Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 166 of 171
Found at i:49149735 original size:6 final size:6
Alignment explanation
Indices: 49149726--49149752 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
49149716 TCTTCTGTTG
49149726 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
49149753 CCACTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:49160444 original size:31 final size:30
Alignment explanation
Indices: 49160399--49160457 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
49160389 AAAGTATTAC
*
49160399 ATTGAAAAAAACTTAGATA-TCAAATTGAAT
1 ATTGAAAAAAACTTAAATACT-AAATTGAAT
*
49160429 ATTGAAACCAAACTTAAATACTAAATTGA
1 ATTGAAA-AAAACTTAAATACTAAATTGA
49160458 GACAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 17 0.68
32 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (30 bp):
ATTGAAAAAAACTTAAATACTAAATTGAAT
Found at i:49162432 original size:15 final size:16
Alignment explanation
Indices: 49162407--49162437 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
49162397 AAGATTGGTT
49162407 TTTATTTAAAAATATA
1 TTTATTTAAAAATATA
49162423 TTTA-TTAAAAATATA
1 TTTATTTAAAAATATA
49162438 ATACACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATTTAAAAATATA
Found at i:49162568 original size:37 final size:40
Alignment explanation
Indices: 49162501--49162586 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
49162491 AAAAGCATTC
* *
49162501 ATATTAGAAAACACTACCATAAATATAATAA-ATTTTATT
1 ATATTAAAAAACACTACAATAAATATAATAATATTTTATT
49162540 ATATTAAAAAACAC-A-AATAAATATAATAATTATTTTATT
1 ATATTAAAAAACACTACAATAAATATAATAA-TATTTTATT
*
49162579 GTATTAAA
1 ATATTAAA
49162587 TATGATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 13 0.31
38 1 0.02
39 28 0.67
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (40 bp):
ATATTAAAAAACACTACAATAAATATAATAATATTTTATT
Found at i:49163217 original size:15 final size:15
Alignment explanation
Indices: 49163198--49163236 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
49163188 AAATTATAAA
49163198 ATAAAAATAAAGATAT
1 ATAAAAATAAA-ATAT
*
49163214 -TAAAAATAAATTAT
1 ATAAAAATAAAATAT
49163228 ATAAAAATA
1 ATAAAAATA
49163237 TTTAATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAAAAATAAAATAT
Found at i:49168608 original size:209 final size:210
Alignment explanation
Indices: 49168230--49168710 Score: 540
Period size: 209 Copynumber: 2.3 Consensus size: 210
49168220 AATATGAAGA
** * ** * *
49168230 GCTTTTCAACCTA-AGGGTTAGGATGTACTGTAGTTGTAATAGACTTGATTACGGCTTAATCATT
1 GCTTTTCAACCTATA-GGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACAGCTTAATCATT
* * * * * *
49168294 CTGGGCCAAATGATCAGATCGGGTTACTGGCTTGATTTTAAAGCTTCTGATGCATTGGTTGGAGC
65 CTGGGCCAAATGATCACATCAGGCTACTGGCCTAATTTTAAAGCTTCTGAAGCATTGGTTGGAGC
* * * *
49168359 ATTACTTGAAAAAGGTAAGTATTTTCAAGCTCAGAAGC-TTT-ATCTGGGATGGGGATTGACCAA
130 ATTACTTAAAAAAGGTAAGTATTCTCAAGCTAAGAAGCTTTTAAT-TGGGATGGGGATCGACCAA
* * *
49168422 TTACGT-TATGAAAAAGT
194 CTACATCT-CGAAAAAGT
* * *
49168439 GTTTTTCAACTTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACAACTTAATCATTC
1 GCTTTTCAACCTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACAGCTTAATCATTC
* * * *
49168504 TGGGCCAAATGATTACATCAGGCTACTGGCCTAATTTTAAAGCTTTTGAAGGATTGGTTGTAGCA
66 TGGGCCAAATGATCACATCAGGCTACTGGCCTAATTTTAAAGCTTCTGAAGCATTGGTTGGAGCA
* * * *
49168569 TTGCTTAAAAAAGGTAAGT-TTACTGAAGCTAATAAGCTTTTAATTGGGATGGGGATCGATCAAC
131 TTACTTAAAAAAGGTAAGTATT-CTCAAGCTAAGAAGCTTTTAATTGGGATGGGGATCGACCAAC
* *
49168633 TGCATCTCGAATAAGT
195 TACATCTCGAAAAAGT
* * * * * *
49168649 GCTTTTCAGCCTATGGGTTTGGATAAATTGTAGTAATAATAGACTTGATGACAGTTTAATCA
1 GCTTTTCAACCTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACAGCTTAATCA
49168711 ATCTAGGTTA
Statistics
Matches: 225, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
208 2 0.01
209 136 0.60
210 84 0.37
211 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (210 bp):
GCTTTTCAACCTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACAGCTTAATCATTC
TGGGCCAAATGATCACATCAGGCTACTGGCCTAATTTTAAAGCTTCTGAAGCATTGGTTGGAGCA
TTACTTAAAAAAGGTAAGTATTCTCAAGCTAAGAAGCTTTTAATTGGGATGGGGATCGACCAACT
ACATCTCGAAAAAGT
Found at i:49173995 original size:210 final size:210
Alignment explanation
Indices: 49173633--49174130 Score: 658
Period size: 210 Copynumber: 2.4 Consensus size: 210
49173623 AATATGAATA
* ** * *
49173633 GCTTTTCAACCTA-AGGGATAGGATGTACTGTAGCTGTAATAGACTTGATGACGGCTTAATCATT
1 GCTTTTCAACCTATA-GGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACGGCTTAATCATT
* * * * * *
49173697 CTGGGCCAAATGATCAGATCGGGTTATTGGCTTGATTTTAAAGATTCTGATGCATTGGTTGGAGC
65 CTAGGCCAAATGATCACATCAGGCTATTGGCTTAATTTTAAAGATTCTGAAGCATTGGTTGGAGC
* * * *
49173762 ATTACTTGAAAAATGTAAGTTTTCTAAAGCTCAGAAGATTTTATTTGGGATGGAGATTGACCAAC
130 ATTACTTGAAAAAGGTAAGTTTTCTAAAGCTAAGAAGATTTTAATTGGGATGGAGATCGACCAAC
* *
49173827 TGC-TTTATGAAGAAGT
195 TGCATCT-CGAAGAAGT
* **
49173843 GCTTTTCAACTTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACAACTTAATCATTC
1 GCTTTTCAACCTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACGGCTTAATCATTC
* * *
49173908 TAGGCCAAATGATTACATCAGGCTATTGGCTTAATTTTAAAGCTTCTGAAGCATTGGTTGTAGCA
66 TAGGCCAAATGATCACATCAGGCTATTGGCTTAATTTTAAAGATTCTGAAGCATTGGTTGGAGCA
* * * *
49173973 TTACTTGAAAAAGGTAAGTTTTCTGAAGCTAAGAAGCTTTTAATTGGGATGGAGATCGATCAATT
131 TTACTTGAAAAAGGTAAGTTTTCTAAAGCTAAGAAGATTTTAATTGGGATGGAGATCGACCAACT
*
49174038 GCATCTCGAATAAGT
196 GCATCTCGAAGAAGT
* * * *
49174053 GCTTTTCAGCCTATGGGTTTGGATAAATTGTAGCAATAATAGACTTGATGACGGCTTAATCATTC
1 GCTTTTCAACCTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACGGCTTAATCATTC
* *
49174118 TAAGCAAAATGAT
66 TAGGCCAAATGAT
49174131 AATATCATGA
Statistics
Matches: 249, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
210 246 0.99
211 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (210 bp):
GCTTTTCAACCTATAGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGACGGCTTAATCATTC
TAGGCCAAATGATCACATCAGGCTATTGGCTTAATTTTAAAGATTCTGAAGCATTGGTTGGAGCA
TTACTTGAAAAAGGTAAGTTTTCTAAAGCTAAGAAGATTTTAATTGGGATGGAGATCGACCAACT
GCATCTCGAAGAAGT
Found at i:49176987 original size:210 final size:210
Alignment explanation
Indices: 49176680--49177142 Score: 581
Period size: 210 Copynumber: 2.2 Consensus size: 210
49176670 TACTGTAGCT
** * * *
49176680 GTAATAGACTTGATGACGGCTTAATCATTCTGGGCCAAATGATCAGATAGGGTTACTGGCTTGAT
1 GTAATAGACTTGATGACAACTTAATCATTCTGGGCCAAATGATCACATAGGGCTACTGGCTTAAT
* * * * *
49176745 TTTACAGCTTCTGATGCATTGGTTGGAGCATTAATTGAAAAAGGTAAGTTTTCTAAAGCTCAGAA
66 TTTAAAGCTTCTAAAGCATTAGTTGGAGCATTAATTGAAAAAGGTAAGTTTTCTAAAGCTAAGAA
* * * * *
49176810 GATTTT-TTCTAGGATGGGGATTGACCAACTGCGT-TATGAAGAAGTACTTTTCAACTTATAGGT
131 GATTTTAAT-TAGGATGGGGATCGACCAACTGCATCT-CGAAGAAGTACTTTTCAACCTATAGGT
**
49176873 TAGGATAAATTGTAGTA
194 TAGGATAAATTGTAACA
* * *
49176890 GTAATAGACTTGATGACAACTTAATCATTCTGGGCCAAATGATTACATCGGGCTACT-GATCTAA
1 GTAATAGACTTGATGACAACTTAATCATTCTGGGCCAAATGATCACATAGGGCTACTGGCT-TAA
* * * *
49176954 TTTTAAAGCTTCTAAAGCATTAGTTGTAGCATTACTTGAAAAAGGTAAGTTTTCTGAAGCTAATA
65 TTTTAAAGCTTCTAAAGCATTAGTTGGAGCATTAATTGAAAAAGGTAAGTTTTCTAAAGCTAAGA
* * * * * *
49177019 AGCTTTTAATTGGGATGGGGATCGATCAACTGCATCTCGAATAAGTGCTTTTCAACCTATGGGTT
130 AGATTTTAATTAGGATGGGGATCGACCAACTGCATCTCGAAGAAGTACTTTTCAACCTATAGGTT
*
49177084 TGGATAAATTGTAACA
195 AGGATAAATTGTAACA
* *
49177100 ATAATAGACTTGATGACAACTTAATCATTCTAGGCCAAATGAT
1 GTAATAGACTTGATGACAACTTAATCATTCTGGGCCAAATGAT
49177143 AATGTCACAG
Statistics
Matches: 217, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
209 2 0.01
210 213 0.98
211 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (210 bp):
GTAATAGACTTGATGACAACTTAATCATTCTGGGCCAAATGATCACATAGGGCTACTGGCTTAAT
TTTAAAGCTTCTAAAGCATTAGTTGGAGCATTAATTGAAAAAGGTAAGTTTTCTAAAGCTAAGAA
GATTTTAATTAGGATGGGGATCGACCAACTGCATCTCGAAGAAGTACTTTTCAACCTATAGGTTA
GGATAAATTGTAACA
Found at i:49179745 original size:210 final size:209
Alignment explanation
Indices: 49179396--49179892 Score: 597
Period size: 210 Copynumber: 2.4 Consensus size: 209
49179386 AATATGAATA
* ** * * *
49179396 GCTTTTCAACCTAAGGGTTAGGATGTACTGTAGCTA-TAATAGACTTGATGACGGCTTAATCATT
1 GCTTTTCAA-CTATGGGTTAGGATAAATTGTAGC-AGTAATAGACTTGATGATGACTTAATCATT
* * ** * * * *
49179460 CTGGGCCAAATGATCAGATCGGGTTACTGGCTTGATTTTAAAGCTTCTGATGCATTGGTTGGAGC
64 CTGAGCCAAATGATCACATCAAGCTACTGGCCTGATTTTAAAGCTTCTAAAGCATTGGTTGGAGC
*
49179525 ATTACTTGAAAAAGGAAAGTTTTCTCAAGCTCAGAAGCTTTT-ATATCGAATGGGGATCGACCAA
129 ATTACTTGAAAAAGGAAAGTTTTCTCAAGCTAAGAAGCTTTTAAT-TCGAATGGGGATCGACCAA
* *
49179589 CTGCGT-TATGAAGAAGT
193 CTACATCT-TGAAGAAGT
49179606 GCTTTTCAACTTATGGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGATGACTTAATCATTC
1 GCTTTTCAAC-TATGGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGATGACTTAATCATTC
* * * *
49179671 TTAGCCAAATGATTACATCAAGCTACTGGCCTGATTTTAAAGCTTCTAAAGCATTGGTTGTAGGA
65 TGAGCCAAATGATCACATCAAGCTACTGGCCTGATTTTAAAGCTTCTAAAGCATTGGTTGGAGCA
* * * * * *
49179736 TTGCTTGAAAAAGGTAAGTTTTCTGAAGCTAAGAAGCTTTTAATTGGGATGGGGATCGATCAACT
130 TTACTTGAAAAAGGAAAGTTTTCTCAAGCTAAGAAGCTTTTAATTCGAATGGGGATCGACCAACT
*
49179801 ACATCTTGAATAAGT
195 ACATCTTGAAGAAGT
* * * * *
49179816 GCTTTTCAGCTATGGGTTTGGATAAATTGTAGTAGTAAGAGACTTGATAACT-ACTTAATCATTC
1 GCTTTTCAACTATGGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGA-TGACTTAATCATTC
* *
49179880 TGGGCTAAATGAT
65 TGAGCCAAATGAT
49179893 AATGTCACGG
Statistics
Matches: 246, Mismatches: 36, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
209 60 0.24
210 183 0.74
211 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (209 bp):
GCTTTTCAACTATGGGTTAGGATAAATTGTAGCAGTAATAGACTTGATGATGACTTAATCATTCT
GAGCCAAATGATCACATCAAGCTACTGGCCTGATTTTAAAGCTTCTAAAGCATTGGTTGGAGCAT
TACTTGAAAAAGGAAAGTTTTCTCAAGCTAAGAAGCTTTTAATTCGAATGGGGATCGACCAACTA
CATCTTGAAGAAGT
Found at i:49182813 original size:210 final size:210
Alignment explanation
Indices: 49182524--49182933 Score: 527
Period size: 210 Copynumber: 2.0 Consensus size: 210
49182514 CTAAATGATT
* * *
49182524 TACTGGCCTAATTTTAAAGCTTCTGATGCATTGGTTGAAACATTGCTTGAAAAAGGTAAGTTTTC
1 TACTGGCCTAATTTTAAAGCTTCTAAAGCATTGGTTGAAACATTGCTTAAAAAAGGTAAGTTTTC
* * * * ** *
49182589 TCAAGCTCAGAAGCTTTT-GTCTGGGAAGGGGATTGACCAACTGTGT-TATGAAGAAGTGCTTTT
66 TAAAGCTAAGAAGCTTTTAAT-TGGGAAGGGGATCGACCAACTGCATCT-CGAAGAAGTGCTTTT
* * * *
49182652 CAACCTATGGGATAGGATAAATTGTAGCAATAATACACTTGATGACGGCTTAATCATTCTGGGCC
129 CAACCCATGAGATAGGATAAATTATAGCAATAATACACTTGATAACGGCTTAATCATTCTGGGCC
49182717 AAATGATTACATTAGGC
194 AAATGATTACATTAGGC
* * * * *
49182734 TACTGGCCTGATTTTAAAGCTTCTAAAGCTTTGGTTGCAGCATTTCTTAAAAAAGGTAAGTTTTC
1 TACTGGCCTAATTTTAAAGCTTCTAAAGCATTGGTTGAAACATTGCTTAAAAAAGGTAAGTTTTC
* *
49182799 TAAAGCTAAGAAGCTTTTAATTGGGATGGGGATCGATCAACTGCATCTCGAAGAAGTGCTTTTCA
66 TAAAGCTAAGAAGCTTTTAATTGGGAAGGGGATCGACCAACTGCATCTCGAAGAAGTGCTTTTCA
* * * * * * * *
49182864 GCCCATGAGTTTGGATAAATTATAGCAGTAATAGACTTGATAACTGTTTAATCATTCTGGGCTAA
131 ACCCATGAGATAGGATAAATTATAGCAATAATACACTTGATAACGGCTTAATCATTCTGGGCCAA
49182929 ATGAT
196 ATGAT
49182934 AATGTCAAGA
Statistics
Matches: 169, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
210 167 0.99
211 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (210 bp):
TACTGGCCTAATTTTAAAGCTTCTAAAGCATTGGTTGAAACATTGCTTAAAAAAGGTAAGTTTTC
TAAAGCTAAGAAGCTTTTAATTGGGAAGGGGATCGACCAACTGCATCTCGAAGAAGTGCTTTTCA
ACCCATGAGATAGGATAAATTATAGCAATAATACACTTGATAACGGCTTAATCATTCTGGGCCAA
ATGATTACATTAGGC
Found at i:49196476 original size:62 final size:61
Alignment explanation
Indices: 49196409--49196530 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
49196399 TTAATGGCTA
** * *
49196409 ATTATTTGTTCAAGTCCGGAAGTTGGTTTAGTATTTTTGAGAGTAAATTTTGTTTGATATTC
1 ATTATTTGTTCAAGTCCAAAAATTGG-TTAGTATTTTTGAGAGTAAATTTTATTTGATATTC
* * * *
49196471 ATTATTTGTTTAAGTTCAAAAATTTGTTAGTATTTTTGAGAGTAAGTTTTATTTGATATT
1 ATTATTTGTTCAAGTCCAAAAATTGGTTAGTATTTTTGAGAGTAAATTTTATTTGATATT
49196531 TAAGAAAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
61 32 0.62
62 20 0.38
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (61 bp):
ATTATTTGTTCAAGTCCAAAAATTGGTTAGTATTTTTGAGAGTAAATTTTATTTGATATTC
Found at i:49200829 original size:12 final size:12
Alignment explanation
Indices: 49200812--49200881 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
49200802 TTAACTTAAT
49200812 CGAACATGTTCA
1 CGAACATGTTCA
**
49200824 CGAACAT-TGGA
1 CGAACATGTTCA
49200835 CGAACATGTTCA
1 CGAACATGTTCA
* * *
49200847 TGAACAT-ATAA
1 CGAACATGTTCA
*
49200858 TTGAACATGTTCA
1 -CGAACATGTTCA
49200871 CGAACAATGTT
1 CGAAC-ATGTT
49200882 AATGAATAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
11 11 0.25
12 26 0.59
13 7 0.16
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:49200838 original size:23 final size:24
Alignment explanation
Indices: 49200808--49200876 Score: 88
Period size: 23 Copynumber: 2.9 Consensus size: 24
49200798 TCATTTAACT
49200808 TAATCGAACATGTTCACGAACAT-
1 TAATCGAACATGTTCACGAACATA
* *
49200831 TGGA-CGAACATGTTCATGAACATA
1 T-AATCGAACATGTTCACGAACATA
*
49200855 TAATTGAACATGTTCACGAACA
1 TAATCGAACATGTTCACGAACA
49200877 ATGTTAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
TAATCGAACATGTTCACGAACATA
Found at i:49203845 original size:31 final size:30
Alignment explanation
Indices: 49203800--49203858 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
49203790 AAAGTTTTAC
*
49203800 ATTGAAAAAAACTTAGATACCAAATTGAAT
1 ATTGAAAAAAACTTAAATACCAAATTGAAT
* *
49203830 ATTGAAACCAAACTTAAATACTAAATTGA
1 ATTGAAA-AAAACTTAAATACCAAATTGA
49203859 GACAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (30 bp):
ATTGAAAAAAACTTAAATACCAAATTGAAT
Found at i:49204211 original size:22 final size:21
Alignment explanation
Indices: 49204186--49204241 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
49204176 TAGACCAATC
49204186 TATATTATTTTTTAAAAATATT
1 TATATTATTTTTTAAAAAT-TT
* * *
49204208 TATATTAATATTTAATAATTT
1 TATATTATTTTTTAAAAATTT
49204229 TATA-TATTTTTTA
1 TATATTATTTTTTA
49204242 TATAGTTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 7 0.24
21 6 0.21
22 16 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTATTTTTTAAAAATTT
Found at i:49205096 original size:9 final size:8
Alignment explanation
Indices: 49205071--49205095 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
49205061 AATATTAATT
49205071 ATAAAAAA
1 ATAAAAAA
49205079 ATAAAAAA
1 ATAAAAAA
49205087 ATAAAAAA
1 ATAAAAAA
49205095 A
1 A
49205096 ACTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:49220624 original size:43 final size:43
Alignment explanation
Indices: 49220576--49220661 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
49220566 AGGAGTTAGC
49220576 TCTATTTTTATTACATTTTAATATGTATAAATACCTCATTAAA
1 TCTATTTTTATTACATTTTAATATGTATAAATACCTCATTAAA
* *
49220619 TCTATTTTTGTTACATTTTCATATGTATAAATACCTCATTAAA
1 TCTATTTTTATTACATTTTAATATGTATAAATACCTCATTAAA
49220662 GTGAGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (43 bp):
TCTATTTTTATTACATTTTAATATGTATAAATACCTCATTAAA
Found at i:49223615 original size:15 final size:16
Alignment explanation
Indices: 49223579--49223620 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
49223569 TATATGATGT
49223579 TATTTTA-ATATTTAA
1 TATTTTATATATTTAA
49223594 TAATTTTATATATTTAA
1 T-ATTTTATATATTTAA
*
49223611 T-TTTTTTATA
1 TATTTTATATA
49223621 CGTACATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 6 0.25
17 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTATATATTTAA
Found at i:49223620 original size:17 final size:17
Alignment explanation
Indices: 49223580--49223611 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49223570 ATATGATGTT
49223580 ATTTTA-ATATTTAATA
1 ATTTTATATATTTAATA
49223596 ATTTTATATATTTAAT
1 ATTTTATATATTTAAT
49223612 TTTTTTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATATATTTAATA
Found at i:49226694 original size:41 final size:41
Alignment explanation
Indices: 49226635--49226726 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
49226625 CTAAAATTAT
* *
49226635 TTATATTAGAAAATACTACCATAAACAAAATAAATATTTTA
1 TTATATTAAAAAACACTACCATAAACAAAATAAATATTTTA
* *
49226676 TTATATTAAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACCATAAACAAAATAAATATTTTA
*
49226717 TTCTATTAAA
1 TTATATTAAA
49226727 TATGATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (41 bp):
TTATATTAAAAAACACTACCATAAACAAAATAAATATTTTA
Found at i:49229619 original size:197 final size:197
Alignment explanation
Indices: 49229278--49229670 Score: 687
Period size: 197 Copynumber: 2.0 Consensus size: 197
49229268 GTGTCAGTGT
* *
49229278 AAATAACCAAAGCCTTTAAAAAGTTTTTTTCCTTGCTAAAAGGCTTTTAAAAGTAAATTTTAGAA
1 AAATAACCAAAGCCTTTAAAAAGTTTTTTTCCTTGCTAAAAAGCCTTTAAAAGTAAATTTTAGAA
* * * *
49229343 TTACTTTGAATTGGAAGACTCTAGATTACTATGACATTTTTACCCTTTAGTTATATCTATGTTTA
66 TTACTTTGAATTGAAAGACTCTAGATTACAATGACATTTTTACCCTTTAATTATACCTATGTTTA
* *
49229408 GGTGTCACTCAAACAAATCTTTTCAATAAGATATAAATTTTATATATAGTTATGGATTGTTTTTT
131 GGTGTCACTCAAACAAATCATTTCAATAAGATATAAAATTTATATATAGTTATGGATTGTTTTTT
49229473 TA
196 TA
49229475 AAATAACCAAAGCCTTTAAAAAGTTTTTTTCCTTGCTAAAAAGCCTTTAAAAGTAAATTTTAGAA
1 AAATAACCAAAGCCTTTAAAAAGTTTTTTTCCTTGCTAAAAAGCCTTTAAAAGTAAATTTTAGAA
*
49229540 TTACTTTGAATTTAAAGACTCTAGATTACAATGACATTTTTACCCTTTAATTATACCTATGTTTA
66 TTACTTTGAATTGAAAGACTCTAGATTACAATGACATTTTTACCCTTTAATTATACCTATGTTTA
* *
49229605 GGTGTCAGTCAAACAAATCATTTCAATAGGATATAAAATTTATATATAGTTATGGATTGTTTTTT
131 GGTGTCACTCAAACAAATCATTTCAATAAGATATAAAATTTATATATAGTTATGGATTGTTTTTT
49229670 T
196 T
49229671 GTAGAAAAAG
Statistics
Matches: 185, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
197 185 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (197 bp):
AAATAACCAAAGCCTTTAAAAAGTTTTTTTCCTTGCTAAAAAGCCTTTAAAAGTAAATTTTAGAA
TTACTTTGAATTGAAAGACTCTAGATTACAATGACATTTTTACCCTTTAATTATACCTATGTTTA
GGTGTCACTCAAACAAATCATTTCAATAAGATATAAAATTTATATATAGTTATGGATTGTTTTTT
TA
Found at i:49229751 original size:81 final size:82
Alignment explanation
Indices: 49229625--49229785 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 82
49229615 AAACAAATCA
*
49229625 TTTCAATAGGATATAAAATTTATATATAGTTATGGATTGT-TTTTTTGTAGAAAAAGGAACTAGA
1 TTTCAATAGGATATAAAATTTATATATAGTTATGGATTGTATTTTTGGTAGAAAAAGGAACTAGA
*
49229689 TAAAAGTCAACAAAAGG
66 TAAAAGTAAACAAAAGG
* * *
49229706 TTTCAATAGGATATAAATTTTGTATATAGTTATGGATTGTATTTTTGGTAGAAAAAGGAATTAGA
1 TTTCAATAGGATATAAAATTTATATATAGTTATGGATTGTATTTTTGGTAGAAAAAGGAACTAGA
49229771 TAAAAGTAAACAAAA
66 TAAAAGTAAACAAAA
49229786 AGTTGTATAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 38 0.51
82 36 0.49
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (82 bp):
TTTCAATAGGATATAAAATTTATATATAGTTATGGATTGTATTTTTGGTAGAAAAAGGAACTAGA
TAAAAGTAAACAAAAGG
Found at i:49233359 original size:16 final size:16
Alignment explanation
Indices: 49233338--49233392 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
49233328 TTGAATTGAT
49233338 TTTAAATTTTTTTAAA
1 TTTAAATTTTTTTAAA
49233354 TTTAAATTTGTTTTAAA
1 TTTAAATTT-TTTTAAA
**
49233371 TTTAAATTTAGTTAAA
1 TTTAAATTTTTTTAAA
49233387 TTTAAA
1 TTTAAA
49233393 ATGGTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
TTTAAATTTTTTTAAA
Found at i:49233361 original size:27 final size:27
Alignment explanation
Indices: 49233317--49233373 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
49233307 ATTTTTGAAT
* *
49233317 TTTTTTTAAGTTTGAA-TTGATTTTAAA
1 TTTTTTTAAATTTAAATTTG-TTTTAAA
49233344 TTTTTTTAAATTTAAATTTGTTTTAAA
1 TTTTTTTAAATTTAAATTTGTTTTAAA
49233371 TTT
1 TTT
49233374 AAATTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (27 bp):
TTTTTTTAAATTTAAATTTGTTTTAAA
Found at i:49233400 original size:33 final size:34
Alignment explanation
Indices: 49233338--49233418 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
49233328 TTGAATTGAT
** * *
49233338 TTTAAATTTTTTTAAATTTAAATTTG-TTTTAAA
1 TTTAAATTTAGTTAAATTTAAAATGGTTTTTAAA
49233371 TTTAAATTTAGTTAAATTTAAAATGGTTTTTAAA
1 TTTAAATTTAGTTAAATTTAAAATGGTTTTTAAA
* *
49233405 CTTATAATTAAGTT
1 TTTA-AATTTAGTT
49233419 TAAAATGTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
33 22 0.55
34 10 0.25
35 8 0.20
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (34 bp):
TTTAAATTTAGTTAAATTTAAAATGGTTTTTAAA
Found at i:49235311 original size:30 final size:29
Alignment explanation
Indices: 49235258--49235410 Score: 108
Period size: 29 Copynumber: 5.2 Consensus size: 29
49235248 AAAAGTCCCT
* *
49235258 AAACTATCCAAAAATTATATTTTAACCCCA
1 AAACT-TCCAAAAATTACATTTTTACCCCA
* **
49235288 AAACTTCTAAAAATTACATTTTTACCCTT
1 AAACTTCCAAAAATTACATTTTTACCCCA
* * ** * * *
49235317 GAATTTTTAGAAATTACATTTTTGCCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCA
* * * ** *
49235346 GAATTTCCCAAAATTGTATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCA
*
49235375 AAACTTCCAAAAATTCCATTTTTTTACCCCA
1 AAACTTCCAAAAATTACA--TTTTTACCCCA
49235406 AAACT
1 AAACT
49235411 CTCGAAATTA
Statistics
Matches: 96, Mismatches: 25, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
29 76 0.79
30 5 0.05
31 15 0.16
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCA
Found at i:49235506 original size:28 final size:27
Alignment explanation
Indices: 49235473--49235573 Score: 78
Period size: 28 Copynumber: 3.6 Consensus size: 27
49235463 AATTTTTCTA
*
49235473 AAAATTACCATTTTATCCTCGAACGTTT
1 AAAATTACCATTTTAACCTCGAA-GTTT
* * *
49235501 AAAATT-TCATTTTTAACCTTGAATTTT
1 AAAATTACCA-TTTTAACCTCGAAGTTT
**
49235528 CCCAAAATTACCATTTTGCCCTCGAAAGTTT
1 ---AAAATTACCATTTTAACCTCG-AAGTTT
*
49235559 AAAATTGCCATTTTA
1 AAAATTACCATTTTA
49235574 CCCCCAAGTA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
27 5 0.09
28 30 0.54
30 14 0.25
31 7 0.12
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAATTACCATTTTAACCTCGAAGTTT
Found at i:49240628 original size:13 final size:12
Alignment explanation
Indices: 49240603--49240674 Score: 67
Period size: 12 Copynumber: 5.8 Consensus size: 12
49240593 TTCAATGAAT
49240603 AAAAGAAAAGAA
1 AAAAGAAAAGAA
49240615 AAAAGAATAAGAA
1 AAAAGAA-AAGAA
*
49240628 AAATA-AAAATAA
1 AAA-AGAAAAGAA
*
49240640 AAAA-ATAAAAAA
1 AAAAGA-AAAGAA
*
49240652 ACAAAGAAGAGAA
1 A-AAAGAAAAGAA
49240665 AAAAGAAAAG
1 AAAAGAAAAG
49240675 GAGAGGTCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
11 2 0.04
12 28 0.56
13 18 0.36
14 2 0.04
ACGTcount: A:0.81, C:0.01, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:49240643 original size:14 final size:15
Alignment explanation
Indices: 49240620--49240650 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
49240610 AAGAAAAAAG
49240620 AATAAGAAAAATAAA
1 AATAAGAAAAATAAA
49240635 AATAA-AAAAATAAA
1 AATAAGAAAAATAAA
49240649 AA
1 AA
49240651 AACAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AATAAGAAAAATAAA
Found at i:49240651 original size:15 final size:16
Alignment explanation
Indices: 49240605--49240651 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
49240595 CAATGAATAA
*
49240605 AAGAAAAGAAAAAAGAAT
1 AAGAAAA-ATAAAA-AAT
49240623 AAGAAAAAT-AAAAAT
1 AAGAAAAATAAAAAAT
49240638 AA-AAAAATAAAAAA
1 AAGAAAAATAAAAAA
49240652 ACAAAGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 10 0.37
16 3 0.11
17 1 0.04
18 7 0.26
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (16 bp):
AAGAAAAATAAAAAAT
Found at i:49241905 original size:50 final size:49
Alignment explanation
Indices: 49241741--49241915 Score: 129
Period size: 50 Copynumber: 3.5 Consensus size: 49
49241731 AGGTTTGACA
* * * * *
49241741 GGGAAAGATCTAAGTCGCGACGGCATATCGTGTACCTCAAAAGACACGAC
1 GGGAAAGATCTAAGACGCAACGGTAGACCGTGTACCTC-AAAGACACGAC
* * * * * * *
49241791 GGGAAAGATCTAAGACCGTAACGGTGGATCC-AGTATCGT-AAAAACACAAAA
1 GGGAAAGATCTAAGA-CGCAACGGTAGA-CCGTGTA-CCTCAAAGACAC-GAC
* * *
49241842 GGAAAAGGTCTAAGAAGCAACGGTAGACCGTGTACCTCAGAAGACACGAC
1 GGGAAAGATCTAAGACGCAACGGTAGACCGTGTACCTCA-AAGACACGAC
*
49241892 GGGAAAGATCTAAGATCGTAACGG
1 GGGAAAGATCTAAGA-CGCAACGG
49241916 CGGATCCATT
Statistics
Matches: 91, Mismatches: 26, Indels: 15
0.69 0.20 0.11
Matches are distributed among these distances:
49 4 0.04
50 48 0.53
51 36 0.40
52 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (49 bp):
GGGAAAGATCTAAGACGCAACGGTAGACCGTGTACCTCAAAGACACGAC
Found at i:49241937 original size:51 final size:50
Alignment explanation
Indices: 49241773--49242069 Score: 167
Period size: 50 Copynumber: 6.0 Consensus size: 50
49241763 GCATATCGTG
* * * *
49241773 TACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAACGGTGGATCCAG
1 TACCGCAAAAGACACAAAGGGAAAGATCTAAGA-CGTAACGGTGGATCCAT
* * * * * * * *
49241824 TATCGTAAAA-ACACAAAAGGAAAAGGTCTAAGAAGCAACGGTAGA-CCGT
1 TACCGCAAAAGACAC-AAAGGGAAAGATCTAAGACGTAACGGTGGATCCAT
* * * * *
49241873 GTACCTCAGAAGACACGACGGGAAAGATCTAAGATCGTAACGGCGGATCCAT
1 -TACCGCAAAAGACACAAAGGGAAAGATCTAAGA-CGTAACGGTGGATCCAT
* * * *** *
49241925 TACCGCAAAAGACA-AAAGGGTAAGATCTAAGACAGCAAAGACAGATCCAG
1 TACCGCAAAAGACACAAAGGGAAAGATCTAAGAC-GTAACGGTGGATCCAT
* * * * * * * **
49241975 TACCGC-GAAGACA-TAAGGGAAAGATTTAAGCCGCAATGGTAGATCCGG
1 TACCGCAAAAGACACAAAGGGAAAGATCTAAGACGTAACGGTGGATCCAT
* * * *
49242023 TACCGC-GAAGACA-TAAGGGAAAGATCTAAGCCGTGACGGTGGATCCA
1 TACCGCAAAAGACACAAAGGGAAAGATCTAAGACGTAACGGTGGATCCA
49242070 ATTCCACGAA
Statistics
Matches: 190, Mismatches: 50, Indels: 15
0.75 0.20 0.06
Matches are distributed among these distances:
48 53 0.28
49 24 0.13
50 65 0.34
51 45 0.24
52 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (50 bp):
TACCGCAAAAGACACAAAGGGAAAGATCTAAGACGTAACGGTGGATCCAT
Found at i:49241962 original size:101 final size:101
Alignment explanation
Indices: 49241769--49241962 Score: 282
Period size: 101 Copynumber: 1.9 Consensus size: 101
49241759 GACGGCATAT
* *
49241769 CGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAACGGTGGATCCAGTATCGTAAAA
1 CGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGTAAAA
*
49241834 ACACAAAAGGAAAAGGTCTAAGAAGCAACGGTAGAC
66 ACACAAAAGGAAAAGATCTAAGAAGCAACGGTAGAC
* * * *
49241870 CGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGATCGTAACGGCGGATCCATTACCG-CAAA
1 CGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGTAAAA
* **
49241934 AGACAAAAGGGTAAGATCTAAGACAGCAA
66 ACACAAAAGGAAAAGATCTAAGA-AGCAA
49241963 AGACAGATCC
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 22 0.27
101 60 0.73
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.14
Consensus pattern (101 bp):
CGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGTAAAA
ACACAAAAGGAAAAGATCTAAGAAGCAACGGTAGAC
Found at i:49241978 original size:101 final size:101
Alignment explanation
Indices: 49241772--49242004 Score: 258
Period size: 101 Copynumber: 2.3 Consensus size: 101
49241762 GGCATATCGT
* * *
49241772 GTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAACGGTGGATCCAGTATCGTAAAAACA
1 GTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGTAAAAACA
* * ** *
49241837 CAAAAGGAAAAGGTCTAAGAAGCAACGGTAGACCGT
66 CAAAAGGAAAAGATCTAAGAAGCAAAGACAGACCGA
* * * *
49241873 GTACCTCAGAAGACACGACGGGAAAGATCTAAGATCGTAACGGCGGATCCATTACCG-CAAAAGA
1 GTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGTAAAAACA
**
49241937 CAAAAGGGTAAGATCTAAGACAGCAAAGACAGATCC-A
66 CAAAAGGAAAAGATCTAAGA-AGCAAAGACAGA-CCGA
* * * *
49241974 GTACCGC-GAAGACA-TAAGGGAAAGATTTAAG
1 GTACCTCAGAAGACACGACGGGAAAGATCTAAG
49242005 CCGCAATGGT
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
99 14 0.12
100 29 0.26
101 67 0.60
102 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.14
Consensus pattern (101 bp):
GTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGTAAAAACA
CAAAAGGAAAAGATCTAAGAAGCAAAGACAGACCGA
Found at i:49242143 original size:49 final size:48
Alignment explanation
Indices: 49241933--49242130 Score: 189
Period size: 48 Copynumber: 4.1 Consensus size: 48
49241923 ATTACCGCAA
* * * * * * * *
49241933 AAGACAAAAGGGTAAGATCTAAGACAGCAAAGACAGATCCAGTACCGCG
1 AAGACATAAGGGAAAGATCTAAG-CCGCGATGGCAGATCCAATACCACG
* * * ** *
49241982 AAGACATAAGGGAAAGATTTAAGCCGCAATGGTAGATCCGGTACCGCG
1 AAGACATAAGGGAAAGATCTAAGCCGCGATGGCAGATCCAATACCACG
* * ** *
49242030 AAGACATAAGGGAAAGATCTAAGCCGTGACGGTGGATCCAATTCCACG
1 AAGACATAAGGGAAAGATCTAAGCCGCGATGGCAGATCCAATACCACG
* *
49242078 AAGACATGAAGAGAAAGATCTAATCCGCGATGGCAGATCCAATACCACG
1 AAGACAT-AAGGGAAAGATCTAAGCCGCGATGGCAGATCCAATACCACG
49242127 AAGA
1 AAGA
49242131 TTTGAAGGGA
Statistics
Matches: 124, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
48 66 0.53
49 58 0.47
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (48 bp):
AAGACATAAGGGAAAGATCTAAGCCGCGATGGCAGATCCAATACCACG
Found at i:49242160 original size:49 final size:48
Alignment explanation
Indices: 49241892--49242160 Score: 196
Period size: 49 Copynumber: 5.5 Consensus size: 48
49241882 AAGACACGAC
* * * * * * * *
49241892 GGGAAAGATCTAAGATCGTAACGGCGGATCCATTACCGCAAAAGACAAAA
1 GGGAAAGATCTAAG-CCGCAATGGCAGATCCAATACCAC-GAAGACATAA
* * * * * *
49241942 GGGTAAGATCTAAGACAGCAAAGACAGATCCAGTACCGCGAAGACATAA
1 GGGAAAGATCTAAG-CCGCAATGGCAGATCCAATACCACGAAGACATAA
* * ** *
49241991 GGGAAAGATTTAAGCCGCAATGGTAGATCCGGTACCGCGAAGACATAA
1 GGGAAAGATCTAAGCCGCAATGGCAGATCCAATACCACGAAGACATAA
** * ** *
49242039 GGGAAAGATCTAAGCCGTGACGGTGGATCCAATTCCACGAAGACATGAA
1 GGGAAAGATCTAAGCCGCAATGGCAGATCCAATACCACGAAGACAT-AA
* * * **
49242088 GAGAAAGATCTAATCCGCGATGGCAGATCCAATACCACGAAGATTTGAA
1 GGGAAAGATCTAAGCCGCAATGGCAGATCCAATACCACGAAGACAT-AA
* * *
49242137 GGGAAAGGTTTAAGTCGCAATGGC
1 GGGAAAGATCTAAGCCGCAATGGC
49242161 GAACCCGGTA
Statistics
Matches: 177, Mismatches: 41, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
48 66 0.37
49 80 0.45
50 31 0.18
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (48 bp):
GGGAAAGATCTAAGCCGCAATGGCAGATCCAATACCACGAAGACATAA
Found at i:49242429 original size:38 final size:37
Alignment explanation
Indices: 49242387--49242459 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 37
49242377 GATTCAAGAA
*
49242387 GGGCAAAATGAAG-ATTCTGATCTCTTACCCTGAGCAAG
1 GGGCAAAATGAAGCATT-TGATCT-TTACCCCGAGCAAG
* *
49242425 GGGCAGATTGAAGCCATTTGATCTTTACCCCGAGC
1 GGGCAAAATGAAG-CATTTGATCTTTACCCCGAGC
49242460 CTAAGGTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
38 21 0.70
39 6 0.20
40 3 0.10
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (37 bp):
GGGCAAAATGAAGCATTTGATCTTTACCCCGAGCAAG
Found at i:49242973 original size:206 final size:205
Alignment explanation
Indices: 49242618--49243216 Score: 827
Period size: 206 Copynumber: 3.0 Consensus size: 205
49242608 CCAACTCAAC
* * *
49242618 GCTCAATGCGAGCAAATCTTCGAACCCTAACTTCCTGAT--G---TGAGAAGCAGGTCGAAGCAA
1 GCTCAATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATGAGAAGCAGGTCGAAGCAA
* *
49242678 TAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTAAGGAGATCC
66 TAAAATGGTTAGCTTCCTGATGAGATATAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCC
* * *
49242743 AGAGAAGCGAATTAAAATAAGTGATACGGTTATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
49242808 TCAAACCCAG
196 TCAAACCCAG
* * *
49242818 GCTCAATGAGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAAGTTGAAGCA
1 GCTCAATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACA-TGAGAAGCAGGTCGAAGCA
* *
49242883 ATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATC
65 ATAAAATGGTTAGCTTCCTGATGAGATATAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATC
* *
49242948 CAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCTTGATGAGACACTGAGAAGAAGACCAA
130 CAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
49243013 ATCAAACCCAG
195 ATCAAACCCAG
* *
49243024 GCTCAATGGGAGCAAATCTTCGAGCCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCA
1 GCTCAATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACA-TGAGAAGCAGGTCGAAGCA
* * * * ** *
49243089 AT-AAGTGGTTAGCTTCCTGATGAGACATAGAGAAGTGAACCAAATCCGTCTCCCTGTTGA-A-A
65 ATAAAATGGTTAGCTTCCTGATGAGATATAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATC
* * * * * * * * *
49243151 CATAGAAGTGGATCAAAACAAGTGACGCAGTCGTCTTCCTGATCAGATACTGAGAAGAAGGCCAA
130 CAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
49243216 A
195 A
49243217 CCAATTAAAT
Statistics
Matches: 352, Mismatches: 41, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
200 35 0.10
202 1 0.00
203 55 0.16
204 1 0.00
205 50 0.14
206 210 0.60
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21
Consensus pattern (205 bp):
GCTCAATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATGAGAAGCAGGTCGAAGCAA
TAAAATGGTTAGCTTCCTGATGAGATATAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCC
AGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAG
Found at i:49243603 original size:26 final size:27
Alignment explanation
Indices: 49243560--49243615 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
49243550 AATTTTTGAT
**
49243560 TTTTTTAAAGTTTGAA-TTGATTTTAAA
1 TTTTTTAAAGTTAAAATTTG-TTTTAAA
49243587 TTTTTTAAA-TTAAAATTTGTTTTAAA
1 TTTTTTAAAGTTAAAATTTGTTTTAAA
49243613 TTT
1 TTT
49243616 AAATTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTTTTAAAGTTAAAATTTGTTTTAAA
Found at i:49243611 original size:17 final size:18
Alignment explanation
Indices: 49243589--49243655 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 18
49243579 ATTTTAAATT
49243589 TTTTAAA-TTAAAATTTG
1 TTTTAAACTTAAAATTTG
*
49243606 TTTTAAA-TTTAAATTTAG
1 TTTTAAACTTAAAATTT-G
* *
49243624 --TTAAATTTAAAA-TGG
1 TTTTAAACTTAAAATTTG
49243639 TTTTTAAACTTAAAATT
1 -TTTTAAACTTAAAATT
49243656 AAGTTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
15 1 0.03
16 6 0.15
17 20 0.50
18 12 0.30
19 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTTAAACTTAAAATTTG
Found at i:49243629 original size:16 final size:15
Alignment explanation
Indices: 49243581--49243634 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 15
49243571 TTGAATTGAT
*
49243581 TTTAAATTTTTTAAA
1 TTTAAATTTGTTAAA
*
49243596 TTAAAATTTGTTTTAAA
1 TTTAAATTTG--TTAAA
49243613 TTTAAATTTAGTTAAA
1 TTTAAATTT-GTTAAA
49243629 TTTAAA
1 TTTAAA
49243635 ATGGTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 11 0.33
17 13 0.39
18 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
TTTAAATTTGTTAAA
Found at i:49245650 original size:58 final size:59
Alignment explanation
Indices: 49245426--49245658 Score: 185
Period size: 58 Copynumber: 3.9 Consensus size: 59
49245416 CCCTAAAAGT
* * * *
49245426 CCCTAAACTATTC-AAAAATT--ATATTTTAA-CCTCGAAACTTCCTAAAATTACATTTTTAC
1 CCCTAAACT-TTCAAAAAATTCCAT-TTTTAACCCT-AAAAC-TCCAAAAATTATATTTTTGC
* * * * * *
49245485 CCCCAAATTTTAAAAAAATTCCATTTTTAACCCTAAAAATTCCTAAAATTATGTTTTTGC
1 CCCTAAACTTTCAAAAAATTCCATTTTTAACCCT-AAAACTCCAAAAATTATATTTTTGC
* * *
49245545 CCCTAAACTTTC-AAAAATTCCA-CTTTAACCTTTAAACCTCCAAAAATTATATTTTTG-
1 CCCTAAACTTTCAAAAAATTCCATTTTTAACC-CTAAAACTCCAAAAATTATATTTTTGC
* * **
49245602 CCCTCGAAC-TTCAAAAAATTCCATTTTTTACCCTAAAACTCCCGAAATTACTATTTT
1 CCCT-AAACTTTCAAAAAATTCCATTTTTAACCCTAAAACTCCAAAAATTA-TATTTT
49245659 ACCCGCAGAT
Statistics
Matches: 140, Mismatches: 25, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
57 7 0.05
58 56 0.40
59 37 0.26
60 32 0.23
61 8 0.06
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (59 bp):
CCCTAAACTTTCAAAAAATTCCATTTTTAACCCTAAAACTCCAAAAATTATATTTTTGC
Found at i:49250486 original size:13 final size:13
Alignment explanation
Indices: 49250468--49250495 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49250458 GTGTGAAAAC
49250468 TATGAATTTAGAA
1 TATGAATTTAGAA
49250481 TATGAATTTAGAA
1 TATGAATTTAGAA
49250494 TA
1 TA
49250496 CAGATAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
TATGAATTTAGAA
Found at i:49253827 original size:5 final size:5
Alignment explanation
Indices: 49253780--49253823 Score: 79
Period size: 5 Copynumber: 8.6 Consensus size: 5
49253770 AAACTCACAC
49253780 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATCA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTA
49253824 CATTGCATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 34 0.89
6 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:49260653 original size:33 final size:33
Alignment explanation
Indices: 49260614--49260681 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
49260604 AGAATTTTTA
49260614 AAAATCATATCTCTACACCAATATATCTAATTT
1 AAAATCATATCTCTACACCAATATATCTAATTT
*
49260647 AAAATCATATCTCTACACCAGTATATCTAATTT
1 AAAATCATATCTCTACACCAATATATCTAATTT
49260680 AA
1 AA
49260682 GTATTAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (33 bp):
AAAATCATATCTCTACACCAATATATCTAATTT
Found at i:49261034 original size:24 final size:23
Alignment explanation
Indices: 49260983--49261034 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
49260973 TAAAATTTAG
49260983 TTTTAGTATTTTTATTTTTAGAA
1 TTTTAGTATTTTTATTTTTAGAA
* *
49261006 ATTTAGTTTTTTTTACTTTTTA-AA
1 TTTTAG-TATTTTTA-TTTTTAGAA
49261030 TTTTA
1 TTTTA
49261035 AAATTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (23 bp):
TTTTAGTATTTTTATTTTTAGAA
Found at i:49261614 original size:9 final size:9
Alignment explanation
Indices: 49261549--49261638 Score: 50
Period size: 9 Copynumber: 10.3 Consensus size: 9
49261539 ATTTAAAAAC
*
49261549 ATTTTTATT
1 ATTTTTATA
* *
49261558 TTTTTTGTA
1 ATTTTTATA
49261567 ATTTTTATA
1 ATTTTTATA
49261576 CATTTTTAATA
1 -ATTTTT-ATA
*
49261587 A-TGTTA-A
1 ATTTTTATA
*
49261594 TTTATTTAATA
1 ATT-TTT-ATA
49261605 ATTTTTATA
1 ATTTTTATA
49261614 ATTTTT-T-
1 ATTTTTATA
49261621 A-TTTTA-A
1 ATTTTTATA
49261628 ATTTTTA-A
1 ATTTTTATA
49261636 ATT
1 ATT
49261639 AGTTAATTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
6 4 0.06
7 3 0.05
8 12 0.19
9 27 0.43
10 11 0.17
11 6 0.10
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTTATA
Found at i:49262359 original size:31 final size:31
Alignment explanation
Indices: 49262289--49262363 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
49262279 ACAAAGGGTT
* * *
49262289 AATATATC-ATTTGGTACATGAGTTTGGCTTT
1 AATAT-TCAATTTGGTACATGAATTTGACTTC
** *
49262320 AAGGTTCAATTTGGTACATTAATTTGACTTC
1 AATATTCAATTTGGTACATGAATTTGACTTC
49262351 AATATTCAATTTG
1 AATATTCAATTTG
49262364 ATACCTAGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (31 bp):
AATATTCAATTTGGTACATGAATTTGACTTC
Found at i:49262525 original size:31 final size:31
Alignment explanation
Indices: 49262484--49262554 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
49262474 TTAATATACC
49262484 ATTTGATACATAAGTTTGGCTTTAAGGTTCA
1 ATTTGATACATAAGTTTGGCTTTAAGGTTCA
* * *
49262515 ATTTGGTACATGAGTTTGGCTTTAATGTTCA
1 ATTTGATACATAAGTTTGGCTTTAAGGTTCA
49262546 ATTTGATAC
1 ATTTGATAC
49262555 CTAGACTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (31 bp):
ATTTGATACATAAGTTTGGCTTTAAGGTTCA
Found at i:49262548 original size:187 final size:187
Alignment explanation
Indices: 49262222--49262602 Score: 609
Period size: 187 Copynumber: 2.0 Consensus size: 187
49262212 GGTCCAATAC
* *
49262222 AATGTATATTAAAACACCAAATCAGCTAGGTTGGTCTTCGGTAACAATTAATACCAGACAAAGGG
1 AATGTATATTAAAACACCAAATCAGCTAGGTTGGTCTTCGGTAACAATTAAGACCAAACAAAGGG
* * * *
49262287 TTAATATATCATTTGGTACATGAGTTTGGCTTTAAGGTTCAATTTGGTACATTAATTTGACTTCA
66 TTAATATACCATTTGATACATAAGTTTGGCTTTAAGGTTCAATTTGGTACATGAATTTGACTTCA
* *
49262352 ATATTCAATTTGATACCTAGACTAAACAATATCATGTGGCCCAAAGAATATTTGACA
131 ATATTCAATTTGATACCTAGACTAAACAATATCATATGGCCCAAAGAATATTTGAAA
* * *
49262409 AATGTATATTAACACACCAAATCAGCTAGGTTGGTCTTTGGTAATAATTAAGACCAAACAAAGGG
1 AATGTATATTAAAACACCAAATCAGCTAGGTTGGTCTTCGGTAACAATTAAGACCAAACAAAGGG
* * *
49262474 TTAATATACCATTTGATACATAAGTTTGGCTTTAAGGTTCAATTTGGTACATGAGTTTGGCTTTA
66 TTAATATACCATTTGATACATAAGTTTGGCTTTAAGGTTCAATTTGGTACATGAATTTGACTTCA
* * *
49262539 ATGTTCAATTTGATACCTAGACTAAACGATATCATATGGCCCAATGAATATTTGAAA
131 ATATTCAATTTGATACCTAGACTAAACAATATCATATGGCCCAAAGAATATTTGAAA
49262596 AATGTAT
1 AATGTAT
49262603 TTTAGTAAAA
Statistics
Matches: 177, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
187 177 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (187 bp):
AATGTATATTAAAACACCAAATCAGCTAGGTTGGTCTTCGGTAACAATTAAGACCAAACAAAGGG
TTAATATACCATTTGATACATAAGTTTGGCTTTAAGGTTCAATTTGGTACATGAATTTGACTTCA
ATATTCAATTTGATACCTAGACTAAACAATATCATATGGCCCAAAGAATATTTGAAA
Found at i:49262768 original size:31 final size:30
Alignment explanation
Indices: 49262732--49262839 Score: 121
Period size: 31 Copynumber: 3.6 Consensus size: 30
49262722 CAAATTGAAA
*
49262732 AAACTCAGGTACCAAACTGAACATTGAAGCT
1 AAACTCAGGTACCAAATTGAACATTGAA-CT
* * * *
49262763 AAACTCAGGTACTAAATTGGGACAAT-AA-A
1 AAACTCAGGTACCAAATT-GAACATTGAACT
*
49262792 AAACTTAGGTACCAAATTGAACATTGAAACT
1 AAACTCAGGTACCAAATTGAACATTG-AACT
49262823 AAACTCAGGTACCAAAT
1 AAACTCAGGTACCAAAT
49262840 AGAATCGCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
28 5 0.08
29 16 0.26
30 2 0.03
31 34 0.55
32 5 0.08
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (30 bp):
AAACTCAGGTACCAAATTGAACATTGAACT
Found at i:49276702 original size:17 final size:17
Alignment explanation
Indices: 49276670--49276701 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
49276660 TGAAAGAGTA
49276670 TAATAAATTATTAAAAC
1 TAATAAATTATTAAAAC
49276687 TAATAAA-TATTAAAA
1 TAATAAATTATTAAAA
49276702 AAAAAGGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATAAATTATTAAAAC
Found at i:49277196 original size:31 final size:31
Alignment explanation
Indices: 49277139--49277209 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
49277129 ATTATCGTTC
*
49277139 TAATATTTTTTTAAAAAAATTCTTTAATAAAT
1 TAATATTTTTTTAAAAAAACTCTTTAA-AAAT
* *
49277171 TAATGTTTTTTTACAAAAACT-TTTAAAAAT
1 TAATATTTTTTTAAAAAAACTCTTTAAAAAT
*
49277201 AAAATATTT
1 -TAATATTT
49277210 ACTTTTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 4 0.12
31 11 0.33
32 18 0.55
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (31 bp):
TAATATTTTTTTAAAAAAACTCTTTAAAAAT
Found at i:49279813 original size:21 final size:21
Alignment explanation
Indices: 49279789--49279828 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
49279779 TTGTTATCGT
49279789 TTTAACAAATTAAGTTCTCAG
1 TTTAACAAATTAAGTTCTCAG
49279810 TTTAACAAATTAAGTTCTC
1 TTTAACAAATTAAGTTCTC
49279829 GATAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTAACAAATTAAGTTCTCAG
Found at i:49282016 original size:20 final size:19
Alignment explanation
Indices: 49281991--49282054 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
49281981 TTTCATGTTA
49281991 ATTTTTTTATTTTTAAATT
1 ATTTTTTTATTTTTAAATT
* *
49282010 -TATTTTTATTTTTAAAAT
1 ATTTTTTTATTTTTAAATT
* *
49282028 ATTTTTATAATTTTTAACTT
1 ATTTTT-TTATTTTTAAATT
49282048 ATTTTTT
1 ATTTTTT
49282055 GAGGTGACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 16 0.43
19 5 0.14
20 16 0.43
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTTTTATTTTTAAATT
Found at i:49282196 original size:54 final size:54
Alignment explanation
Indices: 49282130--49282240 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
49282120 TAATGTTTAT
*
49282130 TAACATTTTCATTGAAGAAAAAAATTGATTTTTTAATATAAAAAACTAAATTAA
1 TAACATTTTCATTGAAGAAAAAAATTGAGTTTTTAATATAAAAAACTAAATTAA
49282184 TAACATTTTCATTGAAGAAAAAAATTGAGTTTTTAATATAAAAAACTAAATTAA
1 TAACATTTTCATTGAAGAAAAAAATTGAGTTTTTAATATAAAAAACTAAATTAA
49282238 TAA
1 TAA
49282241 AAAATTAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.36
Consensus pattern (54 bp):
TAACATTTTCATTGAAGAAAAAAATTGAGTTTTTAATATAAAAAACTAAATTAA
Found at i:49283301 original size:24 final size:23
Alignment explanation
Indices: 49283239--49283303 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
49283229 GGAATTAAAT
**
49283239 TATATATTTTTATTATAGTAAAAA
1 TATATA-TTTTATTATTTTAAAAA
** *
49283263 TATA-ATTTCGTTATTTTAATAA
1 TATATATTTTATTATTTTAAAAA
49283285 TATATATCTTTATTATTTT
1 TATATAT-TTTATTATTTT
49283304 TAAATAATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 16 0.50
23 3 0.09
24 13 0.41
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (23 bp):
TATATATTTTATTATTTTAAAAA
Found at i:49284884 original size:24 final size:24
Alignment explanation
Indices: 49284857--49284902 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
49284847 CCCTTCAAAA
49284857 AATAAAAAAATTACAAATTAATAC
1 AATAAAAAAATTACAAATTAATAC
* * *
49284881 AATAATAAATTTACAATTTAAT
1 AATAAAAAAATTACAAATTAAT
49284903 CCTTCCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAAAAAAATTACAAATTAATAC
Found at i:49285231 original size:21 final size:18
Alignment explanation
Indices: 49285199--49285247 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
49285189 TACTTTTACA
*
49285199 TAAATATATAATTATTTATT
1 TAAATATTTAATT-TTT-TT
49285219 TAATATATTTAATTTTTTT
1 TAA-ATATTTAATTTTTTT
49285238 TAAA-ATTTAA
1 TAAATATTTAA
49285248 AATCCTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.22
18 1 0.04
19 5 0.19
20 6 0.22
21 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATATTTAATTTTTTT
Found at i:49292723 original size:14 final size:14
Alignment explanation
Indices: 49292704--49292772 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
49292694 AAGTAATTTT
*
49292704 TAAACCCTAAATAA
1 TAAACCCTAAATCA
*
49292718 TAAACCATAAATCA
1 TAAACCCTAAATCA
* * *
49292732 TAAACTCTAAACCC
1 TAAACCCTAAATCA
*
49292746 TAAACCCTAAATGA
1 TAAACCCTAAATCA
*
49292760 TAAAACCTAAATC
1 TAAACCCTAAATC
49292773 CTAACACCAT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.52, C:0.25, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:49296877 original size:43 final size:43
Alignment explanation
Indices: 49296816--49297020 Score: 241
Period size: 43 Copynumber: 4.8 Consensus size: 43
49296806 GTTTATGAGG
* * *
49296816 AAAAACGCCGCTATAGAACATGTTCTTTAGTGGCACTTTCCCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCC
* ** * *
49296859 AAAAAGGCCGCTAAAGAACATGGTCTTTAGCAACGC-TTCTTCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTC-CCC
* * * *
49296902 ACAAACGCCGCTAAAGAACATGGTCATTAGCGGCAATTTCACC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCC
* *
49296945 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGTACTTTACCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCC
** *
49296988 GCAAACACCGCTAAAGAACATGGTCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGG
49297021 TGCTTCCCTC
Statistics
Matches: 135, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
42 3 0.02
43 129 0.96
44 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCC
Found at i:49297021 original size:43 final size:42
Alignment explanation
Indices: 49296818--49297045 Score: 240
Period size: 43 Copynumber: 5.3 Consensus size: 42
49296808 TTATGAGGAA
* * * *
49296818 AAACGCCGCTATAGAACATGTTCTTTAGTGGCACTTTCCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTT-CCCAC
* ** * *
49296861 AAAGGCCGCTAAAGAACATGGTCTTTAGCAACGCTTCTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTT-TCCCAC
* * *
49296904 AAACGCCGCTAAAGAACATGGTCATTAGCGGCAATTTCACCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTC-CCAC
* *
49296947 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTACTTTACCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTT-CCCAC
* ** *
49296990 AAACACCGCTAAAGAACATGGTCTTTAGCGGTGCTTCCCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTCC-CAC
*
49297033 AAACGCTGCTAAA
1 AAACGCCGCTAAA
49297046 ATTAACAGAA
Statistics
Matches: 153, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
42 3 0.02
43 148 0.97
44 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCAC
Found at i:49297378 original size:21 final size:21
Alignment explanation
Indices: 49297354--49297393 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49297344 ATTCGCTTTT
*
49297354 CTCGCTGCTGCCTCTTCTTCC
1 CTCGCTGCTGCCTCCTCTTCC
* *
49297375 CTCGTTGTTGCCTCCTCTT
1 CTCGCTGCTGCCTCCTCTT
49297394 TAAGTTGTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.00, C:0.42, G:0.15, T:0.42
Consensus pattern (21 bp):
CTCGCTGCTGCCTCCTCTTCC
Found at i:49301151 original size:3 final size:3
Alignment explanation
Indices: 49301137--49301272 Score: 50
Period size: 3 Copynumber: 49.7 Consensus size: 3
49301127 CCATAGTAGA
* * * * * *
49301137 AAT AAG AAT AAT AAT CAT AAT AAT AAA AAT AAT TAG AA- AA- AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
49301183 AAT AAC AAC AAT AAT GAT AAT AAT AA- ATCT AA- ACA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT
*
49301227 AA- AAT AA- AA- AAT AA- AAT GA- AAT AA- AAT AA- AA- AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49301266 AA- AAT AA
1 AAT AAT AA
49301273 ACAAAATAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
2 26 0.25
3 75 0.74
4 1 0.01
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.22
Consensus pattern (3 bp):
AAT
Found at i:49301234 original size:5 final size:5
Alignment explanation
Indices: 49301217--49301282 Score: 62
Period size: 5 Copynumber: 12.4 Consensus size: 5
49301207 AAATCTAAAC
*
49301217 AAATA ATAATA AAATAAA AAATA AAATG AAATA AAATAAA AAATA AAATA
1 AAATA A-AATA AAAT--A AAATA AAATA AAATA AAAT--A AAATA AAATA
*
49301267 AAAT- AAACA AAATA AA
1 AAATA AAATA AAATA AA
49301283 GAAAAGGGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 3 0.06
5 33 0.65
6 5 0.10
7 10 0.20
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:49301252 original size:22 final size:22
Alignment explanation
Indices: 49301217--49301273 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
49301207 AAATCTAAAC
49301217 AAATAATAATAAAATAAAAAATA
1 AAATAA-AATAAAATAAAAAATA
*
49301240 AAATGAAATAAAATAAAAAATA
1 AAATAAAATAAAATAAAAAATA
49301262 AAATAAAATAAA
1 AAATAAAATAAA
49301274 CAAAATAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAATAAAATAAAAAATA
Found at i:49301270 original size:17 final size:17
Alignment explanation
Indices: 49301224--49301273 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
49301214 AACAAATAAT
49301224 AATAAAATAAAA-AATAA
1 AATAAAATAAAATAA-AA
*
49301241 AATGAAATAAAATAAAA
1 AATAAAATAAAATAAAA
49301258 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
49301274 CAAAATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 28 0.93
18 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (17 bp):
AATAAAATAAAATAAAA
Found at i:49301280 original size:9 final size:9
Alignment explanation
Indices: 49301217--49301287 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
49301207 AAATCTAAAC
49301217 AAATAATAAT
1 AAATAA-AAT
49301227 AAA-ATAAA-
1 AAATA-AAAT
49301235 AAATAAAAT
1 AAATAAAAT
49301244 GAAATAAAAT
1 -AAATAAAAT
49301254 -AA-AAAAT
1 AAATAAAAT
49301261 AAAATAAAAT
1 -AAATAAAAT
*
49301271 AAACAAAAT
1 AAATAAAAT
*
49301280 AAAGAAAA
1 AAATAAAA
49301288 GGGAAGAGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
7 5 0.10
8 8 0.15
9 21 0.40
10 18 0.35
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:49301960 original size:118 final size:118
Alignment explanation
Indices: 49301767--49302115 Score: 325
Period size: 118 Copynumber: 3.0 Consensus size: 118
49301757 TGTCTGCAGG
* * * * * **
49301767 CCGTGTACTATTTCGATATTTTAGAAAATAAGGCTCCAGTAGTCACACGATCTTGGAACACGCCC
1 CCGTGTACTATTTCAAAATTTCAGAAAATAAGGCTCCAATAGTCACACGATCCTAAAACACGCCC
*
49301832 GTGTATGACGG-CTGTAGGTCTGTCTTCGCTTCTCCCA-TGCCCGTGTCTATAAA
66 GTGTATGACGGTC-GTAGGCCTGTCTTCGCTTCTCCCACT-CCCGTGTCTATAAA
* * *
49301885 CCGTGTGCTATTTCAAAATTTCAGAAAATAAGGCTCCAATGGTCACATTG-TCCTAAAACACGCC
1 CCGTGTACTATTTCAAAATTTCAGAAAATAAGGCTCCAATAGTCACA-CGATCCTAAAACACGCC
* *
49301949 CGTGTATGACGGTCGTGGGCCTGTCTTCGCTTCTTCCACTCCCGTGTCTATAAA
65 CGTGTATGACGGTCGTAGGCCTGTCTTCGCTTCTCCCACTCCCGTGTCTATAAA
* * * * * * **
49302003 CCGTGTA-TCGTTTCGAAATGTTTATG-AAATAAGGCTCCAGTAGACACACGGT-C-AGTCACAC
1 CCGTGTACT-ATTTCAAAAT-TTCA-GAAAATAAGGCTCCAATAGTCACACGATCCTA-AAACAC
* ** * * * * *
49302064 GCCCGTGTGTTTCGGTCGTGGGCTTGTCTTCACTTCTTCCACGCCCGTGTCT
62 GCCCGTGTATGACGGTCGTAGGCCTGTCTTCGCTTCTCCCACTCCCGTGTCT
49302116 CCAGGACATG
Statistics
Matches: 194, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
117 2 0.01
118 165 0.85
119 26 0.13
120 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (118 bp):
CCGTGTACTATTTCAAAATTTCAGAAAATAAGGCTCCAATAGTCACACGATCCTAAAACACGCCC
GTGTATGACGGTCGTAGGCCTGTCTTCGCTTCTCCCACTCCCGTGTCTATAAA
Found at i:49304101 original size:25 final size:23
Alignment explanation
Indices: 49304044--49304204 Score: 164
Period size: 23 Copynumber: 6.9 Consensus size: 23
49304034 TTACCGTTCA
*
49304044 GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
49304067 GCACTTTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
*
49304090 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
* *
49304113 GCACTTCGTGTGCCTACTGATTT-
1 GCACTTTGTGTGCTTACTG-TTTC
* * * * *
49304136 GCGCTATGTGCGCCTACTGATT-
1 GCACTTTGTGTGCTTACTGTTTC
*
49304158 GCACTGTGTGTGCTTACTGTTTCC
1 GCACTTTGTGTGCTTACTGTTT-C
* *
49304182 CCAGTACTTGTGTGCTTACTGTT
1 GCACT--TTGTGTGCTTACTGTT
49304205 AAGTACTTCG
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.16
23 77 0.66
24 6 0.05
26 15 0.13
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.42
Consensus pattern (23 bp):
GCACTTTGTGTGCTTACTGTTTC
Found at i:49312767 original size:20 final size:20
Alignment explanation
Indices: 49312740--49312919 Score: 141
Period size: 20 Copynumber: 8.9 Consensus size: 20
49312730 AATGAAGAGG
49312740 TGCCCCTGTTTGCACTTCGA
1 TGCCCCTGTTTGCACTTCGA
* ** *
49312760 TACCCCTGAATGCAC-TCTA
1 TGCCCCTGTTTGCACTTCGA
* *
49312779 GTGCCTCTATTTGCACTTCGA
1 -TGCCCCTGTTTGCACTTCGA
** *
49312800 TGCCCCTGAATGCAC-TCTGG
1 TGCCCCTGTTTGCACTTC-GA
*
49312820 TGCCCCTGTTTGCACTTCAA
1 TGCCCCTGTTTGCACTTCGA
* ** *
49312840 TGCCCTTGAATGCACTTCAA
1 TGCCCCTGTTTGCACTTCGA
*
49312860 TGCCCCTGTTTGCACTTTGA
1 TGCCCCTGTTTGCACTTCGA
**
49312880 TGCCCCTGAATGCAC-TCTGA
1 TGCCCCTGTTTGCACTTC-GA
*
49312900 TGCCCCTATATTGCACTTCG
1 TGCCCCTGT-TTGCACTTCG
49312920 GTACCCCCGT
Statistics
Matches: 120, Mismatches: 33, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
19 6 0.05
20 101 0.84
21 11 0.09
22 2 0.02
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.32
Consensus pattern (20 bp):
TGCCCCTGTTTGCACTTCGA
Found at i:49312792 original size:40 final size:40
Alignment explanation
Indices: 49312739--49312919 Score: 240
Period size: 40 Copynumber: 4.5 Consensus size: 40
49312729 GAATGAAGAG
*
49312739 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACTCTA
1 GTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACTCTA
* * *
49312779 GTGCCTCTATTTGCACTTCGATGCCCCTGAATGCACTCTG
1 GTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACTCTA
* *
49312819 GTGCCCCTGTTTGCACTTCAATGCCCTTGAATGCACT-TCA
1 GTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACTCT-A
* *
49312859 ATGCCCCTGTTTGCACTTTGATGCCCCTGAATGCACTCT-
1 GTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACTCTA
*
49312898 GATGCCCCTATATTGCACTTCG
1 G-TGCCCCTGT-TTGCACTTCG
49312920 GTACCCCCGT
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 110 0.91
41 10 0.08
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.32
Consensus pattern (40 bp):
GTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACTCTA
Found at i:49314292 original size:319 final size:320
Alignment explanation
Indices: 49313708--49314329 Score: 1039
Period size: 319 Copynumber: 1.9 Consensus size: 320
49313698 CACGACTGTG
* * *
49313708 TGTGTGTTTTAGGGTGCAGTACAGTCTATTCGAATAGACACATGGGCTGAGACACAGTCCAAAGC
1 TGTGTGTTTTAGGGTACAGTACACTCTATTCGAATAGACACACGGGCTGAGACACAGTCCAAAGC
49313773 ACGGGCGTGTGATGTAAGTCAGTAAGGTCTTTTCGAGCTTGAACAAAGGCGGGCACACGTGCTGT
66 ACGGGCGTGTGATGTAAGTCAGTAAGGTCTTTTCGAGCTTGAACAAAGGCGGGCACACGTGCTGT
* * ** * *
49313838 TACATGATCGTGTGACCTTATTTCGAAGGTACACATGGGCGAGAACACGGGCTGGCACATGACCA
131 TACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACAGGCTGGCACACGACCA
* *
49313903 TGTGCCCCTGTTTCATATGATTTTCTAGCTTTTCCTTGGACTTTCTGATTGTTTGCAAATGAGCT
196 TGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGATCGTTTGCAAATGAGCT
49313968 TCTAGTCGTATTTAAACTAGTCTTAAGTGAATGAATGTATGTTGATTGTCACACGGCCTA
261 TCTAGTCGTATTTAAACTAGTCTTAAGTGAATGAATGTATGTTGATTGTCACACGGCCTA
* *
49314028 TGTGTGTTTTAGGGTACAGTATACTCTATTCGAATAGACACACGGGCTGAGACACGGTCCAAAGC
1 TGTGTGTTTTAGGGTACAGTACACTCTATTCGAATAGACACACGGGCTGAGACACAGTCCAAAGC
* * *
49314093 ACGGGCGTGTGATGTAAGTCAGTAAGGT-TTTTCGAGCTTGAACACAGGCGGGCGCACGTGTTGT
66 ACGGGCGTGTGATGTAAGTCAGTAAGGTCTTTTCGAGCTTGAACAAAGGCGGGCACACGTGCTGT
** *
49314157 TACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACAGGCTGGCACACGGTCG
131 TACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACAGGCTGGCACACGACCA
* *
49314222 TGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGATCGTTTGCAAATTAGTT
196 TGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGATCGTTTGCAAATGAGCT
*
49314287 TCTAGTTGTATTTAAACTAGTCTTAAGTGAATGAATGTATGTT
261 TCTAGTCGTATTTAAACTAGTCTTAAGTGAATGAATGTATGTT
49314330 TTGAGAATTG
Statistics
Matches: 280, Mismatches: 22, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
319 192 0.69
320 88 0.31
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (320 bp):
TGTGTGTTTTAGGGTACAGTACACTCTATTCGAATAGACACACGGGCTGAGACACAGTCCAAAGC
ACGGGCGTGTGATGTAAGTCAGTAAGGTCTTTTCGAGCTTGAACAAAGGCGGGCACACGTGCTGT
TACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACAGGCTGGCACACGACCA
TGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGATCGTTTGCAAATGAGCT
TCTAGTCGTATTTAAACTAGTCTTAAGTGAATGAATGTATGTTGATTGTCACACGGCCTA
Found at i:49321843 original size:14 final size:15
Alignment explanation
Indices: 49321821--49321850 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
49321811 TTAAATTAGT
49321821 TTTTATTTAAAAATA
1 TTTTATTTAAAAATA
49321836 TTTT-TTTAAAAATA
1 TTTTATTTAAAAATA
49321850 T
1 T
49321851 AATACATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTATTTAAAAATA
Found at i:49322095 original size:26 final size:30
Alignment explanation
Indices: 49322065--49322128 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
49322055 TTTAATATAA
* *
49322065 ATATAAAT-ATATATTTATTATT-TAACAT
1 ATATAATTGATATAATTATTATTATAACAT
*
49322093 ATATAATTGATATAATTATTTTTATAACAT
1 ATATAATTGATATAATTATTATTATAACAT
49322123 AATATA
1 -ATATA
49322129 TTCGGGCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 12 0.40
30 6 0.20
31 5 0.17
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATAATTGATATAATTATTATTATAACAT
Found at i:49328131 original size:10 final size:10
Alignment explanation
Indices: 49328097--49328138 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
49328087 TACTTTATGC
49328097 TTTTTT-TAA
1 TTTTTTATAA
49328106 -TTTTTATGAA
1 TTTTTTAT-AA
49328116 TTTTTTATAA
1 TTTTTTATAA
49328126 TTTTTTA-AA
1 TTTTTTATAA
49328135 TTTT
1 TTTT
49328139 GATTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.17
9 7 0.23
10 11 0.37
11 7 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:49329602 original size:48 final size:48
Alignment explanation
Indices: 49329531--49329626 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
49329521 TAATAATCTG
*
49329531 TATGCACTTCTAATGGAAAACTCACTTGTGGGTTCACATTGCCATACC
1 TATGCACTTCTAATGGAAAACTCACCTGTGGGTTCACATTGCCATACC
49329579 TATGCACTTCTAATGGAAAACTCACCTGTGGGTTCACATTGCCATACC
1 TATGCACTTCTAATGGAAAACTCACCTGTGGGTTCACATTGCCATACC
49329627 AATTCATCAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (48 bp):
TATGCACTTCTAATGGAAAACTCACCTGTGGGTTCACATTGCCATACC
Found at i:49334900 original size:29 final size:27
Alignment explanation
Indices: 49334838--49334901 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
49334828 CACAAATTTA
* * *
49334838 AAATTTAATCCTTGTATTTTTATTTTT
1 AAATTTAATCCATCTATTTTTATTTTC
49334865 AGGAATTTAATCCATCTATTTTTCATGTTTC
1 A--AATTTAATCCATCTATTTTT-AT-TTTC
49334896 AAATTT
1 AAATTT
49334902 TAGGTCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
29 23 0.77
30 2 0.07
31 4 0.13
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (27 bp):
AAATTTAATCCATCTATTTTTATTTTC
Found at i:49336798 original size:329 final size:329
Alignment explanation
Indices: 49336200--49337181 Score: 1964
Period size: 329 Copynumber: 3.0 Consensus size: 329
49336190 TCTATTCCTG
49336200 GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
1 GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
49336265 CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
66 CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
49336330 ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
131 ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
49336395 CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
196 CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
49336460 AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTTG
261 AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTTG
49336525 ATTT
326 ATTT
49336529 GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
1 GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
49336594 CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
66 CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
49336659 ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
131 ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
49336724 CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
196 CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
49336789 AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTTG
261 AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTTG
49336854 ATTT
326 ATTT
49336858 GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
1 GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
49336923 CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
66 CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
49336988 ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
131 ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
49337053 CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
196 CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
49337118 AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTT
261 AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTT
49337182 CAGTTGCATC
Statistics
Matches: 653, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
329 653 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (329 bp):
GATTTCCCTTGCTTCAGCTTCAAGAAGAATCTTATCATAATTCCTCTTAATTGCAAGCTCAATTC
CCAGTTTCATAGCTAAGGCTTCCACAATTTCAGGGCTATCAACCGAAGTTCCAAGATCATTCCTT
ACCACAACTCCCAACCCTGCAGAGCCAGTGTCTTTATCAAAATCTCCATGCCTTTGTGTTAGTCC
CCGAATCTTCAGGCTCTCTCTTTGCTCAATGAGATTTTCCATCTCAGTAGCTGTGCCATTCCTCA
AAGATTTGATCATTTGATTGAGCCAAGAATCAAAAGTACTGATGTATTCTCTTTGGTCTGTCTTG
ATTT
Found at i:49341739 original size:2 final size:2
Alignment explanation
Indices: 49341732--49341782 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
49341722 GAGATAACAT
*
49341732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
49341774 TA TT TA TA T
1 TA TA TA TA T
49341783 TAGATATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:49342405 original size:13 final size:13
Alignment explanation
Indices: 49342325--49342406 Score: 50
Period size: 14 Copynumber: 6.5 Consensus size: 13
49342315 AAAAAATATA
49342325 ATTTTAATTATTT
1 ATTTTAATTATTT
49342338 ATTTTTAA-TA---
1 A-TTTTAATTATTT
* *
49342348 ATTGTAA-TCTTT
1 ATTTTAATTATTT
* *
49342360 ATTTAAAATATTTT
1 ATTTTAATTA-TTT
49342374 ATTTTAACTTATATT
1 ATTTTAA-TTAT-TT
49342389 -TTTTAATTATTT
1 ATTTTAATTATTT
49342401 ATTTTA
1 ATTTTA
49342407 TATATACATA
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
9 6 0.11
10 1 0.02
12 7 0.13
13 13 0.25
14 22 0.42
15 4 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTTAATTATTT
Found at i:49344672 original size:22 final size:22
Alignment explanation
Indices: 49344647--49344690 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49344637 TTACTAGTCC
*
49344647 TATACGTATAATTGTAGATTTA
1 TATACATATAATTGTAGATTTA
49344669 TATACATATAATTGTAGATTTA
1 TATACATATAATTGTAGATTTA
49344691 GTTCATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (22 bp):
TATACATATAATTGTAGATTTA
Found at i:49347779 original size:55 final size:53
Alignment explanation
Indices: 49347714--49347906 Score: 192
Period size: 55 Copynumber: 3.5 Consensus size: 53
49347704 GACATCAGCA
*
49347714 TTTTTTATCAGATAAAAAAAATTTTGGTGTTGGTCAATGC-TTGACTGACACCACC
1 TTTTTTATCAGATAAAAAAAATTTTGGTGTTGG-CAATGCATTG-CT-ACACCACT
* * *
49347769 TTTTTAATCAGATAAAAAATAATTTTTTTGGTGTTGGCCATGCATTGGTAGCACCAGCAT
1 TTTTTTATCAGATAAAAAA-AA---TTTTGGTGTTGGCAATGCATTGCTA-CACCA-C-T
* * **
49347829 TTTTTTATCAGAT-AAAAAAATTTTGGTGTTGGCCAATGCTTTGCCAACAATACT
1 TTTTTTATCAGATAAAAAAAATTTTGGTGTTGG-CAATGCATTG-CTACACCACT
49347883 TTTTTTATCAGATAAAAAAAATTT
1 TTTTTTATCAGATAAAAAAAATTT
49347907 AGAGTTTTGG
Statistics
Matches: 116, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
54 14 0.12
55 41 0.35
56 13 0.11
57 2 0.02
58 13 0.11
59 21 0.18
60 12 0.10
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (53 bp):
TTTTTTATCAGATAAAAAAAATTTTGGTGTTGGCAATGCATTGCTACACCACT
Found at i:49347887 original size:114 final size:114
Alignment explanation
Indices: 49347681--49347906 Score: 305
Period size: 114 Copynumber: 2.0 Consensus size: 114
49347671 TTAAAAAAAA
* *
49347681 TTGGTGTTGGCCATACATTGGCCGACATCAGCATTTTTTATCAGATAAAAAAAATTTTGGTGTTG
1 TTGGTGTTGGCCATACATTGGCAGACACCAGCATTTTTTATCAGATAAAAAAAATTTTGGTGTTG
* ** *
49347746 GTCAATGCTTGACTGACACCACCTTTTTAATCAGATAAAAAATAATTTTT
66 GCCAATGCTTGACCAACAACACCTTTTTAATCAGATAAAAAA-AATTTTT
* *
49347796 TTGGTGTTGGCCATGCATTGGTAG-CACCAGCATTTTTTTATCAGAT-AAAAAAATTTTGGTGTT
1 TTGGTGTTGGCCATACATTGGCAGACACCAGCA-TTTTTTATCAGATAAAAAAAATTTTGGTGTT
* * *
49347859 GGCCAATGCTTTG-CCAACAATACTTTTTTTATCAGATAAAAAAAATTT
65 GGCCAATGC-TTGACCAACAACACCTTTTTAATCAGATAAAAAAAATTT
49347907 AGAGTTTTGG
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
113 5 0.05
114 56 0.57
115 37 0.38
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (114 bp):
TTGGTGTTGGCCATACATTGGCAGACACCAGCATTTTTTATCAGATAAAAAAAATTTTGGTGTTG
GCCAATGCTTGACCAACAACACCTTTTTAATCAGATAAAAAAAATTTTT
Found at i:49347993 original size:53 final size:54
Alignment explanation
Indices: 49347927--49348098 Score: 154
Period size: 55 Copynumber: 3.1 Consensus size: 54
49347917 TCGACGCCGT
*
49347927 TTTTTTATCAGATAAAAAAA-ATTTGGTGGTT-ATC-ATGTGTTGGTCGACACCACC
1 TTTTTTATCAGATAAAAAAATATTTGGT-GTTGA-CAATG-CTTGGTCGACACCACC
* *
49347981 -TTTTTGTCAGATAAAAGAAATTTTTGGTGTTGGACAATGCTTGGTCGACACCACC
1 TTTTTTATCAGATAAAA-AAATATTTGGTGTT-GACAATGCTTGGTCGACACCACC
* * * *
49348036 TTTTTTATCTGATAAAAAAATAATTTTTTTGGTGTTGACCATGCATTGGCCGACACCAAC
1 TTTTTTATCAGATAAAAAAAT-A----TTTGGTGTTGACAATGC-TTGGTCGACACCACC
49348096 TTT
1 TTT
49348099 CCCTCTTTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
53 15 0.15
54 6 0.06
55 26 0.27
56 18 0.19
59 7 0.07
60 25 0.26
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (54 bp):
TTTTTTATCAGATAAAAAAATATTTGGTGTTGACAATGCTTGGTCGACACCACC
Found at i:49348025 original size:55 final size:58
Alignment explanation
Indices: 49347966--49348098 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 58
49347956 TTATCATGTG
* *
49347966 TTGGTCGACACCACCTTTTTGTCAGAT-AAAAGA-AA-TTTTTGGTGTTGGACAATGC-
1 TTGGTCGACACCACCTTTTTATCAGATAAAAAAATAATTTTTTGGTGTT-GACAATGCA
* *
49348021 TTGGTCGACACCACCTTTTTTATCTGATAAAAAAATAATTTTTTTGGTGTTGACCATGCA
1 TTGGTCGACACCACC-TTTTTATCAGATAAAAAAATAA-TTTTTTGGTGTTGACAATGCA
* *
49348081 TTGGCCGACACCAACTTT
1 TTGGTCGACACCACCTTT
49348099 CCCTCTTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 15 0.23
56 10 0.15
57 5 0.08
58 2 0.03
59 10 0.15
60 24 0.36
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (58 bp):
TTGGTCGACACCACCTTTTTATCAGATAAAAAAATAATTTTTTGGTGTTGACAATGCA
Found at i:49348958 original size:18 final size:18
Alignment explanation
Indices: 49348937--49348982 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
49348927 TAATAATTAG
49348937 AAATGAAATTTAAAATAT
1 AAATGAAATTTAAAATAT
*
49348955 AAATTAAATTTAAAATAT
1 AAATGAAATTTAAAATAT
*
49348973 AAACGAAATT
1 AAATGAAATT
49348983 GCAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATGAAATTTAAAATAT
Found at i:49348989 original size:30 final size:30
Alignment explanation
Indices: 49348955--49349040 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
49348945 TTTAAAATAT
*
49348955 AAATTAAATTTAAAATATAAACGAAATTGC
1 AAATTAAATTTAAAATATAAACGAAATTAC
* *
49348985 AAATTAAATTTAAAATAAAAACAAAATTAC
1 AAATTAAATTTAAAATATAAACGAAATTAC
*
49349015 AAATTAAATTTAAAAAATAAACGAAA
1 AAATTAAATTTAAAATATAAACGAAA
49349041 AAAAATCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATTAAATTTAAAATATAAACGAAATTAC
Found at i:49352589 original size:3 final size:3
Alignment explanation
Indices: 49352581--49352617 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
49352571 TTGTCCCTAG
49352581 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
49352618 ACAAGCTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:49354213 original size:59 final size:58
Alignment explanation
Indices: 49354040--49354673 Score: 446
Period size: 59 Copynumber: 11.0 Consensus size: 58
49354030 TGGGCAACAC
* * * *
49354040 AAAAATAATTTTTTTATCAGATAAAAAA-GTGGTGTCGACCAAACATTGTCCAACA-C-
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTCG-CCAAGCATTGGCCAACACCA
* * * * *
49354096 --AAATT-TTTTTTTATTTGATAGAAAAGGTAGT-TCGACCAATGCA-TAGCCAACACAA
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTCG-CCAA-GCATTGGCCAACACCA
* * *
49354151 AAAAATTATTTTTTTATTTGATAAAAAAGGTGGTGTCTGTCAAGCATTGACCAACACCA
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTC-GCCAAGCATTGGCCAACACCA
* *
49354210 AAAAA--A--TTTTTATCTGATAAAAAAGGTAGTGTCGTCCAAGCATTGGCTAACACCAAA
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTCG-CCAAGCATTGGCCAACACC--A
** * *
49354267 AAAAATTATTTTTTTATCTGATAAAAAATTATTGGTGTCAACCACTGCA-TGGCCAACACC-
1 AAAAATTATTTTTTTATCTGATAAAAAA--GGTGGTGTC-GCCA-AGCATTGGCCAACACCA
* * * *
49354327 --AAATTTTTTTTTTATCTGATTAAAAAA-GTGATGTAGGCCAAGCATTGGCCAACACTAA
1 AAAAATTATTTTTTTATCTGA-TAAAAAAGGTGGTGT-CGCCAAGCATTGGCCAACAC-CA
* * *
49354385 AAAAAATATTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGTA-TGGCCAACACTAA
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTC-GCCAA-GCATTGGCCAACAC-CA
* * * *
49354445 AAAAATTA-TATTTTATCTGATTAAAAAGGTGATGTCGACCAAGCATTGGTCAACACCAA
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTCG-CCAAGCATTGGCCAACACC-A
* * * * *
49354504 AAAAATTA-TTTTTTATCTGATTAAAAAAAGTGATGTCAGCCAAGTATTAGCCAACATC-
1 AAAAATTATTTTTTTATCTGA-TAAAAAAGGTGGTGTC-GCCAAGCATTGGCCAACACCA
* * * * *
49354562 AAAAA-TA-TTTTTTATCTAATAAAAATGTTGGTGTCGGTCAATG-AATGGCCAACA-C-
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTC-GCCAA-GCATTGGCCAACACCA
* * * * *
49354617 --TAA--ATTTTTTTATCTGATCAAAATGGTGGTGTCGGTCAAACATTGGCCAACACCA
1 AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTC-GCCAAGCATTGGCCAACACCA
49354672 AA
1 AA
49354674 TTTTTTTTTC
Statistics
Matches: 468, Mismatches: 67, Indels: 85
0.75 0.11 0.14
Matches are distributed among these distances:
52 1 0.00
53 75 0.16
54 12 0.03
55 45 0.10
56 43 0.09
57 26 0.06
58 53 0.11
59 92 0.20
60 78 0.17
61 21 0.04
63 19 0.04
64 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (58 bp):
AAAAATTATTTTTTTATCTGATAAAAAAGGTGGTGTCGCCAAGCATTGGCCAACACCA
Found at i:49354381 original size:119 final size:118
Alignment explanation
Indices: 49354040--49354586 Score: 460
Period size: 119 Copynumber: 4.7 Consensus size: 118
49354030 TGGGCAACAC
* * * * *
49354040 AAAAATAATTTTTTTATCAGAT-AAAAAAGTGGTGTCGACCAA-ACATTGTCCAACAC---AAAT
1 AAAAATTATTTTTTTATCTGATAAAAAAAGTGGTGTCAACCAATGCA-TGGCCAACACAAAAAAT
* * * *
49354100 TTTTTTTTATTTGA-TAGAAAAG-G-TAGTTCGACCAATGCA-TAGCCAACA-C-AA
65 TATTTTTTATCTGATTAAAAAAGTGAT-G-TCGACCAA-GCATTGGCCAACACCAAA
* * *** *
49354151 AAAAATTATTTTTTTATTTGATAAAAAAGGTGGTGTCTGTCAA-GCATTGACCAACACCAAAAAA
1 AAAAATTATTTTTTTATCTGATAAAAAAAGTGGTGTCAACCAATGCA-TGGCCAACA-CAAAAAA
* *
49354215 --A-TTTTTATCTGA-TAAAAAAG-GTAGTGTCGTCCAAGCATTGGCTAACACCAAA
64 TTATTTTTTATCTGATTAAAAAAGTG-A-TGTCGACCAAGCATTGGCCAACACCAAA
* * * *
49354267 AAAAATTATTTTTTTATCTGATAAAAAATTATTGGTGTCAACCACTGCATGGCCAACAC-CAAAT
1 AAAAATTATTTTTTTATCTGATAAAAAA--AGTGGTGTCAACCAATGCATGGCCAACACAAAAAA
* * * *
49354331 TTTTTTTTTATCTGATTAAAAAAGTGATGTAGGCCAAGCATTGGCCAACACTAAA
64 TTATTTTTTATCTGATTAAAAAAGTGATGTCGACCAAGCATTGGCCAACACCAAA
* * *
49354386 AAAAA-TATTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGTATGGCCAACACTAAAAAAA
1 AAAAATTATTTTTTTATCTGATAAAAAAAGTGGTGTCAACCAATGCATGGCCAACAC--AAAAAA
* * *
49354450 TTATATTTTATCTGATTAAAAAGGTGATGTCGACCAAGCATTGGTCAACACC-AA
64 TTATTTTTTATCTGATTAAAAAAGTGATGTCGACCAAGCATTGGCCAACACCAAA
* * * *
49354504 AAAAATTA-TTTTTTATCTGATTAAAAAAAGTGATGTCAGCCAA-GTATTAGCCAACATC-AAAA
1 AAAAATTATTTTTTTATCTGA-TAAAAAAAGTGGTGTCAACCAATGCA-TGGCCAACA-CAAAAA
*
49354566 A-TATTTTTTATCT-AATAAAAA
63 ATTATTTTTTATCTGATTAAAAA
49354587 TGTTGGTGTC
Statistics
Matches: 361, Mismatches: 49, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
111 19 0.05
112 27 0.07
113 22 0.06
114 14 0.04
115 9 0.02
116 71 0.20
117 6 0.02
118 61 0.17
119 121 0.34
120 10 0.03
121 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (118 bp):
AAAAATTATTTTTTTATCTGATAAAAAAAGTGGTGTCAACCAATGCATGGCCAACACAAAAAATT
ATTTTTTATCTGATTAAAAAAGTGATGTCGACCAAGCATTGGCCAACACCAAA
Found at i:49354404 original size:60 final size:57
Alignment explanation
Indices: 49354141--49354586 Score: 301
Period size: 60 Copynumber: 7.6 Consensus size: 57
49354131 CCAATGCATA
* * * * *
49354141 GCCAACACAAAAAAATTATTTTTTTATTTGA-TAAAAAAGGTGGTGTCTGTCAAGCATTG
1 GCCAACACAAAAAAAATA-TTTTTTATCTGATTAAAAAA-GTGATGT-AGCCAAGCATTG
* * *
49354200 ACCAACAC-CAAAAAA-A-TTTTTATCTGA-TAAAAAAG-GTAGTGTCGTCCAAGCATTG
1 GCCAACACAAAAAAAATATTTTTTATCTGATTAAAAAAGTG-A-TGTAG-CCAAGCATTG
* * * * * *
49354255 GCTAACACCAAAAAAAATTATTTTTTTATCTGATAAAAAATTATTGGTGTCAACCACTGCA-TG
1 GCCAACA-CAAAAAAAA-TA-TTTTTTATCTGATTAAAAA--AGTGATGT-AGCCA-AGCATTG
* ** *
49354318 GCCAACAC--CAAATTTTTTTTTTATCTGATTAAAAAAGTGATGTAGGCCAAGCATTG
1 GCCAACACAAAAAAAATATTTTTTATCTGATTAAAAAAGTGATGTA-GCCAAGCATTG
* *
49354374 GCCAACACTAAAAAAAATATTTTTTTATCTGA-TAAAAAAGGTGGTGTCAGCCAATGTA-TG
1 GCCAACAC-AAAAAAAATA-TTTTTTATCTGATTAAAAAA-GTGATGT-AGCCAA-GCATTG
* * * *
49354434 GCCAACACTAAAAAAATTATATTTTATCTGATTAAAAAGGTGATGTCGACCAAGCATTG
1 GCCAACAC-AAAAAAAATATTTTTTATCTGATTAAAAAAGTGATGTAG-CCAAGCATTG
* * * *
49354493 GTCAACACCAAAAAAATTATTTTTTATCTGATTAAAAAAAGTGATGTCAGCCAAGTATTA
1 GCCAACA-CAAAAAAAATATTTTTTATCTGATT-AAAAAAGTGATGT-AGCCAAGCATTG
*
49354553 GCCAACATC---AAAAATATTTTTTATCT-AATAAAAA
1 GCCAACA-CAAAAAAAATATTTTTTATCTGATTAAAAA
49354587 TGTTGGTGTC
Statistics
Matches: 309, Mismatches: 48, Indels: 64
0.73 0.11 0.15
Matches are distributed among these distances:
53 1 0.00
54 2 0.01
55 43 0.14
56 22 0.07
57 23 0.07
58 26 0.08
59 72 0.23
60 80 0.26
61 15 0.05
62 6 0.02
63 14 0.05
64 4 0.01
65 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (57 bp):
GCCAACACAAAAAAAATATTTTTTATCTGATTAAAAAAGTGATGTAGCCAAGCATTG
Found at i:49354679 original size:54 final size:54
Alignment explanation
Indices: 49354564--49354681 Score: 157
Period size: 53 Copynumber: 2.2 Consensus size: 54
49354554 CCAACATCAA
* * ** *
49354564 AAATATTTTTTATCTAATAAAAATGTTGGTGTCGGTCAATGAATGGCCAACACT
1 AAATTTTTTTTATCTAATAAAAATGGTGGTGTCGGTCAAACAATGGCCAACACC
* * *
49354618 AAA-TTTTTTTATCTGATCAAAATGGTGGTGTCGGTCAAACATTGGCCAACACC
1 AAATTTTTTTTATCTAATAAAAATGGTGGTGTCGGTCAAACAATGGCCAACACC
49354671 AAATTTTTTTT
1 AAATTTTTTTT
49354682 TCAAAATCTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 45 0.82
54 10 0.18
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (54 bp):
AAATTTTTTTTATCTAATAAAAATGGTGGTGTCGGTCAAACAATGGCCAACACC
Found at i:49356618 original size:61 final size:61
Alignment explanation
Indices: 49356494--49356608 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
49356484 TCTTAAATCT
* * * *
49356494 AAAAATTCAATAAATTTAATACTCAATATTTACGAAACTTGTCATTTTAGTTCTATTTCTA
1 AAAAATTCAATAAATTTAATACTCAATATTTACCAAAATTGTCAATTTAATTCTATTTCTA
* * *
49356555 AAAAATTCAATAAATTTAATTCTTAATATTTACCAAAATTTTCAATTTAATTCT
1 AAAAATTCAATAAATTTAATACTCAATATTTACCAAAATTGTCAATTTAATTCT
49356609 TGTTTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (61 bp):
AAAAATTCAATAAATTTAATACTCAATATTTACCAAAATTGTCAATTTAATTCTATTTCTA
Found at i:49362974 original size:20 final size:20
Alignment explanation
Indices: 49362949--49362986 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
49362939 TCCTCCAATG
49362949 TTACAACCAAACCAACAAAA
1 TTACAACCAAACCAACAAAA
49362969 TTACAACCAAACCAACAA
1 TTACAACCAAACCAACAA
49362987 TCATGAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.32, G:0.00, T:0.11
Consensus pattern (20 bp):
TTACAACCAAACCAACAAAA
Found at i:49363616 original size:2 final size:2
Alignment explanation
Indices: 49363611--49363644 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49363601 AAAAAAAAAA
49363611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49363645 GTATTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49366171 original size:24 final size:24
Alignment explanation
Indices: 49366144--49366290 Score: 204
Period size: 24 Copynumber: 6.1 Consensus size: 24
49366134 CCACACTAGT
* *
49366144 CCAGAATGGTTAGCTTTTACGAGC
1 CCAGAATGATTAGCTCTTACGAGC
49366168 CCAGAATGATTAGCTCTTACGAGC
1 CCAGAATGATTAGCTCTTACGAGC
*
49366192 CCAGAATGATTAGCTCTTACGAGT
1 CCAGAATGATTAGCTCTTACGAGC
* **
49366216 CCAAAATGATTAAATCTTACGAGC
1 CCAGAATGATTAGCTCTTACGAGC
* *
49366240 CTAGAATGATTAACTCTTACGAGC
1 CCAGAATGATTAGCTCTTACGAGC
* *
49366264 CCAGAATGTTTAGCTCTTACAAGC
1 CCAGAATGATTAGCTCTTACGAGC
49366288 CCA
1 CCA
49366291 AATAGAGTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 109 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (24 bp):
CCAGAATGATTAGCTCTTACGAGC
Found at i:49368163 original size:18 final size:16
Alignment explanation
Indices: 49368132--49368175 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
49368122 GGTTTAGGGT
*
49368132 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
49368149 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
49368163 TTAAAAATTTATT
1 TTAAAAATTTATT
49368176 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:49385782 original size:10 final size:11
Alignment explanation
Indices: 49385754--49385783 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
49385744 GTAACTAAGG
49385754 ACAAATTAATC
1 ACAAATTAATC
49385765 ACAAATTAATC
1 ACAAATTAATC
49385776 A-AAATTAA
1 ACAAATTAA
49385784 AAAAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (11 bp):
ACAAATTAATC
Found at i:49388498 original size:51 final size:51
Alignment explanation
Indices: 49388426--49388552 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 51
49388416 TAAGGAAGAC
* * *
49388426 TCAAGTTCAAGTAA-GGCTGAAGAAGATAAAAAGAGGCAAACTAAGGAAGGA
1 TCAAGTCCAAG-AAGGGTTGAAGAAGATAAAAAGAGGCAAACTAAGAAAGGA
* * * * *
49388477 TTAAGTCCAAGGAGGGTTGAAGAAGATAATAAGGGGTAAACTAAGAAAGGA
1 TCAAGTCCAAGAAGGGTTGAAGAAGATAAAAAGAGGCAAACTAAGAAAGGA
*
49388528 TCAAGTTCAAGAAGGGTTGAA-AAGA
1 TCAAGTCCAAGAAGGGTTGAAGAAGA
49388553 ATGAGCTTTG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 5 0.08
51 59 0.92
ACGTcount: A:0.46, C:0.08, G:0.29, T:0.17
Consensus pattern (51 bp):
TCAAGTCCAAGAAGGGTTGAAGAAGATAAAAAGAGGCAAACTAAGAAAGGA
Found at i:49390958 original size:31 final size:31
Alignment explanation
Indices: 49390921--49390980 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
49390911 AAATAATCAT
49390921 TGAACCATTTAAAAGTTT-TCATTTAAGTCAA
1 TGAACCATTTAAAAGTTTCT-ATTTAAGTCAA
*
49390952 TGAACCATTTGAAAGTTTCTATTTAAGTC
1 TGAACCATTTAAAAGTTTCTATTTAAGTC
49390981 GTTGAGTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (31 bp):
TGAACCATTTAAAAGTTTCTATTTAAGTCAA
Found at i:49402673 original size:31 final size:31
Alignment explanation
Indices: 49402601--49402675 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
49402591 TTAATATATT
* * *
49402601 ATTTGGTACCTAAATTTGACTTTAATGTTCA
1 ATTTGGTACCTGAGTTTGACTTCAATGTTCA
* *
49402632 ATTTGGTACCTGAGTTTGGCTTCAATGTTGA
1 ATTTGGTACCTGAGTTTGACTTCAATGTTCA
* *
49402663 CTTTGTTACCTGA
1 ATTTGGTACCTGA
49402676 ATGCTTTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTGAGTTTGACTTCAATGTTCA
Found at i:49406759 original size:17 final size:18
Alignment explanation
Indices: 49406739--49406773 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
49406729 ATCTTTATAT
49406739 TTTTTAAAA-ACTTAAAA
1 TTTTTAAAAGACTTAAAA
49406756 -TTTTAAAAGACTTAAAA
1 TTTTTAAAAGACTTAAAA
49406773 T
1 T
49406774 ATAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
TTTTTAAAAGACTTAAAA
Found at i:49410680 original size:88 final size:88
Alignment explanation
Indices: 49410570--49410730 Score: 295
Period size: 88 Copynumber: 1.8 Consensus size: 88
49410560 TCTCGATGCG
* * *
49410570 TGTTTTTTCCTTGTTTCTCCTATGTTAAAATATTGAATATTGAAGGATGAATCCGGGTTCGGAGT
1 TGTTTGTTCCTTGTTTCTCCTATATTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGT
49410635 TTAGATACTGTTCTTGATGTATA
66 TTAGATACTGTTCTTGATGTATA
49410658 TGTTTGTTCCTTGTTTCTCCTATATTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGT
1 TGTTTGTTCCTTGTTTCTCCTATATTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGT
49410723 TTAGATAC
66 TTAGATAC
49410731 CATTCTCGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (88 bp):
TGTTTGTTCCTTGTTTCTCCTATATTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGT
TTAGATACTGTTCTTGATGTATA
Found at i:49410761 original size:88 final size:88
Alignment explanation
Indices: 49410576--49410775 Score: 258
Period size: 88 Copynumber: 2.3 Consensus size: 88
49410566 TGCGTGTTTT
* *
49410576 TTCCTTGTTTCTCCTATGTTAAAATATTGAATATTGAAGGATGAATCCGGGTTCGGAGTTTAGAT
1 TTCCATGTTTCTCCTATGTTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGAT
** * ** * **
49410641 ACTGTTCTTGATGTATATGTTTG
66 ACCATTCTCGATACATATCTTCA
* *
49410664 TTCCTTGTTTCTCCTATATTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGAT
1 TTCCATGTTTCTCCTATGTTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGAT
49410729 ACCATTCTCGATACATATCTTCA
66 ACCATTCTCGATACATATCTTCA
**
49410752 TTTGATGTTT-TGCCTATGTTAAAA
1 TTCCATGTTTCT-CCTATGTTAAAA
49410776 GATTTTGTGT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 1 0.01
88 96 0.99
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (88 bp):
TTCCATGTTTCTCCTATGTTAAAATATTGAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGAT
ACCATTCTCGATACATATCTTCA
Found at i:49413915 original size:45 final size:45
Alignment explanation
Indices: 49413864--49413954 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
49413854 AATTGGGTTT
* * ***
49413864 ATGTTCTTCAGGATCTTGTTCAACACCCTTGGTGTTATCATCATC
1 ATGTTCTTCAAGAACTTGTTCAACACCCTCAATGTTATCATCATC
* *
49413909 ATGTTCTTCAAGAACTTGTTTAACCCCCTCAATGTTATCATCATC
1 ATGTTCTTCAAGAACTTGTTCAACACCCTCAATGTTATCATCATC
49413954 A
1 A
49413955 ACTTTCCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.38
Consensus pattern (45 bp):
ATGTTCTTCAAGAACTTGTTCAACACCCTCAATGTTATCATCATC
Found at i:49418344 original size:45 final size:45
Alignment explanation
Indices: 49418294--49418386 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
49418284 TCAATTGGTT
49418294 TCATGTTTTTC-AGAATTTTGTTTAACACCCTCGGTCTTATCACCA
1 TCATGTTTTTCAAGAA-TTTGTTTAACACCCTCGGTCTTATCACCA
* * *
49418339 TCATGTTTTTCAAGAATTTGTTTAACCCCCTCGGTGTTATCATCA
1 TCATGTTTTTCAAGAATTTGTTTAACACCCTCGGTCTTATCACCA
49418384 TCA
1 TCA
49418387 ACTTTCCTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 40 0.91
46 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.42
Consensus pattern (45 bp):
TCATGTTTTTCAAGAATTTGTTTAACACCCTCGGTCTTATCACCA
Found at i:49422405 original size:48 final size:48
Alignment explanation
Indices: 49422334--49422448 Score: 194
Period size: 48 Copynumber: 2.4 Consensus size: 48
49422324 ACAACAATAT
* *
49422334 TAACGAATTAACGATAATATTCAACTGTAACGATGGCTCACATATCAC
1 TAACGAATTAACGATAATATTCAACTGTAACGATGGATCACACATCAC
*
49422382 TAACGAATTAACGATAATATTCAACTGTGACGATGGATCACACATCAC
1 TAACGAATTAACGATAATATTCAACTGTAACGATGGATCACACATCAC
*
49422430 TAACGAATTAACGAGAATA
1 TAACGAATTAACGATAATA
49422449 ATCTAGAATG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (48 bp):
TAACGAATTAACGATAATATTCAACTGTAACGATGGATCACACATCAC
Found at i:49423272 original size:19 final size:19
Alignment explanation
Indices: 49423234--49423273 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49423224 GAAATTTATG
* * *
49423234 TATTTGATGTAAATTTAAA
1 TATTTAATGTAAAATAAAA
49423253 TATTTAATGTAAAATAAAA
1 TATTTAATGTAAAATAAAA
49423272 TA
1 TA
49423274 GTAACATATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
TATTTAATGTAAAATAAAA
Found at i:49423643 original size:29 final size:30
Alignment explanation
Indices: 49423600--49423663 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
49423590 GTTTAATGTT
* * *
49423600 CAATTGTATATATGAACTTT-GATTTTATG
1 CAATTGTATACATGAAATTTCGATTTGATG
*
49423629 CAATTTTATACATGAAATTTCGATTTGATG
1 CAATTGTATACATGAAATTTCGATTTGATG
49423659 CAATT
1 CAATT
49423664 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (30 bp):
CAATTGTATACATGAAATTTCGATTTGATG
Found at i:49423905 original size:31 final size:29
Alignment explanation
Indices: 49423849--49423907 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
49423839 TCACGTGTAT
*
49423849 AATTGCACCAAATTAAAGTTCATGTATAC
1 AATTGCACCAAATCAAAGTTCATGTATAC
*
49423878 AATTGCACCTTAAATCAAAGTTTATGTATA
1 AATTGCACC--AAATCAAAGTTCATGTATA
49423908 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (29 bp):
AATTGCACCAAATCAAAGTTCATGTATAC
Found at i:49423910 original size:29 final size:27
Alignment explanation
Indices: 49423844--49423910 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
49423834 GAGTCTCACG
*
49423844 TGTATAATTGCACCAAATTAAAGTTCA
1 TGTATAATTGCACCAAATCAAAGTTCA
*
49423871 TGTATACAATTGCACCTTAAATCAAAGTTTA
1 TGTAT--AATTGCACC--AAATCAAAGTTCA
49423902 TGTATAATT
1 TGTATAATT
49423911 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 13 0.38
31 16 0.47
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTCA
Found at i:49424427 original size:19 final size:19
Alignment explanation
Indices: 49424389--49424428 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
49424379 GAAATTCATG
* *
49424389 TATTTGATGTAAATTTAAA
1 TATTTGATGTAAAATAAAA
49424408 TATTTGATGTAAAATAAAA
1 TATTTGATGTAAAATAAAA
49424427 TA
1 TA
49424429 GTAGTATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
TATTTGATGTAAAATAAAA
Found at i:49426098 original size:45 final size:45
Alignment explanation
Indices: 49426011--49426143 Score: 178
Period size: 45 Copynumber: 3.0 Consensus size: 45
49426001 TTGGTTTCAA
*
49426011 GTTCTTTAGGATCTTGTTTAA-CCCCTCGGTGTTATCATCATCAT
1 GTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCATCAT
* * *
49426055 GTTCTTCGGGATCTTGTATAACCCCCTCGGTGTTATCAACATCAT
1 GTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCATCAT
* * * **
49426100 GTTTTTCAGGAACTTGTTTAACCCCTTTTGTGTTATCATCATCA
1 GTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCATCA
49426144 ACTTTCCTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
44 18 0.24
45 58 0.76
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (45 bp):
GTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCATCAT
Found at i:49427642 original size:37 final size:37
Alignment explanation
Indices: 49427601--49427674 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
49427591 CTAAAGAGGG
*
49427601 TAACCTTTTTTGCAACTAAGACGAAGTGCCTCATTCA
1 TAACCTTTTTTGCAACTAAAACGAAGTGCCTCATTCA
* * *
49427638 TAACCTTTTTTGCAATTAAAATGAAGTGCCTCTTTCA
1 TAACCTTTTTTGCAACTAAAACGAAGTGCCTCATTCA
49427675 CACTCTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (37 bp):
TAACCTTTTTTGCAACTAAAACGAAGTGCCTCATTCA
Found at i:49432309 original size:19 final size:19
Alignment explanation
Indices: 49432271--49432310 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49432261 GAAATTCATG
* * *
49432271 TATTTGATGTAAATTTAAA
1 TATTTAATGTAAAATAAAA
49432290 TATTTAATGTAAAATAAAA
1 TATTTAATGTAAAATAAAA
49432309 TA
1 TA
49432311 ATAGTATATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
TATTTAATGTAAAATAAAA
Found at i:49432529 original size:17 final size:17
Alignment explanation
Indices: 49432507--49432540 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49432497 TTTGCTAACC
49432507 AAAAACAATAATATTAT
1 AAAAACAATAATATTAT
49432524 AAAAACAATAATATTAT
1 AAAAACAATAATATTAT
49432541 CTATATACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAACAATAATATTAT
Found at i:49432728 original size:29 final size:31
Alignment explanation
Indices: 49432670--49432728 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
49432660 ATATCAAAAT
* **
49432670 TATATATAAATTTTAGTTTTATATGTAATTG
1 TATATATAAATTTTAGATTTATATCCAATTG
49432701 TATATATAAATTTT-GATTTA-ATCCAATT
1 TATATATAAATTTTAGATTTATATCCAATT
49432729 TTCTCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 5 0.20
31 14 0.56
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (31 bp):
TATATATAAATTTTAGATTTATATCCAATTG
Found at i:49433952 original size:45 final size:45
Alignment explanation
Indices: 49433886--49433974 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
49433876 TTGGTTTCAA
*
49433886 GTTCTTTAGGATCTTGCTTAACATCCTCGGTGTTATCATCATCAT
1 GTTCTTTAGGATCTTGCTTAACACCCTCGGTGTTATCATCATCAT
* * *
49433931 GTTCTTTGGGATCTTGTTTAACCCCCTCGGTGTTATCATCATCA
1 GTTCTTTAGGATCTTGCTTAACACCCTCGGTGTTATCATCATCA
49433975 ACTTTCCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.42
Consensus pattern (45 bp):
GTTCTTTAGGATCTTGCTTAACACCCTCGGTGTTATCATCATCAT
Found at i:49438045 original size:45 final size:45
Alignment explanation
Indices: 49437981--49438070 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
49437971 CAATTGGTTC
* * *
49437981 CATGTTCTTTAGGATCTTGTTTAACACCTTCAGTGTTATCATCAT
1 CATGTTCTTCAGGAACTTGTTTAACACCCTCAGTGTTATCATCAT
* *
49438026 CATGTTCTTCAGGAACTTGTTTAACCCCCTCGGTGTTATCATCAT
1 CATGTTCTTCAGGAACTTGTTTAACACCCTCAGTGTTATCATCAT
49438071 TAACTTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (45 bp):
CATGTTCTTCAGGAACTTGTTTAACACCCTCAGTGTTATCATCAT
Done.