Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 35
Found at i:2302832 original size:15 final size:15
Alignment explanation
Indices: 2302778--2302838 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
2302768 ATATTAAGTT
*
2302778 TTATATATATTAATA
1 TTATATATATTACTA
2302793 TTATATATATTAC--
1 TTATATATATTACTA
2302806 TT-T-T-TA--ACTA
1 TTATATATATTACTA
2302816 TTATATATATTACTA
1 TTATATATATTACTA
2302831 TTATATAT
1 TTATATAT
2302839 TACTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
8 2 0.05
10 4 0.11
11 2 0.05
12 2 0.05
13 4 0.11
15 24 0.63
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATATATTACTA
Found at i:2302860 original size:36 final size:38
Alignment explanation
Indices: 2302778--2302865 Score: 153
Period size: 36 Copynumber: 2.4 Consensus size: 38
2302768 ATATTAAGTT
*
2302778 TTATATATATTAATATTATATATATTACTTTTTAACTA
1 TTATATATATTACTATTATATATATTACTTTTTAACTA
2302816 TTATATATATTACTA-T-TATATATTACTTTTTAACTA
1 TTATATATATTACTATTATATATATTACTTTTTAACTA
2302852 TTATATATATTACT
1 TTATATATATTACT
2302866 TTTTCTAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 34 0.69
37 1 0.02
38 14 0.29
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (38 bp):
TTATATATATTACTATTATATATATTACTTTTTAACTA
Found at i:2304677 original size:28 final size:28
Alignment explanation
Indices: 2304645--2304701 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2304635 TTTTTATTTT
* * *
2304645 GCCCCTGGAATTTTATAAGTTCAAGTTC
1 GCCCCTAGAACTTTAAAAGTTCAAGTTC
2304673 GCCCCTAGAACTTTAAAAGTTCAAGTTC
1 GCCCCTAGAACTTTAAAAGTTCAAGTTC
2304701 G
1 G
2304702 TCATCCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (28 bp):
GCCCCTAGAACTTTAAAAGTTCAAGTTC
Found at i:2312347 original size:17 final size:19
Alignment explanation
Indices: 2312325--2312368 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2312315 ATAATTATAT
2312325 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
2312342 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
2312361 ATATATTA
1 AAATATTA
2312369 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:2312360 original size:19 final size:18
Alignment explanation
Indices: 2312312--2312372 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
2312302 TTCTAAATAA
* *
2312312 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
2312329 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
2312346 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
2312365 ATTAATAT
1 A-TAATAT
2312373 AAAAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 4 0.11
19 8 0.23
20 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:2312361 original size:34 final size:34
Alignment explanation
Indices: 2312306--2312413 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 34
2312296 TAATAATTCT
* * *
2312306 AAATAAATAATAATTATATAAATATTATT-TTAATAA
1 AAAT-AATAATATTTACATAAATA-TATTAAT-ATAA
2312342 AAAT-ATAATATTTACATAAATATATTAATATAA
1 AAATAATAATATTTACATAAATATATTAATATAA
* * *
2312375 AAATAATAACTATTTA-A-AAAAATACTAACATAA
1 AAATAATAA-TATTTACATAAATATATTAATATAA
2312408 AAATAA
1 AAATAA
2312414 ATTTCTTACC
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 31 0.49
34 22 0.35
35 6 0.10
36 4 0.06
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (34 bp):
AAATAATAATATTTACATAAATATATTAATATAA
Found at i:2312370 original size:31 final size:33
Alignment explanation
Indices: 2312310--2312383 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
2312300 AATTCTAAAT
*
2312310 AAATAATAATTATATAAATATTATTTTAATA-AA
1 AAATAATAATTACATAAATATTA-TTTAATATAA
*
2312343 AATATAATATTTACATAAATA-TA-TTAATATAA
1 AA-ATAATAATTACATAAATATTATTTAATATAA
2312375 AAATAATAA
1 AAATAATAA
2312384 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 12 0.33
32 4 0.11
33 4 0.11
34 16 0.44
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
AAATAATAATTACATAAATATTATTTAATATAA
Found at i:2313287 original size:71 final size:71
Alignment explanation
Indices: 2313169--2313300 Score: 237
Period size: 71 Copynumber: 1.9 Consensus size: 71
2313159 AGATCCAAGG
*
2313169 GTCTGCATGCGCCGACTGAAGCAACTAGGGTTACAAGACATTGGGGTTTCTTTGGTTGTTGATAT
1 GTCTGCATGCGCCGACTGAAGCAACTAGGGTTACAAGACATTAGGGTTTCTTTGGTTGTTGATAT
2313234 CTAAGT
66 CTAAGT
**
2313240 GTCTGCATGCGCCGACTGAAGCAACTAGGGTTAGGAGACATTAGGGTTTCTTTGGTTGTTG
1 GTCTGCATGCGCCGACTGAAGCAACTAGGGTTACAAGACATTAGGGTTTCTTTGGTTGTTG
2313301 GGCCCATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (71 bp):
GTCTGCATGCGCCGACTGAAGCAACTAGGGTTACAAGACATTAGGGTTTCTTTGGTTGTTGATAT
CTAAGT
Found at i:2313826 original size:2 final size:2
Alignment explanation
Indices: 2313819--2313844 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2313809 ACTAAGTTCA
2313819 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
2313845 TGATACTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2315585 original size:257 final size:257
Alignment explanation
Indices: 2315122--2315640 Score: 966
Period size: 257 Copynumber: 2.0 Consensus size: 257
2315112 CCCTTGAAAA
2315122 GAGATCAATCCCTTGGATTCCATTAGGTTTTTGATTGATCCCTTTTACAAAAGGATCGATCCCTT
1 GAGATCAATCCCTTGGATTCCATTAGGTTTTTGATTGATCCCTTTTACAAAAGGATCGATCCCTT
*
2315187 GTGCATTAAATGTTTTTTTAATTGTAGGTAATGGTTATAATGGTCTTCAACGGCTCCAAACAACT
66 GTGCATTAAATGTTTTTTTAATTGTAGGTAATGGTTATAATGATCTTCAACGGCTCCAAACAACT
2315252 AGAATTGATGGAAAATGTATAAATTGAAGGTCAAAGCATCCCAAGGTCAACTAGAACCATATTGA
131 AGAATTGATGGAAAATGTATAAATTGAAGGTCAAAGCATCCCAAGGTCAACTAGAACCATATTGA
*
2315317 TCAAATATGCCAATGATTAGTATTTAAATTATACATTATTTTATGATTAATTACTCATTGAT
196 TCAAATATGCCAATAATTAGTATTTAAATTATACATTATTTTATGATTAATTACTCATTGAT
* *
2315379 GAGATCGATCCCTTGGATTCCATTAGGTTTTTGATTGATCCCTTTTACAAATGGATCGATCCCTT
1 GAGATCAATCCCTTGGATTCCATTAGGTTTTTGATTGATCCCTTTTACAAAAGGATCGATCCCTT
*
2315444 GTGCATTAAATGTTTTTTTAATTGTAGGTAATGGTTATAATGATCTTCAACGGCTCCAAACAGCT
66 GTGCATTAAATGTTTTTTTAATTGTAGGTAATGGTTATAATGATCTTCAACGGCTCCAAACAACT
*
2315509 AGAATTGATGGGAAATGTATAAATTGAAGGTCAAAGCATCCCAAGGTCAACTAGAACCATATTGA
131 AGAATTGATGGAAAATGTATAAATTGAAGGTCAAAGCATCCCAAGGTCAACTAGAACCATATTGA
*
2315574 TCAAATATGCCAATAATTAGTATTTAAATTATACATTATTTTATGATTAATTACTCCTTGAT
196 TCAAATATGCCAATAATTAGTATTTAAATTATACATTATTTTATGATTAATTACTCATTGAT
*
2315636 TAGAT
1 GAGAT
2315641 AATTTTAGTT
Statistics
Matches: 254, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
257 254 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (257 bp):
GAGATCAATCCCTTGGATTCCATTAGGTTTTTGATTGATCCCTTTTACAAAAGGATCGATCCCTT
GTGCATTAAATGTTTTTTTAATTGTAGGTAATGGTTATAATGATCTTCAACGGCTCCAAACAACT
AGAATTGATGGAAAATGTATAAATTGAAGGTCAAAGCATCCCAAGGTCAACTAGAACCATATTGA
TCAAATATGCCAATAATTAGTATTTAAATTATACATTATTTTATGATTAATTACTCATTGAT
Found at i:2316009 original size:21 final size:21
Alignment explanation
Indices: 2315966--2316009 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2315956 AAATTCAAGG
** **
2315966 TTTTAGGATTTATCTTTTTAT
1 TTTTAGGATTTAAATTTAAAT
2315987 TTTTAGGATTTAAATTTAAAT
1 TTTTAGGATTTAAATTTAAAT
2316008 TT
1 TT
2316010 AAATAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTTAGGATTTAAATTTAAAT
Found at i:2316698 original size:13 final size:13
Alignment explanation
Indices: 2316680--2316723 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
2316670 TTGAATTTTA
2316680 TTTTAAACTTTCT
1 TTTTAAACTTTCT
2316693 TTTTAAA-TTTCT
1 TTTTAAACTTTCT
*
2316705 TTTTAATC-TTC-
1 TTTTAAACTTTCT
2316716 TTTTAAAC
1 TTTTAAAC
2316724 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 14 0.50
13 7 0.25
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTAAACTTTCT
Found at i:2318593 original size:3 final size:3
Alignment explanation
Indices: 2318585--2318628 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
2318575 TTTCATCCTG
* *
2318585 TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA ATA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2318629 TTACATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2318636 original size:18 final size:18
Alignment explanation
Indices: 2318586--2318637 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2318576 TTCATCCTGT
*
2318586 TATTATTATT-ATATTTAT
1 TATTATTATTAATA-TTAA
2318604 TATTATTATTAATATTAA
1 TATTATTATTAATATTAA
2318622 TATTATT-TTACATATT
1 TATTATTATTA-ATATT
2318638 TGGCAGGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 3 0.10
18 25 0.81
19 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTATTAATATTAA
Found at i:2328025 original size:4 final size:4
Alignment explanation
Indices: 2328016--2328069 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
2328006 TTTCCATTCT
* *
2328016 TTTA TTTA TTTA TTTA TTTA TTTC TTT- TTTA TATA -TTA -TTA TTTCA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A
2328062 TTCTA TTT
1 TT-TA TTT
2328070 TGATATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
3 8 0.19
4 28 0.65
5 6 0.14
6 1 0.02
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:2328065 original size:25 final size:25
Alignment explanation
Indices: 2328005--2328075 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
2327995 AAATATCATC
2328005 ATTTCCATTCTTTTATT-TATTTATTT
1 ATTT-CATTCTTTT-TTATATTTATTT
2328031 ATTT-ATTTCTTTTTTATATATTA-TT
1 ATTTCA-TTCTTTTTTATAT-TTATTT
*
2328056 ATTTCATTCTATTTTGATAT
1 ATTTCATTCT-TTTTTATAT
2328076 GGGATAGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
24 3 0.08
25 20 0.51
26 16 0.41
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (25 bp):
ATTTCATTCTTTTTTATATTTATTT
Found at i:2332889 original size:47 final size:48
Alignment explanation
Indices: 2332821--2332951 Score: 192
Period size: 47 Copynumber: 2.8 Consensus size: 48
2332811 ACTTCTCCAT
* *
2332821 ATTTGATATTCCCTTCAGAGTAAGTGGAATATGTCTCTCTTCTTCAAG
1 ATTTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTCATCAAG
* * * *
2332869 ATTTGATATTCCC-TCAGAGTAAGAGGAACATGTTTCTTTTCATCATG
1 ATTTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTCATCAAG
*
2332916 ATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 ATTTGATATTCCCTTCAGAGTAAGTGGAACATGTCT
2332952 GCTTCGATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 41 0.56
48 32 0.44
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (48 bp):
ATTTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTCATCAAG
Found at i:2333083 original size:113 final size:113
Alignment explanation
Indices: 2332867--2333294 Score: 637
Period size: 113 Copynumber: 3.8 Consensus size: 113
2332857 CTCTTCTTCA
* * * * * * *
2332867 AGATTTGATATTCCC-TCAGAGTAAGAGGAACATGTTTCTTTTCATCATGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTT
*
2332931 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCTCCC
66 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCCCCC
* *
2332979 AGATCTGATATTCCCTTCGGAGTAAGCGGAACAGGTTTCTCTTCTTCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTT
*
2333044 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCCCCC
* * * *
2333092 AGATATGATATTCCCTACGGAGTAAGCGGAACATGTCTCTCTTCTTCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTT
2333157 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCCCCC
66 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCCCCC
* * * * *
2333205 AGATCT-AGTATTCCCTCCAGAGTAAGTGGAATAGGTCTCTCTTCTTCAAGATTTGAAATTCCTT
1 AGATCTGA-TATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCT
*
2333269 TCAGAGTAAGCGGAACAAGTCT-CTTC
65 TCAGAGTAAGTGGAACAAGTCTGCTTC
2333295 TTCAAGATTT
Statistics
Matches: 291, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
112 19 0.07
113 272 0.93
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (113 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCCCCC
Found at i:2333291 original size:48 final size:48
Alignment explanation
Indices: 2333214--2333336 Score: 178
Period size: 46 Copynumber: 2.6 Consensus size: 48
2333204 CAGATCTAGT
* * *
2333214 ATTCCCTCCAGAGTAAGTGGAATAGGTCTCTCTTCTTCAAGATTTGAA
1 ATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTTCAAGATTTGAA
* * *
2333262 ATTCCTTTCAGAGTAAGCGGAACAAG--TCTCTTCTTCAAGATTTGAT
1 ATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTTCAAGATTTGAA
2333308 ATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 ATTCCCTTCAGAGTAAGTGGAACAAGTCT
2333337 GTTTCGATTC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
46 43 0.66
48 22 0.34
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (48 bp):
ATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTTCAAGATTTGAA
Found at i:2333418 original size:159 final size:159
Alignment explanation
Indices: 2333092--2333652 Score: 874
Period size: 159 Copynumber: 3.5 Consensus size: 159
2333082 CAACTCCCCC
* * * *
2333092 AGATATGATATTCCCTACGGAGTAAGCGGAACATGTCTCTCTTCTTCAAGATTTGATATTCCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTTCAAGATTTGATATTCCCTT
*
2333157 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCCCCCAGATCT-AGTATTCCCT
64 CAGAGTAAGTGGAACAAGTCTGTTTCGATTCAATGGATCAATTCCCCCAGATCTGA-TATTCCCT
* *
2333221 CCAGAGTAAGTGGAATAGGTCTCTCTTCTTCA
128 TCAGAGTAAGTGGAACAGGTCTCTCTTCTTCA
* *
2333253 AGATTTGAAATTCCTTTCAGAGTAAGCGGAACAAGTCTCTTCTTCAAGATTTGATATTCCCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTTCAAGATTTGATATTCCCTTCA
*
2333318 GAGTAAGTGGAACAAGTCTGTTTCGATTCAATGGATCAATTCTCCCAGATCTGATATTCCCTTCA
66 GAGTAAGTGGAACAAGTCTGTTTCGATTCAATGGATCAATTCCCCCAGATCTGATATTCCCTTCA
*
2333383 GAGTAAGTGGAACAGGTCTATCTTCTTCA
131 GAGTAAGTGGAACAGGTCTCTCTTCTTCA
*
2333412 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTTCAAGATTTGATTTTCCCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTTCAAGATTTGATATTCCCTTCA
* * * *
2333477 GAGTAAGTGGAACAAGTCTGTTTCAATTCAATGGATTAACTCCCCCAGATCTGATATTCCCTTCG
66 GAGTAAGTGGAACAAGTCTGTTTCGATTCAATGGATCAATTCCCCCAGATCTGATATTCCCTTCA
*
2333542 GAGTAAGTGGAACAGGTCTCTTTTCTTCA
131 GAGTAAGTGGAACAGGTCTCTCTTCTTCA
* *
2333571 AGATTTGATATTCCCTTCAGAATAAGCGGAACAAGTCTTTCTTCTTCAAGATTTGATATACCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTC--TCTTCTTCAAGATTTGATATTCCCTT
*
2333636 CAGCA-AAAGTGGAACAA
64 CAG-AGTAAGTGGAACAA
2333653 ATCCCTCTCA
Statistics
Matches: 371, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
159 302 0.81
160 1 0.00
161 67 0.18
162 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (159 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTTCAAGATTTGATATTCCCTTCA
GAGTAAGTGGAACAAGTCTGTTTCGATTCAATGGATCAATTCCCCCAGATCTGATATTCCCTTCA
GAGTAAGTGGAACAGGTCTCTCTTCTTCA
Found at i:2333443 original size:48 final size:47
Alignment explanation
Indices: 2333364--2333495 Score: 212
Period size: 46 Copynumber: 2.8 Consensus size: 47
2333354 CAATTCTCCC
* *
2333364 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTATCTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT-TCTTCTTCA
*
2333412 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTC-TCTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCTTCTTCA
*
2333458 AGATTTGATTTTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
2333496 GTTTCAATTC
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
46 44 0.56
48 34 0.44
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (47 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCTTCTTCA
Found at i:2333570 original size:272 final size:269
Alignment explanation
Indices: 2332798--2333608 Score: 942
Period size: 272 Copynumber: 3.0 Consensus size: 269
2332788 TTTGAACCCA
* * *
2332798 ATTCAATGGATCAACTTCT-CCATATTTGATATTCCCTTCAGAGTAAGTGGAATATGTCTCTCTT
1 ATTCAATGGATCAA-TTCTCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTT
* * *
2332862 CTTCAAGATTTGATATTCCC-TCAGAGTAAGAGGAACATGTTTCTT-TTCATCATGATTTGATAT
65 CTTCAAGATTTGATATTCCCTTCAGAGTAAGAGGAACAAGTCTCTTCTTCA--ATGATTTGATTT
* *
2332925 TCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTCTCCCAGATCTGATAT
128 TCCCTTCAGAGTAAGTGGAACAAGTCTGTTTC-ATTCAATGGATTAA-TC-CCCAGATCTGATAT
*
2332990 TCCCTTCGGAGTAAGCGGAACAGGTTTCTCTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGTG
190 TCCCTTCGGAGTAAGCGGAACAGGTCTCT-TTCTTCAAGATTTGATATTCCCTTCAGAGTAAGTG
2333055 GAACAAGTCTGCTTCG
254 GAACAAGTCTGCTTCG
* * * * *
2333071 ATTCAATGGATCAACTCCCCCAGATATGATATTCCCTACGGAGTAAGCGGAACATGTCTCTCTTC
1 ATTCAATGGATCAATTCTCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTC
*
2333136 TTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAATTC
66 TTCAAGATTTGATATTCCCTTCAGAGTAAGAGGAACAAGTCT-CTTC--TTCAAT-GAT---TT-
* * * *
2333201 CCCCAGATCTAGTATTCCCTCCAGAGTAAGTGGAATAGGTCTCTCTTC-TTCAA--GATT--T--
123 -----GA--T--T-TTCCCTTCAGAGTAAGTGGAACAAGTCTGT-TTCATTCAATGGATTAATCC
* * *
2333259 ---GA----A-ATTCCTTTCAGAGTAAGCGGAACAAGTCTC-TTCTTCAAGATTTGATATTCCCT
177 CCAGATCTGATATTCCCTTCGGAGTAAGCGGAACAGGTCTCTTTCTTCAAGATTTGATATTCCCT
*
2333315 TCAGAGTAAGTGGAACAAGTCTGTTTCG
242 TCAGAGTAAGTGGAACAAGTCTGCTTCG
* * *
2333343 ATTCAATGGATCAATTCTCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTATCTTC
1 ATTCAATGGATCAATTCTCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTC
*
2333408 TTCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTTCAA-GATTTGATTTTCC
66 TTCAAGATTTGATATTCCCTTCAGAGTAAGAGGAACAAGTCTCTTCTTCAATGATTTGATTTTCC
2333472 CTTCAGAGTAAGTGGAACAAGTCTGTTTCAATTCAATGGATTAACTCCCCCAGATCTGATATTCC
131 CTTCAGAGTAAGTGGAACAAGTCTGTTTC-ATTCAATGGATTAA-T-CCCCAGATCTGATATTCC
* * *
2333537 CTTCGGAGTAAGTGGAACAGGTCTCTTTTCTTCAAGATTTGATATTCCCTTCAGAATAAGCGGAA
193 CTTCGGAGTAAGCGGAACAGGTCTC-TTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAA
2333602 CAAGTCT
257 CAAGTCT
2333609 TTCTTCTTCA
Statistics
Matches: 454, Mismatches: 42, Indels: 85
0.78 0.07 0.15
Matches are distributed among these distances:
252 3 0.01
253 26 0.06
254 6 0.01
256 5 0.01
258 2 0.00
259 1 0.00
264 2 0.00
265 2 0.00
267 3 0.01
269 6 0.01
270 26 0.06
271 4 0.01
272 193 0.43
273 73 0.16
274 45 0.10
275 4 0.01
276 2 0.00
277 3 0.01
278 4 0.01
279 2 0.00
280 2 0.00
285 1 0.00
286 2 0.00
288 4 0.01
290 5 0.01
291 25 0.06
292 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (269 bp):
ATTCAATGGATCAATTCTCCCAGATATGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTC
TTCAAGATTTGATATTCCCTTCAGAGTAAGAGGAACAAGTCTCTTCTTCAATGATTTGATTTTCC
CTTCAGAGTAAGTGGAACAAGTCTGTTTCATTCAATGGATTAATCCCCAGATCTGATATTCCCTT
CGGAGTAAGCGGAACAGGTCTCTTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG
TCTGCTTCG
Found at i:2333602 original size:48 final size:48
Alignment explanation
Indices: 2333523--2333682 Score: 182
Period size: 48 Copynumber: 3.3 Consensus size: 48
2333513 TAACTCCCCC
* * * *
2333523 AGATCTGATATTCCCTTCGGAGTAAGTGGAACAGGTCTCTTTTCTTCA
1 AGATTTGATATTCCCTTCAGAATAAGTGGAACAAGTCTCTTTTCTTCA
*
2333571 AGATTTGATATTCCCTTCAGAATAAGCGGAACAAGTCT-TTCTTCTTCA
1 AGATTTGATATTCCCTTCAGAATAAGTGGAACAAGTCTCTT-TTCTTCA
* * * * *
2333619 AGATTTGATATACCCTTCAGCAA-AAGTGGAACAAATC-CCTCTCATGCA
1 AGATTTGATATTCCCTTCAG-AATAAGTGGAACAAGTCTCTTTTC-TTCA
2333667 AGATTTGATATTCCCT
1 AGATTTGATATTCCCT
2333683 GAGTGACAGC
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
47 4 0.04
48 90 0.94
49 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAATAAGTGGAACAAGTCTCTTTTCTTCA
Found at i:2339921 original size:14 final size:14
Alignment explanation
Indices: 2339902--2339931 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2339892 TTTGGCTCAA
2339902 TGGATCAATCCCTT
1 TGGATCAATCCCTT
*
2339916 TGGATCGATCCCTT
1 TGGATCAATCCCTT
2339930 TG
1 TG
2339932 ACTAGAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (14 bp):
TGGATCAATCCCTT
Found at i:2342253 original size:6 final size:6
Alignment explanation
Indices: 2342242--2342317 Score: 125
Period size: 6 Copynumber: 12.7 Consensus size: 6
2342232 ATCATATACA
* *
2342242 ATATAC ATATAC ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
2342290 ATATAT ATATAT ATATAT ATACAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATAT
2342318 CATGAAAGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:2342265 original size:8 final size:8
Alignment explanation
Indices: 2342242--2342317 Score: 125
Period size: 8 Copynumber: 9.5 Consensus size: 8
2342232 ATCATATACA
*
2342242 ATATACAT
1 ATATATAT
*
2342250 ATACATAT
1 ATATATAT
2342258 ATATATAT
1 ATATATAT
2342266 ATATATAT
1 ATATATAT
2342274 ATATATAT
1 ATATATAT
2342282 ATATATAT
1 ATATATAT
2342290 ATATATAT
1 ATATATAT
2342298 ATATATAT
1 ATATATAT
*
2342306 ATATACAT
1 ATATATAT
2342314 ATAT
1 ATAT
2342318 CATGAAAGGT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 64 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (8 bp):
ATATATAT
Found at i:2344568 original size:64 final size:63
Alignment explanation
Indices: 2344500--2344677 Score: 180
Period size: 64 Copynumber: 2.8 Consensus size: 63
2344490 GAACACTTGA
* * *
2344500 TGCATCGGTGCACCAAGTGTGCATCTATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-G
1 TGCATCGATGCA-CAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAG
** * **
2344564 TGCATCGATGCA-TGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGA
1 TGCATCGATGCACAAG--TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGA
2344628 G
63 G
* * * *
2344629 TGCATCGATGCATAGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCACA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
2344678 CAATTAATTC
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
64 49 0.52
65 43 0.46
67 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCACAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
Found at i:2344651 original size:65 final size:65
Alignment explanation
Indices: 2344518--2344677 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
2344508 TGCACCAAGT
* * * ***
2344518 GTGCATCTATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATAGAGA
* **
2344582 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATAGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATAGAG
2344646 A
65 A
* *
2344647 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
2344678 CAATTAATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 35 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATAGAGA
Found at i:2344717 original size:65 final size:65
Alignment explanation
Indices: 2344527--2344726 Score: 191
Period size: 65 Copynumber: 3.1 Consensus size: 65
2344517 TGTGCATCTA
* ** *
2344527 TGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTTG-TGCATC
1 TGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-TGATGCATC
*
2344589 GA
64 GG
* * *
2344591 TGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATAGA--GAGTGCATC
1 TGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA-TGCATC
2344654 GG
64 GG
* *
2344656 TGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGACTGATGCAT
1 TGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGACTGATGCAT
2344718 CGG
63 CGG
2344721 TGCATG
1 TGCATG
2344727 CCTTTGAATA
Statistics
Matches: 114, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 42 0.37
65 59 0.52
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGATGCATCGG
Found at i:2349891 original size:15 final size:15
Alignment explanation
Indices: 2349871--2349909 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2349861 TTCTTGTTCC
2349871 TCTTCATCGGAACTT
1 TCTTCATCGGAACTT
2349886 TCTTCATCGGAACTT
1 TCTTCATCGGAACTT
2349901 TCTTCATCG
1 TCTTCATCG
2349910 CTCCATGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (15 bp):
TCTTCATCGGAACTT
Found at i:2351736 original size:64 final size:64
Alignment explanation
Indices: 2351683--2351845 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
2351673 CGGTGCACCA
*
2351683 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
2351747 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
2351812 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
2351846 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:2351817 original size:19 final size:19
Alignment explanation
Indices: 2351793--2351843 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2351783 GAAAATATTC
2351793 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2351812 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2351831 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2351844 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2351885 original size:65 final size:65
Alignment explanation
Indices: 2351687--2351894 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
2351677 GCACCAAGTG
* * ** *
2351687 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
2351750 G-
64 GA
* * *
2351751 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
2351814 A
65 A
* *
2351815 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
2351877 CTGA
62 CTGA
2351881 TGCATCGGTGCATG
1 TGCATCGGTGCATG
2351895 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 51 0.41
65 60 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:2352476 original size:15 final size:15
Alignment explanation
Indices: 2352458--2352575 Score: 50
Period size: 15 Copynumber: 7.9 Consensus size: 15
2352448 CATAAGTTTA
2352458 TATATAAACTATATTT
1 TATATAAACTATA-TT
2352474 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
** *
2352493 TATTATAAGTTATATA
1 TA-TATAAACTATATT
* **
2352509 TATATAAATTACGTT
1 TATATAAACTATATT
*
2352524 TATATGAA-T-TA--
1 TATATAAACTATATT
*
2352535 TATATAAAC--TATG
1 TATATAAACTATATT
*
2352548 TATATAAACTATATA
1 TATATAAACTATATT
*
2352563 TGTATAAACTATA
1 TATATAAACTATA
2352576 AAAAGTATAT
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
11 9 0.11
13 9 0.11
14 1 0.01
15 31 0.39
16 2 0.03
17 3 0.04
18 24 0.30
19 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:2352483 original size:18 final size:18
Alignment explanation
Indices: 2352432--2352489 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 18
2352422 AAAATATATA
2352432 ATTTATATTAATATAAC-AT
1 ATTTATATT-ATA-AACTAT
2352451 AAGTTTATA-TATAAACTAT
1 -A-TTTATATTATAAACTAT
2352470 ATTTATATTATAAACTAT
1 ATTTATATTATAAACTAT
2352488 AT
1 AT
2352490 AATTATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.17
18 16 0.46
19 5 0.14
20 2 0.06
21 6 0.17
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTATATTATAAACTAT
Found at i:2352496 original size:18 final size:17
Alignment explanation
Indices: 2352455--2352500 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
2352445 TAACATAAGT
*
2352455 TTATATATAAACTATATT
1 TTAT-TATAAACTATATA
2352473 TATATTATAAACTATATAA
1 T-TATTATAAACTATAT-A
2352492 TTATTATAA
1 TTATTATAA
2352501 GTTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTATAAACTATATA
Found at i:2352551 original size:13 final size:13
Alignment explanation
Indices: 2352533--2352575 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2352523 TTATATGAAT
2352533 TATATATAAACTA
1 TATATATAAACTA
*
2352546 TGTATATAAACTA
1 TATATATAAACTA
2352559 TATATGTATAAACTA
1 TATA--TATAAACTA
2352574 TA
1 TA
2352576 AAAAGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2352656 original size:75 final size:75
Alignment explanation
Indices: 2352563--2352705 Score: 250
Period size: 75 Copynumber: 1.9 Consensus size: 75
2352553 AAACTATATA
*
2352563 TGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATATTAATAAATATATATATATA
1 TGTATAAACTAGAAAAAGTATATAGTTTATAAACTATAATTTATATTAATAAATATATATATATA
2352628 TATGTGTGTG
66 TATGTGTGTG
* * *
2352638 TGTATAAACTAGATAAAGTATATAGTTTATAAATTATAATTTATATTAATATATATATATATATA
1 TGTATAAACTAGAAAAAGTATATAGTTTATAAACTATAATTTATATTAATAAATATATATATATA
2352703 TAT
66 TAT
2352706 ATATATATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (75 bp):
TGTATAAACTAGAAAAAGTATATAGTTTATAAACTATAATTTATATTAATAAATATATATATATA
TATGTGTGTG
Found at i:2352693 original size:2 final size:2
Alignment explanation
Indices: 2352686--2352724 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2352676 ATTTATATTA
2352686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2352725 GTTTATAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2353072 original size:19 final size:19
Alignment explanation
Indices: 2353032--2353104 Score: 101
Period size: 20 Copynumber: 3.7 Consensus size: 19
2353022 TACATGTATG
* *
2353032 TATAAAATATGTATAGTATA
1 TATAAACTATATATA-TATA
2353052 TATAAACTATATATATATA
1 TATAAACTATATATATATA
2353071 TATATAACCTATATATATATA
1 TATA-AA-CTATATATATATA
2353092 TATAAACTATATA
1 TATAAACTATATA
2353105 AAGTAAATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 15 0.31
20 17 0.35
21 17 0.35
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:2353074 original size:21 final size:21
Alignment explanation
Indices: 2353038--2353104 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 21
2353028 TATGTATAAA
*
2353038 ATATGTATAGTATATATAAACT
1 ATATATATA-TATATATAAACT
2353060 ATATATATATATATAT-AAC-
1 ATATATATATATATATAAACT
*
2353079 CTATATATATATATATAAACT
1 ATATATATATATATATAAACT
2353100 ATATA
1 ATATA
2353105 AAGTAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
19 15 0.38
20 6 0.15
21 11 0.28
22 8 0.20
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (21 bp):
ATATATATATATATATAAACT
Found at i:2353104 original size:2 final size:2
Alignment explanation
Indices: 2353038--2353095 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
2353028 TATGTATAAA
* * * *
2353038 AT AT GT AT AGT AT AT AT AA ACT AT AT AT AT AT AT AT AT A- AC CT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
2353081 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2353096 AACTATATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
1 1 0.02
2 42 0.91
3 3 0.07
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2353168 original size:14 final size:14
Alignment explanation
Indices: 2353151--2353193 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2353141 CCCTATTCCC
2353151 TAAACACTAAACTA
1 TAAACACTAAACTA
* *
2353165 TAAACCCTAAA-TCC
1 TAAACACTAAACT-A
2353179 TAAACACTAAACTA
1 TAAACACTAAACTA
2353193 T
1 T
2353194 GTATGTATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACACTAAACTA
Found at i:2353381 original size:20 final size:20
Alignment explanation
Indices: 2353353--2353392 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2353343 TATATTACAT
* *
2353353 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
2353373 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
2353393 TAACCTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:2353387 original size:55 final size:55
Alignment explanation
Indices: 2353325--2353458 Score: 162
Period size: 55 Copynumber: 2.4 Consensus size: 55
2353315 TGTATACATG
* * * * * *
2353325 TAAACTATATACGTAACTTATATTACATGTATGTATAAACTATGTATA-GTATATA
1 TAAACTATATATGTAACCTATAGTACATATATATACAAACTATGTATATGT-TATA
* * * *
2353380 TAAACTATATATATAACCTATAGTATATATATATACAATCTATTTATATGTTATA
1 TAAACTATATATGTAACCTATAGTACATATATATACAAACTATGTATATGTTATA
2353435 TAAACTATATATGTAACCTATAGT
1 TAAACTATATATGTAACCTATAGT
2353459 TTATAAACAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
55 65 0.97
56 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (55 bp):
TAAACTATATATGTAACCTATAGTACATATATATACAAACTATGTATATGTTATA
Found at i:2353392 original size:13 final size:13
Alignment explanation
Indices: 2353374--2353408 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2353364 CTATGTATAG
2353374 TATATATAAACTA
1 TATATATAAACTA
*
2353387 TATATATAACCTA
1 TATATATAAACTA
2353400 TAGTATATA
1 TA-TATATA
2353409 TATATACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2353477 original size:21 final size:20
Alignment explanation
Indices: 2353453--2353543 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 20
2353443 ATATGTAACC
2353453 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
**
2353474 TATA-TTAGTGTACTAAATAGTT
1 TATATTTA-TAAAC--AATAGTT
* *
2353496 TATACTTTATAACCAATAGTA
1 TATA-TTTATAAACAATAGTT
*
2353517 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
2353538 TATATT
1 TATATT
2353544 AATGTTAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 29 0.53
22 12 0.22
23 2 0.04
24 3 0.05
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:2353615 original size:21 final size:20
Alignment explanation
Indices: 2353588--2353677 Score: 101
Period size: 21 Copynumber: 4.2 Consensus size: 20
2353578 AATTATAAAC
2353588 TATATTAATA-TAATATAAGT
1 TATATTAATATTAATATAA-T
2353608 TAATATTAATATTAATATTAAT
1 T-ATATTAATATTAATA-TAAT
2353630 TATATTAATATTAATTATAAT
1 TATATTAATATTAA-TATAAT
*
2353651 ATATAATTTATATTAATATTAAT
1 -TAT-ATTAATATTAATA-TAAT
2353674 TATA
1 TATA
2353678 AATAGTTTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
20 1 0.02
21 27 0.44
22 17 0.27
23 17 0.27
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (20 bp):
TATATTAATATTAATATAAT
Found at i:2353616 original size:6 final size:6
Alignment explanation
Indices: 2353589--2353673 Score: 80
Period size: 6 Copynumber: 15.3 Consensus size: 6
2353579 ATTATAAACT
*
2353589 ATATTA ATA-TA ATA-TA A-GTTA ATATTA ATATTA ATATT- A-ATT-
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
2353631 ATATTA ATATTA AT-TATA ATATATA AT-TT- ATATTA ATATTA AT
1 ATATTA ATATTA ATAT-TA ATAT-TA ATATTA ATATTA ATATTA AT
2353674 TATAAATAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 16
0.79 0.02 0.18
Matches are distributed among these distances:
4 6 0.09
5 19 0.28
6 38 0.55
7 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:2353636 original size:15 final size:15
Alignment explanation
Indices: 2353588--2353677 Score: 95
Period size: 15 Copynumber: 6.3 Consensus size: 15
2353578 AATTATAAAC
2353588 TATATTAATA-TAA-
1 TATATTAATATTAAT
2353601 TATAAGTTAATATT-A-
1 TAT-A-TTAATATTAAT
2353616 -ATATTAATATTAAT
1 TATATTAATATTAAT
2353630 TATATTAATATTAAT
1 TATATTAATATTAAT
*
2353645 TATAAT-ATA-TAATT
1 TATATTAATATTAA-T
2353659 TATATTAATATTAAT
1 TATATTAATATTAAT
2353674 TATA
1 TATA
2353678 AATAGTTTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
12 8 0.12
13 8 0.12
14 12 0.18
15 34 0.52
16 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
TATATTAATATTAAT
Found at i:2353649 original size:44 final size:42
Alignment explanation
Indices: 2353588--2353677 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 42
2353578 AATTATAAAC
2353588 TATATTAATATAATATAAGT-TA-ATATTAATATTAATATTAAT
1 TATATTAATATAATATAA-TATATA-ATTAATATTAATATTAAT
*
2353630 TATATTAATATTAATTATAATATATAATTTATATTAATATTAAT
1 TATATTAATA-TAA-TATAATATATAATTAATATTAATATTAAT
2353674 TATA
1 TATA
2353678 AATAGTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 10 0.23
43 4 0.09
44 28 0.65
45 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (42 bp):
TATATTAATATAATATAATATATAATTAATATTAATATTAAT
Found at i:2353661 original size:29 final size:27
Alignment explanation
Indices: 2353607--2353701 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 27
2353597 ATAATATAAG
2353607 TTAATATTAA-TATTAATATTAATTATA
1 TTAATATTAATTA-TAATATTAATTATA
2353634 TTAATATTAATTATAATATATAATTTATA
1 TTAATATTAATTATAATAT-TAA-TTATA
*
2353663 TTAATATTAATTATAA-A-TAGTT-TA
1 TTAATATTAATTATAATATTAATTATA
*
2353687 TTAATATAAATTATA
1 TTAATATTAATTATA
2353702 TAGGGATAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
24 16 0.25
25 2 0.03
26 2 0.03
27 16 0.25
28 6 0.10
29 21 0.33
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAATATTAATTATAATATTAATTATA
Found at i:2354482 original size:18 final size:18
Alignment explanation
Indices: 2354461--2354543 Score: 67
Period size: 18 Copynumber: 4.6 Consensus size: 18
2354451 CCTAAACTTG
*
2354461 AATCTAAACCCGAACCCA
1 AATCTGAACCCGAACCCA
* *
2354479 AATCCGAACCTGAACCCA
1 AATCTGAACCCGAACCCA
* ****
2354497 AATCTGAACCTGAATATG
1 AATCTGAACCCGAACCCA
* *
2354515 AACCTGAACCCAAACCCA
1 AATCTGAACCCGAACCCA
*
2354533 AATCCGAACCC
1 AATCTGAACCC
2354544 AAATTCAAAC
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.41, C:0.36, G:0.10, T:0.13
Consensus pattern (18 bp):
AATCTGAACCCGAACCCA
Found at i:2354506 original size:30 final size:30
Alignment explanation
Indices: 2354472--2354528 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2354462 ATCTAAACCC
*
2354472 GAACCCAAATCCGAACCTGAACCCAAATCT
1 GAACCCAAATACGAACCTGAACCCAAATCT
** *
2354502 GAACCTGAATATGAACCTGAACCCAAA
1 GAACCCAAATACGAACCTGAACCCAAA
2354529 CCCAAATCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (30 bp):
GAACCCAAATACGAACCTGAACCCAAATCT
Found at i:2354559 original size:18 final size:18
Alignment explanation
Indices: 2354515--2354560 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2354505 CCTGAATATG
2354515 AACCTGAACCCAAACCCA
1 AACCTGAACCCAAACCCA
**
2354533 AATCC-GAACCCAAATTCA
1 AA-CCTGAACCCAAACCCA
2354551 AACCTGAACC
1 AACCTGAACC
2354561 TAAAAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.43, C:0.39, G:0.07, T:0.11
Consensus pattern (18 bp):
AACCTGAACCCAAACCCA
Found at i:2357272 original size:18 final size:19
Alignment explanation
Indices: 2357249--2357287 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2357239 ACTGAAACAA
2357249 GTTTTTAT-TGATGCTTCT
1 GTTTTTATATGATGCTTCT
* *
2357267 GTTTTTGTATGTTGCTTCT
1 GTTTTTATATGATGCTTCT
2357286 GT
1 GT
2357288 CCAAAGTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.08, C:0.10, G:0.21, T:0.62
Consensus pattern (19 bp):
GTTTTTATATGATGCTTCT
Found at i:2357772 original size:12 final size:11
Alignment explanation
Indices: 2357744--2357778 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2357734 TTGAATTAAC
2357744 TCAAATGTTAT
1 TCAAATGTTAT
*
2357755 TCAAATTTTAT
1 TCAAATGTTAT
2357766 ATCAAATGTTAT
1 -TCAAATGTTAT
2357778 T
1 T
2357779 TAATTTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (11 bp):
TCAAATGTTAT
Found at i:2358043 original size:23 final size:24
Alignment explanation
Indices: 2358015--2358068 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
2358005 ATTATTTTTC
2358015 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
2358038 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
2358062 TTTACAT
1 TTTACAT
2358069 TTAATCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:2375880 original size:23 final size:25
Alignment explanation
Indices: 2375834--2375881 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2375824 TTACATCTCC
*
2375834 TTTTATAATAAATAAACCTGGTACA
1 TTTTACAATAAATAAACCTGGTACA
*
2375859 TTTTACAA-AAATAACCCT-GTACA
1 TTTTACAATAAATAAACCTGGTACA
2375882 GTAAAGCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (25 bp):
TTTTACAATAAATAAACCTGGTACA
Found at i:2388992 original size:14 final size:15
Alignment explanation
Indices: 2388954--2388993 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2388944 CATATAGTAA
2388954 GCGTCTTTATTATGG
1 GCGTCTTTATTATGG
2388969 GCGTCTTTATTATGG
1 GCGTCTTTATTATGG
2388984 GCG-CTTTATT
1 GCGTCTTTATT
2388994 CTGTCTCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.47
Consensus pattern (15 bp):
GCGTCTTTATTATGG
Found at i:2391496 original size:20 final size:20
Alignment explanation
Indices: 2391467--2391507 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2391457 ATATAGCTAT
* *
2391467 GGTCTGTATTCTCTCTAAAG
1 GGTCTATATTCTCTATAAAG
2391487 GGTCTATATTCTCTATAAAG
1 GGTCTATATTCTCTATAAAG
2391507 G
1 G
2391508 ACCAGAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
GGTCTATATTCTCTATAAAG
Found at i:2399270 original size:18 final size:18
Alignment explanation
Indices: 2399247--2399284 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2399237 TATTCAAAGG
2399247 TGATTACAAGGTAATATT
1 TGATTACAAGGTAATATT
2399265 TGATTACAAGGTAATATT
1 TGATTACAAGGTAATATT
2399283 TG
1 TG
2399285 TTCAAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (18 bp):
TGATTACAAGGTAATATT
Found at i:2401673 original size:3 final size:3
Alignment explanation
Indices: 2401665--2401714 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
2401655 AATATTATAT
2401665 TAA TAA TAA TAA TAA -AA T-A TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2401710 TAA TA
1 TAA TA
2401715 TAAGTATCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2401683 original size:11 final size:11
Alignment explanation
Indices: 2401669--2401717 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
2401659 TTATATTAAT
2401669 AATAATAATAA
1 AATAATAATAA
2401680 AAT-ATAATAA
1 AATAATAATAA
2401690 TAATAATAATAA
1 -AATAATAATAA
*
2401702 TATAATAATAA
1 AATAATAATAA
*
2401713 TATAA
1 AATAA
2401718 GTATCTTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
10 7 0.20
11 21 0.60
12 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATAATAA
Found at i:2401690 original size:22 final size:20
Alignment explanation
Indices: 2401665--2401714 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
2401655 AATATTATAT
2401665 TAATAATAATAATAA-AATA
1 TAATAATAATAATAATAATA
2401684 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
2401704 TAATAATAATA
1 TAATAATAATA
2401715 TAAGTATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:2401717 original size:25 final size:25
Alignment explanation
Indices: 2401652--2401714 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
2401642 CTGATGTATG
* *
2401652 TAAAATATTATATTAATAATAATAA
1 TAAAATATAATAATAATAATAATAA
2401677 TAAAATATAATAATAATAATAATAA
1 TAAAATATAATAATAATAATAATAA
*
2401702 TATAATAATAATA
1 TAAAAT-ATAATA
2401715 TAAGTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 28 0.82
26 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAATATAATAATAATAATAATAA
Found at i:2402404 original size:113 final size:113
Alignment explanation
Indices: 2402287--2403044 Score: 1063
Period size: 113 Copynumber: 6.7 Consensus size: 113
2402277 CTTCTTCTTC
* * * ** *
2402287 CTTCTTCATCCTTCTTTAGATGAGTTCTTTTCATTATGAACTTTTTCTGGAAATGTTGATCCATC
1 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATGTTGATCCATC
* * * *
2402352 GAGTAATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTTATTATGAA
66 AAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * *
2402400 CTTCTTCTTCCTTTTTCAGATGAGTTCTTCTAATTATGAACTTTACCTGGCAATGCTGATCCATC
1 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATGTTGATCCATC
** *
2402465 AAGTGATGGATTTGAGCCAAAGGTTGAACAAATTCTTCTCATTATGAA
66 AAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * * * *
2402513 TTTCTTCTTCCTTCTTTATATGAGTTCTTCTCATTATGAACTCTACTTGGCAATGTTGATCCATC
1 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATGTTGATCCATC
* *
2402578 AAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
66 AAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* *
2402626 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTT-ATCCAT
1 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATG-TTGATCCAT
* *
2402690 CAAGTGATGGATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
65 CAAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
2402739 CTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCAT
1 CTT-CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATGTTGATCCAT
** *
2402804 CAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
65 CAAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * *
2402853 CTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGCAATGCTAATCCAT
1 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CTGGCAATGTTGATCCAT
** * * **
2402917 CGGGTGATGAATTAAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
65 CAAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * *
2402966 CTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGC-ATGTTGATCCATT
1 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATGTTGATCCATC
* *
2403030 GAGTAATGGATTCAA
66 AAGTGATGGATTCAA
2403045 ATCTTTGCTA
Statistics
Matches: 584, Mismatches: 56, Indels: 11
0.90 0.09 0.02
Matches are distributed among these distances:
112 22 0.04
113 450 0.77
114 112 0.19
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAATGTTGATCCATC
AAGTGATGGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
Found at i:2402598 original size:226 final size:226
Alignment explanation
Indices: 2402031--2403028 Score: 1300
Period size: 226 Copynumber: 4.4 Consensus size: 226
2402021 ATTATACAAG
* *
2402031 AGGTTGAACAAGCTCTTCTCATTATGAACTTCCTCTT-CTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
2402095 GAACT-TTCTTTGGAAAAGTTGATCCATCGAGTGATGAA----A--AAAA-ATTGAACAAATTCT
66 GAACTCTAC-TTGGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCT
* *
2402152 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAA
130 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAA
* * * * * * *
2402217 CGCTGATCCATTAAATGGTGAATTCAAACAAA
195 TGCTGATCCATCAAGTGATGGATTTAAGCAAA
* * *
2402249 GGGTTGAACAAGCTCTTCTCATTAGGAACTTCTTCTTCCTTCTTCATCCTTCTTTAGATGAGTTC
1 AGGTTGAACAAGCTCTTCTCATTATGAA-----T-TT-CTTC-T--TCCTTCTTCAGATGAGTTC
* ** * * * *
2402314 TTTTCATTATGAACT-TTTTCTGGAAATGTTGATCCATCGAGTAATGAATTCAAGCAAAAGGTTG
56 TTCTCATTATGAACTCTACT-TGGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTG
* * * *
2402378 AACAAATTCTTCTTATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTAATTATGAACTT
120 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
2402443 TACCTGGCAATGCTGATCCATCAAGTGATGGATTTGAGCCAA
185 TACCTGGCAATGCTGATCCATCAAGTGATGGATTTAAGCAAA
** * *
2402485 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTTATATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
2402550 GAACTCTACTTGGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTT
66 GAACTCTACTTGGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTT
*
2402615 CTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAT
131 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAT
*
2402680 GCTTATCCATCAAGTGATGGATTTAAGCAAA
196 GCTGATCCATCAAGTGATGGATTTAAGCAAA
* *
2402711 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AGGTTGAACAAGCTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
2402776 TGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCT
65 TGAACTCTACTTGGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCT
* *
2402841 TCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGCA
130 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCA
* ** * *
2402905 ATGCTAATCCATCGGGTGATGAATTAAAGCAAA
194 ATGCTGATCCATCAAGTGATGGATTTAAGCAAA
* *
2402938 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
*
2403003 GAACTCTACCTGGC-ATGTTGATCCAT
66 GAACTCTACTTGGCAATGTTGATCCAT
2403029 TGAGTAATGG
Statistics
Matches: 693, Mismatches: 65, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
218 26 0.04
224 2 0.00
225 15 0.02
226 249 0.36
227 209 0.30
228 3 0.00
229 62 0.09
230 2 0.00
231 1 0.00
233 1 0.00
235 4 0.01
236 119 0.17
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (226 bp):
AGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTACTTGGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAT
GCTGATCCATCAAGTGATGGATTTAAGCAAA
Found at i:2402878 original size:340 final size:339
Alignment explanation
Indices: 2402031--2403044 Score: 1334
Period size: 340 Copynumber: 3.0 Consensus size: 339
2402021 ATTATACAAG
*
2402031 AGGTTGAACAAGCTCTTCTCATTATGAACTTCC-TCTT-CTTCTTCAGATGAGTTCTTCTCATTA
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * **
2402094 TGAACTTTCTTTGGAAAAGTTGATCCATCGAGTGAT-GA----A--AAAAAATTGAACAAATTCT
66 TGAACTTAC-CTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
* *
2402152 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAA
130 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTTGGCAA
* * * * * * *
2402217 CGCTGATCCATTAAATGGTGAATTCAAACAAAGGGTTGAACAAGCTCTTCTCATTAGGAACTTCT
195 TGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA-----
* * * ** *
2402282 TCTTCCTTCTTCATCCTTCTTTAGATGAGTTCTTTTCATTATGAACTTTTTCTGGAAATGTTGAT
255 T-TT-CTTC-T--TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT
*
2402347 CCATCGAGTAATGAATTCAAGCAAA
315 CCATCAAGTAATGAATTCAAGCAAA
* * * *
2402372 AGGTTGAACAAATTCTTCTTATTATGAACTT-CTTCTTCCTTTTTCAGATGAGTTCTTCTAATTA
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
2402436 TGAACTTTACCTGGCAATGCTGATCCATCAAGTGATGGATTTGAGCCAAAGGTTGAACAAATTCT
66 TGAAC-TTACCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
* *
2402501 TCTCATTATGAATTTCTTCTTCCTTCTTTATATGAGTTCTTCTCATTATGAACTCTACTTGGCAA
130 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTTGGCAA
* * **
2402566 TGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCT
195 TGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCT
2402631 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTT-ATCCATCAAGT
260 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG-TTGATCCATCAAGT
* * *
2402695 GATGGATTTAAGCAAA
324 AATGAATTCAAGCAAA
2402711 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
2402776 TGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCT
66 TGAACT-TACCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
* * *
2402841 TCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGCA
130 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACT-TGGCA
* ** * *
2402905 ATGCTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
194 ATGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTC
* **
2402970 TTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGC-ATGTTGATCCATTGAGT
259 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAGT
*
2403034 AATGGATTCAA
324 AATGAATTCAA
2403045 ATCTTTGCTA
Statistics
Matches: 593, Mismatches: 65, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
338 2 0.00
339 118 0.20
340 251 0.42
341 33 0.06
342 54 0.09
343 7 0.01
344 1 0.00
347 1 0.00
349 126 0.21
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (339 bp):
AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTACCTGGCAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
CTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTTGGCAAT
GCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTT
CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAGTAA
TGAATTCAAGCAAA
Found at i:2404418 original size:18 final size:18
Alignment explanation
Indices: 2404395--2404429 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2404385 TATATGAAAC
2404395 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
2404413 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
2404430 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:2412129 original size:15 final size:15
Alignment explanation
Indices: 2412106--2412137 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2412096 TGTAATGAAT
2412106 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2412121 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2412136 AA
1 AA
2412138 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2415480 original size:28 final size:29
Alignment explanation
Indices: 2415427--2415482 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2415417 GAAAAATAAA
*
2415427 AATAATGTACATATAAATATTATGAAAAT
1 AATAATGTACATATAAAAATTATGAAAAT
* *
2415456 AATAA-GTATATATAAAAATTTTGAAAA
1 AATAATGTACATATAAAAATTATGAAAA
2415483 GAAAGAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (29 bp):
AATAATGTACATATAAAAATTATGAAAAT
Found at i:2416262 original size:18 final size:20
Alignment explanation
Indices: 2416214--2416262 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
2416204 AAAAAGTAAA
2416214 ATAA-AATATATATTATTTC
1 ATAATAATATATATTATTTC
*
2416233 -TTATATATATATATATATTT-
1 ATAATA-ATATATAT-TATTTC
2416253 ATAATAATAT
1 ATAATAATAT
2416263 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
18 2 0.08
19 1 0.04
20 12 0.50
21 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATAATATATATTATTTC
Found at i:2417586 original size:3 final size:3
Alignment explanation
Indices: 2417580--2417646 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
2417570 TAATATTTAT
* * *
2417580 TAA TAA TAA -AA TAA AAA TAA TGA TAA AAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2417627 TTA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
2417647 TTCAAATGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.08
3 47 0.89
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2417647 original size:9 final size:10
Alignment explanation
Indices: 2417567--2417647 Score: 63
Period size: 9 Copynumber: 8.9 Consensus size: 10
2417557 CTGATGTATG
*
2417567 TAATAATATT
1 TAATAATATA
*
2417577 TATTAATA-A
1 TAATAATATA
2417586 TAA-AATA-A
1 TAATAATATA
*
2417594 AAATAATGATA
1 TAATAAT-ATA
2417605 -AA-AATA-A
1 TAATAATATA
2417612 TAATAATA-A
1 TAATAATATA
2417621 TAATAAT-TA
1 TAATAATATA
2417630 TAATAATATA
1 TAATAATATA
2417640 -AATAATAT
1 TAATAATAT
2417648 TCAAATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
7 1 0.02
8 10 0.17
9 36 0.60
10 12 0.20
11 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (10 bp):
TAATAATATA
Found at i:2419379 original size:22 final size:22
Alignment explanation
Indices: 2419338--2419379 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2419328 GCGGAATTAT
* *
2419338 GAAGATGTTGGTGGCCTTGATG
1 GAAGATGTTGATGGACTTGATG
*
2419360 GAAGATGTTGATGGAGTTGA
1 GAAGATGTTGATGGACTTGA
2419380 AGTTGAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.40, T:0.31
Consensus pattern (22 bp):
GAAGATGTTGATGGACTTGATG
Found at i:2424725 original size:20 final size:20
Alignment explanation
Indices: 2424700--2424738 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2424690 GTAGTGTTTT
2424700 AATATAAATATTAATGATTA
1 AATATAAATATTAATGATTA
**
2424720 AATATATTTATTAATGATT
1 AATATAAATATTAATGATT
2424739 TTAATAGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
AATATAAATATTAATGATTA
Found at i:2439215 original size:22 final size:22
Alignment explanation
Indices: 2439187--2439240 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
2439177 TGGGAAGGTA
*
2439187 GTATCGATACCATAGCATAGGG
1 GTATCGATACCATAGCATAAGG
**
2439209 GTATCGATA-C-TAGGTTAAGG
1 GTATCGATACCATAGCATAAGG
2439229 GTATCGATACCA
1 GTATCGATACCA
2439241 GTAAACATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.59
21 2 0.07
22 9 0.33
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATAGCATAAGG
Found at i:2450124 original size:21 final size:21
Alignment explanation
Indices: 2450098--2450147 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2450088 TTCTACGTGG
* *
2450098 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGCAA
*
2450119 TCCTTCGTAACATATATGCAA
1 TCCTTCGGAACATATATGCAA
*
2450140 TACTTCGG
1 TCCTTCGG
2450148 TACACTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (21 bp):
TCCTTCGGAACATATATGCAA
Found at i:2450431 original size:21 final size:21
Alignment explanation
Indices: 2450407--2450450 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2450397 ATATGATGTG
2450407 TATGTATGTTAAAGATAAGAA
1 TATGTATGTTAAAGATAAGAA
2450428 TATGTATGTTAAAGATAAGAA
1 TATGTATGTTAAAGATAAGAA
2450449 TA
1 TA
2450451 AGATGAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (21 bp):
TATGTATGTTAAAGATAAGAA
Found at i:2453391 original size:7 final size:7
Alignment explanation
Indices: 2453373--2453406 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2453363 CCATAATTCT
2453373 CTTCTT-
1 CTTCTTC
2453379 CTTCTTC
1 CTTCTTC
2453386 CTTCTTC
1 CTTCTTC
2453393 CTTCTTC
1 CTTCTTC
*
2453400 CGTCTTC
1 CTTCTTC
2453407 ATATTTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (7 bp):
CTTCTTC
Found at i:2460778 original size:21 final size:21
Alignment explanation
Indices: 2460726--2460780 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2460716 TCGAGGGTTC
* * *
2460726 TATGTGGTCCTTCGGGACATA
1 TATGTGGTACTTTGGAACATA
**
2460747 TATGTAATACTTTGGAACATA
1 TATGTGGTACTTTGGAACATA
2460768 TATGTGGTACTTT
1 TATGTGGTACTTT
2460781 AGTACACTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (21 bp):
TATGTGGTACTTTGGAACATA
Found at i:2462381 original size:53 final size:53
Alignment explanation
Indices: 2462300--2462414 Score: 185
Period size: 53 Copynumber: 2.2 Consensus size: 53
2462290 ATGAACATCT
* *
2462300 TCAATACCCTGTAAACATTGAATTTAATTTGGGTACCGATACCCTAGTAGTGTA
1 TCAATA-CCTGTAAAAATCGAATTTAATTTGGGTACCGATACCCTAGTAGTGTA
*
2462354 TCAATACCTGTAAAAATCGAATTTAATTTGGGTATCGATACCCTAGTAGTGTA
1 TCAATACCTGTAAAAATCGAATTTAATTTGGGTACCGATACCCTAGTAGTGTA
*
2462407 TCGATACC
1 TCAATACC
2462415 CTTCTAAAGG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 51 0.89
54 6 0.11
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (53 bp):
TCAATACCTGTAAAAATCGAATTTAATTTGGGTACCGATACCCTAGTAGTGTA
Found at i:2463166 original size:59 final size:59
Alignment explanation
Indices: 2462822--2463153 Score: 547
Period size: 59 Copynumber: 5.6 Consensus size: 59
2462812 AAATTACCAA
* * * *
2462822 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACCAAGTATATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2462881 ATGGCACTTTGTGTTCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
2462940 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
2462999 AGGGCACTTTATATACTAAAATGGTAAGGAAATCATACTAAGTGTATGATTTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2463058 AAGGCACTTTGTGTGCTAAAATTGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
2463117 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATA
2463154 TTGATTGTAT
Statistics
Matches: 252, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 252 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:2463951 original size:53 final size:53
Alignment explanation
Indices: 2463870--2463984 Score: 167
Period size: 53 Copynumber: 2.2 Consensus size: 53
2463860 ATGAACATCT
* ** * *
2463870 TCAATACCCTGTAAACATTGAATTTAATTTGGGTACCGATACCCTAGTAGTGTA
1 TCAATA-CCTGTAAAAATCAAATTTAATTTGGGTACCGATACCCCAGTAGTATA
*
2463924 TCAATACCTGTAAAAATCAAATTTAATTTGGGTATCGATACCCCAGTAGTATA
1 TCAATACCTGTAAAAATCAAATTTAATTTGGGTACCGATACCCCAGTAGTATA
2463977 TCAATACC
1 TCAATACC
2463985 CTTCTAAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
53 49 0.89
54 6 0.11
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (53 bp):
TCAATACCTGTAAAAATCAAATTTAATTTGGGTACCGATACCCCAGTAGTATA
Found at i:2464485 original size:59 final size:59
Alignment explanation
Indices: 2464393--2464724 Score: 520
Period size: 59 Copynumber: 5.6 Consensus size: 59
2464383 AAATTACCAA
* * *
2464393 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACCAAGTATATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
2464452 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
2464511 AGGTCACTTTGTGTGCTAAAATGGTAAAGAAATCATACTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * **
2464570 AGGGCACTTTATATGTTAAAATGGTAAGGAAATCATACTAAGTGTATGGTTTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
2464629 AAGGCACTTTGTGTGCTAAAATTGTAAGGAAATCATACTAAGTGTATTAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2464688 AGGGAACTTTGTGTGCTAAAATGGTAAGAAAATCATA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATA
2464725 TTGATTGTAT
Statistics
Matches: 247, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 247 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:2465160 original size:26 final size:23
Alignment explanation
Indices: 2465125--2465178 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
2465115 AGCATATATT
**
2465125 TTTTTGTTTATTTAAGTTAAGATA
1 TTTTTGTTTAAGTAAGTTAA-ATA
2465149 TGTTTTGTTTTAAGTAAGTTAAATA
1 T-TTTTG-TTTAAGTAAGTTAAATA
2465174 TTTTT
1 TTTTT
2465179 ATAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 5 0.19
25 9 0.35
26 12 0.46
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (23 bp):
TTTTTGTTTAAGTAAGTTAAATA
Found at i:2467916 original size:13 final size:13
Alignment explanation
Indices: 2467898--2467922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2467888 TTACTTTACT
2467898 TTATTTTTTTCTA
1 TTATTTTTTTCTA
2467911 TTATTTTTTTCT
1 TTATTTTTTTCT
2467923 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2468035 original size:18 final size:17
Alignment explanation
Indices: 2468003--2468047 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2467993 TGCACACATT
2468003 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
2468020 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
2468038 ATTTTTTTAC
1 ATTTTTTTAC
2468048 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:2468045 original size:17 final size:17
Alignment explanation
Indices: 2468001--2468047 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2467991 TATGCACACA
2468001 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
2468018 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
2468036 TTATTTTTTTAC
1 TTATTTTTTTAC
2468048 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:2470630 original size:106 final size:106
Alignment explanation
Indices: 2470441--2470864 Score: 627
Period size: 106 Copynumber: 4.0 Consensus size: 106
2470431 TATTGTTCCA
* *
2470441 AGTCCAATATCC-TCTGCCGTGAAGTTGAAATTGGTTCTGGAAA-TGGGAAATTGTTTGTTGACA
1 AGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAATTGTTTGTTGACA
* *
2470504 ACCAGCCGTCCCTTCATTGTGAAGTTGAACCTGTGTTGTCTCG
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * *
2470547 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTATTTGTTAACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* *
2470612 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
** * * *
2470653 AGTCCAATGCCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * *
2470718 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTTG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* *
2470759 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTTTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
2470824 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTTGTCTCG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
2470865 GGTTTCGCAA
Statistics
Matches: 285, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
105 4 0.01
106 279 0.98
107 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
Found at i:2471518 original size:49 final size:48
Alignment explanation
Indices: 2471447--2471551 Score: 201
Period size: 49 Copynumber: 2.2 Consensus size: 48
2471437 AAAATTCGTT
2471447 TCAAGGGAAACGATCTCAAAGATATATGTTGTTTCATGAGAAACGGTC
1 TCAAGGGAAACGATCTCAAAGATATATGTTGTTTCATGAGAAACGGTC
2471495 TCAAGGTGAAACGATCTCAAAGATATATGTTGTTTCATGAGAAACGGTC
1 TCAAGG-GAAACGATCTCAAAGATATATGTTGTTTCATGAGAAACGGTC
2471544 TCAAGGGA
1 TCAAGGGA
2471552 GACAAAATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
48 8 0.14
49 48 0.86
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (48 bp):
TCAAGGGAAACGATCTCAAAGATATATGTTGTTTCATGAGAAACGGTC
Found at i:2471841 original size:38 final size:38
Alignment explanation
Indices: 2471768--2471844 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 38
2471758 GAAACAATTT
* *
2471768 CAAAGGTTTTTTTCCAAGCGAAACTGTTTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGCGAAACTGTCTCAAGAGAGA
*
2471806 CAAA-GTTTGTTT-CAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGCGAAACTGTCTCAAGAGAGA
2471842 CAA
1 CAA
2471845 TGGTGAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 25 0.69
37 7 0.19
38 4 0.11
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGCGAAACTGTCTCAAGAGAGA
Found at i:2472351 original size:17 final size:18
Alignment explanation
Indices: 2472331--2472365 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2472321 TGTTGAATCC
*
2472331 CCAAAGATG-CCCAATAT
1 CCAAAAATGCCCCAATAT
2472348 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2472366 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:2473445 original size:16 final size:17
Alignment explanation
Indices: 2473426--2473476 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
2473416 TGATTTTTGC
2473426 TTCTTTTCTTTTTTTT-
1 TTCTTTTCTTTTTTTTA
*
2473442 TTCTTGTTTTTCCTTTTTTCA
1 TTCTT-TTCTT--TTTTTT-A
2473463 TTCTTTTCTTTTTT
1 TTCTTTTCTTTTTT
2473477 GTTCTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.18
17 4 0.14
18 4 0.14
19 6 0.21
20 4 0.14
21 5 0.18
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (17 bp):
TTCTTTTCTTTTTTTTA
Found at i:2473457 original size:21 final size:20
Alignment explanation
Indices: 2473406--2473460 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
2473396 CTTTTCGTCC
2473406 CTTTTCCTTTTGATTTTTGCTT
1 CTTTTCCTTTT--TTTTTGCTT
*
2473428 CTTTT-CTTTTTTTTTTCTT
1 CTTTTCCTTTTTTTTTGCTT
*
2473447 GTTTTTCCTTTTTT
1 -CTTTTCCTTTTTT
2473461 CATTCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 8 0.28
20 4 0.14
21 12 0.41
22 5 0.17
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.76
Consensus pattern (20 bp):
CTTTTCCTTTTTTTTTGCTT
Found at i:2473466 original size:21 final size:20
Alignment explanation
Indices: 2473429--2473467 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2473419 TTTTTGCTTC
**
2473429 TTTTCTTTTTTTTTTCTTGT
1 TTTTCTTTTTTCATTCTTGT
2473449 TTTTCCTTTTTTCATTCTT
1 TTTT-CTTTTTTCATTCTT
2473468 TTCTTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTTTCATTCTTGT
Found at i:2475768 original size:18 final size:17
Alignment explanation
Indices: 2475743--2475796 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
2475733 AATCAAGAAC
2475743 AAAAAAAAGAAGCAAAA
1 AAAAAAAAGAAGCAAAA
*
2475760 AAGAAAAAACAAG-AACAA
1 AA-AAAAAAGAAGCAA-AA
2475778 AAAAGAAAAGAAGCAAAA
1 AAAA-AAAAGAAGCAAAA
2475796 A
1 A
2475797 TCAAGAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAGCAAAA
Found at i:2475768 original size:20 final size:20
Alignment explanation
Indices: 2475743--2475786 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2475733 AATCAAGAAC
2475743 AAAAAA-AAGAAGCAAAAAAG
1 AAAAAACAAGAA-CAAAAAAG
2475763 AAAAAACAAGAACAAAAAAG
1 AAAAAACAAGAACAAAAAAG
2475783 AAAA
1 AAAA
2475787 GAAGCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAACAAGAACAAAAAAG
Found at i:2476757 original size:18 final size:18
Alignment explanation
Indices: 2476734--2476768 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2476724 TTCCCTTGGA
2476734 AAAAAACATTTGAAACAC
1 AAAAAACATTTGAAACAC
*
2476752 AAAAAACCTTTGAAACA
1 AAAAAACATTTGAAACA
2476769 TAAACATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAAACATTTGAAACAC
Found at i:2476973 original size:37 final size:37
Alignment explanation
Indices: 2476903--2476974 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2476893 TGGAACTAAG
* * *
2476903 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
2476940 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
2476975 CATATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:2477781 original size:106 final size:106
Alignment explanation
Indices: 2477592--2478015 Score: 668
Period size: 106 Copynumber: 4.0 Consensus size: 106
2477582 GCGCCACCCG
* * *
2477592 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
* *
2477657 CAGAGCCAATTTAAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCA
* *
2477698 AGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
* ** *
2477763 CAGAGCCAATTTTAACTTCACAGCGAAGGGCATTGGACTCG
66 CAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCA
*
2477804 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTTTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
*
2477869 CAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCA
* * * *
2477910 AGACAACACAGGTTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
* * *
2477975 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTCA
66 CAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCA
2478016 GAACAATACA
Statistics
Matches: 294, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 294 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
CAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCA
Found at i:2479524 original size:20 final size:20
Alignment explanation
Indices: 2479459--2479535 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
2479449 TTATTTTATT
2479459 TATATGTTATATTATATATA
1 TATATGTTATATTATATATA
* * *
2479479 TATAT-TTTTCGGGA-TATACATG
1 TATATGTTAT----ATTATATATA
2479501 TATATGTTATATTATATATA
1 TATATGTTATATTATATATA
2479521 TATATGTTATATTAT
1 TATATGTTATATTAT
2479536 TTACTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 4 0.09
20 26 0.58
22 11 0.24
23 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (20 bp):
TATATGTTATATTATATATA
Found at i:2479954 original size:472 final size:472
Alignment explanation
Indices: 2479070--2479958 Score: 1778
Period size: 472 Copynumber: 1.9 Consensus size: 472
2479060 AAAGAAAATG
2479070 ATTTTTTGTCAATGAACAGGGGCATTTTTCGGGATCTATTTTTATAGATCTAGCCCCCGAGGCTT
1 ATTTTTTGTCAATGAACAGGGGCATTTTTCGGGATCTATTTTTATAGATCTAGCCCCCGAGGCTT
2479135 CTTTTCTTGAGAAAATACTTTGATTTTCGGAATGGGTGTGAAAAATGGGTAATCTCACTCTTGGT
66 CTTTTCTTGAGAAAATACTTTGATTTTCGGAATGGGTGTGAAAAATGGGTAATCTCACTCTTGGT
2479200 CCCCTTGTTTATAAAGGATTTAATTTCCACCCTGAAATCCCAATTCATCCTCAAAGTGCTCCAAA
131 CCCCTTGTTTATAAAGGATTTAATTTCCACCCTGAAATCCCAATTCATCCTCAAAGTGCTCCAAA
2479265 ATTTGTCATTCGATTTTTTATTTTTACATTCTAGTCCGTTTTCTAGATTTGAATTTCAATTTTCT
196 ATTTGTCATTCGATTTTTTATTTTTACATTCTAGTCCGTTTTCTAGATTTGAATTTCAATTTTCT
2479330 TCTTATTTTATTTAATATTACATTATAATATATATTTGATATTACTCCTGTATATTATTATTATT
261 TCTTATTTTATTTAATATTACATTATAATATATATTTGATATTACTCCTGTATATTATTATTATT
2479395 TATTTCCTTTTGTTGTTATGTATATACATGTATCATTATTATTTTATTATTTACTTATTTTATTT
326 TATTTCCTTTTGTTGTTATGTATATACATGTATCATTATTATTTTATTATTTACTTATTTTATTT
2479460 ATATGTTATATTATATATATATATTTTTCGGGATATACATGTATATGTTATATTATATATATATA
391 ATATGTTATATTATATATATATATTTTTCGGGATATACATGTATATGTTATATTATATATATATA
2479525 TGTTATATTATTTACTT
456 TGTTATATTATTTACTT
2479542 ATTTTTTGTCAATGAACAGGGGCATTTTTCGGGATCTATTTTTATAGATCTAGCCCCCGAGGCTT
1 ATTTTTTGTCAATGAACAGGGGCATTTTTCGGGATCTATTTTTATAGATCTAGCCCCCGAGGCTT
2479607 CTTTTCTTGAGAAAATACTTTGATTTTCGGAATGGGTGTGAAAAATGGGTAATCTCACTCTTGGT
66 CTTTTCTTGAGAAAATACTTTGATTTTCGGAATGGGTGTGAAAAATGGGTAATCTCACTCTTGGT
2479672 CCCCTTGTTTATAAAGGATTTAATTTCCACCCTGAAATCCCAATTCATCCTCAAAGTGCTCCAAA
131 CCCCTTGTTTATAAAGGATTTAATTTCCACCCTGAAATCCCAATTCATCCTCAAAGTGCTCCAAA
2479737 ATTTGTCATTCGATTTTTTATTTTTACATTCTAGTCCGTTTTCTAGATTTGAATTTCAATTTTCT
196 ATTTGTCATTCGATTTTTTATTTTTACATTCTAGTCCGTTTTCTAGATTTGAATTTCAATTTTCT
2479802 TCTTATTTTATTTAATATTACATTATAATATATATTTGATATTACTCCTGTATATTATTATTATT
261 TCTTATTTTATTTAATATTACATTATAATATATATTTGATATTACTCCTGTATATTATTATTATT
2479867 TATTTCCTTTTGTTGTTATGTATATACATGTATCATTATTATTTTATTATTTACTTATTTTATTT
326 TATTTCCTTTTGTTGTTATGTATATACATGTATCATTATTATTTTATTATTTACTTATTTTATTT
2479932 ATATGTTATATTATATATATATATTTT
391 ATATGTTATATTATATATATATATTTT
2479959 ACGTTATTTC
Statistics
Matches: 417, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
472 417 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.48
Consensus pattern (472 bp):
ATTTTTTGTCAATGAACAGGGGCATTTTTCGGGATCTATTTTTATAGATCTAGCCCCCGAGGCTT
CTTTTCTTGAGAAAATACTTTGATTTTCGGAATGGGTGTGAAAAATGGGTAATCTCACTCTTGGT
CCCCTTGTTTATAAAGGATTTAATTTCCACCCTGAAATCCCAATTCATCCTCAAAGTGCTCCAAA
ATTTGTCATTCGATTTTTTATTTTTACATTCTAGTCCGTTTTCTAGATTTGAATTTCAATTTTCT
TCTTATTTTATTTAATATTACATTATAATATATATTTGATATTACTCCTGTATATTATTATTATT
TATTTCCTTTTGTTGTTATGTATATACATGTATCATTATTATTTTATTATTTACTTATTTTATTT
ATATGTTATATTATATATATATATTTTTCGGGATATACATGTATATGTTATATTATATATATATA
TGTTATATTATTTACTT
Found at i:2481192 original size:21 final size:21
Alignment explanation
Indices: 2481163--2481210 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2481153 TTTTTTTCTC
*
2481163 TTATGTTTTT-TTGCCATTTAT
1 TTAT-TTTTTATTACCATTTAT
**
2481184 TTATTTTTTATTATTATTTAT
1 TTATTTTTTATTACCATTTAT
2481205 TTATTT
1 TTATTT
2481211 CTATTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (21 bp):
TTATTTTTTATTACCATTTAT
Found at i:2481207 original size:14 final size:14
Alignment explanation
Indices: 2481184--2481225 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2481174 TGCCATTTAT
2481184 TTATTT-TTTATTA
1 TTATTTATTTATTA
2481197 TTATTTATTTATT-
1 TTATTTATTTATTA
2481210 TCTATTTATTT-TTA
1 T-TATTTATTTATTA
2481224 TT
1 TT
2481226 TTACTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTATTA
Found at i:2481218 original size:21 final size:21
Alignment explanation
Indices: 2481178--2481226 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2481168 TTTTTTTGCC
*
2481178 ATTTATTTATTTTTTATTATT
1 ATTTATTTATTTTATATTATT
2481199 ATTTATTTATTTCTAT-TTATT
1 ATTTATTTATTT-TATATTATT
2481220 -TTTATTT
1 ATTTATTT
2481227 TACTAAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 17 0.65
22 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTATTTATTTTATATTATT
Found at i:2484614 original size:21 final size:21
Alignment explanation
Indices: 2484590--2484637 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
2484580 TCAAGAACAA
2484590 AAAAGAA-AAGAATCAAAAAAG
1 AAAAGAACAAGAA-CAAAAAAG
2484611 AAAA-AACAAGAACAAAAAAG
1 AAAAGAACAAGAACAAAAAAG
2484631 AAAAGAA
1 AAAAGAA
2484638 TCAAAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAGAACAAGAACAAAAAAG
Found at i:2484636 original size:15 final size:16
Alignment explanation
Indices: 2484582--2484644 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
2484572 AGATTCAATC
2484582 AAGAA-CAAAAAAGAA
1 AAGAATCAAAAAAGAA
2484597 AAGAATCAAAAAAGAAAAAA
1 AAGAATCAAAAAAG----AA
2484617 CAAGAA-CAAAAAAGAA
1 -AAGAATCAAAAAAGAA
2484633 AAGAATCAAAAA
1 AAGAATCAAAAA
2484645 TCAAAAGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
15 10 0.24
16 16 0.39
20 10 0.24
21 5 0.12
ACGTcount: A:0.78, C:0.08, G:0.11, T:0.03
Consensus pattern (16 bp):
AAGAATCAAAAAAGAA
Found at i:2486168 original size:33 final size:33
Alignment explanation
Indices: 2486126--2486207 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
2486116 AAGTTGGATT
*
2486126 TCAACTTCACGACGAAGGATATCCAATTTCTGC
1 TCAACTTCACGGCGAAGGATATCCAATTTCTGC
2486159 TCAACTTCACGGCGAAGGATATCCAATTTCTGC
1 TCAACTTCACGGCGAAGGATATCCAATTTCTGC
2486192 TCAACTTCACGGCGAA
1 TCAACTTCACGGCGAA
2486208 TGGGCCACCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (33 bp):
TCAACTTCACGGCGAAGGATATCCAATTTCTGC
Found at i:2486307 original size:36 final size:36
Alignment explanation
Indices: 2486260--2486362 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
2486250 CTCACCATTG
2486260 TCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTA
** * *
2486296 TCTCTCTTGAGACAGTTTCCCTTGAAATGAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTA
2486332 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA
2486363 ATCTTTGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTA
Found at i:2487272 original size:106 final size:106
Alignment explanation
Indices: 2487118--2487543 Score: 604
Period size: 106 Copynumber: 4.0 Consensus size: 106
2487108 ACGCGCCACC
* * *
2487118 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAAGGACGACTGGTTGTCAACAAACAATTTCCCAAT
*
2487183 TTCA-AAGCCAATTTCAACTTCACAGTGAAGGATATTGGACT
66 TTCAGAA-CCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * *
2487224 CAAGACAACACAAGTTCAACTTCACAATGAAAGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAAGGACGACTGGTTGTCAACAAACAATTTCCCAAT
* * **
2487289 TTCAGAGCCAATTTCAACTTCACAGTGAAGGGCATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
2487330 CGAGACAACACAAGTTCAACTTCATAAC-AAAGGGACGACTGGTTGTCAACAAACAATTTCCCAA
1 CGAGACAACACAAGTTCAACTTCACAACGAAA-GGACGACTGGTTGTCAACAAACAATTTCCCAA
2487394 TTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
65 TTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * * ** * * *
2487436 CGAGATAAAACAGGTTCAACTTCACAACGATGGGACGACTGGTTGTCAATAAACAATTTCCTAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAAGGACGACTGGTTGTCAACAAACAATTTCCCAAT
* * * *
2487501 TCCAGAACCAATTTTAACTTCACGGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
2487542 CG
1 CG
2487544 GAACAATACA
Statistics
Matches: 289, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
105 3 0.01
106 284 0.98
107 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAAGGACGACTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:2489002 original size:2 final size:2
Alignment explanation
Indices: 2488995--2489025 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2488985 ATTTATATGT
*
2488995 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2489026 TTTACGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2489129 original size:4 final size:4
Alignment explanation
Indices: 2489122--2489198 Score: 52
Period size: 4 Copynumber: 18.5 Consensus size: 4
2489112 CTTCATTTTT
* * *
2489122 TTTA TTTA TTT- TATT- TTTA TTTTC TTTA TTTA TTGA TTCA TTT- TTCCTA
1 TTTA TTTA TTTA T-TTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT--TA
2489171 TTTTA TTTA TTTA TTTA TTTA TCTTA TT
1 -TTTA TTTA TTTA TTTA TTTA T-TTA TT
2489199 CCATTGTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
3 5 0.08
4 43 0.72
5 10 0.17
7 2 0.03
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:2489138 original size:15 final size:15
Alignment explanation
Indices: 2489120--2489152 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2489110 TCCTTCATTT
2489120 TTTTTATTTAT-TTTA
1 TTTTTATTT-TCTTTA
2489135 TTTTTATTTTCTTTA
1 TTTTTATTTTCTTTA
2489150 TTT
1 TTT
2489153 ATTGATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTCTTTA
Found at i:2490302 original size:20 final size:21
Alignment explanation
Indices: 2490279--2490336 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
2490269 TTTCTTGCCA
2490279 TTTATTTTATTATTA-TTATT
1 TTTATTTTATTATTATTTATT
*
2490299 TTTA-TTTATTTTTATTTATT
1 TTTATTTTATTATTATTTATT
*
2490319 TTTATTTTACTAATTATT
1 TTTATTTTA-TTATTATT
2490337 CGCCTTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 9 0.28
20 13 0.41
21 4 0.12
22 6 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTTATTATTATTTATT
Found at i:2490309 original size:10 final size:10
Alignment explanation
Indices: 2490279--2490325 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
2490269 TTTCTTGCCA
2490279 TTTATTTTATT
1 TTTA-TTTATT
*
2490290 ATTA-TTATT
1 TTTATTTATT
2490299 TTTATTTATT
1 TTTATTTATT
2490309 TTTATTTATT
1 TTTATTTATT
2490319 TTTATTT
1 TTTATTT
2490326 TACTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 8 0.24
10 22 0.67
11 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:2494708 original size:38 final size:36
Alignment explanation
Indices: 2494635--2494710 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
2494625 GTGCTCACCA
* *
2494635 TTGTCTCTCTTGAGACAGTTTCCTTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCTTAGAAAAAAACT
*
2494671 TTGTCTCTCTTGAGATAGTTTCCCTTAGAAAAAAAACT
1 TTGTCTCTCTTGAGACAGTTT-CCTTAG-AAAAAAACT
2494709 TT
1 TT
2494711 TGAAATTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 20 0.57
37 5 0.14
38 10 0.29
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCTTAGAAAAAAACT
Found at i:2494955 original size:37 final size:37
Alignment explanation
Indices: 2494885--2494956 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2494875 TGGAACTAAG
* * *
2494885 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
2494922 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
2494957 CATATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:2495731 original size:106 final size:106
Alignment explanation
Indices: 2495574--2496000 Score: 638
Period size: 106 Copynumber: 4.0 Consensus size: 106
2495564 TCATGCCACC
* * * * *
2495574 CGAGACAACACAAGTTCAACTTCATAACGAAGGGACGACTGATTGTGAACAAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
2495639 TTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGTACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * * * *
2495680 CAAGATAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTAAACAAATAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * **
2495745 TTCAGAGCCAATTTCAACTTCCCAGCGAAGGGCATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
2495786 CGAGACATCACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
2495851 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * *
2495892 CGAGACAACACATGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
2495957 TCCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
2495998 CGA
1 CGA
2496001 AATAATACAA
Statistics
Matches: 290, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 290 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Done.