Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 23 of 126
Found at i:5117473 original size:16 final size:14
Alignment explanation
Indices: 5117412--5117473 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
5117402 AATATTATTT
*
5117412 AAATAATATTATAATT
1 AAAT-ATATT-TAATA
5117428 AAATA-ATTTAACTA
1 AAATATATTTAA-TA
5117442 AAATATATTTAA-A
1 AAATATATTTAATA
5117455 AAATAATATTTATATA
1 AAAT-ATATTTA-ATA
5117471 AAA
1 AAA
5117474 ATTAAATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 16 0.40
15 8 0.20
16 8 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATTTAATA
Found at i:5123757 original size:15 final size:16
Alignment explanation
Indices: 5123737--5123809 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
5123727 TCCTTTTTTA
5123737 AAAAAAAT-TACAAAT
1 AAAAAAATATACAAAT
*
5123752 AAAAAAATATATAAAT
1 AAAAAAATATACAAAT
5123768 AATCAAATAA-ATA-AAAT
1 AA--AAA-AATATACAAAT
* * *
5123785 AAACAAATAAACAAAC
1 AAAAAAATATACAAAT
*
5123801 AAATAAATA
1 AAAAAAATA
5123810 AATAGACAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.04
15 12 0.26
16 19 0.40
17 6 0.13
18 6 0.13
19 2 0.04
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAAAATATACAAAT
Found at i:5123779 original size:4 final size:4
Alignment explanation
Indices: 5123748--5123813 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
5123738 AAAAAATTAC
* * * *
5123748 AAAT AAAA AAAT ATAT AAAT -AAT CAAAT AAAT AAAAT AAAC AAAT AAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT
*
5123797 AAAC AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT A
5123814 GACAATTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:5125668 original size:2 final size:2
Alignment explanation
Indices: 5125661--5125687 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5125651 CATTATGTTG
5125661 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5125688 GATTGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5129508 original size:21 final size:20
Alignment explanation
Indices: 5129461--5129511 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
5129451 CCATTCAAAA
5129461 TTTAAAAATTAAATTTTCAC
1 TTTAAAAATTAAATTTTCAC
5129481 TTTAAAAATTAAATTTTCAC
1 TTTAAAAATTAAATTTTCAC
5129501 TTTAAAAATTA
1 TTTAAAAATTA
5129512 TTAGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAATTAAATTTTCAC
Found at i:5133298 original size:16 final size:16
Alignment explanation
Indices: 5133265--5133313 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
5133255 TGACCACATT
5133265 GAATAAATATTATATATA
1 GAATAAATA-T-TATATA
* *
5133283 GCATTAATATTATATA
1 GAATAAATATTATATA
5133299 GAATAAATATTATAT
1 GAATAAATATTATAT
5133314 GTGACAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 19 0.70
17 1 0.04
18 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (16 bp):
GAATAAATATTATATA
Found at i:5137588 original size:22 final size:22
Alignment explanation
Indices: 5137510--5137614 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 22
5137500 TAATACCTTT
* * **
5137510 TTAAAAATTATATCCAAAAATC
1 TTAAAAATTATATTCGAAGGTC
* * * *
5137532 TTAAAAATTATAAGTCAAAGATT
1 TTAAAAATTAT-ATTCGAAGGTC
* * * *
5137555 TTGAATAATTATGTTTGAATGTC
1 TT-AAAAATTATATTCGAAGGTC
5137578 TTAAAAATTATATTCGAAGGTC
1 TTAAAAATTATATTCGAAGGTC
* *
5137600 TTATAAATTAAATTC
1 TTAAAAATTATATTC
5137615 AAAAGTTTTA
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
22 40 0.63
23 15 0.24
24 8 0.13
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (22 bp):
TTAAAAATTATATTCGAAGGTC
Found at i:5139112 original size:19 final size:19
Alignment explanation
Indices: 5139072--5139113 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5139062 TGATTATAAG
*
5139072 ATAATGTCATAAAAATTTC
1 ATAATGTCATAAAAATTAC
*
5139091 ATAATGTCAT-TAAATATAC
1 ATAATGTCATAAAAAT-TAC
5139110 ATAA
1 ATAA
5139114 AAAGTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (19 bp):
ATAATGTCATAAAAATTAC
Found at i:5140796 original size:7 final size:7
Alignment explanation
Indices: 5140784--5140835 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 7
5140774 CACCAAAATT
5140784 TTTTTTA
1 TTTTTTA
5140791 TTTTTTA
1 TTTTTTA
5140798 TTCTATTTA
1 TT-T-TTTA
5140807 TTTTTTTAA
1 -TTTTTT-A
*
5140816 TTTTTAA
1 TTTTTTA
5140823 TTTTTTCA
1 TTTTTT-A
5140831 TTTTT
1 TTTTT
5140836 CTAAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 15 0.39
8 15 0.39
9 6 0.16
10 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:5141295 original size:33 final size:32
Alignment explanation
Indices: 5141256--5141486 Score: 142
Period size: 33 Copynumber: 7.0 Consensus size: 32
5141246 TCTAAAATTG
* *
5141256 ATGACTTTGATTGAATCAAAGTTTGAAAATGAA
1 ATGACTTAGATT-AACCAAAGTTTGAAAATGAA
* * *
5141289 ATGACTTGGACTAAGCCGAAGTTTGAAAATGAA
1 ATGACTTAGATTAA-CCAAAGTTTGAAAATGAA
* * *
5141322 ATGACCTAGACTTAGCCTAAGTTTGAAAATGAA
1 ATGACTTAGA-TTAACCAAAGTTTGAAAATGAA
* * * * *
5141355 ATGACCT-GCACTAAGTCGAAGTCTGAAAATGAA
1 ATGACTTAG-ATTAA-CCAAAGTTTGAAAATGAA
* * * *
5141388 ATGACCTAGACTTAGCCTAAGTATGAAAATGAA
1 ATGACTTAGA-TTAACCAAAGTTTGAAAATGAA
* * **
5141421 AT-AATTTGTATTGAGTCAAAGTTTGAAAATGAA
1 ATGACTTAG-ATT-AACCAAAGTTTGAAAATGAA
* * * *
5141454 ATGACTTAGGTTGAGCTAGAGTTTGAAAATGAA
1 ATGACTTAGATT-AACCAAAGTTTGAAAATGAA
5141487 TTCAATGATC
Statistics
Matches: 158, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
32 10 0.06
33 139 0.88
34 9 0.06
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (32 bp):
ATGACTTAGATTAACCAAAGTTTGAAAATGAA
Found at i:5141351 original size:66 final size:66
Alignment explanation
Indices: 5141274--5141486 Score: 277
Period size: 66 Copynumber: 3.2 Consensus size: 66
5141264 GATTGAATCA
* *
5141274 AAGTTTGAAAATGAAATGACTTGGACTAAGCCGAAGTTTGAAAATGAAATGACCTAGACTTAGCC
1 AAGTTTGAAAATGAAATGACTTGCACTAAGTCGAAGTTTGAAAATGAAATGACCTAGACTTAGCC
5141339 T
66 T
* *
5141340 AAGTTTGAAAATGAAATGACCTGCACTAAGTCGAAGTCTGAAAATGAAATGACCTAGACTTAGCC
1 AAGTTTGAAAATGAAATGACTTGCACTAAGTCGAAGTTTGAAAATGAAATGACCTAGACTTAGCC
5141405 T
66 T
* * * * * * * * *
5141406 AAGTATGAAAATGAAATAATTTGTATTGAGTCAAAGTTTGAAAATGAAATGACTTAG-GTTGAG-
1 AAGTTTGAAAATGAAATGACTTGCACTAAGTCGAAGTTTGAAAATGAAATGACCTAGACTT-AGC
5141469 CT
65 CT
5141471 AGAGTTTGAAAATGAA
1 A-AGTTTGAAAATGAA
5141487 TTCAATGATC
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
65 5 0.04
66 124 0.96
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (66 bp):
AAGTTTGAAAATGAAATGACTTGCACTAAGTCGAAGTTTGAAAATGAAATGACCTAGACTTAGCC
T
Found at i:5141443 original size:99 final size:99
Alignment explanation
Indices: 5141274--5141458 Score: 239
Period size: 99 Copynumber: 1.9 Consensus size: 99
5141264 GATTGAATCA
* * * * *
5141274 AAGTTTGAAAATGAAATGACTTGGACTAAGCCGAAGTTTGAAAATGAAATGACCTAGACTTAGCC
1 AAGTCTGAAAATGAAATGACCTAGACTAAGCCGAAGTATGAAAATGAAATGAACTAGACTTAGCC
*
5141339 TAAGTTTGAAAATGAAATGACCTGCACTAAGTCG
66 AAAGTTTGAAAATGAAATGACCTGCACTAAGTCG
* * * *
5141373 AAGTCTGAAAATGAAATGACCTAGACTTAGCCTAAGTATGAAAATGAAAT-AATTTGTA-TTGAG
1 AAGTCTGAAAATGAAATGACCTAGACTAAGCCGAAGTATGAAAATGAAATGAACTAG-ACTT-AG
*
5141436 TCAAAGTTTGAAAATGAAATGAC
64 CCAAAGTTTGAAAATGAAATGAC
5141459 TTAGGTTGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
98 5 0.07
99 68 0.93
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (99 bp):
AAGTCTGAAAATGAAATGACCTAGACTAAGCCGAAGTATGAAAATGAAATGAACTAGACTTAGCC
AAAGTTTGAAAATGAAATGACCTGCACTAAGTCG
Found at i:5142334 original size:71 final size:71
Alignment explanation
Indices: 5142204--5142379 Score: 174
Period size: 71 Copynumber: 2.5 Consensus size: 71
5142194 CCACTAAATA
* ** * * *
5142204 ATACAAATGCATGGTCCTAGTAATGATGCAAATGCAATTATCAAAACAAAAATTTAAATGCTCAC
1 ATACAAATGCATGATTATAATAATGATGCAAATGCAACTATCAAAACAAAAATTAAAATGCTCAC
*
5142269 CACACG
66 CAAACG
* * ** *
5142275 ATGCAAATGCATGATTATAATAATGATGCAAATGCAACTATTCAAAATAATGA-TAAAATGTTCA
1 ATACAAATGCATGATTATAATAATGATGCAAATGCAACTA-TCAAAACAAAAATTAAAATGCTCA
** *
5142339 TTAAATG
65 CCAAACG
* * *
5142346 ATATAAATGCATGATTATAACAATGATGTAAATG
1 ATACAAATGCATGATTATAATAATGATGCAAATG
5142380 TAAATGCATG
Statistics
Matches: 85, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
71 76 0.89
72 9 0.11
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (71 bp):
ATACAAATGCATGATTATAATAATGATGCAAATGCAACTATCAAAACAAAAATTAAAATGCTCAC
CAAACG
Found at i:5142385 original size:31 final size:31
Alignment explanation
Indices: 5142349--5142411 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
5142339 TTAAATGATA
*
5142349 TAAATGCATGA-TTATAACAATGATGTAAATG
1 TAAATGCATGATTTA-AACAATGATGCAAATG
*
5142380 TAAATGCATGGTTTAAACAATGATGCAAATG
1 TAAATGCATGATTTAAACAATGATGCAAATG
5142411 T
1 T
5142412 GATGATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (31 bp):
TAAATGCATGATTTAAACAATGATGCAAATG
Found at i:5144068 original size:21 final size:21
Alignment explanation
Indices: 5144047--5144086 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5144037 ATGGATATGA
5144047 AATT-AAAGAACTTAAAATTG
1 AATTGAAAGAACTTAAAATTG
* *
5144067 AATTGCAAGAACTTGAAATT
1 AATTGAAAGAACTTAAAATT
5144087 AAAGAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (21 bp):
AATTGAAAGAACTTAAAATTG
Found at i:5144602 original size:24 final size:24
Alignment explanation
Indices: 5144554--5144602 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
5144544 TTGCTTCAAT
*
5144554 TCTTCCATCTTGATCTTGATCTTC
1 TCTTCCATCTTGATCTTGATATTC
5144578 TCTTCCATGCATTGA-CTTGA-ATTC
1 TCTTCCAT-C-TTGATCTTGATATTC
5144602 T
1 T
5144603 TGAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.16, C:0.27, G:0.10, T:0.47
Consensus pattern (24 bp):
TCTTCCATCTTGATCTTGATATTC
Found at i:5147435 original size:60 final size:56
Alignment explanation
Indices: 5147217--5147675 Score: 561
Period size: 60 Copynumber: 7.8 Consensus size: 56
5147207 TTTTTTGTAG
5147217 GGAAAATTGATACTTTCAACTTTTCCCCAAAATA-TTTTTTGGAAAATTTCCTATTTC-AA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAATATTTTTTTGG-AAA-TT--TATTTCTAA
*
5147276 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAACCTCTTTTTTTGGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCC-C--AAAA--TATTTTTTTGG-AAATTTATTTCTAA
5147338 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTT-CCC-AAAATATTTTTTTGGAAATTTA--TTTC---TAA
* *
5147401 GGAAAATTGATACTTTC-ACTTTTCCCTAAATATTTTTTTTGGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAATA-TTTTTTTGGAAATTTATTTCTAA
*
5147457 GGAAAATTGAT-CTTTCAACTCTTCCCCGAAAATATTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACT-TTTCCC-AAAATATTTTTTTGGAAATTTATTTCTAA
*
5147514 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCC--AAAATA--TTTTTTTGGAAATTTATTTCTAA
*
5147574 GGAAAATTGATACTTTCCACTTTTCCCCAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAATATTTTTTTGGAAATTTATTTCTAA
5147630 GG-AAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGGAA
1 GGAAAATTGATACTTTCAACTTTTCCC--AAAATAT-TTTTTTGGAA
5147676 TTTTTTTATT
Statistics
Matches: 361, Mismatches: 13, Indels: 53
0.85 0.03 0.12
Matches are distributed among these distances:
54 3 0.01
55 25 0.07
56 45 0.12
57 43 0.12
58 39 0.11
59 45 0.12
60 54 0.15
61 37 0.10
62 33 0.09
63 25 0.07
64 12 0.03
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.44
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAATATTTTTTTGGAAATTTATTTCTAA
Found at i:5148216 original size:20 final size:19
Alignment explanation
Indices: 5148196--5148233 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5148186 CCGATTTCTG
*
5148196 GGATTCTTCGCCGGAAACT
1 GGATTCGTCGCCGGAAACT
*
5148215 GGATTGGTCGCCGGAAACT
1 GGATTCGTCGCCGGAAACT
5148234 TCAATGTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (19 bp):
GGATTCGTCGCCGGAAACT
Found at i:5148244 original size:19 final size:19
Alignment explanation
Indices: 5148202--5148249 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5148192 TCTGGGATTC
* *
5148202 TTCGCCGGAAACTGGATTG
1 TTCGCCGGAAACTGCAATG
* *
5148221 GTCGCCGGAAACTTCAATG
1 TTCGCCGGAAACTGCAATG
5148240 TTCGCCGGAA
1 TTCGCCGGAA
5148250 TTGTTGCCGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (19 bp):
TTCGCCGGAAACTGCAATG
Found at i:5148262 original size:31 final size:31
Alignment explanation
Indices: 5148224--5148282 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5148214 TGGATTGGTC
*
5148224 GCCGGAAACTTC-AATGTTCGCCGGAATTGTT
1 GCCGGAAAATTCAAAT-TTCGCCGGAATTGTT
5148255 GCCGGAAAATTCAAATTTCGCCGGAATT
1 GCCGGAAAATTCAAATTTCGCCGGAATT
5148283 TTCACCGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (31 bp):
GCCGGAAAATTCAAATTTCGCCGGAATTGTT
Found at i:5148291 original size:31 final size:31
Alignment explanation
Indices: 5148225--5148291 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
5148215 GGATTGGTCG
* *
5148225 CCGGAAACTTCAATGTTCGCCGGAATTGTTG
1 CCGGAAAATTCAATGTTCGCCGGAATTGTTA
5148256 CCGGAAAATTCAAAT-TTCGCCGGAATT-TTCA
1 CCGGAAAATTC-AATGTTCGCCGGAATTGTT-A
5148287 CCGGA
1 CCGGA
5148292 TTCTGGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.06
31 27 0.84
32 3 0.09
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (31 bp):
CCGGAAAATTCAATGTTCGCCGGAATTGTTA
Found at i:5153759 original size:21 final size:22
Alignment explanation
Indices: 5153734--5153775 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5153724 GTGCAAGTTG
5153734 AATTGAAAG-AAATTAACAAGA
1 AATTGAAAGTAAATTAACAAGA
* *
5153755 AATTGAATGTAAATTCACAAG
1 AATTGAAAGTAAATTAACAAG
5153776 GAAAATTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (22 bp):
AATTGAAAGTAAATTAACAAGA
Found at i:5158203 original size:18 final size:19
Alignment explanation
Indices: 5158160--5158195 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5158150 ATTAAAACAT
*
5158160 ATTAAATATTAAGATTTTA
1 ATTAAATATTAAGATTTGA
5158179 ATTAAATATTAA-ATTTG
1 ATTAAATATTAAGATTTG
5158196 GTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATTAAATATTAAGATTTGA
Found at i:5159931 original size:63 final size:63
Alignment explanation
Indices: 5159863--5160030 Score: 166
Period size: 62 Copynumber: 2.7 Consensus size: 63
5159853 AAATATAATT
* * * * * *
5159863 GAATTATTTAAGATTTTTTTTTGTTAGAAAATGCCTTAAATAATCCCCTTCAATTTTTT-TAA
1 GAATTATTTAAGATATTTTTTGGTCAAAAAATACCTTAAATAATCCCATTCAATTTTTTGTAA
* * *
5159925 GCAATTATTCAA-AGCA-TTTTTGGTCAAAAAATACCTTAAATAATCCTATTCAATTTTTTGTAA
1 G-AATTATTTAAGA-TATTTTTTGGTCAAAAAATACCTTAAATAATCCCATTCAATTTTTTGTAA
* * *
5159988 GAGATTATTTAAGATATTTTCTAGT--AAAAATATCTTAAATAAT
1 GA-ATTATTTAAGATATTTTTTGGTCAAAAAATACCTTAAATAAT
5160031 GCCCTAAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
62 57 0.66
63 22 0.26
64 7 0.08
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (63 bp):
GAATTATTTAAGATATTTTTTGGTCAAAAAATACCTTAAATAATCCCATTCAATTTTTTGTAA
Found at i:5160399 original size:62 final size:61
Alignment explanation
Indices: 5160267--5160428 Score: 155
Period size: 62 Copynumber: 2.6 Consensus size: 61
5160257 CCAGAAAACG
* ** * ** * *
5160267 CCTTAAATAATCCTTTCAAGTTTTTTATTAGATTATTTAAGGCATTTTTAGCAAGAAGATG
1 CCTTAAATAATCCTTTCAATTTTTTTAGGAGATTATTCAAAACATTTTTAGCAAGAAAATA
* *
5160328 CCTTAAATAATGCTGTTCAATTTTTTTAGGAGATTATTCAAAACATTTTT-GACTAGAAAATA
1 CCTTAAATAATCCT-TTCAATTTTTTTAGGAGATTATTCAAAACATTTTTAG-CAAGAAAATA
* * * *
5160390 CCTTGAATAATCCCATTCAAATTTTATTAGGGGATTATT
1 CCTTAAATAAT-CCTTTC-AATTTTTTTAGGAGATTATT
5160429 TAAGACAGTA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
61 14 0.17
62 49 0.60
63 19 0.23
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (61 bp):
CCTTAAATAATCCTTTCAATTTTTTTAGGAGATTATTCAAAACATTTTTAGCAAGAAAATA
Found at i:5160583 original size:62 final size:62
Alignment explanation
Indices: 5160506--5160653 Score: 197
Period size: 62 Copynumber: 2.4 Consensus size: 62
5160496 AAATTTTTTC
* * * * * * *
5160506 AAATAATCCTTTTCAATTTTTTTAGGGAATTATTTAAGGCTTTTTTTGTTAGAAGATGCCTT
1 AAATAATCCTATTCAATTTTTTTAGGGAATTATTCAAGGCATTTTTAGCTAGAAAATACCTT
** * *
5160568 AAATAATGTTATTCAATTTTTTTAGGGGATTATTCAAGGCATTTTTAGCTAGAAAATATCTT
1 AAATAATCCTATTCAATTTTTTTAGGGAATTATTCAAGGCATTTTTAGCTAGAAAATACCTT
5160630 AAATAATCCTATTCAATTTTTTTA
1 AAATAATCCTATTCAATTTTTTTA
5160654 TAATGGTTTA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 73 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (62 bp):
AAATAATCCTATTCAATTTTTTTAGGGAATTATTCAAGGCATTTTTAGCTAGAAAATACCTT
Found at i:5160689 original size:64 final size:62
Alignment explanation
Indices: 5160506--5160838 Score: 192
Period size: 62 Copynumber: 5.4 Consensus size: 62
5160496 AAATTTTTTC
* * * * * * * *
5160506 AAATAATCCTTTTCAATTTTTTT-AGGGAATTATTTAAGGCTTTTTTTGTTAGAAGATGCCTT
1 AAATAATCCTATTCAATTTTTTTAAGGG-ATTATTCAAGGCATTTTTAGCTAAAAAATACCTT
** * * *
5160568 AAATAATGTTATTCAATTTTTTTAGGGGATTATTCAAGGCATTTTTAGCTAGAAAATATCTT
1 AAATAATCCTATTCAATTTTTTTAAGGGATTATTCAAGGCATTTTTAGCTAAAAAATACCTT
* * * *
5160630 AAATAATCCTATTCAATTTTTTTATAATGGTTTATTTAAGGTATTTTATAGC-AAAAAATACCTT
1 AAATAATCCTATTCAA-TTTTTT-TAAGGGATTATTCAAGGCATTTT-TAGCTAAAAAATACCTT
* **** * * * * * * *
5160694 AAATAAT--TATCTAAAAAAATTGAAGAAGATTATTTAAGGCATTTCTAGCCAAAAAACACCCT
1 AAATAATCCTAT-TCAATTTTTTTAAG-GGATTATTCAAGGCATTTTTAGCTAAAAAATACCTT
** * * * * * * * * *
5160756 AAATAATGTTATTCAA-TTCTTT-AGGAGATCAATCAAAGTATTTTTTGCTAGAAATTATCTT
1 AAATAATCCTATTCAATTTTTTTAAGG-GATTATTCAAGGCATTTTTAGCTAAAAAATACCTT
*
5160817 AAATAATCATATTCAATTTTTT
1 AAATAATCCTATTCAATTTTTT
5160839 GAGGAGATTA
Statistics
Matches: 205, Mismatches: 55, Indels: 22
0.73 0.20 0.08
Matches are distributed among these distances:
61 44 0.21
62 104 0.51
63 15 0.07
64 38 0.19
65 4 0.02
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (62 bp):
AAATAATCCTATTCAATTTTTTTAAGGGATTATTCAAGGCATTTTTAGCTAAAAAATACCTT
Found at i:5161100 original size:63 final size:61
Alignment explanation
Indices: 5160897--5161126 Score: 198
Period size: 62 Copynumber: 3.7 Consensus size: 61
5160887 ATTAAAGATA
* * * *
5160897 ATTATTTAAGACATTTTTGGTCAAAAAATGCCATAAATAATCTTAGTCAAAATTTTATAGGG
1 ATTATTTAAGACATTTTTGGTCAAAAAATGCCTTAAATAATCTTA-TCAATATTTTTTAAGG
* * * * * *
5160959 ATTATTTAA-AGTATTTTCTAG-CTAGAAACGCCTTAAATAATCATGATCAAT-TTTTTTAAGTG
1 ATTATTTAAGA-CATTTT-TGGTCAAAAAATGCCTTAAATAATC-TTATCAATATTTTTTAAG-G
* * *
5161021 ATTATTTAAGGCATTTTTGGTCAAAAAATACCTTTAATAATCTTATTCAATATTTTTTAATGG
1 ATTATTTAAGACATTTTTGGTCAAAAAATGCCTTAAATAATCTTA-TCAATATTTTTTAA-GG
* * ** *
5161084 TTTATTTAAGATATTTTCTAAT-AAAAAATGACTTAAATAATCT
1 ATTATTTAAGACATTTT-TGGTCAAAAAATGCCTTAAATAATCT
5161127 CTTACAAAAA
Statistics
Matches: 131, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
61 12 0.09
62 71 0.54
63 45 0.34
64 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (61 bp):
ATTATTTAAGACATTTTTGGTCAAAAAATGCCTTAAATAATCTTATCAATATTTTTTAAGG
Found at i:5164383 original size:213 final size:209
Alignment explanation
Indices: 5163866--5164415 Score: 811
Period size: 210 Copynumber: 2.6 Consensus size: 209
5163856 AATTTAATCA
* * * *
5163866 TATTGAAAA-TTTTCTATAAATATTCCAATACGCTGGTAATATTTAAAAAAAAATCTTCTCACCT
1 TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCT
* * * * * * * **
5163930 AGAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCTCATCATTGGATTAAATTTTTT
66 AGAGATTTCGT-AGGCATCACTACTCGGAATACCTTT-GAATCTCATCATCGGATAAAAATTTCC
*
5163995 TCTTCCTATTTTATTACTTATATTTTTTATTTATTAATCAATTTTTATTTATTATTTAAAAAAAA
129 TCTTCCTATTTTATTACTTATATTTTTAATTTATTAATCAATTTTTATTTATTATTTAAAAAAAA
5164060 AAAAAAATCTTTACTG
194 AAAAAAATCTTTACTG
*
5164076 TATTG-AAATTTTTTTATAAATACTCCAATACGCTGGTAGTA-CTTAAAAAAAATCTTCTCACCT
1 TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCT
5164139 AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTC
66 AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTC
* ****
5164204 TTCTCTTATTTTTTATTAGTTATA-TTTTAATTTATTAATCAATTTTTATTTATTATTTTTTTAA
131 TTC-C-TA--TTTTATTACTTATATTTTTAATTTATTAATCAATTTTTATTTATTATTTAAAAAA
*
5164268 AAAAGAAAATCTTTACTG
192 AAAAAAAAATCTTTACTG
5164286 TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTATTTTTAAAAAAAATCTTCTCACC
1 TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTA-TTTTAAAAAAAATCTTCTCACC
*
5164351 TAGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCGTCGGATAAAAATTTCCT
65 TAGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCT
5164416 TTTTCTTTCA
Statistics
Matches: 309, Mismatches: 23, Indels: 13
0.90 0.07 0.04
Matches are distributed among these distances:
207 27 0.09
208 23 0.07
209 35 0.11
210 91 0.29
211 49 0.16
213 84 0.27
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (209 bp):
TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCT
AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTC
TTCCTATTTTATTACTTATATTTTTAATTTATTAATCAATTTTTATTTATTATTTAAAAAAAAAA
AAAAATCTTTACTG
Found at i:5164692 original size:13 final size:15
Alignment explanation
Indices: 5164672--5164714 Score: 65
Period size: 13 Copynumber: 3.1 Consensus size: 15
5164662 CGGTCAACTC
5164672 CTGGTTCGGTTCGG-
1 CTGGTTCGGTTCGGT
5164686 C-GGTTCGGTTCGGT
1 CTGGTTCGGTTCGGT
5164700 CTGGTT-GGTTCGGT
1 CTGGTTCGGTTCGGT
5164714 C
1 C
5164715 CGGCGGTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 12 0.44
14 11 0.41
15 4 0.15
ACGTcount: A:0.00, C:0.21, G:0.42, T:0.37
Consensus pattern (15 bp):
CTGGTTCGGTTCGGT
Found at i:5164712 original size:32 final size:32
Alignment explanation
Indices: 5164673--5164764 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 32
5164663 GGTCAACTCC
*
5164673 TGGTTCGGTTCGGCGGTTCGGTTCGGTCTGGT
1 TGGTTCGGTCCGGCGGTTCGGTTCGGTCTGGT
* *
5164705 TGGTTCGGTCCGGCGGTTCAGTTCGATCTGGT
1 TGGTTCGGTCCGGCGGTTCGGTTCGGTCTGGT
*
5164737 TGGTTTGGTCCGGCGGTTCGGTTCGGTC
1 TGGTTCGGTCCGGCGGTTCGGTTCGGTC
5164765 CAGTCAGACC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.02, C:0.21, G:0.41, T:0.36
Consensus pattern (32 bp):
TGGTTCGGTCCGGCGGTTCGGTTCGGTCTGGT
Found at i:5165604 original size:11 final size:11
Alignment explanation
Indices: 5165583--5165617 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5165573 TTTCTGTTTC
5165583 TTTTGTTTGTT
1 TTTTGTTTGTT
5165594 TATTT-TTTGTT
1 T-TTTGTTTGTT
5165605 TTTTGTTTGTT
1 TTTTGTTTGTT
5165616 TT
1 TT
5165618 GTTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.14
11 16 0.73
12 3 0.14
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (11 bp):
TTTTGTTTGTT
Found at i:5167590 original size:42 final size:42
Alignment explanation
Indices: 5167531--5167616 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
5167521 TTTTGGAGGA
5167531 AAATACCTTAAATGATCATCATTTAAGGCATTTCTTCAACCC
1 AAATACCTTAAATGATCATCATTTAAGGCATTTCTTCAACCC
* *
5167573 AAATGCCTTAAATGATCATCATTTAAGGTATTTCTTCAACCC
1 AAATACCTTAAATGATCATCATTTAAGGCATTTCTTCAACCC
5167615 AA
1 AA
5167617 TATTTATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (42 bp):
AAATACCTTAAATGATCATCATTTAAGGCATTTCTTCAACCC
Found at i:5174258 original size:19 final size:20
Alignment explanation
Indices: 5174226--5174264 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5174216 TATGATGTTG
**
5174226 GAAAATATTTTTAAA-ACAT
1 GAAAATATGATTAAATACAT
5174245 GAAAATATGATTAAATACAT
1 GAAAATATGATTAAATACAT
5174265 AACTTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (20 bp):
GAAAATATGATTAAATACAT
Found at i:5175160 original size:30 final size:30
Alignment explanation
Indices: 5175126--5175184 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5175116 AAACTAAATT
5175126 TAAATGCAAGAAAT-TGAAAATGCTTGAAAG
1 TAAATGCAAGAAATAT-AAAATGCTTGAAAG
* *
5175156 TAAATGCGAGAAATATAAAGTGCTTGAAA
1 TAAATGCAAGAAATATAAAATGCTTGAAA
5175185 ACCAAATCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (30 bp):
TAAATGCAAGAAATATAAAATGCTTGAAAG
Found at i:5177344 original size:19 final size:19
Alignment explanation
Indices: 5177322--5177364 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5177312 TCTTTCTTTG
5177322 CTTTTCATCACTTTATTTT-
1 CTTTTCAT-ACTTTATTTTC
* *
5177341 CTTTTTATTCTTTATTTTC
1 CTTTTCATACTTTATTTTC
5177360 CTTTT
1 CTTTT
5177365 TTAAATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTCATACTTTATTTTC
Found at i:5177396 original size:22 final size:20
Alignment explanation
Indices: 5177355--5177399 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5177345 TTATTCTTTA
*
5177355 TTTTCCTTTTTTAAATCTCT
1 TTTTCCTTTTTTAAAGCTCT
*
5177375 TTTTCTTTCTTTTACAAGCTCT
1 TTTTCCTT-TTTTA-AAGCTCT
5177397 TTT
1 TTT
5177400 CACTTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.13, C:0.20, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTCCTTTTTTAAAGCTCT
Found at i:5180867 original size:195 final size:191
Alignment explanation
Indices: 5180620--5181004 Score: 671
Period size: 195 Copynumber: 2.0 Consensus size: 191
5180610 AGTATGCATC
5180620 CTCTTCTAGGTAAGCATACCAAAATAAGAGGGTAATGGTTTAAGCTCTAACACTGGTGGCTTTAT
1 CTCTTCTAGGTAAGCATACCAAAATAAGAGGGTAATGGTTTAAGCTCTAACACTGGTGGCTTTAT
* *
5180685 AATAGAAGGCTTTAACACTTGAGGGAAAGACTTAGAAACATCTAAAGGTTTAACATTGGTAGGAG
66 AATAGAAGGCTTCAACACTTGAGGGAAAGACTTAGAAACATCTAAAGGTTTAACATTGGCAGGAG
*
5180750 AAAATTGAACTGTAATGATAATTATGATATCTTTATCATCATCATCATTATCTAAATCCATGTT
131 AAAATTGAACTGTAATGATAATTATGATATCTTTATCAT--T-ATCATCATCTAAATCCATGTT
*
5180814 CTCTTCTAGGTAAGCATACCTAAAATGAGAGGGTAATGGTTTAAGCTCTAACACTGGTGGCTTTA
1 CTCTTCTAGGTAAGCATACC-AAAATAAGAGGGTAATGGTTTAAGCTCTAACACTGGTGGCTTTA
*
5180879 TAATAGAGGGCTTCAACACTTGAGGGAAAGACTTAGAAACATCTAAAGGTTTAACATTGGCAGGA
65 TAATAGAAGGCTTCAACACTTGAGGGAAAGACTTAGAAACATCTAAAGGTTTAACATTGGCAGGA
* *
5180944 GAAAATTGAACTGTAGTGATGATTATGATATCTTTATCATTATCATCATCTAAATCCATGT
130 GAAAATTGAACTGTAATGATAATTATGATATCTTTATCATTATCATCATCTAAATCCATGT
5181005 CTACTATATT
Statistics
Matches: 183, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
192 19 0.10
193 1 0.01
194 20 0.11
195 143 0.78
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (191 bp):
CTCTTCTAGGTAAGCATACCAAAATAAGAGGGTAATGGTTTAAGCTCTAACACTGGTGGCTTTAT
AATAGAAGGCTTCAACACTTGAGGGAAAGACTTAGAAACATCTAAAGGTTTAACATTGGCAGGAG
AAAATTGAACTGTAATGATAATTATGATATCTTTATCATTATCATCATCTAAATCCATGTT
Found at i:5181814 original size:153 final size:152
Alignment explanation
Indices: 5181545--5181833 Score: 479
Period size: 153 Copynumber: 1.9 Consensus size: 152
5181535 TATAAATTAA
5181545 TGAACTACACTCACCAATGAGTGTCACTATCTTTTAATATTTTAATCTCTTTTTTCTTGAGATAA
1 TGAACTACACTCACCAATGAGTGTCACTATCTTTTAATATTTTAATCTCTTTTTTCTTGAGATAA
* * ** * *
5181610 TATCTTTTATAAACTTGGCATAAGTAGGTATTTGCACTAAACCATCCATAAAAATGGATCTTGAT
66 TATCCTTCATAAACTTGGCATAAGTAGACATATGCACTAAACCATCCATAAAAATAGATCTTGAT
5181675 ATGAAGTTTCCCTCTAAATCAG
131 ATGAAGTTTCCCTCTAAATCAG
* * *
5181697 TGAAGTACACTCACCAGTGAGTGTCACTATCTTTTAATCTTTTAATCTCTTTTTTTCTTGAGATA
1 TGAACTACACTCACCAATGAGTGTCACTATCTTTTAATATTTTAATCTC-TTTTTTCTTGAGATA
*
5181762 ATATCCTTCATAAACTTGGCATAAGTAGACATATGCACTAAACCATCCATAAAAATAGATGTTGA
65 ATATCCTTCATAAACTTGGCATAAGTAGACATATGCACTAAACCATCCATAAAAATAGATCTTGA
5181827 TATGAAG
130 TATGAAG
5181834 CTTCTTAAAC
Statistics
Matches: 126, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
152 46 0.37
153 80 0.63
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (152 bp):
TGAACTACACTCACCAATGAGTGTCACTATCTTTTAATATTTTAATCTCTTTTTTCTTGAGATAA
TATCCTTCATAAACTTGGCATAAGTAGACATATGCACTAAACCATCCATAAAAATAGATCTTGAT
ATGAAGTTTCCCTCTAAATCAG
Found at i:5182042 original size:29 final size:30
Alignment explanation
Indices: 5181999--5182089 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
5181989 ATTAACATCC
*
5181999 TTACCTTTTTCTTTCTTTTAAACTTCAACT
1 TTACCTTTTTCTTTCTTTTGAACTTCAACT
5182029 TTACC-TTTTCTTTCTTTTGAACTTCAACT
1 TTACCTTTTTCTTTCTTTTGAACTTCAACT
*
5182058 TTACCTTTTTCTTTCTTTTGAACTTTAACT
1 TTACCTTTTTCTTTCTTTTGAACTTCAACT
5182088 TT
1 TT
5182090 TTTTTGTTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 28 0.48
30 30 0.52
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (30 bp):
TTACCTTTTTCTTTCTTTTGAACTTCAACT
Found at i:5187310 original size:24 final size:25
Alignment explanation
Indices: 5187263--5187310 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5187253 GGAAAAGAAA
*
5187263 GGTTTTCACTCAAAAAGTTTATAAT
1 GGTTTTCACTCAAAAAGTTGATAAT
5187288 GGTTTTCAC-CAAAAA-TTAGATAA
1 GGTTTTCACTCAAAAAGTT-GATAA
5187311 GCCATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 10 0.48
25 9 0.43
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (25 bp):
GGTTTTCACTCAAAAAGTTGATAAT
Found at i:5190473 original size:44 final size:44
Alignment explanation
Indices: 5190330--5190473 Score: 166
Period size: 44 Copynumber: 3.3 Consensus size: 44
5190320 TAATATTTAC
*
5190330 TCATAATTACAAAGAAACTCACAGCATAATCATACT-CAGCATAA
1 TCATAATTATAAAGAAACTCACAGCATAATCATA-TACAGCATAA
* * * **
5190374 TCATAATTATAAAGAAACTTATAGCACAATCAT-TCACAATATAA
1 TCATAATTATAAAGAAACTCACAGCATAATCATAT-ACAGCATAA
* * *
5190418 TCGTAATTATAAAGAAACTCACAGCATAATCATATAGAGCACAA
1 TCATAATTATAAAGAAACTCACAGCATAATCATATACAGCATAA
*
5190462 TCATAAATATAA
1 TCATAATTATAA
5190474 CAACAGTTAT
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
42 1 0.01
44 79 0.98
45 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (44 bp):
TCATAATTATAAAGAAACTCACAGCATAATCATATACAGCATAA
Found at i:5203036 original size:21 final size:20
Alignment explanation
Indices: 5203010--5203051 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
5203000 ATTATTTGTT
5203010 ATTTTT-ATATTATTTAATATA
1 ATTTTTAATA-TATTTAA-ATA
5203031 ATTTTTAATATATTTAAATA
1 ATTTTTAATATATTTAAATA
5203051 A
1 A
5203052 AATAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTAATATATTTAAATA
Found at i:5206358 original size:92 final size:94
Alignment explanation
Indices: 5206238--5206417 Score: 222
Period size: 92 Copynumber: 1.9 Consensus size: 94
5206228 AAGAATCTAA
** * * ** * *
5206238 CTCGATAAAAGAGCTCATTTCAACAAATTA-CTATCATAAAGGCCTAGTTCGACAAAAGAGCTTA
1 CTCGATAAAAGAGCTCAGCTAAAAAAATTACCT-TCATAAAGGCAGAGTTCAACAAAAGAGCTCA
*
5206302 GCATGAC-AAATTGCTTTCATAAAGGTAAT
65 ACATGACAAAATTGCTTTCATAAAGGTAAT
*
5206331 CTCGAT-AAAGAGCTCAGCTAAAAAAATTACCTTTATAAAGGCAGAGTTCAACAAAAGAGCTCAA
1 CTCGATAAAAGAGCTCAGCTAAAAAAATTACCTTCATAAAGGCAGAGTTCAACAAAAGAGCTCAA
* *
5206395 CTTGACAAAATTTCTTTCATAAA
66 CATGACAAAATTGCTTTCATAAA
5206418 AGCCCAACTA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
92 50 0.68
93 23 0.32
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (94 bp):
CTCGATAAAAGAGCTCAGCTAAAAAAATTACCTTCATAAAGGCAGAGTTCAACAAAAGAGCTCAA
CATGACAAAATTGCTTTCATAAAGGTAAT
Found at i:5206687 original size:47 final size:47
Alignment explanation
Indices: 5206541--5206693 Score: 146
Period size: 47 Copynumber: 3.3 Consensus size: 47
5206531 CAACTCAATG
* * * * * *
5206541 AAATTGCCTTCACATAGGCCCAATTTGGTAAAATAGCTCATCTTGAT
1 AAATTGTCTTCACAAAGGCCCAACTTAGCAAAATAGCTCATCTTGAC
** * * * *
5206588 AAATTACCTTCATAAAGGCCCAACTTAGCAATATAACTCATCTTAAC
1 AAATTGTCTTCACAAAGGCCCAACTTAGCAAAATAGCTCATCTTGAC
* * * *
5206635 AAATTGTTTTCACAAAGGCCTAGC-TAGGCAAAATAGCTCAACTTGAC
1 AAATTGTCTTCACAAAGGCCCAACTTA-GCAAAATAGCTCATCTTGAC
5206682 AAATTGTCTTCA
1 AAATTGTCTTCA
5206694 TAAAAACTTA
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
46 2 0.02
47 82 0.98
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (47 bp):
AAATTGTCTTCACAAAGGCCCAACTTAGCAAAATAGCTCATCTTGAC
Found at i:5206824 original size:47 final size:46
Alignment explanation
Indices: 5206588--5206842 Score: 154
Period size: 47 Copynumber: 5.4 Consensus size: 46
5206578 TCATCTTGAT
* * * * * ** *
5206588 AAATTACCTTCATAAAGGCCCAACTTAGCAATATAACTCATCTTAAC
1 AAATTGCCTTCATAAAGG-CCAGCTTGGCAAAAGATTTCAGCTTAAC
** * * * ** * *
5206635 AAATTGTTTTCACAAAGGCCTAGCTAGGCAAAATAGCTCAACTTGAC
1 AAATTGCCTTCATAAAGGCC-AGCTTGGCAAAAGATTTCAGCTTAAC
* ** *
5206682 AAATTGTCTTCATAAAAACTTAGCTTGGCAAAAGAGTTT-AG-TTAGAC
1 AAATTGCCTTCATAAAGGC-CAGCTTGGCAAAAGA-TTTCAGCTTA-AC
* * * * * * * *
5206729 AAATTGCCTACTTAAAGGCTTAACTTGGCAAAAGAATCCATCTCAAC
1 AAATTGCCTTCATAAAGGC-CAGCTTGGCAAAAGATTTCAGCTTAAC
5206776 AAATTGCCTTCATACAAGGCCAGCTTGGCAAAAGATTTCAGCTTAAC
1 AAATTGCCTTCATA-AAGGCCAGCTTGGCAAAAGATTTCAGCTTAAC
* *
5206823 AAATTACCTTTATAAAGGCC
1 AAATTGCCTTCATAAAGGCC
5206843 TAACTCGACA
Statistics
Matches: 159, Mismatches: 42, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
46 11 0.07
47 140 0.88
48 8 0.05
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (46 bp):
AAATTGCCTTCATAAAGGCCAGCTTGGCAAAAGATTTCAGCTTAAC
Found at i:5206855 original size:47 final size:47
Alignment explanation
Indices: 5206727--5206885 Score: 131
Period size: 47 Copynumber: 3.4 Consensus size: 47
5206717 GTTTAGTTAG
* * * * *
5206727 ACAAATTGCCTACTTAAAGGCTTAACTTGGCAAAAGAATCCATCTCA
1 ACAAATTACCTTCATAAAGGCCTAACTTGGCAAAAGAATCCAGCTCA
* * * * *
5206774 ACAAATTGCCTTCATACAAGGCC-AGCTTGGCAAAAGATTTCAGCTTA
1 ACAAATTACCTTCATA-AAGGCCTAACTTGGCAAAAGAATCCAGCTCA
* * * * ** * *
5206821 ACAAATTACCTTTATAAAGGCCTAACTCGACAAAAAAATTTATCTCG
1 ACAAATTACCTTCATAAAGGCCTAACTTGGCAAAAGAATCCAGCTCA
*
5206868 ACAAATTACATTCATAAA
1 ACAAATTACCTTCATAAA
5206886 AGCTCAGCTA
Statistics
Matches: 89, Mismatches: 21, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
46 6 0.07
47 78 0.88
48 5 0.06
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.26
Consensus pattern (47 bp):
ACAAATTACCTTCATAAAGGCCTAACTTGGCAAAAGAATCCAGCTCA
Found at i:5206894 original size:94 final size:94
Alignment explanation
Indices: 5206690--5206894 Score: 220
Period size: 94 Copynumber: 2.2 Consensus size: 94
5206680 ACAAATTGTC
* * * * *
5206690 TTCATAAAAACTTAGCTTGGCAAAAGAGTTTAGTTAGACAAATTGCCTACTTAAAGGCTTAACTT
1 TTCATAAAAGCTCAGCTTGGCAAAAGAGTTTAGTTAGACAAATTACCTACTTAAAGGCCTAACTC
* * * *
5206755 GGCAAAAGAATCCATCTCAACAAATTGCC
66 GACAAAAAAATCCATCTCAACAAATTACA
* *
5206784 TTCATACAAGGC-CAGCTTGGCAAAAGA-TTTCAGCTTA-ACAAATTACCT-TTATAAAGGCCTA
1 TTCATA-AAAGCTCAGCTTGGCAAAAGAGTTT-AG-TTAGACAAATTACCTACT-TAAAGGCCTA
** *
5206845 ACTCGACAAAAAAATTTATCTCGACAAATTACA
62 ACTCGACAAAAAAATCCATCTCAACAAATTACA
5206878 TTCATAAAAGCTCAGCT
1 TTCATAAAAGCTCAGCT
5206895 AAAAAAGAAG
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
93 8 0.09
94 77 0.85
95 6 0.07
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (94 bp):
TTCATAAAAGCTCAGCTTGGCAAAAGAGTTTAGTTAGACAAATTACCTACTTAAAGGCCTAACTC
GACAAAAAAATCCATCTCAACAAATTACA
Found at i:5207145 original size:31 final size:31
Alignment explanation
Indices: 5207104--5207180 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
5207094 CTTTTTAGGG
* *
5207104 AAATTACTTTCATAAAAGACTCAGCTT-AATC
1 AAATTTCTTTCATAAAAGAATCAG-TTCAATC
* *
5207135 AAATTTCTTTCAT-AAAGAATTAGTTCAGTC
1 AAATTTCTTTCATAAAAGAATCAGTTCAATC
5207165 AAATTTCTTTCATAAA
1 AAATTTCTTTCATAAA
5207181 TGATTAGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 2 0.05
30 24 0.60
31 14 0.35
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (31 bp):
AAATTTCTTTCATAAAAGAATCAGTTCAATC
Found at i:5207192 original size:26 final size:27
Alignment explanation
Indices: 5207132--5207192 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
5207122 ACTCAGCTTA
5207132 ATCAAATTTCTTTCATAAAGAATTAGTT
1 ATCAAATTTCTTTCATAAAGAATTAG-T
5207160 CAGTCAAATTTCTTTCATAAATG-ATTAG-
1 -A-TCAAATTTCTTTCATAAA-GAATTAGT
5207188 ATCAA
1 ATCAA
5207193 CCAAAAGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
29 1 0.03
30 23 0.77
31 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (27 bp):
ATCAAATTTCTTTCATAAAGAATTAGT
Found at i:5207317 original size:30 final size:31
Alignment explanation
Indices: 5207283--5207452 Score: 113
Period size: 30 Copynumber: 5.6 Consensus size: 31
5207273 TAGCTTAGCT
* *
5207283 AAATTGCCTTCATAAAGGCTCAA-TTGAGTC
1 AAATTACCTTCATAAAGGATCAACTTGAGTC
* *
5207313 AAATTACTTTCATAAAGGATCAACTTGA-CC
1 AAATTACCTTCATAAAGGATCAACTTGAGTC
* * *
5207343 AAA-TACCTTTCATAAAAAGATCAA-TTCAATC
1 AAATTACC-TTCAT-AAAGGATCAACTTGAGTC
* * * *
5207374 -AATTTCCTTTATAAAGGATCAACTTTA-CC
1 AAATTACCTTCATAAAGGATCAACTTGAGTC
* * ** *
5207403 AAAATACCTTTATAAAATATCAACTCGA--C
1 AAATTACCTTCATAAAGGATCAACTTGAGTC
5207432 AAAATTACCTTCATAAAGGAT
1 -AAATTACCTTCATAAAGGAT
5207453 TAGTTTGACA
Statistics
Matches: 109, Mismatches: 23, Indels: 16
0.74 0.16 0.11
Matches are distributed among these distances:
29 14 0.13
30 78 0.72
31 17 0.16
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (31 bp):
AAATTACCTTCATAAAGGATCAACTTGAGTC
Found at i:5207355 original size:60 final size:60
Alignment explanation
Indices: 5207291--5207452 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 60
5207281 CTAAATTGCC
* * * *
5207291 TTCATAAAGGCTCAATTGAGTCAAATTACTTTCATAAAGGATCAACTTGACC-AAATACCT
1 TTCATAAAAGATCAATTCAATCAAATTACTTT-ATAAAGGATCAACTTGACCAAAATACCT
* * *
5207351 TTCATAAAAAGATCAATTCAATCAATTTCCTTTATAAAGGATCAACTTTACCAAAATACCT
1 TTCAT-AAAAGATCAATTCAATCAAATTACTTTATAAAGGATCAACTTGACCAAAATACCT
* * * *
5207412 TT-ATAAAATATCAACTCGA-CAAAATTACCTTCATAAAGGAT
1 TTCATAAAAGATCAATTCAATC-AAATTA-CTTTATAAAGGAT
5207453 TAGTTTGACA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 16 0.19
60 37 0.44
61 31 0.36
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (60 bp):
TTCATAAAAGATCAATTCAATCAAATTACTTTATAAAGGATCAACTTGACCAAAATACCT
Found at i:5207518 original size:29 final size:30
Alignment explanation
Indices: 5207312--5207546 Score: 118
Period size: 30 Copynumber: 7.9 Consensus size: 30
5207302 TCAATTGAGT
* * * **
5207312 CAAATTACTTTCATAAAGGATCAACTTGAC
1 CAAATTACCTTCATAAAAGATTAACTCAAC
* * *
5207342 CAAA-TACCTTTCATAAAAAGATCAATTCAAT
1 CAAATTACC-TTCAT-AAAAGATTAACTCAAC
* * * * **
5207373 C-AATTTCCTTTATAAAGGATCAACTTTAC
1 CAAATTACCTTCATAAAAGATTAACTCAAC
* * * * *
5207402 CAAAATACCTTTATAAAATATCAACTCGAC
1 CAAATTACCTTCATAAAAGATTAACTCAAC
* * ** **
5207432 AAAATTACCTTCATAAAGGATTAGTTTGAC
1 CAAATTACCTTCATAAAAGATTAACTCAAC
* * **
5207462 AAAATTATCTTCATAAATA-ATTTGCTCAA-
1 CAAATTACCTTCATAAA-AGATTAACTCAAC
* *
5207491 TAAATTACCTTCATAAAAGCTTAACTCAAC
1 CAAATTACCTTCATAAAAGATTAACTCAAC
* *
5207521 CAAATTTCTTTCATAAAAGATTAACT
1 CAAATTACCTTCATAAAAGATTAACT
5207547 TAGCCAATCG
Statistics
Matches: 155, Mismatches: 43, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
28 1 0.01
29 37 0.24
30 102 0.66
31 15 0.10
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (30 bp):
CAAATTACCTTCATAAAAGATTAACTCAAC
Found at i:5208192 original size:31 final size:31
Alignment explanation
Indices: 5208154--5208262 Score: 78
Period size: 31 Copynumber: 3.5 Consensus size: 31
5208144 TAACATTTAT
5208154 TATATATTCACCTTAGTGTAAATCACCTCAG
1 TATATATTCACCTTAGTGTAAATCACCTCAG
* * * *
5208185 TATATATTTAGC-TCGTTGTAAATCA-CTTAGG
1 TATATATTCACCTTAG-TGTAAATCACCTCA-G
* * * * * *
5208216 TATATATTTAGCTCAATATAAATCACCTCAA
1 TATATATTCACCTTAGTGTAAATCACCTCAG
**
5208247 TATGGATTCACCTTAG
1 TATATATTCACCTTAG
5208263 CACATATTCA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
30 5 0.09
31 50 0.86
32 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (31 bp):
TATATATTCACCTTAGTGTAAATCACCTCAG
Found at i:5210572 original size:12 final size:12
Alignment explanation
Indices: 5210555--5210579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5210545 AATCAAGCTG
5210555 TTTTTCTCTTTC
1 TTTTTCTCTTTC
5210567 TTTTTCTCTTTC
1 TTTTTCTCTTTC
5210579 T
1 T
5210580 CTTTGTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTCTTTC
Found at i:5211436 original size:3 final size:3
Alignment explanation
Indices: 5211428--5211454 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5211418 AAATATACTT
5211428 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
5211455 ATTTGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5212153 original size:3 final size:3
Alignment explanation
Indices: 5212145--5212172 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5212135 TTAACAAATA
5212145 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5212173 TGGAAACGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5212794 original size:21 final size:22
Alignment explanation
Indices: 5212768--5212809 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
5212758 TCATAATGTA
5212768 AAATTTAAAAT-ATTCAAATTC
1 AAATTTAAAATAATTCAAATTC
5212789 AAATTTAAAATAATTCAAATT
1 AAATTTAAAATAATTCAAATT
5212810 TACAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTTAAAATAATTCAAATTC
Found at i:5212825 original size:16 final size:16
Alignment explanation
Indices: 5212784--5212819 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5212774 AAAATATTCA
5212784 AATTCAAATTTAAAAT
1 AATTCAAATTTAAAAT
*
5212800 AATTCAAATTTACAAT
1 AATTCAAATTTAAAAT
5212816 AATT
1 AATT
5212820 TGAATTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTCAAATTTAAAAT
Found at i:5213894 original size:36 final size:37
Alignment explanation
Indices: 5213853--5213929 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
5213843 AAAAAAAATA
5213853 ATTTATT-TCAAAAATAT-TATCCAATATGTTAGTAAG
1 ATTTATTGTCAAAAATATCT-TCCAATATGTTAGTAAG
* * *
5213889 ATTTATTGTTAAAATTATCTTCTAATATGTTAGTAAG
1 ATTTATTGTCAAAAATATCTTCCAATATGTTAGTAAG
5213926 ATTT
1 ATTT
5213930 TATAAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.19
37 28 0.78
38 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (37 bp):
ATTTATTGTCAAAAATATCTTCCAATATGTTAGTAAG
Found at i:5216279 original size:17 final size:16
Alignment explanation
Indices: 5216212--5216304 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 16
5216202 AAACTTTCAA
* *
5216212 ATTCGCAAGAACTTAT
1 ATTCGCAAGAATTTAG
*
5216228 ATTCGCAAGAATTTCAT
1 ATTCGCAAGAATTT-AG
* * * *
5216245 ATTTGTAAAAACTTAG
1 ATTCGCAAGAATTTAG
5216261 ATTCGCAAGAATTTTAG
1 ATTCGCAAGAA-TTTAG
** *
5216278 ATTTACAAGCATTTAG
1 ATTCGCAAGAATTTAG
*
5216294 ATTTGCAAGAA
1 ATTCGCAAGAA
5216305 ACTTAAAGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
16 36 0.60
17 24 0.40
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (16 bp):
ATTCGCAAGAATTTAG
Found at i:5216602 original size:44 final size:43
Alignment explanation
Indices: 5216536--5216634 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 43
5216526 ACATTTGAAA
* * * *
5216536 AATTCAAAGATTCTCATAAAAAATTTTCA-AGGCTCACATCCAC
1 AATTCAAAGATTCCCATAAAAAATCTT-AGAGACTCACACCCAC
* * *
5216579 AATTCAAAGATTCACCTTAAAAAATCTTAGAGATTCACACCCAT
1 AATTCAAAGATTC-CCATAAAAAATCTTAGAGACTCACACCCAC
5216623 AATTCAAAGATT
1 AATTCAAAGATT
5216635 TTTATTTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 14 0.30
44 33 0.70
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.28
Consensus pattern (43 bp):
AATTCAAAGATTCCCATAAAAAATCTTAGAGACTCACACCCAC
Found at i:5216692 original size:46 final size:45
Alignment explanation
Indices: 5216624--5216776 Score: 132
Period size: 45 Copynumber: 3.4 Consensus size: 45
5216614 CACACCCATA
*
5216624 ATTC-AAAGATTTTTATTTAAAAAACTTTAGAAATTCACATCTAAG
1 ATTCTAAAGATTTTGA-TTAAAAAACTTTAGAAATTCACATCTAAG
* * ** * * * *
5216669 ATTCTAAGGATTTTGATTAAAAAA-TTTTGAGTTTTATATCCAAA
1 ATTCTAAAGATTTTGATTAAAAAACTTTAGAAATTCACATCTAAG
* * * *
5216713 ATTTCAAAAAATTTT-ATTCGAAAAACTTTAGAAATTCACATATAAG
1 A-TTCTAAAGATTTTGATT-AAAAAACTTTAGAAATTCACATCTAAG
*
5216759 ATTCTAAAGATTCTGATT
1 ATTCTAAAGATTTTGATT
5216777 TGAAAAGTTT
Statistics
Matches: 79, Mismatches: 24, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
44 17 0.22
45 37 0.47
46 25 0.32
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (45 bp):
ATTCTAAAGATTTTGATTAAAAAACTTTAGAAATTCACATCTAAG
Found at i:5216719 original size:90 final size:90
Alignment explanation
Indices: 5216595--5216810 Score: 272
Period size: 90 Copynumber: 2.4 Consensus size: 90
5216585 AAGATTCACC
* * * * * * *
5216595 TTAAAAAATCTTAGAGATTCACACCCATAATTCAAAGATTTTTATTTAAAAAACTTTAGAAATTC
1 TTAAAAAAT-TTAGAGTTTTACATCCAAAATTCAAAAAATTTTATTCAAAAAACTTTAGAAATTC
* * *
5216660 ACATCTAAGATTCTAAGGATTTTGA-
65 ACATATAAGATTCTAAAGATTCTGAT
* * *
5216685 TTAAAAAATTTTGAGTTTTATATCCAAAATTTCAAAAAATTTTATTCGAAAAACTTTAGAAATTC
1 TTAAAAAATTTAGAGTTTTACATCCAAAA-TTCAAAAAATTTTATTCAAAAAACTTTAGAAATTC
5216750 ACATATAAGATTCTAAAGATTCTGAT
65 ACATATAAGATTCTAAAGATTCTGAT
* *
5216776 TTGAAAAGTTTAGAGTTTTACATCCAAAATTCAAA
1 TTAAAAAATTTAGAGTTTTACATCCAAAATTCAAA
5216811 TATTCAAATT
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
89 14 0.13
90 68 0.64
91 25 0.23
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (90 bp):
TTAAAAAATTTAGAGTTTTACATCCAAAATTCAAAAAATTTTATTCAAAAAACTTTAGAAATTCA
CATATAAGATTCTAAAGATTCTGAT
Found at i:5217030 original size:22 final size:22
Alignment explanation
Indices: 5217016--5217059 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5217006 AATTGTGCAC
* *
5217016 GAAGGTCTTATAAATCATGCCT
1 GAAGGTCTTAGAAATTATGCCT
5217038 GAAGGTCTTAGAAATTATGCCT
1 GAAGGTCTTAGAAATTATGCCT
5217060 ATTAATAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (22 bp):
GAAGGTCTTAGAAATTATGCCT
Found at i:5217469 original size:11 final size:11
Alignment explanation
Indices: 5217453--5217480 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5217443 TTCAAACACC
5217453 AATGCAAACAT
1 AATGCAAACAT
5217464 AATGCAAACAT
1 AATGCAAACAT
5217475 AATGCA
1 AATGCA
5217481 TGCAATGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (11 bp):
AATGCAAACAT
Found at i:5218616 original size:17 final size:16
Alignment explanation
Indices: 5218590--5218624 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5218580 CTCACATTTG
5218590 TTTTTTTTTTTCCTTT
1 TTTTTTTTTTTCCTTT
*
5218606 TTTTTTCTTTTTTCTTT
1 TTTTTT-TTTTTCCTTT
5218623 TT
1 TT
5218625 CTTCACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTTTCCTTT
Found at i:5218623 original size:13 final size:12
Alignment explanation
Indices: 5218590--5218627 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
5218580 CTCACATTTG
5218590 TTTTTTTTTTTC
1 TTTTTTTTTTTC
*
5218602 -CTTTTTTTTTC
1 TTTTTTTTTTTC
5218613 TTTTTTCTTTTTC
1 TTTTTT-TTTTTC
5218626 TT
1 TT
5218628 CACAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 4 0.18
13 8 0.36
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:5221596 original size:1 final size:1
Alignment explanation
Indices: 5221590--5221617 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5221580 ATGCAGAAGA
5221590 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
5221618 ATCGTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5223323 original size:29 final size:27
Alignment explanation
Indices: 5223291--5223380 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 27
5223281 TTATCTAATT
*
5223291 AAGGAAATAAAAACAAAAAAAAATAAAAA
1 AAGGAAA-AAGAACAAAAAAAAA-AAAAA
* *
5223320 AAGGTAAAAAGGACAAAAATGAAAAAAAA
1 AAGG-AAAAAGAACAAAAA-AAAAAAAAA
* *
5223349 AAGAAAAGGAAGAACAAAATAAAAAAAAA
1 AAGGAAA--AAGAACAAAAAAAAAAAAAA
5223378 AAG
1 AAG
5223381 TTTATAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.06
29 32 0.64
30 15 0.30
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.06
Consensus pattern (27 bp):
AAGGAAAAAGAACAAAAAAAAAAAAAA
Found at i:5226687 original size:13 final size:13
Alignment explanation
Indices: 5226669--5226700 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5226659 CTAGCTGAAA
*
5226669 CTAACCTGAAACC
1 CTAACCTAAAACC
5226682 CTAACCTAAAACC
1 CTAACCTAAAACC
5226695 CTAACC
1 CTAACC
5226701 CTAGCCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.41, G:0.03, T:0.16
Consensus pattern (13 bp):
CTAACCTAAAACC
Found at i:5226719 original size:19 final size:19
Alignment explanation
Indices: 5226671--5226719 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
5226661 AGCTGAAACT
5226671 AACCTGAAACCCTAACCTAA
1 AACC-GAAACCCTAACCTAA
** *
5226691 AACCCTAACCCTAGCCTAA
1 AACCGAAACCCTAACCTAA
*
5226710 AATCGAAACC
1 AACCGAAACC
5226720 TTAAACCACC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.43, C:0.37, G:0.06, T:0.14
Consensus pattern (19 bp):
AACCGAAACCCTAACCTAA
Found at i:5226748 original size:22 final size:22
Alignment explanation
Indices: 5226715--5226779 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
5226705 CCTAAAATCG
*
5226715 AAACC-TTAAACCACCTAAACC
1 AAACCTTTAAACCACTTAAACC
5226736 AAACCTTTAAACCACTTAAATCC
1 AAACCTTTAAACCACTTAAA-CC
* *
5226759 TAA-TTTTAAACCACTTAAACC
1 AAACCTTTAAACCACTTAAACC
5226780 CTAACACTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 7 0.18
22 28 0.72
23 4 0.10
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACCTTTAAACCACTTAAACC
Found at i:5227538 original size:32 final size:32
Alignment explanation
Indices: 5227479--5227559 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
5227469 CTTTTCCATG
* * *
5227479 AAACCCTAAACCTAAGCCTTAAGCCCTAATCC
1 AAACCCTAAACCTAAACCTTAAACCCTAAACC
*
5227511 TAAACCCTAAA-GTAAACCTTAAACCCTAAACC
1 -AAACCCTAAACCTAAACCTTAAACCCTAAACC
* *
5227543 AAACCTTAATCCTAAAC
1 AAACCCTAAACCTAAAC
5227560 TCTAAATCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 8 0.20
32 22 0.55
33 10 0.25
ACGTcount: A:0.43, C:0.33, G:0.04, T:0.20
Consensus pattern (32 bp):
AAACCCTAAACCTAAACCTTAAACCCTAAACC
Found at i:5227559 original size:18 final size:19
Alignment explanation
Indices: 5227511--5227551 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5227501 GCCCTAATCC
**
5227511 TAAACCCTAAAGTAAACCT
1 TAAACCCTAAACCAAACCT
5227530 TAAACCCTAAACCAAACCT
1 TAAACCCTAAACCAAACCT
5227549 TAA
1 TAA
5227552 TCCTAAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAACCCTAAACCAAACCT
Found at i:5229236 original size:47 final size:46
Alignment explanation
Indices: 5229140--5229237 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 46
5229130 GATATCTATA
* * *
5229140 AATACATATGTATAAATATAAACCATAAATAAGAACTTAATTAATAT
1 AATACATATGTATAAATATAAA-CATAAATAAGAACTAAAATAAGAT
*
5229187 AATACATATGTATAAATATAAA-ATTAAATGAATAA-TAAAATATAGAT
1 AATACATATGTATAAATATAAACA-TAAAT-AAGAACTAAAATA-AGAT
5229234 AATA
1 AATA
5229238 AAAATATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
45 1 0.02
46 10 0.23
47 33 0.75
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (46 bp):
AATACATATGTATAAATATAAACATAAATAAGAACTAAAATAAGAT
Found at i:5229676 original size:20 final size:19
Alignment explanation
Indices: 5229599--5229677 Score: 52
Period size: 19 Copynumber: 4.0 Consensus size: 19
5229589 TTGGTCTCAC
** *
5229599 TTTTAAAAAAATGGAAAAAT
1 TTTT-AAAAAATAAAAAAAA
* * *
5229619 TTTTATAAAATATAACAAA
1 TTTTAAAAAATAAAAAAAA
*
5229638 TTTGAAAAAA-ACAATAAAAA
1 TTTTAAAAAATA-AA-AAAAA
5229658 GTTTTAAAAAATAAAAAAAA
1 -TTTTAAAAAATAAAAAAAA
5229678 AAATTTAACA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
19 19 0.42
20 13 0.29
21 11 0.24
22 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
TTTTAAAAAATAAAAAAAA
Found at i:5229915 original size:20 final size:19
Alignment explanation
Indices: 5229871--5229917 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5229861 ATTTATAAAC
*
5229871 TTTAAAAAAATCTAAAAAA
1 TTTAAAAAAAACTAAAAAA
* *
5229890 TCTAAAATAAAACTAAAAAT
1 TTTAAAA-AAAACTAAAAAA
5229910 TTTAAAAA
1 TTTAAAAA
5229918 GAAAAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (19 bp):
TTTAAAAAAAACTAAAAAA
Found at i:5232492 original size:28 final size:28
Alignment explanation
Indices: 5232461--5232524 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
5232451 GGAATAAATG
*
5232461 AAAATGACATGGA-CAAATCCAAAGTCTA
1 AAAATGACATGGATAAAAT-CAAAGTCTA
* *
5232489 AAAATGGACTTGGATAAAATCAATGTCTA
1 AAAAT-GACATGGATAAAATCAAAGTCTA
5232518 AAAATGA
1 AAAATGA
5232525 AATAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (28 bp):
AAAATGACATGGATAAAATCAAAGTCTA
Found at i:5232685 original size:42 final size:43
Alignment explanation
Indices: 5232489--5232874 Score: 231
Period size: 43 Copynumber: 9.1 Consensus size: 43
5232479 CCAAAGTCTA
* * * * *
5232489 AAAATGGACTTGGATAAAATCAATGTCTAAAAATGAAATAAATA
1 AAAAT-GATTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
*
5232533 AAAATGACTTT-AATGAAACCAAAGTCTAAAAATGAAATAAATG
1 AAAATGA-TTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
* * ** *
5232576 AAAACGAATTGGACAAAACCAAAG-CTTAAACATGAAATAAATG
1 AAAATGATTTGGATGAAACCAAAGTC-TAAAAATGAAATAAATG
* * * *
5232619 ACAAA-AACTTGGATGAAACCAAAGTTTAAAAATGAAATAGAT-
1 A-AAATGATTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
* * *
5232661 AAAATGATTTGGATGAAACTAAAGTCTAAAAATGAAATGATTG
1 AAAATGATTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
* * * ** * * *
5232704 AGACAA--A-AT-CA-CAATTCAAAGATGT---AATCAAATAAATA
1 A-A-AATGATTTGGATGAAACCAAAG-TCTAAAAATGAAATAAATG
** * * *
5232742 AAAATGACATGGATTAAACTAAAGTCTAAAAATAAAATAAATG
1 AAAATGATTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
** * ** *
5232785 AAAATGACCTAGACAAAACCAAAGTCTAAAAATGGAATAAATG
1 AAAATGATTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
* * * * *
5232828 AAAAAGACTTGGACGAAACCAAA-ACTTAAACATGAAATAAATG
1 AAAATGATTTGGATGAAACCAAAGTC-TAAAAATGAAATAAATG
5232871 AAAA
1 AAAA
5232875 AAAAAAAAAA
Statistics
Matches: 264, Mismatches: 59, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
36 2 0.01
37 1 0.00
38 11 0.04
39 2 0.01
40 9 0.03
41 12 0.05
42 36 0.14
43 178 0.67
44 11 0.04
45 2 0.01
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (43 bp):
AAAATGATTTGGATGAAACCAAAGTCTAAAAATGAAATAAATG
Found at i:5232826 original size:252 final size:252
Alignment explanation
Indices: 5232487--5232954 Score: 615
Period size: 252 Copynumber: 1.8 Consensus size: 252
5232477 ATCCAAAGTC
* * * * **
5232487 TAAAAATGGACTTGGATAAAATCAATGTCTAAAAATGAAATAAATAAAAATGACTTTAATGAAAC
1 TAAAAATGGACATGGATAAAATCAAAGTCTAAAAATAAAATAAATAAAAATGACTCTAACAAAAC
* *
5232552 CAAAGTCTAAAAATGAAATAAATGAAAACGAATTGGACAAAACCAAAGCTTAAACATGAAATAAA
66 CAAAGTCTAAAAATGAAATAAATGAAAAAGAATTGGACAAAACCAAAACTTAAACATGAAATAAA
* * * *
5232617 TG-ACAAAAACTTGGATGAAACCAAAGTTTAAAAATGAAATAGATAAAA-TGA-TTTGGATGAAA
131 TGAAAAAAAAC-TGAATGAAACCAAAGTCTAAAAATGAAATAGATAAAACTAACTTT-GATG-AA
*
5232679 CTAAAGTCTAAAAATGAAATGATTGAGACAAAATCACAATTCAAAGATGTAATCAAATAAA
193 CCAAAGTCT-AAAATGAAATGATTGAGACAAAATCACAATTCAAAGATGTAATCAAATAAA
* *
5232740 TAAAAAT-GACATGGATTAAA-CTAAAGTCTAAAAATAAAATAAATGAAAATGAC-CTAGACAAA
1 TAAAAATGGACATGGATAAAATC-AAAGTCTAAAAATAAAATAAATAAAAATGACTCTA-ACAAA
* * *
5232802 ACCAAAGTCTAAAAATGGAATAAATGAAAAAGACTTGGACGAAACCAAAACTTAAACATGAAATA
64 ACCAAAGTCTAAAAATGAAATAAATGAAAAAGAATTGGACAAAACCAAAACTTAAACATGAAATA
*
5232867 AATGAAAAAAAAAAAAAACTGAATGAAATCAAAGTCTAAAAATGAAATAGATAAAACTAACTTTG
129 AATG------AAAAAAAACTGAATGAAACCAAAGTCTAAAAATGAAATAGATAAAACTAACTTTG
5232932 ATGAACCAAAGTCTAAAATGAAA
188 ATGAACCAAAGTCTAAAATGAAA
5232955 GGAACGTGAC
Statistics
Matches: 185, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
251 3 0.02
252 106 0.57
253 7 0.04
257 9 0.05
258 44 0.24
259 13 0.07
260 3 0.02
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (252 bp):
TAAAAATGGACATGGATAAAATCAAAGTCTAAAAATAAAATAAATAAAAATGACTCTAACAAAAC
CAAAGTCTAAAAATGAAATAAATGAAAAAGAATTGGACAAAACCAAAACTTAAACATGAAATAAA
TGAAAAAAAACTGAATGAAACCAAAGTCTAAAAATGAAATAGATAAAACTAACTTTGATGAACCA
AAGTCTAAAATGAAATGATTGAGACAAAATCACAATTCAAAGATGTAATCAAATAAA
Found at i:5233077 original size:34 final size:33
Alignment explanation
Indices: 5233039--5233116 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
5233029 ACGAAATAAT
* *
5233039 AAGTCTAAATATACAAGGACTATGAAAAAATCAC
1 AAGTCTAAA-ATACAACGACTAGGAAAAAATCAC
* * * *
5233073 AAGTCTATGAATGCAACGATTAGGACAAAATCAC
1 AAGTCTA-AAATACAACGACTAGGAAAAAATCAC
5233107 AAGTCTAAAA
1 AAGTCTAAAA
5233117 ATGAAATGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
33 2 0.06
34 33 0.92
35 1 0.03
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (33 bp):
AAGTCTAAAATACAACGACTAGGAAAAAATCAC
Found at i:5233134 original size:34 final size:34
Alignment explanation
Indices: 5233065--5233326 Score: 169
Period size: 34 Copynumber: 7.7 Consensus size: 34
5233055 GGACTATGAA
** * *
5233065 AAAATCACAAGTCTATGAATGCAACGATTAGGAC
1 AAAATCACAAGTCTAAAAATGAAATGATTAGGAC
* *
5233099 AAAATCACAAGTCTAAAAATGAAATGATCAAGAC
1 AAAATCACAAGTCTAAAAATGAAATGATTAGGAC
* ** * * * *
5233133 AAGAA-CACAAGTTTATGAGTGCAACGATTAAGGGC
1 AA-AATCACAAGTCTAAAAATGAAATGATT-AGGAC
* * **
5233168 AAAACCACAAGTTTAAAAATTCAATGATTAGGA-
1 AAAATCACAAGTCTAAAAATGAAATGATTAGGAC
** * ** *
5233201 TGAATCTATAAGTCTAAAAAT-ACAATGATCGGGAT
1 AAAATC-ACAAGTCTAAAAATGA-AATGATTAGGAC
5233236 AAAATCACAAGTCTAAAAATGCAAA-GATTAGGAC
1 AAAATCACAAGTCTAAAAATG-AAATGATTAGGAC
* * * *
5233270 AAACT-ACAAGTCTAAAAAT-ATAAT-AATCGAGAT
1 AAAATCACAAGTCTAAAAATGA-AATGATTAG-GAC
5233303 AAAATCACAAGTCTAAAAATGAAA
1 AAAATCACAAGTCTAAAAATGAAA
5233327 CAAATATTTA
Statistics
Matches: 175, Mismatches: 40, Indels: 26
0.73 0.17 0.11
Matches are distributed among these distances:
31 1 0.01
32 5 0.03
33 23 0.13
34 112 0.64
35 33 0.19
36 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (34 bp):
AAAATCACAAGTCTAAAAATGAAATGATTAGGAC
Found at i:5233308 original size:67 final size:68
Alignment explanation
Indices: 5233168--5233323 Score: 215
Period size: 67 Copynumber: 2.3 Consensus size: 68
5233158 GATTAAGGGC
* * * * * * * * *
5233168 AAAACCACAAGTTTAAAAATTCAATGATTAGGATGAATCTATAAGTCTAAAAATACAATGATCGG
1 AAAATCACAAGTCTAAAAATGCAAAGATTAGGATCAAACTACAAGTCTAAAAATACAATAATCGA
5233233 GAT
66 GAT
*
5233236 AAAATCACAAGTCTAAAAATGCAAAGATTAGGA-CAAACTACAAGTCTAAAAATATAATAATCGA
1 AAAATCACAAGTCTAAAAATGCAAAGATTAGGATCAAACTACAAGTCTAAAAATACAATAATCGA
5233300 GAT
66 GAT
5233303 AAAATCACAAGTCTAAAAATG
1 AAAATCACAAGTCTAAAAATG
5233324 AAACAAATAT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 49 0.63
68 29 0.37
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (68 bp):
AAAATCACAAGTCTAAAAATGCAAAGATTAGGATCAAACTACAAGTCTAAAAATACAATAATCGA
GAT
Found at i:5235229 original size:16 final size:16
Alignment explanation
Indices: 5235208--5235242 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5235198 TTTCATAGCA
*
5235208 TGCTACAAACTCAGAT
1 TGCTACAAACTCAAAT
5235224 TGCTACAAACTCAAAT
1 TGCTACAAACTCAAAT
5235240 TGC
1 TGC
5235243 ATGGTAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (16 bp):
TGCTACAAACTCAAAT
Found at i:5244131 original size:17 final size:17
Alignment explanation
Indices: 5244098--5244135 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5244088 TGTTGGCCAT
5244098 TAAATATAGAAAAAAAA
1 TAAATATAGAAAAAAAA
*
5244115 TAAATTATA-AAATAAAA
1 TAAA-TATAGAAAAAAAA
5244132 TAAA
1 TAAA
5244136 AAAATAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TAAATATAGAAAAAAAA
Found at i:5244154 original size:12 final size:12
Alignment explanation
Indices: 5244109--5244153 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5244099 AAATATAGAA
5244109 AAAAAATAAATT
1 AAAAAATAAATT
* *
5244121 ATAAAATAAAATA
1 AAAAAAT-AAATT
*
5244134 AAAAAATAGATT
1 AAAAAATAAATT
5244146 AAAAAATA
1 AAAAAATA
5244154 GGTTTTAGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
AAAAAATAAATT
Found at i:5244878 original size:28 final size:25
Alignment explanation
Indices: 5244832--5244885 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 25
5244822 AAATTGGTAG
5244832 AAAAAGGGAAGTAGCGTAAACAAAAA
1 AAAAAGGGAAGTAGCGTAAA-AAAAA
5244858 AAAAAGAGAGAAGT-GCAGTAAAAAAAA
1 AAAAAG-G-GAAGTAGC-GTAAAAAAAA
5244885 A
1 A
5244886 TAGTAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.24
27 9 0.36
28 10 0.40
ACGTcount: A:0.65, C:0.06, G:0.22, T:0.07
Consensus pattern (25 bp):
AAAAAGGGAAGTAGCGTAAAAAAAA
Found at i:5245799 original size:59 final size:59
Alignment explanation
Indices: 5245690--5246139 Score: 563
Period size: 58 Copynumber: 7.7 Consensus size: 59
5245680 TTGTGTAGGA
* *** *
5245690 AAAATTAATACTTTCAACTTTTCCTCAAAAAT-CCATTTTTGAAAACTTATTTTTAACG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAACTTATTTTTAAGG
*
5245748 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAACTTATTTTTAAGG
* * * **
5245807 AAACTTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTTTGGAAATTTATTTTTAAAA
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATA-TTTTTTTTGAAAACTTATTTTTAAGG
* * *
5245867 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTGGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAACTTATTTTTAAGG
*** *
5245925 AAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTTTGAAAACTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAACTTATTTTTAAGG
** * *
5245983 AAAATTGATACTTTCAACTTTTCCTC-AAAA-CCTTTTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAACTTATTTTTAAGG
* * * * *
5246040 AAAATTGATACTTTTAACTTTT-TTCTAAAAATATTTTTTTGGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTGAAAACTTATTTTTAAGG
* *
5246099 AAAATTGATACTTTCAACTTTTCTTCAATAATATTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT
5246140 TGGATTTTAT
Statistics
Matches: 343, Mismatches: 40, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
56 2 0.01
57 48 0.14
58 130 0.38
59 106 0.31
60 57 0.17
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAACTTATTTTTAAGG
Found at i:5246189 original size:17 final size:16
Alignment explanation
Indices: 5246156--5246320 Score: 97
Period size: 17 Copynumber: 9.9 Consensus size: 16
5246146 TTATTTAAAG
5246156 AAAATAAAATAATAAAAT
1 AAAAT-AAA-AATAAAAT
*
5246174 AAAATAAAAGTAAAAAT
1 AAAATAAAAAT-AAAAT
5246191 AAAA-AAAAAGTAAAAT
1 AAAATAAAAA-TAAAAT
*
5246207 AAAAATAGAAATAAAAT
1 -AAAATAAAAATAAAAT
5246224 AAAGATAAAAATAAAAAT
1 AAA-ATAAAAAT-AAAAT
* * *
5246242 AAAAGAATATTAAACA-
1 AAAATAAAAATAAA-AT
* * *
5246258 AATATAACAATAATA-
1 AAAATAAAAATAAAAT
*
5246273 AAAATAATAATAATAAT
1 AAAATAAAAATAA-AAT
* *
5246290 AAATATATAAA-AAACT
1 AAA-ATAAAAATAAAAT
5246306 AAAATGAAAAA-AAAA
1 AAAAT-AAAAATAAAA
5246321 CTTGAAACTA
Statistics
Matches: 116, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
15 14 0.12
16 39 0.34
17 41 0.35
18 22 0.19
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:5246193 original size:6 final size:6
Alignment explanation
Indices: 5246156--5246245 Score: 91
Period size: 6 Copynumber: 15.5 Consensus size: 6
5246146 TTATTTAAAG
* *
5246156 AAAAT- AAAATA ATAAA-A TAAAATA AAAGTA AAAATA AAAA-A AAAGT-
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
* *
5246202 AAAATA AAAATA GAAAT- AAAATA AAGATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
5246246 GAATATTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
5 17 0.24
6 48 0.69
7 5 0.07
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:5246255 original size:23 final size:23
Alignment explanation
Indices: 5246152--5246248 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 23
5246142 GATTTTATTT
5246152 AAAGAAA-AT-AAAATAATAAAATA
1 AAAGAAAGATAAAAAT-A-AAAATA
*
5246175 AAATAAA-AGTAAAAATAAAAA-A
1 AAAGAAAGA-TAAAAATAAAAATA
*
5246197 AAAGTAAA-ATAAAAATAGAAATA
1 AAAG-AAAGATAAAAATAAAAATA
*
5246220 AAATAAAGATAAAAATAAAAATA
1 AAAGAAAGATAAAAATAAAAATA
5246243 AAAGAA
1 AAAGAA
5246249 TATTAAACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
22 18 0.29
23 38 0.60
24 2 0.03
25 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAGAAAGATAAAAATAAAAATA
Found at i:5246273 original size:9 final size:9
Alignment explanation
Indices: 5246161--5246302 Score: 60
Period size: 9 Copynumber: 16.4 Consensus size: 9
5246151 TAAAGAAAAT
5246161 AAAATAAT-
1 AAAATAATA
5246169 AAAATAA-A
1 AAAATAATA
*
5246177 ATAAA-AGTA
1 A-AAATAATA
5246186 AAAATAA-A
1 AAAATAATA
5246194 AAAA-AAGT-
1 AAAATAA-TA
5246202 AAAATAA-A
1 AAAATAATA
5246210 AATAGA-AAT-
1 AA-A-ATAATA
5246219 AAAATAA-A
1 AAAATAATA
5246227 GATAAA-AATA
1 -A-AAATAATA
5246237 AAAATAA-A
1 AAAATAATA
* *
5246245 AGAATATTA
1 AAAATAATA
5246254 AACAA-ATATA
1 AA-AATA-ATA
*
5246264 ACAATAATA
1 AAAATAATA
5246273 AAAATAATA
1 AAAATAATA
*
5246282 ATAATAATA
1 AAAATAATA
*
5246291 AATAT-ATA
1 AAAATAATA
5246299 AAAA
1 AAAA
5246303 ACTAAAATGA
Statistics
Matches: 101, Mismatches: 12, Indels: 42
0.65 0.08 0.27
Matches are distributed among these distances:
7 3 0.03
8 41 0.41
9 46 0.46
10 11 0.11
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:5247184 original size:25 final size:25
Alignment explanation
Indices: 5247151--5247221 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
5247141 CCAGTCGAAA
5247151 AAATCAAAAAAATCAAATAAAAAATC
1 AAAT-AAAAAAATCAAATAAAAAATC
* * * *
5247177 AAATAAAAAATAT-TAATAGATAATT
1 AAATAAAAAA-ATCAAATAAAAAATC
* *
5247202 AAAGAAAAAAATCAGATAAA
1 AAATAAAAAAATCAAATAAA
5247222 TCAAAATATT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
24 2 0.06
25 27 0.77
26 6 0.17
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATAAAAAAATCAAATAAAAAATC
Found at i:5247194 original size:13 final size:12
Alignment explanation
Indices: 5247157--5247187 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5247147 GAAAAAATCA
5247157 AAAAAATCAAAT
1 AAAAAATCAAAT
5247169 AAAAAATCAAAT
1 AAAAAATCAAAT
5247181 AAAAAAT
1 AAAAAAT
5247188 ATTAATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATCAAAT
Found at i:5247255 original size:36 final size:39
Alignment explanation
Indices: 5247215--5247287 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
5247205 GAAAAAAATC
*
5247215 AGATAAATCA-AA-ATATTAACAGATAAA-AATAATACT
1 AGATAAATCATAACATATAAACAGATAAATAATAATACT
* *
5247251 AGATAAATTATAACATATAAATAGATAAATAATAATA
1 AGATAAATCATAACATATAAACAGATAAATAATAATA
5247288 AATATATAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.29
37 2 0.06
38 13 0.42
39 7 0.23
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (39 bp):
AGATAAATCATAACATATAAACAGATAAATAATAATACT
Found at i:5247413 original size:21 final size:20
Alignment explanation
Indices: 5247399--5247446 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
5247389 ATATAAAGGA
5247399 AAAAATATAAAATATAAAAT
1 AAAAATATAAAATATAAAAT
5247419 AAAAATA-AAAATAATAAAAT
1 AAAAATATAAAAT-ATAAAAT
5247439 ATAAAATA
1 A-AAAATA
5247447 CAAGATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.19
20 15 0.58
21 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATATAAAATATAAAAT
Found at i:5247434 original size:22 final size:24
Alignment explanation
Indices: 5247409--5247461 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 24
5247399 AAAAATATAA
5247409 AATATAAAATA-AAAATA-AAAAT
1 AATATAAAATATAAAATACAAAAT
*
5247431 -A-ATAAAATATAAAATACAAGAT
1 AATATAAAATATAAAATACAAAAT
*
5247453 AATAAAAAA
1 AATATAAAA
5247462 ACAAAGTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.32
21 7 0.28
22 4 0.16
23 1 0.04
24 5 0.20
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (24 bp):
AATATAAAATATAAAATACAAAAT
Found at i:5247442 original size:7 final size:7
Alignment explanation
Indices: 5247400--5247446 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
5247390 TATAAAGGAA
5247400 AAAATAT
1 AAAATAT
5247407 AAAATAT
1 AAAATAT
5247414 AAAATA-
1 AAAATAT
5247420 AAAATA-
1 AAAATAT
5247426 AAAATAAT
1 AAAAT-AT
5247434 AAAATAT
1 AAAATAT
5247441 AAAATA
1 AAAATA
5247447 CAAGATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.29
7 22 0.58
8 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATAT
Found at i:5247772 original size:41 final size:41
Alignment explanation
Indices: 5247726--5248105 Score: 458
Period size: 41 Copynumber: 9.1 Consensus size: 41
5247716 AATGAATAAA
* * * *
5247726 GCTCCTCTAAACAAAGGCTCAATGAATTTAGAAAA-TAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTT-GAAAAGTAAATG
* * * *
5247767 GCTCCTCTAATTAGAGGCTTAACGACTTTGAAAAAT-AACG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATG
*
5247807 GCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATG
5247848 GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTG-AAAAGTAAATG
* * * *
5247891 ACTCATCTAATCAGACGCTCAACGACCTTGAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATG
*
5247932 GCTCCTCTAATCAGAGGTTCAACGACTTTTGAAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTG-AAAAGTAAATG
* * * *
5247975 GCTCATCTAATCAGAGGCTCAACAACTTTGAAGAGTAAATAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAAT--G
* *
5248018 GCTCCTCTAATCAGACGCTCAACAACTTTTGAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAGTAAATG
* * *
5248060 GCTCATCTAATAAGAGGCTCAACGACTTTGAAAAATAAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGT-AAATG
5248102 GCTC
1 GCTC
5248106 ATTGACAATC
Statistics
Matches: 293, Mismatches: 36, Indels: 19
0.84 0.10 0.05
Matches are distributed among these distances:
40 40 0.14
41 103 0.35
42 45 0.15
43 92 0.31
44 13 0.04
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATG
Found at i:5247930 original size:84 final size:84
Alignment explanation
Indices: 5247726--5248105 Score: 509
Period size: 84 Copynumber: 4.5 Consensus size: 84
5247716 AATGAATAAA
* * * * * * *
5247726 GCTCCTCTAAACAAAGGCTCAATGAATTTAGAAAA-TAAATGGCTCCTCTAATTAGAGGCTTAAC
1 GCTCATCTAATCAGAGGCTCAACGACTTT-GAAAAGTAAATGGCTCCTCTAATCAGAGGCTCAAC
*
5247790 GAC-TTTGAAAAA-T-AACG
65 GACTTTTGAAAAAGTAAATG
*
5247807 GCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATGGCTCCTCTAATCAGAGGCTCAACG
1 GCTCATCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATGGCTCCTCTAATCAGAGGCTCAACG
5247872 ACTTTTGAAAAAGTAAATG
66 ACTTTTGAAAAAGTAAATG
* * * *
5247891 ACTCATCTAATCAGACGCTCAACGACCTTGAAAAGTAAATGGCTCCTCTAATCAGAGGTTCAACG
1 GCTCATCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATGGCTCCTCTAATCAGAGGCTCAACG
5247956 ACTTTTGAAAAAGTAAATG
66 ACTTTTGAAAAAGTAAATG
* * * *
5247975 GCTCATCTAATCAGAGGCTCAACAACTTTGAAGAGTAAATAAAGCTCCTCTAATCAGACGCTCAA
1 GCTCATCTAATCAGAGGCTCAACGACTTTGAAAAGTAAAT--GGCTCCTCTAATCAGAGGCTCAA
*
5248040 CAACTTTTG-AAAAGTAAATG
64 CGACTTTTGAAAAAGTAAATG
* *
5248060 GCTCATCTAATAAGAGGCTCAACGACTTTGAAAAATAAAATGGCTC
1 GCTCATCTAATCAGAGGCTCAACGACTTTGAAAAGT-AAATGGCTC
5248106 ATTGACAATC
Statistics
Matches: 265, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
80 5 0.02
81 54 0.20
82 9 0.03
83 1 0.00
84 121 0.46
85 43 0.16
86 32 0.12
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (84 bp):
GCTCATCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATGGCTCCTCTAATCAGAGGCTCAACG
ACTTTTGAAAAAGTAAATG
Found at i:5248135 original size:127 final size:127
Alignment explanation
Indices: 5247758--5248107 Score: 390
Period size: 127 Copynumber: 2.8 Consensus size: 127
5247748 TGAATTTAGA
* * * * * * * * *
5247758 AAATAAATGGCTCCTCTAATTAGAGGCTTAACGACTTTGAAAAAT-AACGGCTCTTCTAATCAGA
1 AAATAAA--GCTCCTCTAATCAGACGCTCAACAACCTTGAAAAGTAAATGGCTCATCTAATAAGA
* * * * *
5247822 GGCTCAACGAC-TTTG-AAAAGTAAATGGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAAAG
64 GGCTCAACGACTTTTGAAAAAGTAAATGGCTCATCTAATCAGAGGCTCAACAAC-GTCG-AAGAG
5247885 T
127 T
* * * * *
5247886 AAAT-GA-CTCATCTAATCAGACGCTCAACGACCTTGAAAAGTAAATGGCTCCTCTAATCAGAGG
1 AAATAAAGCTCCTCTAATCAGACGCTCAACAACCTTGAAAAGTAAATGGCTCATCTAATAAGAGG
* * *
5247949 TTCAACGACTTTTGAAAAAGTAAATGGCTCATCTAATCAGAGGCTCAACAACTTTGAAGAGT
66 CTCAACGACTTTTGAAAAAGTAAATGGCTCATCTAATCAGAGGCTCAACAACGTCGAAGAGT
*
5248011 AAATAAAGCTCCTCTAATCAGACGCTCAACAACTTTTGAAAAGTAAATGGCTCATCTAATAAGAG
1 AAATAAAGCTCCTCTAATCAGACGCTCAACAAC-CTTGAAAAGTAAATGGCTCATCTAATAAGAG
5248076 GCTCAACGAC-TTTGAAAAA-TAAAATGGCTCAT
65 GCTCAACGACTTTTGAAAAAGT-AAATGGCTCAT
5248108 TGACAATCAT
Statistics
Matches: 195, Mismatches: 20, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
124 29 0.15
125 36 0.18
126 10 0.05
127 79 0.41
128 41 0.21
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (127 bp):
AAATAAAGCTCCTCTAATCAGACGCTCAACAACCTTGAAAAGTAAATGGCTCATCTAATAAGAGG
CTCAACGACTTTTGAAAAAGTAAATGGCTCATCTAATCAGAGGCTCAACAACGTCGAAGAGT
Found at i:5249075 original size:24 final size:24
Alignment explanation
Indices: 5249048--5249098 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5249038 AGTCATCCTA
*
5249048 TTTCATTCACTTTTTTTTTCATTT
1 TTTCATTCACATTTTTTTTCATTT
* **
5249072 TTTCTTTTTCATTTTTTTTCATTT
1 TTTCATTCACATTTTTTTTCATTT
5249096 TTT
1 TTT
5249099 TCATATTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTCATTCACATTTTTTTTCATTT
Found at i:5249081 original size:14 final size:13
Alignment explanation
Indices: 5249058--5249090 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
5249048 TTTCATTCAC
5249058 TTTTTTTTTCATT
1 TTTTTTTTTCATT
5249071 TTTTCTTTTTCATT
1 TTTT-TTTTTCATT
5249085 TTTTTT
1 TTTTTT
5249091 CATTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTCATT
Found at i:5259665 original size:59 final size:58
Alignment explanation
Indices: 5259490--5259703 Score: 324
Period size: 59 Copynumber: 3.7 Consensus size: 58
5259480 TTGTGTAGGA
* *** * * *
5259490 AAAATTGATACTTTCAACTTTTCCTCAAGAATCCATTTTT-GAAAACTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCT-AAAAATATTTTTTTGGAAAGCTTATTTTCAAGG
5259548 AAAATTGATACTTTCAACTTTTCCTAAAAATA-TTTTTTGGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTGGAAAGCTTATTTTCAAGG
5259605 AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTGGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAAC-TTTTCCTAAAAATATTTTTTTGGAAAGCTTATTTTCAAGG
5259664 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTT-CCTAAAAATATTTTTTT
5259704 TGGATTTTAT
Statistics
Matches: 146, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
56 5 0.03
57 38 0.26
58 43 0.29
59 60 0.41
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTGGAAAGCTTATTTTCAAGG
Found at i:5259758 original size:27 final size:27
Alignment explanation
Indices: 5259730--5259809 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
5259720 AAAATAAAAT
5259730 AATAAAATAAAATAAAAGTAAAAATATA
1 AATAAAATAAAATAAAA-TAAAAATATA
* *
5259758 AATAAAGA-AAAGTAAAATATAAATATA
1 AATAAA-ATAAAATAAAATAAAAATATA
5259785 AATAAAATAAAGATAAAAATAAAAA
1 AATAAAATAAA-AT-AAAATAAAAA
5259810 AATATTAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 1 0.02
27 18 0.41
28 15 0.34
29 10 0.23
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (27 bp):
AATAAAATAAAATAAAATAAAAATATA
Found at i:5259800 original size:6 final size:5
Alignment explanation
Indices: 5259720--5259883 Score: 79
Period size: 5 Copynumber: 30.8 Consensus size: 5
5259710 TTATTTAAAG
5259720 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT AAAAAT ATAAAT AAAGA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT A-AAAT AAA-AT
*
5259766 AAAGT AAAAT ATAAAT ATAAAT AAAAT AAAGAT AAAAAT AAAA- AAATAT
1 AAAAT AAAAT A-AAAT A-AAAT AAAAT AAA-AT -AAAAT AAAAT AAA-AT
* * ** **
5259815 TAAA- CAAAT CTAAT CTAAT AATAAT AATAAT AAAAT AAATAT ATATATAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAAT AAA-AT A-A-A-AT
5259865 AAAAT AAAAT GAAAA- AAAA
1 AAAAT AAAAT -AAAAT AAAA
5259884 ACCTAAAACA
Statistics
Matches: 134, Mismatches: 7, Indels: 37
0.75 0.04 0.21
Matches are distributed among these distances:
3 3 0.02
4 10 0.07
5 63 0.47
6 44 0.33
7 9 0.07
8 5 0.04
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:5259818 original size:17 final size:17
Alignment explanation
Indices: 5259720--5259808 Score: 80
Period size: 17 Copynumber: 5.2 Consensus size: 17
5259710 TTATTTAAAG
5259720 AAAATAAA-ATAATAAAAT
1 AAAATAAAGAT-A-AAAAT
5259738 AAAATAAA-AGTAAAAAT
1 AAAATAAAGA-TAAAAAT
*
5259755 ATAAATAAAG--AAAAGT
1 A-AAATAAAGATAAAAAT
*
5259771 AAAATATAA-ATATAAAT
1 AAAATA-AAGATAAAAAT
5259788 AAAATAAAGATAAAAAT
1 AAAATAAAGATAAAAAT
5259805 AAAA
1 AAAA
5259809 AAATATTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.08
16 10 0.17
17 27 0.45
18 17 0.28
19 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATAAAGATAAAAAT
Found at i:5260734 original size:25 final size:25
Alignment explanation
Indices: 5260701--5260771 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
5260691 CGAACCGAAA
5260701 AAATCAAAAAAATCAAATAAAAAATC
1 AAAT-AAAAAAATCAAATAAAAAATC
* * * *
5260727 AAATAAAAAATAT-TAATAGATAATT
1 AAATAAAAAA-ATCAAATAAAAAATC
* *
5260752 AAAGAAAAAAATCAGATAAA
1 AAATAAAAAAATCAAATAAA
5260772 TCAAAATATT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
24 2 0.06
25 27 0.77
26 6 0.17
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATAAAAAAATCAAATAAAAAATC
Found at i:5260744 original size:13 final size:12
Alignment explanation
Indices: 5260707--5260737 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5260697 GAAAAAATCA
5260707 AAAAAATCAAAT
1 AAAAAATCAAAT
5260719 AAAAAATCAAAT
1 AAAAAATCAAAT
5260731 AAAAAAT
1 AAAAAAT
5260738 ATTAATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATCAAAT
Found at i:5260815 original size:17 final size:16
Alignment explanation
Indices: 5260774--5260807 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5260764 CAGATAAATC
* *
5260774 AAAATATTAATAGATA
1 AAAATAATACTAGATA
5260790 AAAATAATACTAGATA
1 AAAATAATACTAGATA
5260806 AA
1 AA
5260808 TTATAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAATAATACTAGATA
Found at i:5260895 original size:24 final size:25
Alignment explanation
Indices: 5260851--5260944 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 25
5260841 ATGTAACTAG
*
5260851 ATAAATAAAATATATACATATTAAC
1 ATAAATAAAATAAATACATATTAAC
* *
5260876 ATAAA-AAAATAAATATATATTAAT
1 ATAAATAAAATAAATACATATTAAC
5260900 A-AATAGTAATAATAAATA-A-A-TAA-
1 ATAA-A-TAA-AATAAATACATATTAAC
5260923 ATAAATAAATAATAAATACATA
1 ATAAAT-AA-AATAAATACATA
5260945 AGATATAAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
22 1 0.02
23 15 0.26
24 24 0.41
25 7 0.12
26 3 0.05
27 8 0.14
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (25 bp):
ATAAATAAAATAAATACATATTAAC
Found at i:5260904 original size:4 final size:4
Alignment explanation
Indices: 5260876--5260945 Score: 63
Period size: 4 Copynumber: 17.0 Consensus size: 4
5260866 ACATATTAAC
* *
5260876 ATAA AAAA ATAA ATATA TATTA ATAA ATAGTA AT-A ATAA ATAA ATAA
1 ATAA ATAA ATAA ATA-A -ATAA ATAA ATA--A ATAA ATAA ATAA ATAA
*
5260923 ATAA ATAA AT-A ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA
5260946 GATATAAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
3 6 0.11
4 41 0.76
5 2 0.04
6 5 0.09
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:5260952 original size:15 final size:15
Alignment explanation
Indices: 5260876--5261008 Score: 74
Period size: 14 Copynumber: 9.3 Consensus size: 15
5260866 ACATATTAAC
*
5260876 ATAAAAAAATAAAT-
1 ATAAATAAATAAATA
* *
5260890 ATATATTAATAAATA
1 ATAAATAAATAAATA
*
5260905 GT-AAT-AATAAATAA
1 ATAAATAAATAAAT-A
5260919 ATAAATAAATAAATA
1 ATAAATAAATAAATA
*
5260934 ATAAATACATAAGAT-
1 ATAAATAAATAA-ATA
*
5260949 ATAAAGGAAA-AAAT-
1 ATAAA-TAAATAAATA
*
5260963 ATAAA-ATATAAAATA
1 ATAAATAAAT-AAATA
5260978 A-AAAT-AA-AAATA
1 ATAAATAAATAAATA
5260990 A-AAAT-AATAAAATA
1 ATAAATAAAT-AAATA
5261004 ATAAA
1 ATAAA
5261009 ATATAAAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
12 14 0.15
13 7 0.07
14 36 0.38
15 27 0.28
16 11 0.12
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAATAAATAAATA
Found at i:5260978 original size:26 final size:26
Alignment explanation
Indices: 5260957--5261031 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 26
5260947 ATATAAAGGA
5260957 AAAAATATAAAAT-ATAAAATAAAAAT
1 AAAAATA-AAAATAATAAAATAAAAAT
5260983 AAAAATAAAAATAATAAAATAATAAAAT
1 AAAAATAAAAATAATAAAAT-A-AAAAT
*
5261011 ATAAAATACAAGATAATAAAA
1 A-AAAATA-AAAATAATAAAA
5261032 AAATAAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
25 5 0.12
26 14 0.33
27 1 0.02
28 6 0.14
29 6 0.14
30 11 0.26
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (26 bp):
AAAAATAAAAATAATAAAATAAAAAT
Found at i:5260978 original size:41 final size:41
Alignment explanation
Indices: 5260958--5261041 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 41
5260948 TATAAAGGAA
*
5260958 AAAAT-ATAAAATATAAAATAAAAATAAAAATAAAAATAAT
1 AAAATAATAAAATATAAAATAAAAATAAAAATAAAAAGAAT
*
5260998 AAAATAATAAAATATAAAATACAAGAT---AATAAAAA-AAT
1 AAAATAATAAAATATAAAATA-AAAATAAAAATAAAAAGAAT
5261036 AAAATA
1 AAAATA
5261042 GGTCTACCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
38 9 0.22
39 8 0.20
40 5 0.12
41 15 0.37
42 4 0.10
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (41 bp):
AAAATAATAAAATATAAAATAAAAATAAAAATAAAAAGAAT
Found at i:5261003 original size:8 final size:8
Alignment explanation
Indices: 5260907--5261041 Score: 83
Period size: 8 Copynumber: 17.5 Consensus size: 8
5260897 AATAAATAGT
5260907 AATAAT-A
1 AATAATAA
5260914 AATAA-ATA
1 AATAATA-A
5260922 AATAA-ATA
1 AATAATA-A
5260930 AATAAT-A
1 AATAATAA
5260937 AATACATAA
1 AATA-ATAA
*
5260946 GAT-ATAA
1 AATAATAA
**
5260953 AGGAA-AA
1 AATAATAA
5260960 AAT-ATAA
1 AATAATAA
5260967 AAT-ATAA
1 AATAATAA
*
5260974 AATAAAAA
1 AATAATAA
*
5260982 TAAAAATAAA
1 -AATAAT-AA
5260992 AATAATAA
1 AATAATAA
5261000 AATAATAA
1 AATAATAA
5261008 AAT-ATAA
1 AATAATAA
*
5261015 AAT-ACAA
1 AATAATAA
*
5261022 GATAATAA
1 AATAATAA
*
5261030 AAAAATAA
1 AATAATAA
5261038 AATA
1 AATA
5261042 GGTCTACCCA
Statistics
Matches: 101, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
6 1 0.01
7 41 0.41
8 45 0.45
9 12 0.12
10 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.22
Consensus pattern (8 bp):
AATAATAA
Found at i:5261016 original size:7 final size:7
Alignment explanation
Indices: 5260958--5261041 Score: 84
Period size: 7 Copynumber: 11.9 Consensus size: 7
5260948 TATAAAGGAA
5260958 AAAATAT
1 AAAATAT
5260965 AAAATAT
1 AAAATAT
5260972 AAAATA-
1 AAAATAT
5260978 AAAATA-
1 AAAATAT
5260984 AAAATA-
1 AAAATAT
5260990 AAAATAAT
1 AAAAT-AT
5260998 AAAATAAT
1 AAAAT-AT
5261006 AAAATAT
1 AAAATAT
*
5261013 AAAATAC
1 AAAATAT
*
5261020 AAGATAAT
1 AAAAT-AT
*
5261028 AAAAAAAT
1 -AAAATAT
5261036 AAAATA
1 AAAATA
5261042 GGTCTACCCA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
6 17 0.25
7 31 0.46
8 16 0.24
9 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (7 bp):
AAAATAT
Found at i:5261027 original size:30 final size:28
Alignment explanation
Indices: 5260907--5261041 Score: 104
Period size: 30 Copynumber: 4.7 Consensus size: 28
5260897 AATAAATAGT
5260907 AATAAT-AAATAA-ATAAATAAATAAATAATA
1 AATAATAAAATAATA-AAAT-AA-AAATAA-A
*
5260937 AATACATAAGAT-ATAAAGGA-AAAAATATAA
1 AATA-ATAAAATAATAAA--ATAAAAATA-AA
5260967 AAT-ATAAAAT-A-AAAATAAAAATAAA
1 AATAATAAAATAATAAAATAAAAATAAA
5260992 AATAATAAAATAATAAAATATAAAATACAA
1 AATAATAAAATAATAAAATA-AAAATA-AA
* *
5261022 GATAATAAAAAAATAAAATA
1 AATAATAAAATAATAAAATA
5261042 GGTCTACCCA
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
25 6 0.07
26 14 0.16
27 4 0.04
28 13 0.15
29 6 0.07
30 33 0.37
31 8 0.09
32 4 0.04
33 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.22
Consensus pattern (28 bp):
AATAATAAAATAATAAAATAAAAATAAA
Found at i:5261076 original size:20 final size:20
Alignment explanation
Indices: 5261051--5261089 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5261041 AGGTCTACCC
*
5261051 ATTTGGACTAGGCCCAAATG
1 ATTTGGACTAGGACCAAATG
*
5261071 ATTTGGACTTGGACCAAAT
1 ATTTGGACTAGGACCAAAT
5261090 TGGGTGTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (20 bp):
ATTTGGACTAGGACCAAATG
Done.