCGCTTTCGCAAAAACGCACTAAATCCCTGAGCATTAGCGGCACTTCCT
65 GCGCTTTCGCAAAAACGCACTAAAGCCCTGAGCATTAGCAGCACTTCCC
* * * *
40651278 TAAAAACGCCGCTAAATCTCCCGAAAGCT-AGGAAAACGACATCGTTGGGCTTAGG-TATTTTGC
1 CAAAAACGCCGCTAAATC-CCCGAAAGCTCA-GAAAACGACGTCGTTGGGCTTAGGTTTTTTTGT
40651341 GGCGCTTTCGCAAAAACGC
64 GGCGCTTTCGCAAAAACGC
40651360 CGCTAATGCT
Statistics
Matches: 173, Mismatches: 20, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
113 25 0.14
114 91 0.53
115 57 0.33
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (113 bp):
CAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGTGG
CGCTTTCGCAAAAACGCACTAAAGCCCTGAGCATTAGCAGCACTTCCC
Found at i:40651383 original size:39 final size:40
Alignment explanation
Indices: 40651335--40651423 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
40651325 GGCTTAGGTA
* *
40651335 TTTT-GCGGCGCTTTCGCA-AAAACGCCGCTAATGCT-TAT
1 TTTTAGCGGCGCTTTC-CATAAAACGCCGCTAATGATCGAT
* *
40651373 TTTTAGCGGCGTTTTCCATGAAACGCCGCTAATGATCGAT
1 TTTTAGCGGCGCTTTCCATAAAACGCCGCTAATGATCGAT
40651413 TTTTAGCGGCG
1 TTTTAGCGGCG
40651424 TTTTTTATCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
38 6 0.14
39 25 0.57
40 13 0.30
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (40 bp):
TTTTAGCGGCGCTTTCCATAAAACGCCGCTAATGATCGAT
Found at i:40652241 original size:16 final size:16
Alignment explanation
Indices: 40652187--40652242 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
40652177 ATGACATTTA
*
40652187 AAAAATTATTAAAAAAG
1 AAAAA-TATTAAAAAAT
*
40652204 AAAAA-ACTTAAAAAGT
1 AAAAATA-TTAAAAAAT
* *
40652220 ATAAATATTAAAAATT
1 AAAAATATTAAAAAAT
40652236 AAAAATA
1 AAAAATA
40652243 CAACAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.03
16 25 0.78
17 6 0.19
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (16 bp):
AAAAATATTAAAAAAT
Found at i:40653528 original size:21 final size:21
Alignment explanation
Indices: 40653502--40653542 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40653492 TTAGATTCGC
* *
40653502 TATAAAAAAAATTCTAAAAAG
1 TATAAAAAAAAATCCAAAAAG
40653523 TATAAAAAAAAATCCAAAAA
1 TATAAAAAAAAATCCAAAAA
40653543 ATGAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (21 bp):
TATAAAAAAAAATCCAAAAAG
Found at i:40653935 original size:3 final size:3
Alignment explanation
Indices: 40653922--40653952 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
40653912 AAGACTATTT
40653922 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
40653953 AAACCTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40654929 original size:14 final size:15
Alignment explanation
Indices: 40654902--40654936 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
40654892 TGTCGCCACC
40654902 GTTTTTGTCCTTTTT
1 GTTTTTGTCCTTTTT
*
40654917 GTTTTTGT-TTTTTT
1 GTTTTTGTCCTTTTT
40654931 GTTTTT
1 GTTTTT
40654937 ACTTGCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (15 bp):
GTTTTTGTCCTTTTT
Found at i:40674466 original size:135 final size:137
Alignment explanation
Indices: 40674316--40674569 Score: 352
Period size: 135 Copynumber: 1.9 Consensus size: 137
40674306 CTAACAAACA
** * * *
40674316 AATAATTAATAAATTAGTACTAACAATCCAACATGAATTACACTAATACAAGATTTAAAACTCAG
1 AATAATTAATAAATTAGTAAGAACAATCCAACATGAATAACACTAATACAAGATCTAAAACTAAG
* * * * *
40674381 TTAATATA-G-CAAACAGATTCAATGGAAATTAATAAGAACAA-AATATATGAACAAATTCAACA
66 TTAATATAGGAAAAAAAAACTCAATGAAAATTAATAAGAA-AATAATATATGAACAAATTCAACA
40674443 GGAATAAC
130 GGAATAAC
* * * *
40674451 AATAATTAATAAATTAGTAAGAATAATCCAACATTAATAACACTAATACAAGATCTAGAATTAAG
1 AATAATTAATAAATTAGTAAGAACAATCCAACATGAATAACACTAATACAAGATCTAAAACTAAG
40674516 TTAATATAGGAAAAAAAAACTCAATGAAAATTAATAAGAAAATAATATATGAAC
66 TTAATATAGGAAAAAAAAACTCAATGAAAATTAATAAGAAAATAATATATGAAC
40674570 CATGGAAGCA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
135 64 0.63
136 3 0.03
137 35 0.34
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.26
Consensus pattern (137 bp):
AATAATTAATAAATTAGTAAGAACAATCCAACATGAATAACACTAATACAAGATCTAAAACTAAG
TTAATATAGGAAAAAAAAACTCAATGAAAATTAATAAGAAAATAATATATGAACAAATTCAACAG
GAATAAC
Found at i:40674663 original size:15 final size:14
Alignment explanation
Indices: 40674635--40674675 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
40674625 ATTCACCATG
40674635 AATAAATA-TAATT
1 AATAAATAGTAATT
40674648 AATAAATCAGTAATT
1 AATAAAT-AGTAATT
40674663 AATAAATAAGTAA
1 AATAAAT-AGTAA
40674676 GAACAATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.28
14 1 0.04
15 17 0.68
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (14 bp):
AATAAATAGTAATT
Found at i:40674811 original size:21 final size:21
Alignment explanation
Indices: 40674787--40674826 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40674777 AAACTAGGAT
40674787 TTAACTAACAAATAGATAATA
1 TTAACTAACAAATAGATAATA
* * *
40674808 TTAATTAATAAATTGATAA
1 TTAACTAACAAATAGATAA
40674827 GAACAATCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
TTAACTAACAAATAGATAATA
Found at i:40675308 original size:170 final size:170
Alignment explanation
Indices: 40675021--40675527 Score: 633
Period size: 172 Copynumber: 3.0 Consensus size: 170
40675011 TAATAACAAT
* * * * * *
40675021 CCAACTTGAATGACACTAATACAAGATTAATAACTCAATTAATACAACAAACAAATTCAATGAAA
1 CCAACTTGAATGACACTAATACAAGATTTAGAATTCAATTAATATAGCAAACAAATTCAATGGAA
* ** *
40675086 ATTGATAAGCACAAGATTGAGATTTAATTAAACTGAAACTAACAAGCAAACAAATAAC-TATGTA
66 ATTAATAAAAACAAGATTGAGATTTAATTAAACTGGAACTAACAA-CAAACAAATAACATATGTA
* *
40675150 AGATCCAACAAACCTCTTCAATGAGGTCCAGAACATCCATA
130 AGATCCAACAAACCTTTTCAATAAGGTCCAGAACATCCATA
* * * * **
40675191 CCAACTTGAGTGACACTAATAAAAGATTTAGAATTCAGTTAATATAGCAATCAAATTTGATGGAA
1 CCAACTTGAATGACACTAATACAAGATTTAGAATTCAATTAATATAGCAAACAAATTCAATGGAA
* * * *
40675256 ATTAATAAAAACAAGATTCATATTTAACTAAACTGGAACTAACTAACAAACAAATAACAGTTTGT
66 ATTAATAAAAACAAGATTGAGATTTAATTAAACTGGAACTAAC-AACAAACAAATAACA-TATGT
* * **
40675321 ACGATCCAACAAACCTTTTCAATAAGGTCTAGAACATCTTTA
129 AAGATCCAACAAACCTTTTCAATAAGGTCCAGAACATCCATA
* * * *
40675363 CCAACATT-AATGACACTTATACAATATTTAGAATTCAATTAATATAGTAAACAAATTCAATAGA
1 CCAAC-TTGAATGACACTAATACAAGATTTAGAATTCAATTAATATAGCAAACAAATTCAATGGA
* * *
40675427 AATTAATAAAAACAAGATTGGGATTTAATTAAACTAGAAC-AACAAACAAACAAATAACAATCTG
65 AATTAATAAAAACAAGATTGAGATTTAATTAAACTGGAACTAAC-AACAAACAAATAAC-ATATG
*
40675491 TAAGATCCAACAGACCTTTTCAATAAGGTCCAGAACA
128 TAAGATCCAACAAACCTTTTCAATAAGGTCCAGAACA
40675528 CCTGATTATC
Statistics
Matches: 286, Mismatches: 46, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
170 101 0.35
171 56 0.20
172 127 0.44
173 2 0.01
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (170 bp):
CCAACTTGAATGACACTAATACAAGATTTAGAATTCAATTAATATAGCAAACAAATTCAATGGAA
ATTAATAAAAACAAGATTGAGATTTAATTAAACTGGAACTAACAACAAACAAATAACATATGTAA
GATCCAACAAACCTTTTCAATAAGGTCCAGAACATCCATA
Found at i:40677087 original size:16 final size:15
Alignment explanation
Indices: 40677066--40677096 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
40677056 GGAGCAAGAT
40677066 TGAGATTTAACTAAAC
1 TGAGATTTAAC-AAAC
40677082 TGAGATTTAACAAAC
1 TGAGATTTAACAAAC
40677097 AAACAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TGAGATTTAACAAAC
Found at i:40678008 original size:135 final size:135
Alignment explanation
Indices: 40677844--40678092 Score: 401
Period size: 135 Copynumber: 1.8 Consensus size: 135
40677834 ATAGACAAAC
*
40677844 AATTAATAAATCAATAAAAACAATCCAACATGAATGAAACTAATACAAGATTTAGTATTCAATTA
1 AATTAATAAATCAATAAAAACAATCCAACATGAATGAAACTAATACAAGATTTAGAATTCAATTA
* * *
40677909 ATATAGCAAACAAATTCTATGGAAATTAATAAGAACAAAATATATGAACAAATTCAACATGAATG
66 ATATAACAAACAAATTCAATGAAAATTAATAAGAACAAAATATATGAACAAATTCAACATGAATG
40677974 ATAAT
131 ATAAT
* * * * *
40677979 AATTAATAAATTAGTAATAACTAAT-CAACATGAATGACACTAATACAAGGTTTAGAATTCAATT
1 AATTAATAAATCAATAAAAAC-AATCCAACATGAATGAAACTAATACAAGATTTAGAATTCAATT
40678043 AATATAACAAACAAATTCAATGAAAATTAATAAGAACAAAATATATGAAC
65 AATATAACAAACAAATTCAATGAAAATTAATAAGAACAAAATATATGAAC
40678093 TGTGGAAGCA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 101 0.97
136 3 0.03
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (135 bp):
AATTAATAAATCAATAAAAACAATCCAACATGAATGAAACTAATACAAGATTTAGAATTCAATTA
ATATAACAAACAAATTCAATGAAAATTAATAAGAACAAAATATATGAACAAATTCAACATGAATG
ATAAT
Found at i:40680241 original size:13 final size:14
Alignment explanation
Indices: 40680204--40680244 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
40680194 ATGACAGATG
40680204 CAGATAA-CAGAAT
1 CAGATAACCAGAAT
*
40680217 CAGATAAGCAGAA-
1 CAGATAACCAGAAT
*
40680230 CAGATATCCAGAAT
1 CAGATAACCAGAAT
40680244 C
1 C
40680245 CTACCCCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (14 bp):
CAGATAACCAGAAT
Found at i:40680709 original size:17 final size:17
Alignment explanation
Indices: 40680665--40680711 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
40680655 TTTTTAGGAT
40680665 TATGGACCCACATGCCCG
1 TATGG-CCCACATGCCCG
* *
40680683 TGTGGGCCCACATGCCTG
1 TAT-GGCCCACATGCCCG
40680701 TATGGCCCACA
1 TATGGCCCACA
40680712 CAGCCTAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 8 0.32
18 15 0.60
19 2 0.08
ACGTcount: A:0.19, C:0.36, G:0.26, T:0.19
Consensus pattern (17 bp):
TATGGCCCACATGCCCG
Found at i:40686268 original size:14 final size:15
Alignment explanation
Indices: 40686241--40686269 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40686231 TCAAACCCCA
40686241 CTCTTTTCATTTTTC
1 CTCTTTTCATTTTTC
40686256 CTCTTTT-ATTTTTC
1 CTCTTTTCATTTTTC
40686270 AGCAATTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
CTCTTTTCATTTTTC
Found at i:40687856 original size:45 final size:45
Alignment explanation
Indices: 40687729--40687858 Score: 106
Period size: 45 Copynumber: 2.9 Consensus size: 45
40687719 ATCTGCATGT
*
40687729 TGTGTATTCACAACCATCTGGTAGCATATTAACCTGCAACCTTGA
1 TGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACCTTGA
* * * * * * * * *
40687774 TG-GT-TCGCCCACCCAT-TATCTAGCAATTTTTATCTGCAA-TTATGC
1 TGTGTAT-TCACAACCATCTA-GTAGC-ATATTAACCTGCAACCT-TGA
40687819 TGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAAC
1 TGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAAC
40687859 ATTTGGTTGC
Statistics
Matches: 60, Mismatches: 17, Indels: 15
0.65 0.18 0.16
Matches are distributed among these distances:
43 2 0.03
44 14 0.23
45 28 0.47
46 13 0.22
47 3 0.05
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (45 bp):
TGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACCTTGA
Found at i:40687964 original size:91 final size:91
Alignment explanation
Indices: 40687725--40687967 Score: 317
Period size: 91 Copynumber: 2.7 Consensus size: 91
40687715 TTTTATCTGC
* * **
40687725 ATGTTGTGTATTCACAACCATCTGGTAGCATATTAACCTGCAAC-CTTGATGGTTCGCCCACCCA
1 ATGTTGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACATTTGATGGTTCATCCACCCA
* *
40687789 TTATCTAGCAATTTTTATCTGCAATT
66 TTATCTAGCAACTTTTATCTACAATT
* * * *
40687815 ATGCTGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACATTTGGTTGCTCATCCACCCA
1 ATGTTGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACATTTGATGGTTCATCCACCCA
* * *
40687880 TTATCTGGCAGCTTTTATCTACATTT
66 TTATCTAGCAACTTTTATCTACAATT
*** * *
40687906 ATGTTGTGTATTCACAATTGTCTAGTAACGTATTAACCTGCAACATTTGATGGTTCATCCAC
1 ATGTTGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACATTTGATGGTTCATCCAC
40687968 AACCCGGTGT
Statistics
Matches: 130, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
90 42 0.32
91 88 0.68
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (91 bp):
ATGTTGTGTATTCACAACCATCTAGTAGCATATTAACCTGCAACATTTGATGGTTCATCCACCCA
TTATCTAGCAACTTTTATCTACAATT
Found at i:40690848 original size:113 final size:111
Alignment explanation
Indices: 40690723--40690925 Score: 264
Period size: 113 Copynumber: 1.8 Consensus size: 111
40690713 CGTTTTGAAA
* ** * * **
40690723 AAAGCGCGGCAAAAAATCCTAAGTCC-AACGGCACTATTTTCTTAACTTTTGGGGGATTTAGCGG
1 AAAGCGCCGCAAAAAAAACTAAG-CCGAACGACACCATTTTCGGAACTTTT-GGGGATTTAGCGG
40690787 CATTTTTTAAGAAAGCGCCGCTAATGCTTCCTTTAGCGGCGTTTTCGGG
64 CATTTTTT-AGAAAGCGCCGCTAATGCTTCCTTTAGCGGCGTTTTCGGG
* * *
40690836 AAAGCGCCGCAAAAAAAACTAAGCCGAACGACGCCGTTTTCGGAGCTTTTGGGGATTTAGCGGCA
1 AAAGCGCCGCAAAAAAAACTAAGCCGAACGACACCATTTTCGGAACTTTTGGGGATTTAGCGGCA
* *
40690901 TTTTTTGGGAAGCGCCGCTAATGCT
66 TTTTTTAGAAAGCGCCGCTAATGCT
40690926 CAGGCATTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
111 17 0.22
112 23 0.30
113 37 0.48
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (111 bp):
AAAGCGCCGCAAAAAAAACTAAGCCGAACGACACCATTTTCGGAACTTTTGGGGATTTAGCGGCA
TTTTTTAGAAAGCGCCGCTAATGCTTCCTTTAGCGGCGTTTTCGGG
Found at i:40691389 original size:20 final size:20
Alignment explanation
Indices: 40691366--40691417 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
40691356 ATGTGTTAGA
40691366 GTTTGAGTTTGGGGTTTAAG
1 GTTTGAGTTTGGGGTTTAAG
* *
40691386 GTTTGAGTTTAGGGTTTTAGG
1 GTTTGAGTTT-GGGGTTTAAG
40691407 GTTT-AGTTTGG
1 GTTTGAGTTTGG
40691418 AAATTGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.48
Consensus pattern (20 bp):
GTTTGAGTTTGGGGTTTAAG
Found at i:40691576 original size:7 final size:6
Alignment explanation
Indices: 40691554--40691612 Score: 64
Period size: 7 Copynumber: 8.8 Consensus size: 6
40691544 CAAAAAATAG
40691554 GGTTTA GGTTTA GGTTTA CGGTTTA GGGTTTA CGGTTTA GAGTTTA GAGTTTCA
1 GGTTTA GGTTTA GGTTTA -GGTTTA -GGTTTA -GGTTTA G-GTTTA G-GTTT-A
40691608 GGTTT
1 GGTTT
40691613 GGGGTTTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
6 13 0.27
7 33 0.69
8 2 0.04
ACGTcount: A:0.17, C:0.05, G:0.32, T:0.46
Consensus pattern (6 bp):
GGTTTA
Found at i:40691585 original size:14 final size:14
Alignment explanation
Indices: 40691551--40691599 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
40691541 TTCCAAAAAA
40691551 TAGGGTTTA-GGTT
1 TAGGGTTTACGGTT
40691564 TA-GGTTTACGGTT
1 TAGGGTTTACGGTT
40691577 TAGGGTTTACGGTT
1 TAGGGTTTACGGTT
*
40691591 TAGAGTTTA
1 TAGGGTTTA
40691600 GAGTTTCAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 6 0.18
13 8 0.24
14 19 0.58
ACGTcount: A:0.18, C:0.04, G:0.33, T:0.45
Consensus pattern (14 bp):
TAGGGTTTACGGTT
Found at i:40691611 original size:21 final size:19
Alignment explanation
Indices: 40691554--40691641 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 19
40691544 CAAAAAATAG
40691554 GGTTTAG-GTTTAGGTTTA
1 GGTTTAGAGTTTAGGTTTA
*
40691572 CGGTTTAGGGTTTACGGTTTA
1 -GGTTTAGAGTTTA-GGTTTA
*
40691593 GAGTTTAGAGTTTCAGGTTTGG
1 G-GTTTAGAGTTT-AGGTTT-A
* *
40691615 GGTTTAGAATTTATGATTTAA
1 GGTTTAGAGTTTA-GGTTT-A
40691636 GGTTTA
1 GGTTTA
40691642 TGGTATATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.12
20 7 0.12
21 41 0.72
22 2 0.04
ACGTcount: A:0.20, C:0.03, G:0.31, T:0.45
Consensus pattern (19 bp):
GGTTTAGAGTTTAGGTTTA
Found at i:40692300 original size:115 final size:115
Alignment explanation
Indices: 40692098--40692333 Score: 409
Period size: 115 Copynumber: 2.1 Consensus size: 115
40692088 GCGCTTCAGA
* ***
40692098 AAAAACGTCGCTAAAGGTGATATATTACCGGCATTTTGTGAAGAAACGCCACAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATATATTACCGGCATTTTACAAAGAAACGCCACAAATTTCCTTTAA
*
40692163 CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCGTTTG
66 CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTG
*
40692213 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTACAAAGAAACGCCACAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATATATTACCGGCATTTTACAAAGAAACGCCACAAATTTCCTTTAA
*
40692278 CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTT
66 CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTG
40692328 AAAAAC
1 AAAAAC
40692334 ACCACAAATA
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (115 bp):
AAAAACGCCGCTAAAGGTGATATATTACCGGCATTTTACAAAGAAACGCCACAAATTTCCTTTAA
CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTG
Found at i:40693647 original size:21 final size:21
Alignment explanation
Indices: 40693621--40693672 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
40693611 TGGCAACGAA
* *
40693621 GGAAGCAGCGGCTGTAGCGAG
1 GGAAGCAGAGGCTGCAGCGAG
40693642 GGAAGCAGAGGCTGCAGCGAG
1 GGAAGCAGAGGCTGCAGCGAG
*
40693663 AGAAGCAGAG
1 GGAAGCAGAG
40693673 CAGAGCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.46, T:0.06
Consensus pattern (21 bp):
GGAAGCAGAGGCTGCAGCGAG
Found at i:40694108 original size:42 final size:42
Alignment explanation
Indices: 40694037--40694248 Score: 190
Period size: 42 Copynumber: 5.0 Consensus size: 42
40694027 TTTGTGAATA
* *
40694037 AAGCGCTGCTAAAGAACATTATCTTTAGCGGCGTTTTTTTTG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTG
* * * *******
40694079 AAGCGCCGCTAAAGATCATGTTCTATAGCGGCGCTTGAACAAA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTTG
* ** * * *
40694122 AAACGCCGCTAAAGAACATGGCCTATAGCGACGTTTTTTTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTG
* * * *
40694164 AAGCGCCGCTAAAGAACATAACCTTTAGCAGCGTTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTG
* *
40694206 AAGCGCCACTAAAGAACATGATCTTTAGCTGCGTTTATTTTTG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTTG
40694249 TAAACGCTGC
Statistics
Matches: 132, Mismatches: 36, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
42 97 0.73
43 35 0.27
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTG
Found at i:40695886 original size:19 final size:21
Alignment explanation
Indices: 40695849--40695891 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40695839 TTGTAATTTG
40695849 TTTTTACAATTTTAAATAA-T
1 TTTTTACAATTTTAAATAACT
*
40695869 TTTTTACAATTTT-TATAACT
1 TTTTTACAATTTTAAATAACT
40695889 TTT
1 TTT
40695892 ATGATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTACAATTTTAAATAACT
Found at i:40695891 original size:10 final size:9
Alignment explanation
Indices: 40695849--40695966 Score: 53
Period size: 9 Copynumber: 12.6 Consensus size: 9
40695839 TTGTAATTTG
*
40695849 TTTTTACAA
1 TTTTTATAA
*
40695858 TTTTAAATAA
1 TTTT-TATAA
*
40695868 TTTTTTACAA
1 -TTTTTATAA
40695878 TTTTTATAA
1 TTTTTATAA
* *
40695887 CTTTTATGA
1 TTTTTATAA
40695896 --TTTATAA
1 TTTTTATAA
40695903 TTTTTTTATAA
1 --TTTTTATAA
*
40695914 TTTTCAATAAA
1 TTTT-TAT-AA
*
40695925 TTTTTTTAA
1 TTTTTATAA
***
40695934 AAATTATAAA
1 TTTTTAT-AA
40695944 TTTTTAT-A
1 TTTTTATAA
40695952 TTTTTATTAA
1 TTTTTA-TAA
40695962 TTTTT
1 TTTTT
40695967 TTATAAAGAA
Statistics
Matches: 80, Mismatches: 18, Indels: 21
0.67 0.15 0.18
Matches are distributed among these distances:
7 6 0.08
8 7 0.09
9 29 0.36
10 21 0.26
11 17 0.21
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40695909 original size:18 final size:19
Alignment explanation
Indices: 40695888--40695972 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 19
40695878 TTTTTATAAC
*
40695888 TTTTATGATTTAT-AATTT
1 TTTTATAATTTATAAATTT
40695906 TTTTATAATTTTCAATAAATTT
1 TTTTATAA-TTT--ATAAATTT
* *
40695928 TTTTAAAAATTATAAATTT
1 TTTTATAATTTATAAATTT
* * *
40695947 TTATAT-TTTTATTAATTT
1 TTTTATAATTTATAAATTT
40695965 TTTTATAA
1 TTTTATAA
40695973 AGAAAAATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
18 21 0.40
19 15 0.29
21 4 0.08
22 12 0.23
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTATAAATTT
Found at i:40701629 original size:115 final size:113
Alignment explanation
Indices: 40701508--40701747 Score: 261
Period size: 114 Copynumber: 2.1 Consensus size: 113
40701498 ATAGAATATC
* * *
40701508 ATTAGCGGCGTTTACCACACAGCGCCGCAAA-ATATCAAGACCAACACGCAGCGTTCTGGTCTTG
1 ATTAGCGGCGCTTACCACA-AGCGCCGCAAACATAT-AA-ACCAAAACGCAGAGTT-TGGTCTTG
* * * **
40701572 ATGTATATTGGC-ATTTGTGGCGCTTACGAA-AAAATACCGGTAATGTATAGT
62 ATGTATATT-GCAATTAGTGGCGCTTACAAATAAAACACCACTAATGTATAGT
**** * *
40701623 ATTAGCGGCGCTTATGGGAAGCGCCGCAAACGATGTTAACCAAAACGCAGAGTTTGGTCTTGATG
1 ATTAGCGGCGCTTACCACAAGCGCCGCAAAC-ATATAAACCAAAACGCAGAGTTTGGTCTTGATG
* *
40701688 TATATTGCAATTAGTGGCGCTTATAAATAAAACGCCACTAATGTATAGT
65 TATATTGCAATTAGTGGCGCTTACAAATAAAACACCACTAATGTATAGT
40701737 ATTAGCGGCGC
1 ATTAGCGGCGC
40701748 ATAGCATTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
112 2 0.02
113 32 0.30
114 53 0.50
115 15 0.14
116 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (113 bp):
ATTAGCGGCGCTTACCACAAGCGCCGCAAACATATAAACCAAAACGCAGAGTTTGGTCTTGATGT
ATATTGCAATTAGTGGCGCTTACAAATAAAACACCACTAATGTATAGT
Found at i:40701731 original size:114 final size:113
Alignment explanation
Indices: 40701547--40702205 Score: 498
Period size: 114 Copynumber: 5.8 Consensus size: 113
40701537 AAATATCAAG
* * * * * * * * ** *
40701547 ACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGCATTTGTGGCGCTT-ACGAAAAAATACCG
1 ACCAAAACGCAGAGTTTTGGTCTTGATGGATATTAGAATTAGTGGCGCTTGA-TAAAAAACGCCA
* * * *
40701611 GTAATGTATAGTATTAGCGGCGCTTATGGGAAGCGCCGCAAACGATGTTA
65 CTAAAGTATAGTATTAGCGGCGCTTGTGGGAAGCGCCGCAAAC-ATCTTA
*
40701661 ACCAAAACGCAGAG-TTTGGTCTTGATGTATATT-GCAATTAGTGGCGCTT-ATAAATAAAACGC
1 ACCAAAACGCAGAGTTTTGGTCTTGATGGATATTAG-AATTAGTGGCGCTTGAT-AA-AAAACGC
* * **** * * *
40701723 CACTAATGTATAGTATTAGCGGCGCATAGCATTAAACGCCGCAAGATATCCTA
63 CACTAAAGTATAGTATTAGCGGCGC-TTGTGGGAAGCGCCGCAA-ACATCTTA
* *** * * * *
40701776 ATCAAAACGCTTCGTTTTGGACTTGATGTATACTATAATTAGTGGCG-TT--TAAGGAAAACGCC
1 ACCAAAACGCAGAGTTTTGGTCTTGATGGATATTAGAATTAGTGGCGCTTGATAA--AAAACGCC
* * * * * * *
40701838 AGTAAAGGATAGT-TATAGCAGCGTTTGGTGGGAAGCGCCTCCAGATATCTTA
64 ACTAAAGTATAGTAT-TAGCGGCGCTT-GTGGGAAGCGCC-GCAAACATCTTA
* *
40701890 ACCAAAACGTAGAGTTTTGGTCTTTA-GGAGTATTAGAATTAGTGGCGCTTGAT-AAAAACGCCA
1 ACCAAAACGCAGAGTTTTGGTCTTGATGGA-TATTAGAATTAGTGGCGCTTGATAAAAAACGCCA
* * * * * *
40701953 CTAAAGTATA-TCATCAGCAGCGTTTGTCGGATGCGCCACAAATCATCTTA
65 CTAAAGTATAGT-ATTAGCGGCGCTTGTGGGAAGCGCCGCAAA-CATCTTA
* * *
40702003 ACCAAAACGCAGAGTTTTGGTCTTTA-GGAGTATTAGAATTAGTGGCGCTTGATTAAAAACGCCG
1 ACCAAAACGCAGAGTTTTGGTCTTGATGGA-TATTAGAATTAGTGGCGCTTGATAAAAAACGCCA
* ** * *
40702067 CTAAAGTATA-TCATCAGCGGCATTTGTCGGATGCGCCGCAAATCATCTTA
65 CTAAAGTATAGT-ATTAGCGGCGCTTGTGGGAAGCGCCGCAAA-CATCTTA
* * * * * *
40702117 ACCAAAACGCAGAGTTTTGGTCTTTAGGGGTATTAGAATTAGTGGCGCTTGGTTAAAAACGCCGC
1 ACCAAAACGCAGAGTTTTGGTCTTGATGGATATTAGAATTAGTGGCGCTTGATAAAAAACGCCAC
*
40702182 TGAAGTATAGTATTAGCGGCGCTT
66 TAAAGTATAGTATTAGCGGCGCTT
40702206 TTACAAAAAC
Statistics
Matches: 453, Mismatches: 71, Indels: 42
0.80 0.13 0.07
Matches are distributed among these distances:
112 4 0.01
113 108 0.24
114 275 0.61
115 35 0.08
116 30 0.07
117 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (113 bp):
ACCAAAACGCAGAGTTTTGGTCTTGATGGATATTAGAATTAGTGGCGCTTGATAAAAAACGCCAC
TAAAGTATAGTATTAGCGGCGCTTGTGGGAAGCGCCGCAAACATCTTA
Found at i:40702028 original size:113 final size:113
Alignment explanation
Indices: 40701812--40702190 Score: 519
Period size: 114 Copynumber: 3.3 Consensus size: 113
40701802 TGTATACTAT
* * ** * * * * *
40701812 AATTAGTGGCGTTTAAGGAAAACGCCAGTAAAGGATAGTTAT-AGCAGCGTTTGGTGGGAAGCGC
1 AATTAGTGGCGCTTGATAAAAACGCCACTAAAGTATA-TCATCAGCAGCGTTT-GTCGGATGCGC
* * *
40701876 CTCCAGAT-ATCTTAACCAAAACGTAGAGTTTTGGTCTTTAGGAGTATTAG
64 C-ACAAATCATCTTAACCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAG
40701926 AATTAGTGGCGCTTGATAAAAACGCCACTAAAGTATATCATCAGCAGCGTTTGTCGGATGCGCCA
1 AATTAGTGGCGCTTGATAAAAACGCCACTAAAGTATATCATCAGCAGCGTTTGTCGGATGCGCCA
40701991 CAAATCATCTTAACCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAG
66 CAAATCATCTTAACCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAG
* * *
40702039 AATTAGTGGCGCTTGATTAAAAACGCCGCTAAAGTATATCATCAGCGGCATTTGTCGGATGCGCC
1 AATTAGTGGCGCTTGA-TAAAAACGCCACTAAAGTATATCATCAGCAGCGTTTGTCGGATGCGCC
* *
40702104 GCAAATCATCTTAACCAAAACGCAGAGTTTTGGTCTTTAGGGGTATTAG
65 ACAAATCATCTTAACCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAG
* * *
40702153 AATTAGTGGCGCTTGGTTAAAAACGCCGCTGAAGTATA
1 AATTAGTGGCGCTT-GATAAAAACGCCACTAAAGTATA
40702191 GTATTAGCGG
Statistics
Matches: 242, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
112 4 0.02
113 70 0.29
114 167 0.69
115 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (113 bp):
AATTAGTGGCGCTTGATAAAAACGCCACTAAAGTATATCATCAGCAGCGTTTGTCGGATGCGCCA
CAAATCATCTTAACCAAAACGCAGAGTTTTGGTCTTTAGGAGTATTAG
Found at i:40702328 original size:18 final size:18
Alignment explanation
Indices: 40702307--40702342 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
40702297 TCATTTTATA
40702307 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
40702325 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
40702343 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:40702473 original size:20 final size:20
Alignment explanation
Indices: 40702448--40702486 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40702438 TGATTGATTT
40702448 ATAATTT-ATATATATATTAA
1 ATAATTTCATATATA-ATTAA
40702468 ATAATTTCATATATAATTA
1 ATAATTTCATATATAATTA
40702487 TAAAAGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATTTCATATATAATTAA
Found at i:40703278 original size:7 final size:7
Alignment explanation
Indices: 40703256--40703331 Score: 75
Period size: 7 Copynumber: 10.9 Consensus size: 7
40703246 TTACTGCTCG
*
40703256 GGGTTTT
1 GGGTTTA
40703263 GGTGTTTA
1 GG-GTTTA
40703271 GGGTTTA
1 GGGTTTA
40703278 GGGTTT-
1 GGGTTTA
40703284 GGGATTTA
1 GGG-TTTA
*
40703292 GGGTTTG
1 GGGTTTA
40703299 GGGTTTA
1 GGGTTTA
* *
40703306 AGGATTA
1 GGGTTTA
40703313 GGGTTT-
1 GGGTTTA
*
40703319 GGGTTTG
1 GGGTTTA
40703326 GGGTTT
1 GGGTTT
40703332 GGTTTTTGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
6 9 0.16
7 40 0.69
8 9 0.16
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.45
Consensus pattern (7 bp):
GGGTTTA
Found at i:40705786 original size:16 final size:16
Alignment explanation
Indices: 40705765--40705800 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
40705755 GTATTTATAA
*
40705765 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
40705781 TTATCGATTTACAATT
1 TTATCGATTTACAATT
40705797 TTAT
1 TTAT
40705801 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:40705937 original size:67 final size:67
Alignment explanation
Indices: 40705860--40705998 Score: 244
Period size: 67 Copynumber: 2.1 Consensus size: 67
40705850 ATTAATTGAT
* *
40705860 TGAATGTCAATGAATTATCAGTTTTGGTTA-TGTAATTGATTGAATGTTTTATAAATTCATTATA
1 TGAATGTCAATGAATTATCAATTTTGGTTAGT-TAATTGATTGAATGTTTAATAAATTCATTATA
40705924 TAA
65 TAA
40705927 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
40705992 AA
66 AA
40705994 TGAAT
1 TGAAT
40705999 TCTCAACAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
67 68 0.99
68 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.45
Consensus pattern (67 bp):
TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
AA
Found at i:40706220 original size:76 final size:76
Alignment explanation
Indices: 40706123--40706359 Score: 435
Period size: 76 Copynumber: 3.2 Consensus size: 76
40706113 ATTTCATTTA
*
40706123 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTGAATATATATTATTAAGTA
1 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
40706188 TATTTTACACG
66 TATTTTACACG
40706199 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
1 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
*
40706264 TATTTTACATG
66 TATTTTACACG
40706275 ACTTATTAAT--ATAT-TATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
1 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
40706337 TATTTTACACG
66 TATTTTACACG
40706348 ACTTATTAATGA
1 ACTTATTAATGA
40706360 TATCTTACAT
Statistics
Matches: 156, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
73 68 0.44
74 4 0.03
76 84 0.54
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (76 bp):
ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
TATTTTACACG
Found at i:40706362 original size:57 final size:57
Alignment explanation
Indices: 40706300--40706418 Score: 222
Period size: 57 Copynumber: 2.1 Consensus size: 57
40706290 ATTTTAAAAT
40706300 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
*
40706357 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAA
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
40706414 T-ATAT
1 TGATAT
40706419 TATTTTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 4 0.07
57 57 0.93
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (57 bp):
TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
Found at i:40706373 original size:130 final size:130
Alignment explanation
Indices: 40706227--40706492 Score: 532
Period size: 130 Copynumber: 2.0 Consensus size: 130
40706217 ATTTTAAAAT
40706227 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
40706292 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
66 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
40706357 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
40706422 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
66 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
40706487 TGATAT
1 TGATAT
40706493 ATATATTTTA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 136 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (130 bp):
TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
Found at i:40706546 original size:77 final size:76
Alignment explanation
Indices: 40706357--40706569 Score: 387
Period size: 77 Copynumber: 2.8 Consensus size: 76
40706347 GACTTATTAA
*
40706357 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATT-A--ATATAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATATAT
40706419 TATTTTAAAAT
66 TATTTTAAAAT
40706430 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATATAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATATAT
40706495 ATATTTTAAAAT
66 -TATTTTAAAAT
40706507 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATAT
40706570 CTTACATTAC
Statistics
Matches: 135, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
73 54 0.40
74 1 0.01
76 6 0.04
77 74 0.55
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (76 bp):
TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATATAT
TATTTTAAAAT
Found at i:40706563 original size:207 final size:203
Alignment explanation
Indices: 40706151--40706689 Score: 979
Period size: 207 Copynumber: 2.6 Consensus size: 203
40706141 ATTTTAAAAT
* *
40706151 TGATATCTTACATTACTTGAATATATATTATTAAGTATATTTTACACGACTTATTAATGAATATA
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAAT--ATAT-
40706216 TATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTAT
63 TATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTAT
40706281 TAATATATTATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACA
128 TAATATATTATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACA
40706346 CGACTTATTAA
193 CGACTTATTAA
40706357 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
*
40706422 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
66 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATT-A
40706487 TGATATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTAC
130 --ATATAT-TATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTAC
40706552 ACGACTTATTAA
192 ACGACTTATTAA
40706564 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
*
40706629 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTACATTTTACATGACTTA
66 TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTA
40706690 CATTACTTAC
Statistics
Matches: 324, Mismatches: 5, Indels: 7
0.96 0.01 0.02
Matches are distributed among these distances:
203 65 0.20
204 5 0.02
206 62 0.19
207 192 0.59
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (203 bp):
TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAATATATTAT
TTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAA
TATATTATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGA
CTTATTAA
Found at i:40706570 original size:57 final size:57
Alignment explanation
Indices: 40706507--40706625 Score: 222
Period size: 57 Copynumber: 2.1 Consensus size: 57
40706497 ATTTTAAAAT
40706507 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
*
40706564 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATTAA
1 TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
40706621 T-ATAT
1 TGATAT
40706626 TATTTTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 4 0.07
57 57 0.93
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (57 bp):
TGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAA
Found at i:40706655 original size:39 final size:36
Alignment explanation
Indices: 40706557--40706689 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 36
40706547 TTTACACGAC
40706557 TTATTAA-TGATATCTTACATTACTTAAATATA-TA
1 TTATTAAGTGATATCTTACATTACTTAAATATATTA
* *
40706591 TTATTAAGT-ATATTTTACATGACTTATTAATATATTA
1 TTATTAAGTGATATCTTACATTACTTA--AATATATTA
*
40706628 TT-TTAAAATTGATATCTTACATTACTTAAATATA-TA
1 TTATT--AAGTGATATCTTACATTACTTAAATATATTA
* * *
40706664 TTATTAAGT-ACATTTTACATGACTTA
1 TTATTAAGTGATATCTTACATTACTTA
40706690 CATTACTTAC
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
34 36 0.44
35 4 0.05
36 12 0.15
37 12 0.15
38 3 0.04
39 15 0.18
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (36 bp):
TTATTAAGTGATATCTTACATTACTTAAATATATTA
Found at i:40706689 original size:34 final size:34
Alignment explanation
Indices: 40706350--40706559 Score: 172
Period size: 34 Copynumber: 5.8 Consensus size: 34
40706340 TTTACACGAC
* *
40706350 TTATTAA-TGATATCTTACATTACTTAAATATATA
1 TTATTAAGT-ATATTTTACATGACTTAAATATATA
40706384 TTATTAAGTATATTTTACATGACTTATTAATATATTA
1 TTATTAAGTATATTTTACATGACTTA--AATATA-TA
* * *
40706421 TT-TTAAAATTGATATCTTACATTACTTAAATATATA
1 TTATT--AAGT-ATATTTTACATGACTTAAATATATA
*
40706457 TTATTAAGTATATTTTACACGACTTATTAATGATATA
1 TTATTAAGTATATTTTACATGACTTA--AAT-ATATA
* * *
40706494 TATATTTTAAAATTGATATCTTACATTACTTAAATATATA
1 T-TA--TT--AAGT-ATATTTTACATGACTTAAATATATA
*
40706534 TTATTAAGTATATTTTACACGACTTA
1 TTATTAAGTATATTTTACATGACTTA
40706560 TTAATGATAT
Statistics
Matches: 142, Mismatches: 17, Indels: 34
0.74 0.09 0.18
Matches are distributed among these distances:
34 50 0.35
35 7 0.05
36 15 0.11
37 20 0.14
38 5 0.04
39 17 0.12
40 8 0.06
41 3 0.02
42 3 0.02
43 14 0.10
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (34 bp):
TTATTAAGTATATTTTACATGACTTAAATATATA
Found at i:40706727 original size:130 final size:132
Alignment explanation
Indices: 40706432--40706689 Score: 360
Period size: 130 Copynumber: 2.0 Consensus size: 132
40706422 TTTAAAATTG
* * * * *
40706432 ATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATTAATGATATATAT
1 ATATCTAAAATTACTTAAATAGACATAATTAAGTATATTTTACACGACTTATTAA-GATATATAT
*
40706497 ATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACACGACTTATT
65 ATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTACATTTTACACGACTTATT
40706562 AAT
130 AAT
* * * * * *
40706565 GATATCTTACATTACTTAAATATATATTATTAAGTATATTTTACATGACTTATT-A-ATATAT-T
1 -ATATCTAAAATTACTTAAATAGACATAATTAAGTATATTTTACACGACTTATTAAGATATATAT
*
40706627 ATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTACATTTTACATGACTTA
65 ATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTACATTTTACACGACTTA
40706690 CATTACTTAC
Statistics
Matches: 121, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
130 62 0.51
131 6 0.05
133 1 0.01
134 52 0.43
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (132 bp):
ATATCTAAAATTACTTAAATAGACATAATTAAGTATATTTTACACGACTTATTAAGATATATATA
TTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTACATTTTACACGACTTATTA
AT
Found at i:40706798 original size:16 final size:16
Alignment explanation
Indices: 40706777--40706819 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
40706767 ACACTTATTA
40706777 AACTTACATAATACAT
1 AACTTACATAATACAT
40706793 AACTTACATAATACAT
1 AACTTACATAATACAT
* *
40706809 GACTTATATAA
1 AACTTACATAA
40706820 AATTCTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:40706920 original size:9 final size:9
Alignment explanation
Indices: 40706861--40707068 Score: 130
Period size: 9 Copynumber: 23.8 Consensus size: 9
40706851 AGTTACATAT
*
40706861 TAACTTATA
1 TAACTTACA
40706870 TAAGCTTACA
1 TAA-CTTACA
*
40706880 TAA-TACACA
1 TAACT-TACA
*
40706889 TTACTTACA
1 TAACTTACA
* * *
40706898 TAGCATCCA
1 TAACTTACA
40706907 TAACTTACA
1 TAACTTACA
* *
40706916 CAACTTAAA
1 TAACTTACA
40706925 TAA--TACA
1 TAACTTACA
*
40706932 AAACTTACA
1 TAACTTACA
40706941 TAACTTACA
1 TAACTTACA
*
40706950 TAACCTACA
1 TAACTTACA
*
40706959 TAATACATA-A
1 T-A-ACTTACA
40706969 TAACTTAC-
1 TAACTTACA
40706977 -AACTTACA
1 TAACTTACA
*
40706985 TAACATACA
1 TAACTTACA
* **
40706994 TTACTTTGA
1 TAACTTACA
*
40707003 AAACTTACA
1 TAACTTACA
40707012 TAACTTACA
1 TAACTTACA
40707021 T-AC-TACA
1 TAACTTACA
* *
40707028 CAACTTAAA
1 TAACTTACA
* *
40707037 TAGCTTACT
1 TAACTTACA
40707046 TAA--TACA
1 TAACTTACA
40707053 TAACTTACA
1 TAACTTACA
40707062 TAACTTA
1 TAACTTA
40707069 TACATGTACA
Statistics
Matches: 147, Mismatches: 38, Indels: 28
0.69 0.18 0.13
Matches are distributed among these distances:
7 22 0.15
8 9 0.06
9 100 0.68
10 12 0.08
11 4 0.03
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
TAACTTACA
Found at i:40706993 original size:62 final size:61
Alignment explanation
Indices: 40706906--40707027 Score: 138
Period size: 62 Copynumber: 2.0 Consensus size: 61
40706896 CATAGCATCC
*
40706906 ATAACTTACACAACTTAAATAATACAAAACTTACATAACTTACATAACCTACATAATACATA
1 ATAACTTA-ACAACTTAAATAATACAAAACTTACAAAACTTACATAACCTACATAATACATA
* ** ** * *
40706968 ATAACTT-ACAACTTACATAACATACATTACTTTGAAAACTTACATAACTTACATACTACA
1 ATAACTTAACAACTTAAAT-A-ATACAAAACTTACAAAACTTACATAACCTACATAATACA
40707028 CAACTTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 10 0.20
61 1 0.02
62 39 0.78
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.30
Consensus pattern (61 bp):
ATAACTTAACAACTTAAATAATACAAAACTTACAAAACTTACATAACCTACATAATACATA
Found at i:40707043 original size:25 final size:25
Alignment explanation
Indices: 40706928--40707068 Score: 88
Period size: 25 Copynumber: 5.4 Consensus size: 25
40706918 ACTTAAATAA
* * *
40706928 TACAAAACTTACATAACTTACATAACC
1 TACATAACTTACATAA--TACACAACT
40706955 TACATAA--TACATAATAACTTACAACT
1 TACATAACTTACATAAT-AC--ACAACT
* * ** *
40706981 TACATAACATACATTACTTTGAAAACT
1 TACATAACTTACA-TA-ATACACAACT
*
40707008 TACATAACTTACATACTACACAACT
1 TACATAACTTACATAATACACAACT
* * * *
40707033 TAAATAGCTTACTTAATACATAACT
1 TACATAACTTACATAATACACAACT
40707058 TACATAACTTA
1 TACATAACTTA
40707069 TACATGTACA
Statistics
Matches: 88, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 42 0.48
26 13 0.15
27 23 0.26
28 4 0.05
29 2 0.02
30 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:40711373 original size:21 final size:21
Alignment explanation
Indices: 40711347--40711412 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
40711337 CAACAACTTA
* *
40711347 AAGCAGAGGCGACAGCGCGAG
1 AAGCAGAAGCGACAGCGAGAG
*
40711368 AAGCAGAAGCTACAGCGAGAG
1 AAGCAGAAGCGACAGCGAGAG
*
40711389 AAGCAGAAGCTG-CAGCAAGAG
1 AAGCAGAAGC-GACAGCGAGAG
40711410 AAG
1 AAG
40711413 TAGAGCAGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.36, T:0.03
Consensus pattern (21 bp):
AAGCAGAAGCGACAGCGAGAG
Found at i:40711918 original size:42 final size:41
Alignment explanation
Indices: 40711777--40712023 Score: 325
Period size: 42 Copynumber: 5.9 Consensus size: 41
40711767 TAAGAATAAA
* * *
40711777 CGCCGCTAAAGAGCAT-TGTCTTTAGCGGCATTTCTTTTTAAAG
1 CGCCGCTAAAGAACATGT-TCTTTAGCGGCGTTT-TTTCT-AAG
*
40711820 CGCCGCTAAAGAACATTTTCTTTAGCGGCGTTTCTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TT-TTTTCTAAG
*
40711863 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTTATAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TTCTAAG
* *
40711905 CGCCGCAAAAGAACATGTTCTTTAGCAGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTCTAAG
40711947 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTT-CTAAG
* * *
40711989 CGCCGCTAAAGAACATGGTCTCTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
40712024 ATTTGAAAAC
Statistics
Matches: 185, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
41 8 0.04
42 107 0.58
43 62 0.34
44 7 0.04
45 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTAAG
Found at i:40717352 original size:35 final size:35
Alignment explanation
Indices: 40717299--40717425 Score: 139
Period size: 35 Copynumber: 3.6 Consensus size: 35
40717289 TACTATCTTT
* *
40717299 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTTGATTGGACTAGCTCTTATGAGCA
40717334 TTGGTGTGTTTTGATTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTTGATTGGACTAGCTCTTATGAGCA
* * * * * * *
40717369 TTGCTGTGTTTTGGA-GGGATTGGCCCGTGTGAGCA
1 TTGGTGTGTTTT-GATTGGACTAGCTCTTATGAGCA
*
40717404 TCTGGTGTGTTTTGGTTGGACT
1 T-TGGTGTGTTTTGATTGGACT
40717426 GACGATGTAC
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
35 60 0.79
36 16 0.21
ACGTcount: A:0.13, C:0.13, G:0.34, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTTGATTGGACTAGCTCTTATGAGCA
Found at i:40727701 original size:44 final size:43
Alignment explanation
Indices: 40727632--40727796 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 43
40727622 TCCGATATAC
* *
40727632 GATTT-CGTGTAAGACCACGTATGGGACGTTGGCATCAATTTGA
1 GATTTACGTGTAAGACCATGTCTGGGACGTTGGCATCAATTT-A
* * *
40727675 GATTTACGTGTAAGACCATGTCTGGGACATTGGCATC-GTATA
1 GATTTACGTGTAAGACCATGTCTGGGACGTTGGCATCAATTTA
* *
40727717 TGATTTACGTGTAAGACCCTGTGTGGGACAG-TGGCATCTATATTT-
1 -GATTTACGTGTAAGACCATGTCTGGGAC-GTTGGCATC-A-ATTTA
* *
40727762 GA-TTACATGTAAGA-CATCGTCTGGGACGATGGCAT
1 GATTTACGTGTAAGACCAT-GTCTGGGACGTTGGCAT
40727797 TGTACGAGCT
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
42 4 0.04
43 65 0.64
44 30 0.30
46 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
GATTTACGTGTAAGACCATGTCTGGGACGTTGGCATCAATTTA
Found at i:40727795 original size:86 final size:85
Alignment explanation
Indices: 40727627--40727796 Score: 199
Period size: 86 Copynumber: 2.0 Consensus size: 85
40727617 AGAATTCCGA
*
40727627 TATACGATTTCGTGTAAGACCACGTATGGGACGTTGGCATCAATTTGAGATTTACGTGTAAGACC
1 TATACGATTTCGTGTAAGACCACGTATGGGACGTTGGCATCAATTT-AGATTTACATGTAAGACC
40727692 ATGTCTGGGACATTGGCATCG
65 ATGTCTGGGACATTGGCATCG
* *
40727713 TATATGATTTACGTGTAAGACC-CTGTGTGGGACAG-TGGCATCTATATTT-GA-TTACATGTAA
1 TATACGATTT-CGTGTAAGACCAC-GTATGGGAC-GTTGGCATC-A-ATTTAGATTTACATGTAA
40727774 GA-CATCGTCTGGGACGA-TGGCAT
61 GACCAT-GTCTGGGAC-ATTGGCAT
40727797 TGTACGAGCT
Statistics
Matches: 74, Mismatches: 3, Indels: 14
0.81 0.03 0.15
Matches are distributed among these distances:
85 3 0.04
86 36 0.49
87 29 0.39
88 2 0.03
89 4 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (85 bp):
TATACGATTTCGTGTAAGACCACGTATGGGACGTTGGCATCAATTTAGATTTACATGTAAGACCA
TGTCTGGGACATTGGCATCG
Found at i:40735508 original size:22 final size:22
Alignment explanation
Indices: 40735480--40735521 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40735470 GGTTTGGCAG
40735480 AAAAATCCAAAAGAATGAAAGA
1 AAAAATCCAAAAGAATGAAAGA
**
40735502 AAAAATCGTAAAGAATGAAA
1 AAAAATCCAAAAGAATGAAA
40735522 TAACATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.07, G:0.14, T:0.12
Consensus pattern (22 bp):
AAAAATCCAAAAGAATGAAAGA
Found at i:40739273 original size:21 final size:20
Alignment explanation
Indices: 40739247--40739294 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
40739237 GTATATGTGT
*
40739247 GTATATTTACAAAATAAAAAA
1 GTATATATACAAAAT-AAAAA
* *
40739268 GTATATATATAAAATATAAA
1 GTATATATACAAAATAAAAA
40739288 GTATATA
1 GTATATA
40739295 AAAGATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (20 bp):
GTATATATACAAAATAAAAA
Found at i:40739461 original size:24 final size:24
Alignment explanation
Indices: 40739429--40739474 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40739419 ACGTTTATGT
*
40739429 ATAGAAAAT-ATAATAATTATAATG
1 ATAGAAAATGAT-ATAATAATAATG
*
40739453 ATAGTAAATGATATAATAATAA
1 ATAGAAAATGATATAATAATAA
40739475 ATAATGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (24 bp):
ATAGAAAATGATATAATAATAATG
Found at i:40739487 original size:27 final size:27
Alignment explanation
Indices: 40739436--40739498 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
40739426 TGTATAGAAA
*
40739436 ATATAATAATTATAATGATAGTAAATG
1 ATATAATAATAATAATGATAGTAAATG
*
40739463 ATATAATAATAAATAATGGTA-TAAATG
1 ATATAATAAT-AATAATGATAGTAAATG
40739490 -TAATAATAA
1 AT-ATAATAA
40739499 AAAAACAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 23 0.72
28 8 0.25
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.35
Consensus pattern (27 bp):
ATATAATAATAATAATGATAGTAAATG
Found at i:40745570 original size:104 final size:103
Alignment explanation
Indices: 40745277--40745647 Score: 600
Period size: 105 Copynumber: 3.6 Consensus size: 103
40745267 TAGCCGTTAT
** *
40745277 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
40745342 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
40745380 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
40745445 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
40745484 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
* *
40745549 GAATCAGCACATACCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
40745589 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
40745648 TTTATATACA
Statistics
Matches: 253, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
103 78 0.31
104 86 0.34
105 88 0.35
106 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:40750558 original size:23 final size:23
Alignment explanation
Indices: 40750532--40750579 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
40750522 CCGAGAGCAA
40750532 AAAAAGCATGTCA-ACAGACAGAG
1 AAAAAGCATGTCATA-AGACAGAG
40750555 AAAAAGCATGTCATAAGACAGAG
1 AAAAAGCATGTCATAAGACAGAG
40750578 AA
1 AA
40750580 CTTCATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.54, C:0.15, G:0.21, T:0.10
Consensus pattern (23 bp):
AAAAAGCATGTCATAAGACAGAG
Found at i:40753366 original size:30 final size:30
Alignment explanation
Indices: 40753332--40753395 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
40753322 GCTCCTAAAC
* * *
40753332 TTTTCAAAAATTATATTTTGACCCCCAACT
1 TTTTCAAAAATTACATATTGACCCCCAACA
* * *
40753362 TTTTCTAAATTTACATATTGACCCCTAACA
1 TTTTCAAAAATTACATATTGACCCCCAACA
40753392 TTTT
1 TTTT
40753396 GTAAATTACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTTCAAAAATTACATATTGACCCCCAACA
Found at i:40753371 original size:29 final size:29
Alignment explanation
Indices: 40753339--40753408 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 29
40753329 AACTTTTCAA
* *
40753339 AAATTATATTTTGACCCCCAACTTTTTCT
1 AAATTACATTTTGACCCCCAACATTTTCT
* * *
40753368 AAATTTACATATTGACCCCTAACATTTTGT
1 AAA-TTACATTTTGACCCCCAACATTTTCT
40753398 AAATTACATTT
1 AAATTACATTT
40753409 AGGCCCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (29 bp):
AAATTACATTTTGACCCCCAACATTTTCT
Found at i:40754028 original size:13 final size:13
Alignment explanation
Indices: 40753998--40754046 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
40753988 GGCCTGAAGA
*
40753998 AGAAGAAAAAAAAA
1 AGAAG-AAAAAAAG
*
40754012 AGAAGAAAAAGAG
1 AGAAGAAAAAAAG
40754025 AGAAGAAAAAAAG
1 AGAAGAAAAAAAG
40754038 AGAA-AAAAA
1 AGAAGAAAAA
40754047 TATATATCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 5 0.16
13 22 0.69
14 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAG
Found at i:40754045 original size:24 final size:23
Alignment explanation
Indices: 40753997--40754044 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
40753987 CGGCCTGAAG
40753997 AAGAAGAAAAAAAAAAGAAGAAA
1 AAGAAGAAAAAAAAAAGAAGAAA
*
40754020 AAGAGAGAAGAAAAAAAG-AGAAA
1 AAGA-AGAAAAAAAAAAGAAGAAA
40754043 AA
1 AA
40754045 AATATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
AAGAAGAAAAAAAAAAGAAGAAA
Found at i:40754814 original size:17 final size:17
Alignment explanation
Indices: 40754792--40755113 Score: 204
Period size: 17 Copynumber: 17.5 Consensus size: 17
40754782 CGATACGTCT
40754792 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
40754809 TTTCAAAAATTTCTCGTG
1 TTTCAAAAATTT-TCGTG
40754827 TTCTCAAAAAAATTCTT-GTG
1 TT-TC--AAAAATT-TTCGTG
*
40754847 TTT-AAAAATTTTCGTA
1 TTTCAAAAATTTTCGTG
*
40754863 TTTCAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTG
*
40754880 TTT-AAAAATTTTTCGCG
1 TTTCAAAAA-TTTTCGTG
40754897 TTTTCAAAAAAATTTTCGTG
1 -TTTC--AAAAATTTTCGTG
*
40754917 TTTCAAAAATTTTCGCG
1 TTTCAAAAATTTTCGTG
* *
40754934 TTTTCAAAAAAAAATTTCATG
1 -TTTC---AAAAATTTTCGTG
40754955 TTTCAAAGAA-TTTCGTG
1 TTTCAAA-AATTTTCGTG
*
40754972 TTTTCAAAAAAAATTCTCGTG
1 -TTTC---AAAAATTTTCGTG
40754993 TTT-AAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
** *
40755009 TTTTCAAAAAAAAAGTTCTTG
1 -TTTC---AAAAATTTTCGTG
*
40755030 TTTCAAAAGTTTTCGTG
1 TTTCAAAAATTTTCGTG
* *
40755047 TTTTTAAAAAAGTTTCGTG
1 --TTTCAAAAATTTTCGTG
*
40755066 TTTCCAAAAAAATTTCTTGTG
1 TTT-C--AAAAATTT-TCGTG
* *
40755087 CTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
40755104 TTTTCAAAAA
1 -TTTCAAAAA
40755114 ATTATTATGG
Statistics
Matches: 241, Mismatches: 30, Indels: 67
0.71 0.09 0.20
Matches are distributed among these distances:
15 2 0.01
16 29 0.12
17 71 0.29
18 36 0.15
19 21 0.09
20 33 0.14
21 48 0.20
22 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:40754848 original size:38 final size:36
Alignment explanation
Indices: 40754791--40755075 Score: 289
Period size: 37 Copynumber: 7.8 Consensus size: 36
40754781 ACGATACGTC
*
40754791 TTTTC-AAAAATTTTCGTGTTTCAAAAATTTCTCGTG
1 TTTTCAAAAAAATTTCGTGTTTCAAAAATTT-TCGTG
* *
40754827 TTCTCAAAAAAATTCTTGTGTTT-AAAAATTTTCGT-
1 TTTTCAAAAAAATT-TCGTGTTTCAAAAATTTTCGTG
* *
40754862 ATTTC--AAAAATTCTCGTGTTT-AAAAATTTTTCGCG
1 TTTTCAAAAAAATT-TCGTGTTTCAAAAA-TTTTCGTG
*
40754897 TTTTCAAAAAAATTTTCGTGTTTCAAAAATTTTCGCG
1 TTTTCAAAAAAA-TTTCGTGTTTCAAAAATTTTCGTG
*
40754934 TTTTCAAAAAAAAATTTCATGTTTCAAAGAA-TTTCGTG
1 TTTTC--AAAAAAATTTCGTGTTTCAAA-AATTTTCGTG
40754972 TTTTCAAAAAAAATTCTCGTGTTT-AAAAATTTTCGTG
1 TTTTC-AAAAAAATT-TCGTGTTTCAAAAATTTTCGTG
* * *
40755009 TTTTCAAAAAAAAAGTTCTTGTTTCAAAAGTTTTCGTG
1 TTTTC--AAAAAAATTTCGTGTTTCAAAAATTTTCGTG
* *
40755047 TTTTTAAAAAAGTTTCGTGTTTCCAAAAA
1 TTTTCAAAAAAATTTCGTGTTT-CAAAAA
40755076 AATTTCTTGT
Statistics
Matches: 214, Mismatches: 19, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
33 20 0.09
34 6 0.03
35 7 0.03
36 24 0.11
37 78 0.36
38 70 0.33
39 9 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTTCAAAAAAATTTCGTGTTTCAAAAATTTTCGTG
Found at i:40754858 original size:54 final size:56
Alignment explanation
Indices: 40754791--40755114 Score: 187
Period size: 54 Copynumber: 5.8 Consensus size: 56
40754781 ACGATACGTC
* *
40754791 TTTTCAAAAATTTTCGTGTTTCAAAAATTTCTCGTGTTCTCAAAAAAATTCTT-GTG
1 TTTTAAAAAATTTTCGTGTTTCAAAAATTTCTCGTGTT-TCAAAAAAATTCTTCGCG
* *
40754847 -TTT-AAAAATTTTCGTATTTCAAAAA-TTCTCGTGTTT---AAAAATTTTTCGCG
1 TTTTAAAAAATTTTCGTGTTTCAAAAATTTCTCGTGTTTCAAAAAAATTCTTCGCG
* * **
40754897 TTTTCAAAAAAATTTTCGTGTTTCAAAAATTT-TCGCGTTTTCAAAAAAAAAT-TTCATG
1 TTTT--AAAAAATTTTCGTGTTTCAAAAATTTCTCGTG-TTTC-AAAAAAATTCTTCGCG
* * * *
40754955 TTTCAAAGAA-TTTCGTGTTTTCAAAAAAAATTCTCGTGTTT---AAAAATT-TTCGTG
1 TTTTAAAAAATTTTCGTG-TTTC--AAAAATTTCTCGTGTTTCAAAAAAATTCTTCGCG
** * * ** * *
40755009 TTTTCAAAAAAAAAGTTCTTGTTTCAAAAGTTT-TCGTGTTTTTAAAAAAGT-TTCGTG
1 TTTT---AAAAAATTTTCGTGTTTCAAAAATTTCTCGTGTTTCAAAAAAATTCTTCGCG
* * *
40755066 TTTCCAAAAAAATTTCTTGTGCTTCAAAAATTTC-CGTGTTTTCAAAAAA
1 TTT--TAAAAAATTT-TCGTGTTTCAAAAATTTCTCGTG-TTTCAAAAAA
40755115 TTATTATGGT
Statistics
Matches: 211, Mismatches: 30, Indels: 52
0.72 0.10 0.18
Matches are distributed among these distances:
49 9 0.04
50 2 0.01
51 3 0.01
52 1 0.00
53 10 0.05
54 68 0.32
55 21 0.10
56 16 0.08
57 41 0.19
58 30 0.14
59 10 0.05
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (56 bp):
TTTTAAAAAATTTTCGTGTTTCAAAAATTTCTCGTGTTTCAAAAAAATTCTTCGCG
Found at i:40755074 original size:37 final size:37
Alignment explanation
Indices: 40754796--40755075 Score: 292
Period size: 38 Copynumber: 7.6 Consensus size: 37
40754786 ACGTCTTTTC
* *
40754796 AAAAATTTTCGTGTTTCAAAAATTTCTCGTGTTCTC-A
1 AAAAAATTTCGTGTTTCAAAAATTT-TCGTGTTTTCAA
* *
40754833 AAAAAATTCTTGTGTTT-AAAAATTTTCGT-ATTTC--
1 AAAAAATT-TCGTGTTTCAAAAATTTTCGTGTTTTCAA
*
40754867 -AAAAATTCTCGTGTTT-AAAAATTTTTCGCGTTTTCAA
1 AAAAAATT-TCGTGTTTCAAAAA-TTTTCGTGTTTTCAA
* *
40754904 AAAAATTTTCGTGTTTCAAAAATTTTCGCGTTTTCAAA
1 AAAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC-AA
*
40754942 AAAAAATTTCATGTTTCAAAGAA-TTTCGTGTTTTCAA
1 AAAAAATTTCGTGTTTCAAA-AATTTTCGTGTTTTCAA
40754979 AAAAAATTCTCGTGTTT-AAAAATTTTCGTGTTTTCAAA
1 AAAAAATT-TCGTGTTTCAAAAATTTTCGTGTTTTC-AA
* * * *
40755017 AAAAAAGTTCTTGTTTCAAAAGTTTTCGTGTTTT-TA
1 AAAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTCAA
*
40755053 AAAAAGTTTCGTGTTTCCAAAAA
1 AAAAAATTTCGTGTTT-CAAAAA
40755076 AATTTCTTGT
Statistics
Matches: 209, Mismatches: 20, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
33 20 0.10
34 6 0.03
35 7 0.03
36 20 0.10
37 73 0.35
38 81 0.39
39 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (37 bp):
AAAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTCAA
Found at i:40763280 original size:76 final size:76
Alignment explanation
Indices: 40763063--40763690 Score: 830
Period size: 76 Copynumber: 8.3 Consensus size: 76
40763053 AGAATTATAT
40763063 TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTC-ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
*
40763127 CATCTTGAGGTA
65 CATCCTGAGGTA
40763139 TTTTCATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
40763203 ATCCTGAGGTA
66 ATCCTGAGGTA
* *
40763214 TTTTCATTTCTGTTTTTCAAAACAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
*
40763279 ATTCTGAGGTA
66 ATCCTGAGGTA
* *
40763290 TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
*
40763355 --GCTGAGGTA
66 ATCCTGAGGTA
* *
40763364 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGCTGAGTTGAGCCTT-GGTCA
1 TTTTC-ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
*
40763428 C--GCTGAGGTA
65 CATCCTGAGGTA
* *
40763438 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCTG
1 TTTTC-ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG-T-
*
40763503 CAC-GCC-GAGGTA
63 CACATCCTGAGGTA
* * * * *
40763515 TTTTTAATTTCT-TTTTTTAAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCA
1 -TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
*
40763579 CATGCTGAGGTATA
65 CATCCTGAGG--TA
* * ** * * *
40763593 TTTTAATTTCT-ATTTTCCGAAAAATCAACTTATATTGCGAAAGGTGAGTTGAGCCTTGGGTCAT
1 TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
40763657 ATGCC-GAGGTA
66 AT-CCTGAGGTA
*
40763668 TTTTTCAATTTCTATTTTTCAAA
1 -TTTTC-ATTTCTGTTTTTCAAA
40763691 GGTCAACTCA
Statistics
Matches: 498, Mismatches: 39, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
74 86 0.17
75 142 0.29
76 175 0.35
77 81 0.16
78 14 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (76 bp):
TTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
ATCCTGAGGTA
Found at i:40763374 original size:151 final size:150
Alignment explanation
Indices: 40763063--40763690 Score: 865
Period size: 151 Copynumber: 4.1 Consensus size: 150
40763053 AGAATTATAT
*
40763063 TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCA
*
40763127 CATCTTGAGGTATTTTCATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
66 CAGC-TGAGGTATTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
40763191 GCCTTGGGTCACATCCTGAGGTA
130 GCCTCGGGTCAC-GCC-GAGGTA
*
40763214 TTTTC-ATTTCTGTTTTTCAAAACAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCA
* *
40763278 CATTCTGAGGTATTTTCATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGA
66 CA-GCTGAGGTATTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
*
40763343 GCCTCGGGTCACGCTGAGGTA
130 GCCTCGGGTCACGCCGAGGTA
* * *
40763364 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGCTGAGTTGAGCCTT-GGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCA
*
40763428 C-GCTGAGGTATTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
66 CAGCTGAGGTATTTTC-ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
40763492 GCCTCGGGCTGCACGCCGAGGTA
130 GCCTCGGG-T-CACGCCGAGGTA
* * * *
40763515 TTTTTAATTTCT-TTTTTTAAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCA
* * ** * *
40763579 CATGCTGAGGTATATTTTAATTTCT-ATTTTCCGAAAAATCAACTTATATTGCGAAAGGTGAGTT
66 CA-GCTGAGG--TATTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
40763643 GAGCCTTGGGTCATATGCCGAGGTA
128 GAGCCTCGGGTC--ACGCCGAGGTA
*
40763668 TTTTTCAATTTCTATTTTTCAAA
1 -TTTTCAATTTCTGTTTTTCAAA
40763691 GGTCAACTCA
Statistics
Matches: 430, Mismatches: 31, Indels: 28
0.88 0.06 0.06
Matches are distributed among these distances:
148 13 0.03
149 54 0.13
150 71 0.17
151 154 0.36
152 47 0.11
153 60 0.14
154 17 0.04
155 14 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (150 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTCA
CAGCTGAGGTATTTTCATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCGGGTCACGCCGAGGTA
Found at i:40764096 original size:30 final size:30
Alignment explanation
Indices: 40764039--40764096 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
40764029 ACAAAAATAC
* * *
40764039 AAATTAAATTTTAGCCCCTAAATTTTTCAA
1 AAATTAAATTTTAACCCCCAAACTTTTCAA
* *
40764069 AAATTATATTTTAACCCCCAACCTTTTC
1 AAATTAAATTTTAACCCCCAAACTTTTC
40764097 TAAATTTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (30 bp):
AAATTAAATTTTAACCCCCAAACTTTTCAA
Found at i:40764930 original size:21 final size:21
Alignment explanation
Indices: 40764904--40764949 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40764894 CAAACTGTAG
* * *
40764904 AAAAAAAA-AGAAGAAAAAGA
1 AAAAAAAACAAAACAAAAACA
40764924 AAAAAAAACAAAACAAAAACA
1 AAAAAAAACAAAACAAAAACA
40764945 AAAAA
1 AAAAA
40764950 GGCCCGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAACAAAAACA
Found at i:40765507 original size:37 final size:37
Alignment explanation
Indices: 40765408--40765786 Score: 339
Period size: 38 Copynumber: 10.2 Consensus size: 37
40765398 CAATACGTCT
40765408 TTTCAAAAATTTTCGTG-TTTC--AAAAATTTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTT-TCGTG
** * *
40765443 TTTTCAAAAAAATTCTTGTGTTT---AAAAATTTTCGTA
1 -TTTCAAAAATTTTCGTGT-TTTCAAAAAAATTTTCGTG
* *
40765479 TTTCAAAAATTTTCATGTTTTCAAAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAATTTTCGTG
* * *
40765517 TTT-AAAAATTTTTCGCGTTTTCAAAAAATTTTTTGTG
1 TTTCAAAAA-TTTTCGTGTTTTCAAAAAAATTTTCGTG
** **
40765554 TTTCAAAAATTTTCGCATTTTCAAAAAAAAAATTCGTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAATTTTCGTG
* *
40765592 TTTCAAAGAA-TTTCGTGCTTTCAAAAAAAATTCTCGTG
1 TTTCAAA-AATTTTCGTGTTTTC-AAAAAAATTTTCGTG
** *
40765630 TTT-AAAAATTTTCGTGTTTTCAAAAAAAAGTTCTTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTTCGTG
* *
40765666 TTTCAAAAGTTTTCGTGTTTCCAAAAAAAATTTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAATTT-TCGTG
* *
40765705 TTTCAAAAATTTTCGTGTTTTCAAAAAATTATTATGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAA--ATTTTCGTG
* *
40765744 TTTCAAAAA-TCTCGTGTTTT-AAAAAATATATATCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAA-AT-TTTCGTG
40765781 TTTCAA
1 TTTCAA
40765787 TCGGATCACG
Statistics
Matches: 285, Mismatches: 41, Indels: 33
0.79 0.11 0.09
Matches are distributed among these distances:
34 3 0.01
35 15 0.05
36 37 0.13
37 88 0.31
38 100 0.35
39 39 0.14
40 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTTCGTG
Found at i:40765530 original size:38 final size:38
Alignment explanation
Indices: 40765408--40765786 Score: 358
Period size: 37 Copynumber: 10.2 Consensus size: 38
40765398 CAATACGTCT
*
40765408 TTTCAAAAATTTTCGTG-TTTC--AAAAATTTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTCTCGTG
** * * *
40765443 TTTTCAAAAAAATTCTTGTGTTT----AAAAATTTTCGTA
1 -TTTCAAAAATTTTCGTGT-TTTCAAAAAAAATTCTCGTG
*
40765479 TTTCAAAAATTTTCATGTTTTCAAAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTCTCGTG
* * * *
40765517 TTT-AAAAATTTTTCGCGTTTTC-AAAAAATTTTTTGTG
1 TTTCAAAAA-TTTTCGTGTTTTCAAAAAAAATTCTCGTG
** *
40765554 TTTCAAAAATTTTCGCATTTTCAAAAAAAAAAT-TCGTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAAATTCTCGTG
*
40765592 TTTCAAAGAA-TTTCGTGCTTTCAAAAAAAATTCTCGTG
1 TTTCAAA-AATTTTCGTGTTTTCAAAAAAAATTCTCGTG
40765630 TTT-AAAAATTTTCGTGTTTTCAAAAAAAAGTTCT--TG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAA-TTCTCGTG
* *
40765666 TTTCAAAAGTTTTCGTGTTTCCAAAAAAAATTTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAA-TTCTCGTG
* * *
40765705 TTTCAAAAATTTTCGTGTTTTCAAAAAATTATTATGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAA-AATTCTCGTG
* * *
40765744 TTTCAAAAA-TCTCGTGTTTT-AAAAAATATATATCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAT-TCTCGTG
40765781 TTTCAA
1 TTTCAA
40765787 TCGGATCACG
Statistics
Matches: 289, Mismatches: 35, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.01
35 15 0.05
36 34 0.12
37 109 0.38
38 75 0.26
39 52 0.18
40 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (38 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTCTCGTG
Found at i:40765575 original size:75 final size:75
Alignment explanation
Indices: 40765408--40765786 Score: 338
Period size: 75 Copynumber: 5.1 Consensus size: 75
40765398 CAATACGTCT
* ** *
40765408 TTTCAAAAATTTTCGTG-TTTC--AAAAATTTCTCGTGTTTTCAAAAAAATTCTTGTGTTT---A
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTCTCGTG-TTT-AAAAATTTTCGTGT-TTTCAAA
*
40765467 AAAATTT-TCGTA
63 AAAATTTCTCGTG
* *
40765479 TTTCAAAAATTTTCATGTTTTCAAAAAAAATTCTCGTGTTTAAAAATTTTTCGCGTTTTC-AAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTCTCGTGTTTAAAAA-TTTTCGTGTTTTCAAAAA
* *
40765543 AATTTTTTGTG
65 AATTTCTCGTG
** * *
40765554 TTTCAAAAATTTTCGCATTTTCAAAAAAAAAAT-TCGTGTTTCAAAGAA-TTTCGTGCTTTCAAA
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAAATTCTCGTGTTT-AAA-AATTTTCGTGTTTTCAAA
*
40765617 AAAAATTCTCGTG
63 AAAATTTCTCGTG
* *
40765630 TTT-AAAAATTTTCGTGTTTTCAAAAAAAAGTTCT--TGTTTCAAAAGTTTTCGTGTTTCCAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAA-TTCTCGTGTTT-AAAAATTTTCGTGTTTTC-AAA
40765692 AAAATTTCTCGTG
63 AAAATTTCTCGTG
* * * *
40765705 TTTCAAAAATTTTCGTGTTTTCAAAAAATTATTATGGTGTTTCAAAAA-TCTCGTGTTTT-AAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAA-AATTCTCGTGTTT-AAAAATTTTCGTGTTTTCAAAA
* *
40765768 AATATATATCGTG
64 AA-ATTTCTCGTG
40765781 TTTCAA
1 TTTCAA
40765787 TCGGATCACG
Statistics
Matches: 257, Mismatches: 31, Indels: 35
0.80 0.10 0.11
Matches are distributed among these distances:
71 16 0.06
72 12 0.05
73 9 0.04
74 48 0.19
75 81 0.32
76 69 0.27
77 12 0.05
78 10 0.04
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (75 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTCTCGTGTTTAAAAATTTTCGTGTTTTCAAAAAA
ATTTCTCGTG
Found at i:40766869 original size:19 final size:18
Alignment explanation
Indices: 40766819--40766869 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
40766809 ATTAATTAAT
*
40766819 TTTTTAAAAATTAAAATA
1 TTTTTAAAATTTAAAATA
**
40766837 TTTTATAATTTTTAAAATAA
1 TTTT-TAAAATTTAAAAT-A
40766857 TTTTTAAAATTTA
1 TTTTTAAAATTTA
40766870 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 4 0.15
19 17 0.65
20 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTAAAATTTAAAATA
Found at i:40766872 original size:13 final size:12
Alignment explanation
Indices: 40766841--40766876 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
40766831 AAAATATTTT
40766841 ATAATTTTTAAA
1 ATAATTTTTAAA
40766853 ATAATTTTTAAA
1 ATAATTTTTAAA
*
40766865 ATTTATTTTTAA
1 A-TAATTTTTAA
40766877 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAATTTTTAAA
Done.