Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 15 of 120
Found at i:4156431 original size:21 final size:22
Alignment explanation
Indices: 4156369--4156431 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
4156359 TATTTTTTTG
* *
4156369 TTGTTATTTTTGTTGCTGTTTTGA
1 TTGTTATTTTT-ATGC-GTTTGGA
* *
4156393 TTGTTATTTTGAT-TGTTTGGA
1 TTGTTATTTTTATGCGTTTGGA
4156414 -TGTTATTTTTATGCGTTT
1 TTGTTATTTTTATGCGTTT
4156432 TTACTATTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.34
21 10 0.31
23 1 0.03
24 10 0.31
ACGTcount: A:0.11, C:0.03, G:0.21, T:0.65
Consensus pattern (22 bp):
TTGTTATTTTTATGCGTTTGGA
Found at i:4156616 original size:38 final size:38
Alignment explanation
Indices: 4156533--4156614 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
4156523 ATATAAAGAA
* *
4156533 TTTTTAATGTATTTTAAATTTATTTATTTTTTAATATT
1 TTTTTAATGTATTTTAAATTTATTTATATATTAATATT
*
4156571 TATTTTAATGT-TTTTAAGTTTATTTGATATATTACATATT
1 T-TTTTAATGTATTTTAAATTTATTT-ATATATTA-ATATT
4156611 TTTT
1 TTTT
4156615 AAATTTGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 14 0.37
39 18 0.47
40 6 0.16
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (38 bp):
TTTTTAATGTATTTTAAATTTATTTATATATTAATATT
Found at i:4157350 original size:24 final size:24
Alignment explanation
Indices: 4157315--4157371 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
4157305 TCTCCCCCTT
*
4157315 TTCTTCAC-TTTCA-CCATCTAATCC
1 TTCTTC-CTTTTCATCCA-CTAATAC
*
4157339 TTCTTCCTTTTCATCCACTACTAC
1 TTCTTCCTTTTCATCCACTAATAC
4157363 TTCTTCCTT
1 TTCTTCCTT
4157372 ATCTTCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.03
24 25 0.86
25 3 0.10
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (24 bp):
TTCTTCCTTTTCATCCACTAATAC
Found at i:4170602 original size:30 final size:32
Alignment explanation
Indices: 4170541--4170604 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 32
4170531 ATTTTTAAAT
*
4170541 TAAATAATTCAAGTTATTCGGATCAATTCGAA
1 TAAATAATTCAAGTTATTCGGATCAACTCGAA
* * *
4170573 TAAA-AATT-AAGTTTTTCGGTTTAACTCGAA
1 TAAATAATTCAAGTTATTCGGATCAACTCGAA
4170603 TA
1 TA
4170605 TGAATTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.71
31 4 0.14
32 4 0.14
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (32 bp):
TAAATAATTCAAGTTATTCGGATCAACTCGAA
Found at i:4175012 original size:26 final size:30
Alignment explanation
Indices: 4174960--4175030 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 30
4174950 TTTTTTAAAA
*
4174960 AATATTTATATTATATTATTTCAATTT-TT-
1 AATATTTTTA-TATATTATTTCAATTTATTG
*
4174989 AATATTTTTATATATT-TTT-TATTTATTG
1 AATATTTTTATATATTATTTCAATTTATTG
4175017 AA-ATTTTTTATATA
1 AATA-TTTTTATATA
4175031 ATCATCCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 4 0.11
27 6 0.16
28 18 0.49
29 9 0.24
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (30 bp):
AATATTTTTATATATTATTTCAATTTATTG
Found at i:4188835 original size:18 final size:17
Alignment explanation
Indices: 4188812--4188846 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4188802 AATTAGAATT
*
4188812 ATAAAAAATATTTAAAAA
1 ATAAAAAA-ATTCAAAAA
4188830 ATAAAAAAATTCAAAAA
1 ATAAAAAAATTCAAAAA
4188847 CAAAGGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAAAAAATTCAAAAA
Found at i:4189210 original size:29 final size:25
Alignment explanation
Indices: 4189144--4189197 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
4189134 CTCTTTGTAC
*
4189144 ATTTGAAATTTAGTCCCCTACTTTT
1 ATTTAAAATTTAGTCCCCTACTTTT
4189169 ATTACTAAGAATTTAGTCCCTCTACTTTT
1 ATT--TAA-AATTTAGTCCC-CTACTTTT
4189198 TAGATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
27 2 0.08
28 11 0.46
29 8 0.33
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (25 bp):
ATTTAAAATTTAGTCCCCTACTTTT
Found at i:4198527 original size:372 final size:372
Alignment explanation
Indices: 4197842--4198585 Score: 1290
Period size: 372 Copynumber: 2.0 Consensus size: 372
4197832 GAATTGAGGC
*
4197842 GTCAATTGTAGCATATTGGTTAGGCACTTAGGATGAATTATTTAAGTTGTGTTTTGGCATGTTTT
1 GTCAATTGTAGCATATTGGTTAGGCACTTAGGATGAATTATTTAAGTTGTGTTTTGGCATGTATT
* * *
4197907 TAGTGTATTTGAACATATTAAGGAATGGTATGTTGCATGGTTATAGTGTATTTGAGTGTTTGGAG
66 TAGTGTATTTGAACAGATTAAAGAATGATATGTTGCATGGTTATAGTGTATTTGAGTGTTTGGAG
* * *
4197972 TTGTAACTTGCCTTGTAGGGTATCTTTTTTGCACACATGATCTGACACACAACCGTGTGACACAC
131 TTGTAACTTACCTTGTAGGGTATCTTTTTTGCACACACGATCTGACACACAACCGTGTAACACAC
*
4198037 ATGGCCATGTGGCACGGTCATGTAGTCTTTATGTTTTGAGAGGTTATTGATGTACATGGCCTCAG
196 ATGGCCATGTGGCACGATCATGTAGTCTTTATGTTTTGAGAGGTTATTGATGTACATGGCCTCAG
* * *
4198102 TGATTTACACGGTTTGGATACACGACCGTGTTACTCTAGCTTACACGGCCTCAGCTTGTTACACG
261 TGATTTACACGGTTTGGATACACGACCGTGTGACTCCAGCTTACACGGCCTCAGCCTGTTACACG
* *
4198167 GTTCAAGACACAACTATGTGACTTTTGTTAGTAATTTGCATTTAGGT
326 GTTCAAGACACAACTATATGACTTTTGTTAGTAATTTACATTTAGGT
* *
4198214 GTCAATTGTGGCATATTGGTTAGGCATTTAGGATGAATTATTTAAGTTGTGTTTTGGCATGTATT
1 GTCAATTGTAGCATATTGGTTAGGCACTTAGGATGAATTATTTAAGTTGTGTTTTGGCATGTATT
* *
4198279 TAGTGTATTTGAACAGATTAAAGAATGATATGTTGCGTGGTTATAGTGTATTTGTGTGTTTGGAG
66 TAGTGTATTTGAACAGATTAAAGAATGATATGTTGCATGGTTATAGTGTATTTGAGTGTTTGGAG
4198344 TTGTAACTTACCTTGTAGGGTATCTTTTTTGCACACACGATCTGACACACAACCGTGTAACACAC
131 TTGTAACTTACCTTGTAGGGTATCTTTTTTGCACACACGATCTGACACACAACCGTGTAACACAC
* * * *
4198409 ATGGCCATGTGGCATGATCGTGTAGTCTTTATGTTTTGAGAGGTTATTGATGTATATGGCCTTAG
196 ATGGCCATGTGGCACGATCATGTAGTCTTTATGTTTTGAGAGGTTATTGATGTACATGGCCTCAG
4198474 TGATTTACACGGTTTGGATACACGACCGTGTGACTCCAGCTTACACGGCCTCAGCCTGTTACACG
261 TGATTTACACGGTTTGGATACACGACCGTGTGACTCCAGCTTACACGGCCTCAGCCTGTTACACG
*
4198539 GTTCAAGACACGACTATATGACTTTTGTTAGTAATTTACATTTAGGT
326 GTTCAAGACACAACTATATGACTTTTGTTAGTAATTTACATTTAGGT
4198586 CCACATGACT
Statistics
Matches: 350, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
372 350 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (372 bp):
GTCAATTGTAGCATATTGGTTAGGCACTTAGGATGAATTATTTAAGTTGTGTTTTGGCATGTATT
TAGTGTATTTGAACAGATTAAAGAATGATATGTTGCATGGTTATAGTGTATTTGAGTGTTTGGAG
TTGTAACTTACCTTGTAGGGTATCTTTTTTGCACACACGATCTGACACACAACCGTGTAACACAC
ATGGCCATGTGGCACGATCATGTAGTCTTTATGTTTTGAGAGGTTATTGATGTACATGGCCTCAG
TGATTTACACGGTTTGGATACACGACCGTGTGACTCCAGCTTACACGGCCTCAGCCTGTTACACG
GTTCAAGACACAACTATATGACTTTTGTTAGTAATTTACATTTAGGT
Found at i:4199763 original size:12 final size:12
Alignment explanation
Indices: 4199746--4199770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4199736 GCCAGCCAAA
4199746 TCATTTTAAAAT
1 TCATTTTAAAAT
4199758 TCATTTTAAAAT
1 TCATTTTAAAAT
4199770 T
1 T
4199771 AAATTTATTA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:4199800 original size:17 final size:16
Alignment explanation
Indices: 4199762--4199839 Score: 77
Period size: 17 Copynumber: 4.7 Consensus size: 16
4199752 TAAAATTCAT
*
4199762 TTTAAAATTAAATTTA
1 TTTAAATTTAAATTTA
4199778 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTT-A
*
4199794 TTTAAATTTAGAATTAA
1 TTTAAATTTA-AATTTA
* *
4199811 TGTAAAATTTAAAATTA
1 T-TTAAATTTAAATTTA
4199828 TTATAAATTTAA
1 TT-TAAATTTAA
4199840 TAGAGTGTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.25
16 2 0.04
17 24 0.47
18 12 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:4201525 original size:22 final size:23
Alignment explanation
Indices: 4201485--4201528 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4201475 GTCCTTCCTT
*
4201485 TTTTTAATTCTTTTAATTTAATC
1 TTTTTAATACTTTTAATTTAATC
*
4201508 TTTTTCATACTTTT-ATTTAAT
1 TTTTTAATACTTTTAATTTAAT
4201529 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAATACTTTTAATTTAATC
Found at i:4201836 original size:30 final size:30
Alignment explanation
Indices: 4201800--4202081 Score: 270
Period size: 30 Copynumber: 9.4 Consensus size: 30
4201790 CCCTAGAGGT
* * *
4201800 CCCTAAACTGTCCAAAAATTATATTTTGAC
1 CCCTAAACTTTCTAAAAATTACATTTTGAC
* * *
4201830 CCCTAAACTTT-TCCAAAATTATATTTT-AA
1 CCCTAAACTTTCT-AAAAATTACATTTTGAC
*
4201859 CCTTAAAACTTTCTAAAAATTACATTTTGA-
1 CCCT-AAACTTTCTAAAAATTACATTTTGAC
* *
4201889 CCCTAAAACTTTCTAAAAAGTACATTTTG-G
1 CCCT-AAACTTTCTAAAAATTACATTTTGAC
*
4201919 CCCTAAAACTTTTTAAAAATTACATTTTGAC
1 CCCT-AAACTTTCTAAAAATTACATTTTGAC
* ** *
4201950 CCCTAAACTTTCTAAGAATTATGTTTT-AG
1 CCCTAAACTTTCTAAAAATTACATTTTGAC
*
4201979 CCCTAAAACTTTCTAAAAATTACATTTTGAT
1 CCCT-AAACTTTCTAAAAATTACATTTTGAC
*
4202010 CCCTAAACTTTCTAAAAGTTACATTTTTGAC
1 CCCTAAACTTTCTAAAAATTACA-TTTTGAC
* * * *
4202041 CCCCAAACTTTTTCCAAAATTAGATTTT-AC
1 CCCTAAACTTTCT-AAAAATTACATTTTGAC
*
4202071 CTCTAAACTTT
1 CCCTAAACTTT
4202082 TCAAAATCCC
Statistics
Matches: 212, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.04
30 164 0.77
31 32 0.15
32 7 0.03
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTCTAAAAATTACATTTTGAC
Found at i:4209294 original size:11 final size:11
Alignment explanation
Indices: 4209280--4209307 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4209270 TATCCAAATA
4209280 ATAATAACAAT
1 ATAATAACAAT
4209291 ATAATAACAAT
1 ATAATAACAAT
4209302 ATAATA
1 ATAATA
4209308 GCGAAATAAT
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:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAACAAT
Found at i:4212012 original size:18 final size:18
Alignment explanation
Indices: 4211989--4212026 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4211979 AAAAATTGAC
4211989 TTCTTA-AATTGTGAAATT
1 TTCTTATAATT-TGAAATT
4212007 TTCTTATTAATTTGAAATT
1 TTCTTA-TAATTTGAAATT
4212026 T
1 T
4212027 ATAAAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (18 bp):
TTCTTATAATTTGAAATT
Found at i:4212546 original size:18 final size:18
Alignment explanation
Indices: 4212507--4212544 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4212497 TTGATTGATA
4212507 TTTAAGTTTTTTTTCAAT
1 TTTAAGTTTTTTTTCAAT
*
4212525 TTTATGTTTTTTTT-AAT
1 TTTAAGTTTTTTTTCAAT
4212542 TTT
1 TTT
4212545 TAATGGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTAAGTTTTTTTTCAAT
Found at i:4213795 original size:18 final size:18
Alignment explanation
Indices: 4213759--4213796 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4213749 TAAATTTTCG
*
4213759 AATTCGAATAACTCAAAT
1 AATTCGAATAACACAAAT
4213777 AATTCGAATAA-ACAGAAT
1 AATTCGAATAACACA-AAT
4213795 AA
1 AA
4213797 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCGAATAACACAAAT
Found at i:4214134 original size:5 final size:5
Alignment explanation
Indices: 4214124--4214148 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4214114 GAACAAATAT
4214124 ATTCG ATTCG ATTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG
4214149 GTTCAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:4216310 original size:17 final size:18
Alignment explanation
Indices: 4216276--4216316 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4216266 AATTTCAATA
4216276 AATAC-AAAATAAATTGT
1 AATACAAAAATAAATTGT
*
4216293 AATACAAAAATTAA-TGT
1 AATACAAAAATAAATTGT
*
4216310 AAAACAA
1 AATACAA
4216317 CTTTAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (18 bp):
AATACAAAAATAAATTGT
Found at i:4217241 original size:58 final size:57
Alignment explanation
Indices: 4217153--4217262 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 57
4217143 TTGGCCATGC
* * * **
4217153 AATGGCTGACACCACTTTTTTGTCAGAAAAAAATACAATTTTTTTGTGTCGGCTATCA
1 AATGGCTGACACCACCTTTTTCTCAAAAAAAAATAC-ATTTTTGGGTGTCGGCTATCA
*
4217211 AATGGCTGACACC-CCTTTTTCTCGAAAAAAAATTACATTTTTGGGTGTCGGC
1 AATGGCTGACACCACCTTTTTCTC-AAAAAAAAATACATTTTTGGGTGTCGGC
4217263 CATGTCGAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
57 22 0.49
58 23 0.51
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (57 bp):
AATGGCTGACACCACCTTTTTCTCAAAAAAAAATACATTTTTGGGTGTCGGCTATCA
Found at i:4217259 original size:57 final size:58
Alignment explanation
Indices: 4217153--4217262 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 58
4217143 TTGGCCATGC
* * **
4217153 AATGGCTGACACCACTTTTTTGTCAGAAAAAAATACAATTTTTTTGTGTCGGCTATCA
1 AATGGCTGACACCACCTTTTTCTCAGAAAAAAATACAATTTTTGGGTGTCGGCTATCA
4217211 AATGGCTGACACC-CCTTTTTCTC-GAAAAAAAATTAC-ATTTTTGGGTGTCGGC
1 AATGGCTGACACCACCTTTTTCTCAG-AAAAAAA-TACAATTTTTGGGTGTCGGC
4217263 CATGTCGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 1 0.02
57 29 0.63
58 16 0.35
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (58 bp):
AATGGCTGACACCACCTTTTTCTCAGAAAAAAATACAATTTTTGGGTGTCGGCTATCA
Found at i:4217374 original size:34 final size:34
Alignment explanation
Indices: 4217331--4217395 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
4217321 CTTTTTTCGA
4217331 AAAAAAATTTCAAAATTTTTGGGTGTTGGCCTCG
1 AAAAAAATTTCAAAATTTTTGGGTGTTGGCCTCG
* *
4217365 AAAAAAATTTTAAAATTTTTTGGTGTTGGCC
1 AAAAAAATTTCAAAATTTTTGGGTGTTGGCC
4217396 ATCAAATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (34 bp):
AAAAAAATTTCAAAATTTTTGGGTGTTGGCCTCG
Found at i:4217399 original size:94 final size:96
Alignment explanation
Indices: 4217177--4217454 Score: 311
Period size: 95 Copynumber: 2.9 Consensus size: 96
4217167 CTTTTTTGTC
* * * *
4217177 AGAAAAAAA-T-ACAATTTTTTTGTGTCGGCTATCAAATGGCTGACA-CCCCTTTTTCTCGAAAA
1 AGAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCAGACACCCCCTTTTT-TCGAAAA
* *
4217239 AAAA-TT--ACATTTTTGGGTGTCGGCCATGTCG
65 AAAATTTCAAAATTTTTGGGTGTTGGCCA--TCG
*
4217270 AGAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGACAGACACCCCCTTTTTTCGAAAAA
1 AGAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCAGACACCCCCTTTTTTCGAAAAA
4217335 AAATTTCAAAATTTTTGGGTGTTGGCC-TCG
66 AAATTTCAAAATTTTTGGGTGTTGGCCATCG
* * * * ** * *
4217365 A-AAAAAATTTTAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCTTCTTTTCTCAAGAAA
1 AGAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCAGACACCCCCTTTTTTCGA-AAA
*
4217429 AAAATTTCAAAATTTTTTTGGTGTTG
65 AAAATTTCAAAA-TTTTTGGGTGTTG
4217455 ATCATGTAAT
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
93 9 0.06
94 51 0.32
95 60 0.38
96 23 0.14
98 17 0.11
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (96 bp):
AGAAAAAAATTCAAAATTTTTTTGTGTTGGCCATCAAATGGCAGACACCCCCTTTTTTCGAAAAA
AAATTTCAAAATTTTTGGGTGTTGGCCATCG
Found at i:4217668 original size:31 final size:31
Alignment explanation
Indices: 4217633--4217692 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4217623 TACAATCGAA
* *
4217633 TTTCGGGGTTGAGCTATATACTGTCATGTAT
1 TTTCGGAGTTGAACTATATACTGTCATGTAT
*
4217664 TTTCGGAGTTGAATTATATACTGTCATGT
1 TTTCGGAGTTGAACTATATACTGTCATGT
4217693 GAAGCGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (31 bp):
TTTCGGAGTTGAACTATATACTGTCATGTAT
Found at i:4221221 original size:11 final size:12
Alignment explanation
Indices: 4221181--4221229 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
4221171 TATTTGTGTA
4221181 AAAATTAATTTG
1 AAAATTAATTTG
4221193 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
4221207 TTGAAATTAATTTG
1 --AAAATTAATTTG
4221221 AAAATTAAT
1 AAAATTAAT
4221230 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:4221300 original size:25 final size:25
Alignment explanation
Indices: 4221271--4221325 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
4221261 CATAATTATA
*
4221271 TAAATTTGAATTTAAAATTCTACTT
1 TAAATTTGAAGTTAAAATTCTACTT
4221296 TAAATTTGAAGTTAAAATTCTACTT
1 TAAATTTGAAGTTAAAATTCTACTT
4221321 TAAAT
1 TAAAT
4221326 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (25 bp):
TAAATTTGAAGTTAAAATTCTACTT
Found at i:4221387 original size:48 final size:46
Alignment explanation
Indices: 4221335--4221486 Score: 103
Period size: 48 Copynumber: 3.5 Consensus size: 46
4221325 TAAAAAAATT
4221335 ATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATAC
1 ATTATT-TATTACAATTTATATCAAATA-TGTGTTAATTTGACAATAC
* ** *
4221383 ATTATTTA-T-CAAATT-T-TC--ATA--T-TTAAAGT-ACAA-ATT
1 ATTATTTATTACAATTTATATCAAATATGTGTTAATTTGACAATA-C
* * *
4221419 ATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 ATTATT-TATTACAATTTATATCAAAT-ATGTGTTAATTTGACAATAC
*
4221467 ATTATTTATTA-ATTTTATAT
1 ATTATTTATTACAATTTATAT
4221487 ATTTAAATAA
Statistics
Matches: 78, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
35 1 0.01
36 10 0.13
37 7 0.09
38 2 0.03
39 4 0.05
40 1 0.01
41 5 0.06
43 4 0.05
44 2 0.03
45 5 0.06
46 9 0.12
47 11 0.14
48 16 0.21
49 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (46 bp):
ATTATTTATTACAATTTATATCAAATATGTGTTAATTTGACAATAC
Found at i:4221480 original size:45 final size:45
Alignment explanation
Indices: 4221421--4221565 Score: 123
Period size: 45 Copynumber: 3.4 Consensus size: 45
4221411 TACAAATTAT
*
4221421 TATTATATTA-TAATTTTTATCAAATAATGTGTTGATTTGACAATA
1 TATTAT-TTATTAATTTTTATCAAATAATGTGTTGATTTGAAAATA
* ** *
4221466 CATTATTTATTAA-TTTTAT---AT-A--T-TT-AAATAAAAAT-
1 TATTATTTATTAATTTTTATCAAATAATGTGTTGATTTGAAAATA
*
4221501 TATTATTATACTATAATTTTTATCAAATAATGTGTTGATTTGATAATA
1 TATTATT-TA-T-TAATTTTTATCAAATAATGTGTTGATTTGAAAATA
4221549 TATTATTTATTAATTTT
1 TATTATTTATTAATTTT
4221566 ATATATTGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 28
0.67 0.09 0.25
Matches are distributed among these distances:
35 6 0.08
36 8 0.11
37 3 0.04
38 4 0.05
39 6 0.08
40 1 0.01
41 2 0.03
42 2 0.03
43 1 0.01
44 9 0.12
45 16 0.21
46 3 0.04
47 8 0.11
48 7 0.09
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (45 bp):
TATTATTTATTAATTTTTATCAAATAATGTGTTGATTTGAAAATA
Found at i:4221506 original size:35 final size:36
Alignment explanation
Indices: 4221467--4221596 Score: 93
Period size: 35 Copynumber: 3.3 Consensus size: 36
4221457 TTGACAATAC
4221467 ATTATT-TATTAATTTTATATATTTAAATAAAAATT
1 ATTATTATATTAATTTTATATATTTAAATAAAAATT
** * *
4221502 ATTATTATACTATAATTTTTATCAAATAATGTGTTGATTTGATAATAT
1 ATTATTATA-T-TAA-TTTTAT---AT-A--T-TT-AAATAAAAAT-T
*
4221550 ATTATT-TATTAATTTTATATATTGAAATAAAAATT
1 ATTATTATATTAATTTTATATATTTAAATAAAAATT
4221585 ATTATTATATTA
1 ATTATTATATTA
4221597 TAATTTTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 27
0.67 0.08 0.25
Matches are distributed among these distances:
35 13 0.18
36 13 0.18
37 2 0.03
38 4 0.06
39 6 0.08
40 1 0.01
41 2 0.03
42 2 0.03
43 1 0.01
44 6 0.08
45 4 0.06
46 3 0.04
47 8 0.11
48 7 0.10
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (36 bp):
ATTATTATATTAATTTTATATATTTAAATAAAAATT
Found at i:4221530 original size:83 final size:83
Alignment explanation
Indices: 4221319--4221608 Score: 438
Period size: 83 Copynumber: 3.5 Consensus size: 83
4221309 AAAATTCTAC
* * * *
4221319 TTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACA
1 TTTAAAT--AAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACA
* *
4221384 TTATTTATCAAATTTT-CATA
64 TTATTTAT-TAATTTTATATA
*
4221404 TTTAAAGTACAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACAT
1 TTTAAA-TAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACAT
4221469 TATTTATTAATTTTATATA
65 TATTTATTAATTTTATATA
* * *
4221488 TTTAAATAAAAATTATTATTATACTATAATTTTTATCAAATAATGTGTTGATTTGATAATATATT
1 TTTAAATAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACATT
4221553 ATTTATTAATTTTATATA
66 ATTTATTAATTTTATATA
*
4221571 TTGAAATAAAAATTATTATTATATTATAATTTTTATCA
1 TTTAAATAAAAATTATTATTATATTATAATTTTTATCA
4221609 TATTTTAAAT
Statistics
Matches: 190, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
83 115 0.61
84 68 0.36
85 6 0.03
86 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (83 bp):
TTTAAATAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACATT
ATTTATTAATTTTATATA
Found at i:4224046 original size:30 final size:30
Alignment explanation
Indices: 4223959--4224056 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 30
4223949 TCCGTTTACT
* * *
4223959 TTTTAAATTTAATTTGTAATTTCGTT-TTTA
1 TTTTAATTTTAATTTCTAATTTC-TTGTATA
* *
4223989 TTTTAAATTTAATTTCTAATTTTTTGTATA
1 TTTTAATTTTAATTTCTAATTTCTTGTATA
**
4224019 TTTTAATTTTTCTTTCTAATTTCTTGTATA
1 TTTTAATTTTAATTTCTAATTTCTTGTATA
*
4224049 TTCTAATT
1 TTTTAATT
4224057 ATTATTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 57 0.97
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTAATTTTAATTTCTAATTTCTTGTATA
Found at i:4224054 original size:17 final size:16
Alignment explanation
Indices: 4224002--4224056 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
4223992 TAAATTTAAT
4224002 TTCTAATTTTTTGTATA
1 TTCTAA-TTTTTGTATA
* *
4224019 TTTTAA-TTTT-TCT-
1 TTCTAATTTTTGTATA
4224032 TTCTAATTTCTTGTATA
1 TTCTAATTT-TTGTATA
4224049 TTCTAATT
1 TTCTAATT
4224057 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 5 0.17
14 4 0.13
15 6 0.20
16 2 0.07
17 13 0.43
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (16 bp):
TTCTAATTTTTGTATA
Found at i:4224230 original size:29 final size:29
Alignment explanation
Indices: 4224201--4224255 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4224191 ATAAGCAACA
4224201 AATTAAAT-TTACATA-TACAATAAATTAC
1 AATTAAATGTTA-ATATTACAATAAATTAC
**
4224229 AATTATTTGTTAATATTACAATAAATT
1 AATTAAATGTTAATATTACAATAAATT
4224256 TACATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (29 bp):
AATTAAATGTTAATATTACAATAAATTAC
Found at i:4226720 original size:17 final size:17
Alignment explanation
Indices: 4226698--4226737 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4226688 AGGTGGAGAA
* *
4226698 CTTGTTTGTTGAGAGTT
1 CTTGTTTGTAGAGAATT
4226715 CTTGTTTGTAGAGAATT
1 CTTGTTTGTAGAGAATT
4226732 CTTGTT
1 CTTGTT
4226738 AAGGTGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.25, T:0.53
Consensus pattern (17 bp):
CTTGTTTGTAGAGAATT
Found at i:4226771 original size:41 final size:41
Alignment explanation
Indices: 4226726--4226821 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
4226716 TTGTTTGTAG
*
4226726 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGATAGAATTGGGTGACT
4226767 AGAATTCTTGTTAAGGTGGAGATTGATAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGATAGAATTGGGTGACT
4226808 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
4226822 AATAAGATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGATAGAATTGGGTGACT
Found at i:4228826 original size:27 final size:28
Alignment explanation
Indices: 4228796--4228856 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
4228786 TACAAAGTTA
*
4228796 GCCACAAAGGCTATCTTTATAGAGG-TT
1 GCCACAAAGGCTATCCTTATAGAGGTTT
* * *
4228823 GCCACGAAGGTTTTCCTTATAGAGGTTT
1 GCCACAAAGGCTATCCTTATAGAGGTTT
4228851 GCCACA
1 GCCACA
4228857 CAGACTTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (28 bp):
GCCACAAAGGCTATCCTTATAGAGGTTT
Found at i:4228974 original size:28 final size:28
Alignment explanation
Indices: 4228793--4228975 Score: 92
Period size: 28 Copynumber: 6.5 Consensus size: 28
4228783 CCTTACAAAG
* * *
4228793 TTAGCCACAAAGGCTATCTTTATAGAGG
1 TTAGCCACAAAGGCTTTCTTCATAGAGT
* *
4228821 TT-GCCACGAAGGTTTTCCTT-ATAGAGGT
1 TTAGCCACAAAGGCTTT-CTTCATAGA-GT
* * *
4228849 TT-GCCACACAGACTTACTTTCCA-A-AGT
1 TTAGCCACAAAGGCTTTC-TT-CATAGAGT
* * *
4228876 TTAGCCACGAAGGCTTTCCATTCA-AAAAT
1 TTAGCCACAAAGGCTTT-C-TTCATAGAGT
** * *
4228905 TT-GCCATGAAGGCTTTTCTTTACAGAGTT
1 TTAGCCACAAAGGC-TTTCTTCATAGAG-T
* *
4228934 TTAACCATAAAGGCTTTCTTCATAGAGT
1 TTAGCCACAAAGGCTTTCTTCATAGAGT
4228962 TTAGCCACAAAGGC
1 TTAGCCACAAAGGC
4228976 ATTACTCACA
Statistics
Matches: 118, Mismatches: 25, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
27 24 0.20
28 59 0.50
29 25 0.21
30 10 0.08
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (28 bp):
TTAGCCACAAAGGCTTTCTTCATAGAGT
Found at i:4230312 original size:22 final size:22
Alignment explanation
Indices: 4230251--4230317 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
4230241 TGCACTAATG
* *
4230251 AACAAAGAGCACTAAGGTGCTA
1 AACAGAGAGCACTAATGTGCTA
* *
4230273 TACAGAGAGCA-TGCATGTGCTA
1 AACAGAGAGCACT-AATGTGCTA
4230295 AAC-GAGGAGCACTAATGTGCTA
1 AACAGA-GAGCACTAATGTGCTA
4230317 A
1 A
4230318 TAATCGGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
21 3 0.08
22 32 0.89
23 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (22 bp):
AACAGAGAGCACTAATGTGCTA
Found at i:4231130 original size:16 final size:17
Alignment explanation
Indices: 4231109--4231142 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4231099 TATATTTTAC
*
4231109 ATTTCTATCCTA-AATA
1 ATTTCTATACTACAATA
4231125 ATTTCTATACTACAATA
1 ATTTCTATACTACAATA
4231142 A
1 A
4231143 AAAACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTCTATACTACAATA
Found at i:4241942 original size:23 final size:23
Alignment explanation
Indices: 4241912--4242001 Score: 141
Period size: 23 Copynumber: 4.0 Consensus size: 23
4241902 TCTCGTGGTT
*
4241912 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
4241935 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
4241958 ATTAGCACTTTGTGTGCTCTCT-
1 ATTAGCACTTTGTGTGCTCTCTG
4241980 ATTTAGCAC--TGTGTGCTCTCTG
1 A-TTAGCACTTTGTGTGCTCTCTG
4242002 TTGCCCAGCA
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
21 12 0.19
22 1 0.02
23 51 0.80
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (23 bp):
ATTAGCACTTTGTGTGCTCTCTG
Found at i:4248577 original size:22 final size:21
Alignment explanation
Indices: 4248549--4248603 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
4248539 TAAATTTAAA
4248549 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
* *
4248570 ACAAAACATTATAAGGAGAGTT
1 AC-AAACATAATGAGGAGAGTT
*
4248592 GCAAACATAATG
1 ACAAACATAATG
4248604 TTTTGTAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:4251953 original size:25 final size:24
Alignment explanation
Indices: 4251916--4251964 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
4251906 GAAATCCAAT
*
4251916 GTGAAATGTTTTGATTGTTGATGTG
1 GTGAAATGTTTTGAAT-TTGATGTG
4251941 GTGATAATG-TTTGAATTTGATGTG
1 GTGA-AATGTTTTGAATTTGATGTG
4251965 ATCCTACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (24 bp):
GTGAAATGTTTTGAATTTGATGTG
Found at i:4253871 original size:23 final size:23
Alignment explanation
Indices: 4253828--4253875 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
4253818 TCTATCACCA
4253828 AAAATAGAACAGGAATTTTGAGAG
1 AAAATAGAACA-GAATTTTGAGAG
4253852 AAAATATGAACA-AATTTTGAGAG
1 AAAATA-GAACAGAATTTTGAGAG
4253875 A
1 A
4253876 GAGCAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.52
24 6 0.26
25 5 0.22
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (23 bp):
AAAATAGAACAGAATTTTGAGAG
Found at i:4255193 original size:26 final size:27
Alignment explanation
Indices: 4255140--4255193 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
4255130 AAATCGATTG
4255140 GGAAATCAATTAATAGGGTTAAGAGTT
1 GGAAATCAATTAATAGGGTTAAGAGTT
*
4255167 GGAAATCAATT-TTAGGGTTTAAG-GTT
1 GGAAATCAATTAATAGGG-TTAAGAGTT
4255193 G
1 G
4255194 CATAATTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (27 bp):
GGAAATCAATTAATAGGGTTAAGAGTT
Found at i:4255710 original size:11 final size:12
Alignment explanation
Indices: 4255685--4255725 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
4255675 TAAATTATTC
4255685 AAATA-TGATTCA
1 AAATATTGATT-A
*
4255697 AAATATT-TTTA
1 AAATATTGATTA
4255708 AAATATTGATTA
1 AAATATTGATTA
4255720 AAATAT
1 AAATAT
4255726 AATTATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 8 0.32
12 16 0.64
13 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (12 bp):
AAATATTGATTA
Found at i:4256261 original size:24 final size:23
Alignment explanation
Indices: 4256200--4256261 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
4256190 GTTATTGACT
*
4256200 GTTATGTGCATTATATTGTTTTG
1 GTTATGTGCATGATATTGTTTTG
*
4256223 GATTAAAGTGCATGATTATTG-TTTG
1 G-TT-ATGTGCATGA-TATTGTTTTG
4256248 GTTATTGTGCATGA
1 GTTA-TGTGCATGA
4256262 CAAAAATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 2 0.06
24 12 0.38
25 13 0.41
26 5 0.16
ACGTcount: A:0.23, C:0.05, G:0.24, T:0.48
Consensus pattern (23 bp):
GTTATGTGCATGATATTGTTTTG
Found at i:4256342 original size:152 final size:152
Alignment explanation
Indices: 4255986--4257123 Score: 1431
Period size: 153 Copynumber: 7.4 Consensus size: 152
4255976 AAATGGATTC
* * * * *
4255986 TTTTGTGTTGGTTATTGACTGCCATTTTATTAAATTGTAGTAAAGTATTTGGTTATTGTCTGTCA
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTCA
*
4256051 TGTGCATGATACTG-TTTGGATTCAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAAT
66 TGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAAT
* * *
4256115 GGATTTTTTTTTATGTTAAATTAT
131 -G-TATATTTTTGTGTTAAATTAT
* ** * *
4256139 TTTTGTATTGGTTATTGTCT-CTTATTTTATTAAGTTGCGTTAAAGTGTTTGGTTATTGACTGTT
1 TTTTGTATTGGTTATTGTCTGC-CATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTC
* * *
4256203 ATGTGCATTATATTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTGCATGACAAAAA
65 ATGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAA
**
4256268 TGTATATTTTTGTGTTAAATTGC
130 TGTATATTTTTGTGTTAAATTAT
* * * *
4256291 TTTTGTATTGGTTATAGTTTGCCATTTTATTAAGTTGTATTAAAGTTTTTGGTTATTGTCTATCA
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTCA
* * * ** *
4256356 TGTGCATAATATTGTTTTGGATTAAAATGCATGATTGGTGTTTGGTTATTGTACATGACAGAAAT
66 TGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAAT
* * * *
4256421 GGACATTTTTGTATTAAATTGT
131 GTATATTTTTGTGTTAAATTAT
*
4256443 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAATTGTATTAAAGTGTTTGGTTATTGTCT-TCC
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGT-C
* * * *
4256507 GTGTGCATGATACTGTTTTTGATTAAAGTGCATGATTAATGTTTGGTTATTGTACGTGACAAAAA
65 ATGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAA
* *
4256572 TGAATTATTTTTGTGTTAAATTGT
130 TGTA-TATTTTTGTGTTAAATTAT
* * *
4256596 TTTTGTATTGGTTATTGTCTCCCATTTTATTAAGTTATATTAAAGTGTTTGGTTATTATCTGTCA
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTCA
** * * * * *
4256661 TGTATATCATACTATTTTGGATTAAAGTGCATGATTATTATTTGGTTATTGTACATGATAAGAAT
66 TGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAAT
* *
4256726 GGAGT-TATCTTGTGTTAAATTAT
131 GTA-TAT-TTTTGTGTTAAATTAT
* * * *
4256749 TTTTGAATTGGTTATTGTCTGTCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTATGCCA
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTCA
* * * ** *
4256814 CGCGCATGATAATGTTTTGGATTAAAGTGCATGAAAATTGTTTGGTTATTGTACATGACAGAAAT
66 TGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAAT
* * * *
4256879 GAATTTTTTTGTGTTAATTTTTT
131 GTATATTTTTGTGTTAA-ATTAT
* *
4256902 TTTTGTATTGGTTATTGTTTGTCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTG-CT
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTC-
* * * *
4256966 ATGTGCATGATATTGTTTTGGATTAAAGTGCATGGTTATTGTTTGGTTATTGTACGTGACAGAAA
65 ATGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAA
* * *
4257031 TGTAATTCCTTTTTGTATTAAATTAC
130 TGT-A-T-ATTTTTGTGTTAAATTAT
* * *
4257057 TTTTGTATTGGTTATTATCTGTCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTTTGTCA
1 TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTCA
4257122 TG
66 TG
4257124 GGTATGACAG
Statistics
Matches: 855, Mismatches: 116, Indels: 26
0.86 0.12 0.03
Matches are distributed among these distances:
151 1 0.00
152 278 0.33
153 449 0.53
154 50 0.06
155 65 0.08
156 12 0.01
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.50
Consensus pattern (152 bp):
TTTTGTATTGGTTATTGTCTGCCATTTTATTAAGTTGTATTAAAGTGTTTGGTTATTGTCTGTCA
TGTGCATGATACTGTTTTGGATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAAAAAT
GTATATTTTTGTGTTAAATTAT
Found at i:4259668 original size:56 final size:55
Alignment explanation
Indices: 4259551--4259711 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 55
4259541 TGAAATAACC
* * * * * * *
4259551 TTACGCTCTAACCG-AGACGTAAGCAAACCAGAGCTCTACCCAAGTTGTAATAGCT
1 TTACGCTCTAA-CGAAGACGTAAGCAGATCAAAGCTCTACCTAAGCTATAATAGCA
* * *
4259606 TTACGCTCTAATTG-AGACGTAAGCATG-TCCCAAGCTCTACCTGAGCTATAATAGCA
1 TTACGCTCTAA-CGAAGACGTAAGCA-GAT-CAAAGCTCTACCTAAGCTATAATAGCA
4259662 TTACGCTCTAACGAAGACGTAAGCAGATCAAAGCTCTACCTAAGCTATAA
1 TTACGCTCTAACGAAGACGTAAGCAGATCAAAGCTCTACCTAAGCTATAA
4259712 ATGAATTAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
55 45 0.51
56 43 0.49
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (55 bp):
TTACGCTCTAACGAAGACGTAAGCAGATCAAAGCTCTACCTAAGCTATAATAGCA
Found at i:4263881 original size:12 final size:12
Alignment explanation
Indices: 4263848--4263894 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
4263838 ATCGTTTCAA
*
4263848 ATTTATAAATAT
1 ATTTAAAAATAT
4263860 -TTTAAAAATAT
1 ATTTAAAAATAT
*
4263871 ATTTAATAATAT
1 ATTTAAAAATAT
*
4263883 ATATGAAAAATA
1 AT-TTAAAAATA
4263895 AATATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 10 0.34
12 12 0.41
13 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:4264543 original size:7 final size:7
Alignment explanation
Indices: 4264533--4264564 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
4264523 GAGGTTTGGG
4264533 TTTTAGA
1 TTTTAGA
4264540 TTTTGAGA
1 TTTT-AGA
4264548 TTTTAGA
1 TTTTAGA
4264555 TTTTAGA
1 TTTTAGA
4264562 TTT
1 TTT
4264565 AGGGTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (7 bp):
TTTTAGA
Found at i:4264553 original size:15 final size:14
Alignment explanation
Indices: 4264533--4264564 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
4264523 GAGGTTTGGG
4264533 TTTTAGATTTTGAGA
1 TTTTAGATTTT-AGA
4264548 TTTTAGATTTTAGA
1 TTTTAGATTTTAGA
4264562 TTT
1 TTT
4264565 AGGGTTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (14 bp):
TTTTAGATTTTAGA
Found at i:4265118 original size:21 final size:21
Alignment explanation
Indices: 4265092--4265140 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
4265082 AAAGTATTAC
4265092 ATCATGTGGAACATGTGTTGT
1 ATCATGTGGAACATGTGTTGT
4265113 ATCATGTGGAACATGTGTTGT
1 ATCATGTGGAACATGTGTTGT
4265134 ATCATGT
1 ATCATGT
4265141 TCCACCGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (21 bp):
ATCATGTGGAACATGTGTTGT
Found at i:4266039 original size:62 final size:59
Alignment explanation
Indices: 4265931--4266047 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
4265921 ATCACTTTAA
* *
4265931 TATTAAATTAATATAATACTTATTAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATTAAGATAAATATTAAATTAAATTTAATATTAAATCT
* *
4265990 TATTAAATTAATAGAATATTTATTTACAAGTTAAATATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAATACTTA-TT--AAGATAAATATTAAATTAAATTTAATATTAA
4266048 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.39
60 2 0.04
62 29 0.57
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATTAAGATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:4266498 original size:18 final size:18
Alignment explanation
Indices: 4266475--4266514 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
4266465 GTGACCATGT
*
4266475 TGACTTTTCATAGTTGGG
1 TGACTTTTCATAGTTAGG
4266493 TGACTTTTCATAGTTAGG
1 TGACTTTTCATAGTTAGG
4266511 TGAC
1 TGAC
4266515 CAAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (18 bp):
TGACTTTTCATAGTTAGG
Found at i:4267520 original size:22 final size:22
Alignment explanation
Indices: 4267486--4267541 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
4267476 TTTTATATTT
*
4267486 TTTATATTTTTAAAATTTTAAAA
1 TTTAT-TTTTTAAAATTATAAAA
4267509 TTTATTTTTTAAAATTATAAAA
1 TTTATTTTTTAAAATTATAAAA
4267531 TTATATTTTTT
1 TT-TATTTTTT
4267542 TAGGATTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATTTTTTAAAATTATAAAA
Found at i:4269717 original size:2 final size:2
Alignment explanation
Indices: 4269710--4269734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4269700 GAAATTTATC
4269710 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4269735 GTGGCCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4270552 original size:25 final size:24
Alignment explanation
Indices: 4270509--4270559 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
4270499 ACTGACATAC
* *
4270509 ATAGACTAGTTTTTAACAATAAAA
1 ATAGACTAATTTTTAACAAAAAAA
4270533 ATAGACTATATTTTTAACAAAAAAA
1 ATAGACTA-ATTTTTAACAAAAAAA
4270558 AT
1 AT
4270560 TAGTTTACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (24 bp):
ATAGACTAATTTTTAACAAAAAAA
Found at i:4270726 original size:6 final size:6
Alignment explanation
Indices: 4270715--4270749 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
4270705 GGTAGTCGTT
4270715 ATATAA ATATAA ATATAA ATATAA ATATAA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
4270750 GTATGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:4270927 original size:17 final size:17
Alignment explanation
Indices: 4270878--4270926 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
4270868 TATGACATTA
4270878 ATAA-AAATTATAAAAT
1 ATAATAAATTATAAAAT
*
4270894 CTAATAAATTATTAAAAT
1 ATAATAAATTA-TAAAAT
4270912 AT-ATAAATTATAAAA
1 ATAATAAATTATAAAA
4270927 AACATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 8 0.28
17 14 0.48
18 7 0.24
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAAATTATAAAAT
Found at i:4270928 original size:18 final size:18
Alignment explanation
Indices: 4270882--4270933 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
4270872 ACATTAATAA
**
4270882 AAATTATAAAATCTA-AT
1 AAATTATAAAAAATATAT
*
4270899 AAATTAT-TAAAATATAT
1 AAATTATAAAAAATATAT
*
4270916 AAATTATAAAAAACATAT
1 AAATTATAAAAAATATAT
4270934 TTAAAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 8 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTATAAAAAATATAT
Found at i:4270928 original size:44 final size:44
Alignment explanation
Indices: 4270837--4270927 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
4270827 TTTTTTTCTC
* *
4270837 AAAATTATAAAAACTATTAAATATTAAAAAATATGACATTAATA
1 AAAATTATAAAAACTAATAAATATTAAAAAATATGAAATTAATA
* *
4270881 AAAATTATAAAATCTAATAAATTATTAAAATATAT-AAATT-ATA
1 AAAATTATAAAAACTAATAAA-TATTAAAAAATATGAAATTAATA
4270924 AAAA
1 AAAA
4270928 ACATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 7 0.17
44 23 0.55
45 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (44 bp):
AAAATTATAAAAACTAATAAATATTAAAAAATATGAAATTAATA
Found at i:4271017 original size:9 final size:9
Alignment explanation
Indices: 4270837--4271005 Score: 73
Period size: 9 Copynumber: 18.4 Consensus size: 9
4270827 TTTTTTTCTC
4270837 AAAATTATA
1 AAAATTATA
*
4270846 AAAACTATTA
1 AAAATTA-TA
*
4270856 AATATTA-A
1 AAAATTATA
4270864 AAAA-TAT-
1 AAAATTATA
* *
4270871 GACATTAATA
1 AAAATT-ATA
4270881 AAAATTAT-
1 AAAATTATA
4270889 AAAATCTA-A
1 AAAAT-TATA
* *
4270898 TAAATTATT
1 AAAATTATA
4270907 AAAA-TATA
1 AAAATTATA
*
4270915 TAAATTATAAA
1 AAAATTAT--A
*
4270926 AAACATATTTA
1 AAA-AT-TATA
4270937 AAATATTATA
1 AAA-ATTATA
* *
4270947 AAGATGTATT
1 AAAAT-TATA
*
4270957 AAAATTCTAA
1 AAAATTAT-A
* *
4270967 AAAATCACA
1 AAAATTATA
4270976 AAAATTAT-
1 AAAATTATA
*
4270984 AATATTATA
1 AAAATTATA
4270993 AAAATTATA
1 AAAATTATA
4271002 AAAA
1 AAAA
4271006 AAATCATAAA
Statistics
Matches: 115, Mismatches: 29, Indels: 32
0.65 0.16 0.18
Matches are distributed among these distances:
7 4 0.03
8 25 0.22
9 45 0.39
10 28 0.24
11 9 0.08
12 2 0.02
13 2 0.02
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:4271611 original size:9 final size:9
Alignment explanation
Indices: 4271597--4271677 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
4271587 ATTTTTTATT
4271597 TTTATAATA
1 TTTATAATA
4271606 TTTATAAGT-
1 TTTATAA-TA
4271615 TTT-T-ATA
1 TTTATAATA
*
4271622 TATAT-ATA
1 TTTATAATA
4271630 TTTATAAT-
1 TTTATAATA
*
4271638 TTTAATAA-G
1 TTT-ATAATA
*
4271647 TTTATAACGA
1 TTTATAA-TA
4271657 TTT-TAATA
1 TTTATAATA
*
4271665 TTTTTAATA
1 TTTATAATA
4271674 TTTA
1 TTTA
4271678 ATATTTTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
6 1 0.02
7 3 0.05
8 20 0.34
9 30 0.52
10 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (9 bp):
TTTATAATA
Found at i:4271630 original size:24 final size:24
Alignment explanation
Indices: 4271589--4271640 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
4271579 TTACTAAAAT
* *
4271589 TTTTTATTTTTATAATATTTATAA
1 TTTTTATATATATAATATTTATAA
4271613 GTTTTTATATATAT-ATATTTATAA
1 -TTTTTATATATATAATATTTATAA
4271637 TTTT
1 TTTT
4271641 AATAAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 10 0.40
25 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTTATATATATAATATTTATAA
Found at i:4271679 original size:16 final size:14
Alignment explanation
Indices: 4271656--4271699 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 14
4271646 GTTTATAACG
4271656 ATTTTAATATTTTT
1 ATTTTAATATTTTT
4271670 AATATTTAATATTTTT
1 -AT-TTTAATATTTTT
*
4271686 ATTTTTATATTTTT
1 ATTTTAATATTTTT
4271700 TCTGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.41
15 4 0.15
16 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTAATATTTTT
Found at i:4271709 original size:18 final size:18
Alignment explanation
Indices: 4271686--4271739 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
4271676 TAATATTTTT
*
4271686 ATTTTTATATTTTTTCTG
1 ATTTTTATATTTTTTATG
* *
4271704 ATTTTTTTATAATTTTATG
1 ATTTTTATAT-TTTTTATG
4271723 ATTTTTAATAATTTTTT
1 ATTTTT-AT-ATTTTTT
4271740 TGTGAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 9 0.32
19 12 0.43
20 5 0.18
21 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
ATTTTTATATTTTTTATG
Found at i:4271712 original size:20 final size:19
Alignment explanation
Indices: 4271687--4271737 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
4271677 AATATTTTTA
* *
4271687 TTTTTATATTTTTTCTGATT
1 TTTTTATA-ATTTTATGATT
4271707 TTTTTATAATTTTATGA-T
1 TTTTTATAATTTTATGATT
*
4271725 TTTTAATAATTTT
1 TTTTTATAATTTT
4271738 TTTGTGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.46
19 7 0.25
20 8 0.29
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTTATAATTTTATGATT
Found at i:4282274 original size:21 final size:21
Alignment explanation
Indices: 4282244--4282292 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4282234 TTTAAAAACA
* * *
4282244 TAATAATTTATTAATATAATT
1 TAATATTTTAATAAAATAATT
*
4282265 TAATATTTTAATAAAATTATT
1 TAATATTTTAATAAAATAATT
4282286 TAATATT
1 TAATATT
4282293 ATGATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATATTTTAATAAAATAATT
Found at i:4282358 original size:20 final size:20
Alignment explanation
Indices: 4282300--4282397 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 20
4282290 ATTATGATTT
*
4282300 TATTTTAATAATAGAATTTAA
1 TATTTTAATAATA-ATTTTAA
*
4282321 CA--TTAATAATAATTTTAA
1 TATTTTAATAATAATTTTAA
4282339 -ATTTTAAGTAAT-ATTCTTAA
1 TATTTTAA-TAATAATT-TTAA
* *
4282359 TATTTTATTGAAAACATTATTTTAA
1 TA--TT-TT-AATA-ATAATTTTAA
4282384 TATTTTAATAATAA
1 TATTTTAATAATAA
4282398 ATATATACTA
Statistics
Matches: 61, Mismatches: 5, Indels: 23
0.69 0.06 0.26
Matches are distributed among these distances:
17 1 0.02
18 6 0.10
19 16 0.26
20 11 0.18
21 5 0.08
22 2 0.03
23 4 0.07
24 3 0.05
25 10 0.16
26 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATTTTAATAATAATTTTAA
Found at i:4282941 original size:26 final size:27
Alignment explanation
Indices: 4282894--4282947 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
4282884 AAAAATTATT
*
4282894 ATATTATATTATATTATATGTG-TGAA
1 ATATAATATTATATTATATGTGCTGAA
* * *
4282920 ATATAATATTTTATTGTTTGTGCTGAA
1 ATATAATATTATATTATATGTGCTGAA
4282947 A
1 A
4282948 ATGTTGCTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (27 bp):
ATATAATATTATATTATATGTGCTGAA
Found at i:4286288 original size:52 final size:52
Alignment explanation
Indices: 4286210--4286505 Score: 475
Period size: 52 Copynumber: 5.7 Consensus size: 52
4286200 ATTTCATTTC
*
4286210 ATTCATATACTCACGGTGACACATAGCCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
*
4286262 ATTCATATGCTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
4286314 ACTCATATACTCACAATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * * *
4286366 ATTCATATAGTCACGATGACACATAGTCACCGGACCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * *
4286418 ATTCATATATTCACGATGACACATAGTCACCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
4286470 ATTCATATACTCACGATGACACTTAGTCATCGGACC
1 ATTCATATACTCACGATGACACATAGCCATCGGACC
4286506 CTTTTTCATT
Statistics
Matches: 228, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 228 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
Found at i:4288711 original size:22 final size:22
Alignment explanation
Indices: 4288683--4288741 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
4288673 TTATACTAAA
4288683 TTTTAATTCAATAATTAAAATT
1 TTTTAATTCAATAATTAAAATT
4288705 TTTTAATTCAATAATTAAAATT
1 TTTTAATTCAATAATTAAAATT
*
4288727 CTTTAATTCAA-AATT
1 TTTTAATTCAATAATT
4288742 CCATATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAATTCAATAATTAAAATT
Found at i:4295163 original size:51 final size:51
Alignment explanation
Indices: 4295097--4295316 Score: 228
Period size: 51 Copynumber: 4.3 Consensus size: 51
4295087 GTCCGATGAC
*
4295097 TGTCATCGT-ATGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAA
1 TGTCATCGTGA-GTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAG
* * * *
4295148 TATCATCGTCAGTAAATGAATCCTTTACGGGTTAAAAGTCCGATGACTAAG
1 TGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAG
* * * * * *
4295199 TGTTATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCTGATGACTCAG
1 TGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAG
* * * * **
4295250 GGTCATCATGAGTATATGAATTCCTATACGGAACAAGAGGTCCGATGACTATA-
1 TGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTCCGATGACTA-AG
*
4295303 CGTCATCGTGAGTA
1 TGTCATCGTGAGTA
4295317 TTAAATGAAA
Statistics
Matches: 137, Mismatches: 28, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
51 102 0.74
52 10 0.07
53 24 0.18
54 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (51 bp):
TGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAG
Found at i:4298117 original size:30 final size:29
Alignment explanation
Indices: 4298074--4298153 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
4298064 ATTTTTATTA
* * *
4298074 AAAAAATTTAATAATTCAGTGATTTAAAT
1 AAAAATTTTAATAATTCAATGACTTAAAT
*
4298103 AAAAATTTTAAATAATTAAATGACTTAAAT
1 AAAAATTTT-AATAATTCAATGACTTAAAT
4298133 AAAAATATTTTAATAATTCAA
1 -AAAA-ATTTTAATAATTCAA
4298154 CGACCATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 8 0.19
30 17 0.40
31 13 0.30
32 5 0.12
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAAATTTTAATAATTCAATGACTTAAAT
Found at i:4308281 original size:22 final size:24
Alignment explanation
Indices: 4308252--4308309 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
4308242 TTATATGAAA
4308252 ATAAATAATAAA-TTTTATAATAT
1 ATAAATAATAAATTTTTATAATAT
*
4308275 -TAAATAAATAAAATTTTTATTATAT
1 ATAAAT-AAT-AAATTTTTATAATAT
4308300 ATAAA-AATAA
1 ATAAATAATAA
4308310 TTAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
24 6 0.20
25 10 0.33
26 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAATAATAAATTTTTATAATAT
Found at i:4308284 original size:26 final size:26
Alignment explanation
Indices: 4308250--4308304 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
4308240 ATTTATATGA
4308250 AAATAAATAATAAATTTTATAATAT-T
1 AAATAAATAA-AAATTTTATAATATAT
* *
4308276 AAATAAATAAAATTTTTATTATATAT
1 AAATAAATAAAAATTTTATAATATAT
4308302 AAA
1 AAA
4308305 AATAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAATAAATAAAAATTTTATAATATAT
Found at i:4308455 original size:22 final size:22
Alignment explanation
Indices: 4308430--4308499 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 22
4308420 TTTTAATATC
4308430 TATTATTAAATATTTTATATTT
1 TATTATTAAATATTTTATATTT
* *
4308452 TATTATATTTAATATTTTATAATAT
1 TA-T-TATTAAATATTTTAT-ATTT
* * *
4308477 TAATATTAACTATTTCA-ATTT
1 TATTATTAAATATTTTATATTT
4308498 TA
1 TA
4308500 AATATTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
21 5 0.13
22 2 0.05
23 12 0.32
24 14 0.37
25 5 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATTAAATATTTTATATTT
Found at i:4308479 original size:16 final size:17
Alignment explanation
Indices: 4308438--4308483 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
4308428 TCTATTATTA
*
4308438 AATATTTTATATTTTAT
1 AATATTTAATATTTTAT
*
4308455 TATATTTAATATTTTAT
1 AATATTTAATATTTTAT
4308472 AATA-TTAATATT
1 AATATTTAATATT
4308484 AACTATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATTTAATATTTTAT
Found at i:4313525 original size:59 final size:59
Alignment explanation
Indices: 4313419--4313791 Score: 581
Period size: 59 Copynumber: 6.4 Consensus size: 59
4313409 TATGGATACC
* * *
4313419 CGGGGGTAAAATGGTAATTTT-GGTGTAATCGGGATTAAAAGTGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * **
4313477 CGGGGGTAAAATGGAAATTTTCGGTGTAATCGGGGTTAAAAACAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
4313536 C-GAGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
4313594 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTCAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
4313653 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
4313712 CGAGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
4313771 CGGGGGTCAAAAT-GTAATTTT
1 CGGGGGT-AAAATGGTAATTTT
4313792 TGGACAATTT
Statistics
Matches: 290, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
58 72 0.25
59 213 0.73
60 5 0.02
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:4313686 original size:176 final size:177
Alignment explanation
Indices: 4313419--4313794 Score: 650
Period size: 176 Copynumber: 2.1 Consensus size: 177
4313409 TATGGATACC
* * *
4313419 CGGGGGTAAAATGGTAA-TTTTGGTGTAATCGGGATTAAAAGTGGAATTTTAAAAGATTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTCAAAAGATTCGGGGG
*
4313483 TAAAATGGAAATTTTCGGTGTAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGA-GGTAAAAT
66 TAAAATGGAAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGTAAAAT
4313547 GGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
131 GGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
*
4313594 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTCAAAAGATTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTCAAAAGATTCGGGGG
* * *
4313659 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAAAAGATTCGAGGGTAAAAT
66 TAAAATGGAAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGTAAAAT
4313724 GGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
131 GGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
4313771 CGGGGGTCAAAAT-GTAATTTTTGG
1 CGGGGGT-AAAATGGTAATTTTTGG
4313795 ACAATTTAGG
Statistics
Matches: 190, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
175 17 0.09
176 95 0.50
177 73 0.38
178 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (177 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTCAAAAGATTCGGGGG
TAAAATGGAAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGAGGGTAAAAT
GGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:4313789 original size:29 final size:28
Alignment explanation
Indices: 4313454--4313791 Score: 165
Period size: 29 Copynumber: 11.5 Consensus size: 28
4313444 TAATCGGGAT
4313454 TAAAAGTGGAATTTTAAAAGATTCGGGGG
1 TAAAA-TGGAATTTTAAAAGATTCGGGGG
**** * *
4313483 TAAAATGGAAATTTTCGGTGTAATCGGGGT
1 TAAAATGG-AATTTTAAAAG-ATTCGGGGG
** *
4313513 TAAAAACAGAATTTTAAAAGATTC-GAGG
1 T-AAAATGGAATTTTAAAAGATTCGGGGG
**** * * *
4313541 TAAAATGGTAATTTTCGGTGAAATCAGGGT
1 TAAAATGG-AATTTTAAAAG-ATTCGGGGG
4313571 TAAAAATGGAATTTTAAAAGATTCGGGGG
1 T-AAAATGGAATTTTAAAAGATTCGGGGG
**** * *
4313600 TAAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAATGG-AATTTTAAAAG-ATTCGGGGG
*
4313630 TAAAAATGGAATTTCAAAAGATTCGGGGG
1 T-AAAATGGAATTTTAAAAGATTCGGGGG
**** * *
4313659 TAAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAATGG-AATTTTAAAAG-ATTCGGGGG
* *
4313689 TAAAAACGGAATTTTAAAAGATTCGAGGG
1 T-AAAATGGAATTTTAAAAGATTCGGGGG
**** * * *
4313718 TAAAATGGTAATTTTCGGTGAAATCAGGGT
1 TAAAATGG-AATTTTAAAAG-ATTCGGGGG
4313748 TAAAAATGGAATTTTAAAAGATTCGGGGG
1 T-AAAATGGAATTTTAAAAGATTCGGGGG
*
4313777 TCAAAATGTAATTTT
1 T-AAAATGGAATTTT
4313792 TGGACAATTT
Statistics
Matches: 216, Mismatches: 77, Indels: 32
0.66 0.24 0.10
Matches are distributed among these distances:
27 5 0.02
28 33 0.15
29 79 0.37
30 67 0.31
31 32 0.15
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (28 bp):
TAAAATGGAATTTTAAAAGATTCGGGGG
Found at i:4314094 original size:163 final size:163
Alignment explanation
Indices: 4313866--4314536 Score: 1057
Period size: 163 Copynumber: 4.1 Consensus size: 163
4313856 GTATCTAGAG
* * * * *
4313866 GTCAAGGGACCAATTTGAAAATCTTG-AAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTCG
1 GTCAAAGGACTAATTTGAAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCG
4313930 ATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAT
66 ATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAT
4313995 ATGACACGTGGTAACCTCTGGTGCAGTCAAACA
131 ATGACACGTGGTAACCTCTGGTGCAGTCAAACA
* * * *
4314028 GTCAAAGGACCAATTTGAAAATCTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTCG
1 GTCAAAGGACTAATTTGAAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCG
4314093 ATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAT
66 ATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAT
4314158 ATGACACGTGGTAACCTCTGGTGCAGTCAAACA
131 ATGACACGTGGTAACCTCTGGTGCAGTCAAACA
* *
4314191 GTCAAAGGACTAGTTT-ATAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAATAAAAGTC
1 GTCAAAGGACTAATTTGA-AAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTC
4314255 GATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAA
65 GATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAA
4314320 TATGACACGTGGTAACCTCTGGTGCAGTCAAACA
130 TATGACACGTGGTAACCTCTGGTGCAGTCAAACA
* *
4314354 GTCAAAGGACTAGTTT-ATAAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGT
1 GTCAAAGGACTAATTTGA-AAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATA-AAAGT
* * * *
4314417 TGATTT-GGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAA
64 CGATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAA
* ** * *
4314481 A-AGTGACACGTGGCAGTCTATGGTACAGTCAAACA
129 ATA-TGACACGTGGTAACCTCTGGTGCAGTCAAACA
*
4314516 GTCAAAGGACTAAATTGAAAA
1 GTCAAAGGACTAATTTGAAAA
4314537 GCAATTAAAA
Statistics
Matches: 486, Mismatches: 18, Indels: 10
0.95 0.04 0.02
Matches are distributed among these distances:
161 1 0.00
162 127 0.26
163 358 0.74
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (163 bp):
GTCAAAGGACTAATTTGAAAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCG
ATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAT
ATGACACGTGGTAACCTCTGGTGCAGTCAAACA
Found at i:4315402 original size:23 final size:21
Alignment explanation
Indices: 4315352--4315403 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
4315342 ATTATTATTA
* *
4315352 TTATTAATGTTATTAATGTCT
1 TTATTAATCTTATTAATGCCT
4315373 TTCATTAATCCTTATTAATGCCAT
1 TT-ATTAAT-CTTATTAATGCC-T
4315397 TTATTAA
1 TTATTAA
4315404 ATTCAGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 6 0.23
23 15 0.58
24 3 0.12
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.52
Consensus pattern (21 bp):
TTATTAATCTTATTAATGCCT
Found at i:4316100 original size:6 final size:6
Alignment explanation
Indices: 4316084--4316192 Score: 95
Period size: 6 Copynumber: 18.3 Consensus size: 6
4316074 TTAAATTTGT
*
4316084 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GTTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
4316134 TTTAAA TTTAAGA --TAGA TTTAAA TTTAAA --TAAA TTTAAA -ATCAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4316178 TTTAAA CTTTAAA TT
1 TTTAAA -TTTAAA TT
4316193 AAAGCAAAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
4 5 0.06
5 9 0.11
6 53 0.63
7 11 0.13
8 6 0.07
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:4316107 original size:30 final size:30
Alignment explanation
Indices: 4316089--4316171 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 30
4316079 TTTGTTTTAT
4316089 AATTTAAAT-TTAAATTTAAATTTAAGTTA
1 AATTTAAATATTAAATTTAAATTTAAGTTA
*
4316118 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAAT-ATTAAATTTAAATTTAAGTTA
*
4316149 GATTTAAAT-TTAAA--TAAATTTAA
1 AATTTAAATATTAAATTTAAATTTAA
4316172 AATCAATTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.18
29 14 0.28
31 27 0.54
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (30 bp):
AATTTAAATATTAAATTTAAATTTAAGTTA
Found at i:4316120 original size:17 final size:16
Alignment explanation
Indices: 4316084--4316192 Score: 96
Period size: 17 Copynumber: 6.5 Consensus size: 16
4316074 TTAAATTTGT
4316084 TTTATAATTTAAATTTAAA
1 TTTA-AATTT-AA-TTAAA
4316103 TTTAAATTTAAGTTAAA
1 TTTAAATTTAA-TTAAA
4316120 TTTAAA--TAATTAAA
1 TTTAAATTTAATTAAA
* *
4316134 TTTAAATTTAAGATAGA
1 TTTAAATTTAA-TTAAA
*
4316151 TTTAAATTTAAATAAA
1 TTTAAATTTAATTAAA
* *
4316167 TTTAAAATCAATTTAAA
1 TTTAAATTTAA-TTAAA
4316184 CTTTAAATT
1 -TTTAAATT
4316193 AAAGCAAAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
14 11 0.14
15 3 0.04
16 16 0.21
17 31 0.40
18 12 0.16
19 4 0.05
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:4316136 original size:37 final size:38
Alignment explanation
Indices: 4316087--4316172 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 38
4316077 AATTTGTTTT
4316087 ATAATTTAAATTTAAATTTAA-ATTTA-AGTTAAATTTAA
1 ATAATTTAAATTTAAATTTAAGA--TAGAGTTAAATTTAA
*
4316125 ATAA-TTAAATTTAAATTTAAGATAGATTTAAATTTAA
1 ATAATTTAAATTTAAATTTAAGATAGAGTTAAATTTAA
4316162 ATAAATTTAAA
1 AT-AATTTAAA
4316173 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
36 2 0.05
37 29 0.67
38 7 0.16
39 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (38 bp):
ATAATTTAAATTTAAATTTAAGATAGAGTTAAATTTAA
Found at i:4316556 original size:68 final size:68
Alignment explanation
Indices: 4316472--4316939 Score: 679
Period size: 68 Copynumber: 6.8 Consensus size: 68
4316462 AAGACTTCGC
* * * *
4316472 TATCCAACTTTACTTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGAC
*
4316537 GTGT
65 ATGT
*
4316541 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGACA
4316606 TGT
66 TGT
* * *
4316609 TATCCACTCTATTTCAATTTCAAGGGGATGACGTCGCTCTTACTTCAATTTCAGAGAG-GAAGTC
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG-GTGAAGAC
* *
4316673 TTGA
65 ATGT
* *
4316677 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGAC
4316742 ATGT
65 ATGT
* *
4316746 TATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAG-GAAGTC
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG-GTGAAGAC
* *
4316810 TTGA
65 ATGT
* * *
4316814 TATCCAACTCTACTTCAATTTCAAGGGAATGACTTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGAC
*
4316879 GTGT
65 ATGT
*
4316883 TATCCACTCTACTTCAATTTCAAGGGGATGACTTTGCTCTTACTTCAATTTCAGAGG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGG
4316940 GGATGACGAC
Statistics
Matches: 359, Mismatches: 34, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
68 234 0.65
69 125 0.35
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (68 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGACA
TGT
Found at i:4316722 original size:137 final size:136
Alignment explanation
Indices: 4316485--4316938 Score: 759
Period size: 137 Copynumber: 3.3 Consensus size: 136
4316475 CCAACTTTAC
* * * * * *
4316485 TTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCAGAG-GTAAAGACGTGTTATCC-AC
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAG-GAAGTCTTGATATCCAAC
4316548 TCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATC
65 TCTACTTCAATTTCAA-GGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATC
4316613 CACTCTAT
129 CACTCTAT
*
4316621 TTCAATTTCAAGGGGATGACGTCGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
4316686 CTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
66 CTACTTCAATTTCAAG-GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
4316751 ACTCTAT
130 ACTCTAT
4316758 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
* *
4316823 CTACTTCAATTTCAAGGGAATGACTTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC
66 CTACTTCAATTTCAAGGG-ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
*
4316888 ACTCTAC
130 ACTCTAT
*
4316895 TTCAATTTCAAGGGGATGACTTTGCTCTTACTTCAATTTCAGAG
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
4316939 GGGATGACGA
Statistics
Matches: 302, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
136 55 0.18
137 247 0.82
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (136 bp):
TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
CTACTTCAATTTCAAGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
CTCTAT
Found at i:4316894 original size:205 final size:205
Alignment explanation
Indices: 4316472--4316938 Score: 738
Period size: 205 Copynumber: 2.3 Consensus size: 205
4316462 AAGACTTCGC
* * *
4316472 TATCCAACTTTACTTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
* *
4316537 GTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAA
66 ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
* * *
4316602 GACATGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTCGCTCTTACTTCAATTTCAGAGAG
131 GACATGATATCCACTCTACTTCAATTTCAAGGGAATGACGTCGCTCTTACTTCAATTTCAGAGAG
* *
4316667 GAAGTCTTGA
196 GAAGACGTGA
*
4316677 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
*
4316742 ATGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
66 ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
* * * *
4316807 GTCTTGATATCCAACTCTACTTCAATTTCAAGGGAATGACTTTGCTCTTACTTCAATTTCAGAGA
131 GACATGATATCC-ACTCTACTTCAATTTCAAGGGAATGACGTCGCTCTTACTTCAATTTCAGAGA
* *
4316872 TGAAGACGTGT
195 GGAAGACGTGA
* *
4316883 TATCC-ACTCTACTTCAATTTCAAGGGGATGACTTTGCTCTTACTTCAATTTCAGAG
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAG
4316939 GGGATGACGA
Statistics
Matches: 241, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
205 181 0.75
206 60 0.25
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (205 bp):
TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
GACATGATATCCACTCTACTTCAATTTCAAGGGAATGACGTCGCTCTTACTTCAATTTCAGAGAG
GAAGACGTGA
Found at i:4328884 original size:29 final size:28
Alignment explanation
Indices: 4328852--4329135 Score: 133
Period size: 29 Copynumber: 9.8 Consensus size: 28
4328842 TATGGATACC
4328852 CGGGGGTAAAATGGTAATTTT-GGTGTAAT
1 CGGGGGTAAAATGG-AATTTTAGGTG-AAT
** *** *
4328881 CGGGATTAAAAGTGGAATTTTAAAAGATT
1 CGGGGGTAAAA-TGGAATTTTAGGTGAAT
*
4328910 CGGGGGTAAAATGGAAATTTTTGGTGTAAT
1 CGGGGGTAAAATGG-AATTTTAGGTG-AAT
* * *** *
4328940 CGGGGTTAAAAACGGAATTTTAAAAGATT
1 CGGGGGT-AAAATGGAATTTTAGGTGAAT
* *
4328969 C-GAGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGG-AATTTTAGGTG-AAT
* * *** *
4328998 CAGGGTTAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGAATTTTAGGTGAAT
* *
4329026 CGTGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGG-AATTTTAGGTG-AAT
* *** *
4329056 C-GGGGTAAAAACGGAATTTTAAAAGATT
1 CGGGGGT-AAAATGGAATTTTAGGTGAAT
* *
4329084 CGAGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGG-AATTTTAGGTG-AAT
* *
4329114 CAGGGTTAAAAATGGAATTTTA
1 CGGGGGT-AAAATGGAATTTTA
4329136 AAAGATTCGG
Statistics
Matches: 179, Mismatches: 61, Indels: 29
0.67 0.23 0.11
Matches are distributed among these distances:
27 6 0.03
28 35 0.20
29 75 0.42
30 50 0.28
31 13 0.07
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (28 bp):
CGGGGGTAAAATGGAATTTTAGGTGAAT
Found at i:4329025 original size:116 final size:116
Alignment explanation
Indices: 4328855--4329155 Score: 491
Period size: 116 Copynumber: 2.6 Consensus size: 116
4328845 GGATACCCGG
*
4328855 GGGTAAAATGGTAATTTT-GGTGTAATC-GGGATTAAAAGTGGAATTTTAAAAGATTCGGGGGTA
1 GGGTAAAATGGTAATTTTCGGTGAAATCAGGG-TTAAAA-TGGAATTTTAAAAGATTCGGGGGTA
* *
4328918 AAATGGAAATTTTTGGTGTAATCGGGGTTAAAAACGGAATTTTAAAAGATTCGA
64 AAATGGAAATTTTCGGTGAAATCGGGG-TAAAAACGGAATTTTAAAAGATTCGA
*
4328972 -GGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAATGGAATTTTAAAAGATTCGTGGGTAAA
1 GGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAATGGAATTTTAAAAGATTCGGGGGTAAA
*
4329036 ATGGTAATTTTCGGTGAAATCGGGGTAAAAACGGAATTTTAAAAGATTCGA
66 ATGGAAATTTTCGGTGAAATCGGGGTAAAAACGGAATTTTAAAAGATTCGA
4329087 GGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTCA
1 GGGTAAAATGGTAATTTTCGGTGAAATCAGGGTT-AAAATGGAATTTTAAAAGATTCGGGGGT-A
4329152 AAAT
64 AAAT
4329156 ATAATTTTTG
Statistics
Matches: 173, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
115 26 0.15
116 98 0.57
117 41 0.24
118 8 0.05
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (116 bp):
GGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAATGGAATTTTAAAAGATTCGGGGGTAAA
ATGGAAATTTTCGGTGAAATCGGGGTAAAAACGGAATTTTAAAAGATTCGA
Found at i:4329161 original size:59 final size:58
Alignment explanation
Indices: 4328852--4329163 Score: 443
Period size: 58 Copynumber: 5.4 Consensus size: 58
4328842 TATGGATACC
* *
4328852 CGGGGGTAAAATGGTAATTTT-GGTGTAATCGGGATTAAAAGTGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGG-TTAAAAATGGAATTTTAAAAGATT
* * * *
4328910 CGGGGGTAAAATGGAAATTTTTGGTGTAATCGGGGTTAAAAACGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATC-GGGTTAAAAATGGAATTTTAAAAGATT
*
4328969 C-GAGGTAAAATGGTAATTTTCGGTGAAATCAGGGTT-AAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATC-GGGTTAAAAATGGAATTTTAAAAGATT
* * *
4329026 CGTGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAACGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGTTAAAAATGGAATTTTAAAAGATT
*
4329084 CGAGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATC-GGGTTAAAAATGGAATTTTAAAAGATT
*
4329143 CGGGGGTCAAAAT-ATAATTTT
1 CGGGGGT-AAAATGGTAATTTT
4329164 TGGACAATTT
Statistics
Matches: 230, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
57 25 0.11
58 127 0.55
59 70 0.30
60 8 0.03
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:4329476 original size:162 final size:162
Alignment explanation
Indices: 4329260--4329898 Score: 1104
Period size: 162 Copynumber: 3.9 Consensus size: 162
4329250 ATTTGAAAAT
* * *
4329260 CTTGAAAAAATT-TTGGACCAATTTTGTAATT-AAATAAAAGTCGATTTAAGGATTAAATTAAAA
1 CTTG-AAAAATTATTGGGCCAATTTCGTAATTAAAAT-AAAGTTGATTT-AGGATTAAATTAAAA
4329323 CAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTG
63 CAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTG
4329388 GTGCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
128 GTGCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
*
4329423 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTAGGATTAAATTAAAACCA
1 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTAGGATTAAATTAAAACAA
4329488 ATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTGGTG
66 ATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTGGTG
4329553 CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
131 CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
*
4329585 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTAGGATTAAATTAAAACCA
1 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTAGGATTAAATTAAAACAA
4329650 ATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTGGTG
66 ATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTGGTG
4329715 CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
131 CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* *
4329747 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTGGGATTAAATTAAAATAA
1 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTAGGATTAAATTAAAACAA
* * ** *
4329812 ATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAA-AGTGACACGTGGCAGTCTATGGT
66 ATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATA-TGACACGTGGCAACCTCTGGT
*
4329876 ACAGTCAAACAGTCAAAGGACTA
130 GCAGTCAAACAGTCAAAGGACTA
4329899 AATTGAAAAG
Statistics
Matches: 460, Mismatches: 13, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
161 1 0.00
162 424 0.92
163 31 0.07
164 4 0.01
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (162 bp):
CTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGTTGATTTAGGATTAAATTAAAACAA
ATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAATATGACACGTGGCAACCTCTGGTG
CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:4330771 original size:23 final size:21
Alignment explanation
Indices: 4330721--4330772 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
4330711 ATTATTATTA
* *
4330721 TTATTAATGTTATTAATGTCT
1 TTATTAATCTTATTAATGCCT
4330742 TTCATTAATCCTTATTAATGCCAT
1 TT-ATTAAT-CTTATTAATGCC-T
4330766 TTATTAA
1 TTATTAA
4330773 ATTCAGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 6 0.23
23 15 0.58
24 3 0.12
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.52
Consensus pattern (21 bp):
TTATTAATCTTATTAATGCCT
Found at i:4331469 original size:6 final size:6
Alignment explanation
Indices: 4331453--4331561 Score: 95
Period size: 6 Copynumber: 18.3 Consensus size: 6
4331443 TTAAATTTGT
*
4331453 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GTTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
4331503 TTTAAA TTTAAGA --TAGA TTTAAA TTTAAA --TAAA TTTAAA -ATCAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4331547 TTTAAA CTTTAAA TT
1 TTTAAA -TTTAAA TT
4331562 AAAGCAAAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
4 5 0.06
5 9 0.11
6 53 0.63
7 11 0.13
8 6 0.07
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:4331476 original size:30 final size:30
Alignment explanation
Indices: 4331458--4331540 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 30
4331448 TTTGTTTTAT
4331458 AATTTAAAT-TTAAATTTAAATTTAAGTTA
1 AATTTAAATATTAAATTTAAATTTAAGTTA
*
4331487 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAAT-ATTAAATTTAAATTTAAGTTA
*
4331518 GATTTAAAT-TTAAA--TAAATTTAA
1 AATTTAAATATTAAATTTAAATTTAA
4331541 AATCAATTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.18
29 14 0.28
31 27 0.54
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (30 bp):
AATTTAAATATTAAATTTAAATTTAAGTTA
Found at i:4331489 original size:17 final size:16
Alignment explanation
Indices: 4331453--4331561 Score: 96
Period size: 17 Copynumber: 6.5 Consensus size: 16
4331443 TTAAATTTGT
4331453 TTTATAATTTAAATTTAAA
1 TTTA-AATTT-AA-TTAAA
4331472 TTTAAATTTAAGTTAAA
1 TTTAAATTTAA-TTAAA
4331489 TTTAAA--TAATTAAA
1 TTTAAATTTAATTAAA
* *
4331503 TTTAAATTTAAGATAGA
1 TTTAAATTTAA-TTAAA
*
4331520 TTTAAATTTAAATAAA
1 TTTAAATTTAATTAAA
* *
4331536 TTTAAAATCAATTTAAA
1 TTTAAATTTAA-TTAAA
4331553 CTTTAAATT
1 -TTTAAATT
4331562 AAAGCAAAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
14 11 0.14
15 3 0.04
16 16 0.21
17 31 0.40
18 12 0.16
19 4 0.05
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:4331505 original size:37 final size:38
Alignment explanation
Indices: 4331456--4331541 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 38
4331446 AATTTGTTTT
4331456 ATAATTTAAATTTAAATTTAA-ATTTA-AGTTAAATTTAA
1 ATAATTTAAATTTAAATTTAAGA--TAGAGTTAAATTTAA
*
4331494 ATAA-TTAAATTTAAATTTAAGATAGATTTAAATTTAA
1 ATAATTTAAATTTAAATTTAAGATAGAGTTAAATTTAA
4331531 ATAAATTTAAA
1 AT-AATTTAAA
4331542 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
36 2 0.05
37 29 0.67
38 7 0.16
39 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (38 bp):
ATAATTTAAATTTAAATTTAAGATAGAGTTAAATTTAA
Found at i:4331925 original size:68 final size:68
Alignment explanation
Indices: 4331841--4332308 Score: 679
Period size: 68 Copynumber: 6.8 Consensus size: 68
4331831 AAGACTTCGC
* * * *
4331841 TATCCAACTTTACTTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGAC
*
4331906 GTGT
65 ATGT
*
4331910 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGACA
4331975 TGT
66 TGT
* * *
4331978 TATCCACTCTATTTCAATTTCAAGGGGATGACGTCGCTCTTACTTCAATTTCAGAGAG-GAAGTC
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG-GTGAAGAC
* *
4332042 TTGA
65 ATGT
* *
4332046 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGAC
4332111 ATGT
65 ATGT
* *
4332115 TATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAG-GAAGTC
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG-GTGAAGAC
* *
4332179 TTGA
65 ATGT
* * *
4332183 TATCCAACTCTACTTCAATTTCAAGGGAATGACTTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGAC
*
4332248 GTGT
65 ATGT
*
4332252 TATCCACTCTACTTCAATTTCAAGGGGATGACTTTGCTCTTACTTCAATTTCAGAGG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGG
4332309 GGATGACGAC
Statistics
Matches: 359, Mismatches: 34, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
68 234 0.65
69 125 0.35
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (68 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGGTGAAGACA
TGT
Found at i:4332091 original size:137 final size:136
Alignment explanation
Indices: 4331854--4332307 Score: 759
Period size: 137 Copynumber: 3.3 Consensus size: 136
4331844 CCAACTTTAC
* * * * * *
4331854 TTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCAGAG-GTAAAGACGTGTTATCC-AC
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAG-GAAGTCTTGATATCCAAC
4331917 TCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATC
65 TCTACTTCAATTTCAA-GGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATC
4331982 CACTCTAT
129 CACTCTAT
*
4331990 TTCAATTTCAAGGGGATGACGTCGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
4332055 CTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
66 CTACTTCAATTTCAAG-GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
4332120 ACTCTAT
130 ACTCTAT
4332127 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
* *
4332192 CTACTTCAATTTCAAGGGAATGACTTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC
66 CTACTTCAATTTCAAGGG-ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
*
4332257 ACTCTAC
130 ACTCTAT
*
4332264 TTCAATTTCAAGGGGATGACTTTGCTCTTACTTCAATTTCAGAG
1 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
4332308 GGGATGACGA
Statistics
Matches: 302, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
136 55 0.18
137 247 0.82
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (136 bp):
TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAAGTCTTGATATCCAACT
CTACTTCAATTTCAAGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
CTCTAT
Found at i:4332263 original size:205 final size:205
Alignment explanation
Indices: 4331841--4332307 Score: 738
Period size: 205 Copynumber: 2.3 Consensus size: 205
4331831 AAGACTTCGC
* * *
4331841 TATCCAACTTTACTTCAATTTCGAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
* *
4331906 GTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAA
66 ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
* * *
4331971 GACATGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTCGCTCTTACTTCAATTTCAGAGAG
131 GACATGATATCCACTCTACTTCAATTTCAAGGGAATGACGTCGCTCTTACTTCAATTTCAGAGAG
* *
4332036 GAAGTCTTGA
196 GAAGACGTGA
*
4332046 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
*
4332111 ATGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
66 ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
* * * *
4332176 GTCTTGATATCCAACTCTACTTCAATTTCAAGGGAATGACTTTGCTCTTACTTCAATTTCAGAGA
131 GACATGATATCC-ACTCTACTTCAATTTCAAGGGAATGACGTCGCTCTTACTTCAATTTCAGAGA
* *
4332241 TGAAGACGTGT
195 GGAAGACGTGA
* *
4332252 TATCC-ACTCTACTTCAATTTCAAGGGGATGACTTTGCTCTTACTTCAATTTCAGAG
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAG
4332308 GGGATGACGA
Statistics
Matches: 241, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
205 181 0.75
206 60 0.25
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (205 bp):
TATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAGGAA
GACATGATATCCACTCTACTTCAATTTCAAGGGAATGACGTCGCTCTTACTTCAATTTCAGAGAG
GAAGACGTGA
Found at i:4334374 original size:13 final size:12
Alignment explanation
Indices: 4334352--4334394 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
4334342 AAAAAAATAC
4334352 AAAAATTATTTT
1 AAAAATTATTTT
4334364 AAAAATATATTTT
1 AAAAAT-TATTTT
*
4334377 -AAAATT-TTTA
1 AAAAATTATTTT
4334387 AAAAATTA
1 AAAAATTA
4334395 ATCAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 11 0.41
13 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:4335600 original size:139 final size:139
Alignment explanation
Indices: 4335450--4335712 Score: 508
Period size: 139 Copynumber: 1.9 Consensus size: 139
4335440 TTTTTTCTGT
4335450 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
1 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
*
4335515 AAGTGCTGCTGATGTACTCAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTCTTTTTCTGTT
66 AAGTGCTGCTGACGTACTCAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTCTTTTTCTGTT
4335580 ATTCTTTTA
131 ATTCTTTTA
4335589 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
1 TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
*
4335654 AAGTGCTGCTGACGTACTTAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTCTTTT
66 AAGTGCTGCTGACGTACTCAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTCTTTT
4335713 ATTTGTATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 122 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (139 bp):
TTTTCTTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
AAGTGCTGCTGACGTACTCAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTCTTTTTCTGTT
ATTCTTTTA
Found at i:4350541 original size:18 final size:19
Alignment explanation
Indices: 4350505--4350547 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4350495 CAAAAATTAC
*
4350505 ATAAAATTCAAAATAATTT
1 ATAAAATTAAAAATAATTT
*
4350524 TTAAAATTAAAAAT-ATTT
1 ATAAAATTAAAAATAATTT
4350542 ATAAAA
1 ATAAAA
4350548 AAATCAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAATTAAAAATAATTT
Found at i:4371477 original size:154 final size:153
Alignment explanation
Indices: 4371307--4371598 Score: 478
Period size: 154 Copynumber: 1.9 Consensus size: 153
4371297 TCATATACAA
*
4371307 CTTTTCCTGATATAGATTTTGTTTTACT-TATCTGCATGCTGATAGTTCCCTTTCTTCGTCTGAA
1 CTTTTCCTGATATAGATTTTGTTTTA-TATATCTGCATGCTGATAGTTCCCTTTCTTCATCTGAA
** **
4371371 TATAAGTGTACGGAATTAGTTTTTGCATATGCCAACTTTTTGCAGGTAAGATCAAACTAAATAAT
65 TATAAGTACACGGAATTAG-TTTTGCATACACCAACTTTTTGCAGGTAAGATCAAACTAAATAAT
4371436 CTATGGTAGAATTCATATACATTTT
129 CTATGGTAGAATTCATATACATTTT
*
4371461 CTTTTCCTGATATAGATTTTGTTTTATATATCTGCATGCTGATAGTTCCCTTTCTTCATTTGAAT
1 CTTTTCCTGATATAGATTTTGTTTTATATATCTGCATGCTGATAGTTCCCTTTCTTCATCTGAAT
* * *
4371526 ATAAGTACACGGAATTAGTTTTGTATACACTAACTTTTTGCAGGTAAGATCAAACTAAATCATCT
66 ATAAGTACACGGAATTAGTTTTGCATACACCAACTTTTTGCAGGTAAGATCAAACTAAATAATCT
4371591 ATGGTAGA
131 ATGGTAGA
4371599 CGCTATTCTC
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
153 51 0.40
154 77 0.60
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (153 bp):
CTTTTCCTGATATAGATTTTGTTTTATATATCTGCATGCTGATAGTTCCCTTTCTTCATCTGAAT
ATAAGTACACGGAATTAGTTTTGCATACACCAACTTTTTGCAGGTAAGATCAAACTAAATAATCT
ATGGTAGAATTCATATACATTTT
Found at i:4383976 original size:14 final size:15
Alignment explanation
Indices: 4383957--4383989 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4383947 ATCAACCAGG
*
4383957 TTTT-CCTTTGTTTT
1 TTTTCCCTTTCTTTT
4383971 TTTTCCCTTTCTTTT
1 TTTTCCCTTTCTTTT
4383986 TTTT
1 TTTT
4383990 TTTCACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCCCTTTCTTTT
Found at i:4383990 original size:18 final size:19
Alignment explanation
Indices: 4383962--4383998 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4383952 CCAGGTTTTC
*
4383962 CTTTGTTTTTTTTCCCTTT
1 CTTTGTTTTTTTTCACTTT
4383981 CTTT-TTTTTTTTCACTTT
1 CTTTGTTTTTTTTCACTTT
4383999 GGTTTCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (19 bp):
CTTTGTTTTTTTTCACTTT
Found at i:4393101 original size:2 final size:2
Alignment explanation
Indices: 4393094--4393120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4393084 AATCCGGGTT
4393094 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4393121 TTCTGTTTGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4396599 original size:29 final size:29
Alignment explanation
Indices: 4396554--4396668 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 29
4396544 AAAAATTTGA
*
4396554 GGTCGAAAAT-GTGATTTTTGGATGTTCGG
1 GGTC-AAAATGGTAATTTTTGGATGTTCGG
* *
4396583 GGTCAAAATGGTAATTTTTGGGTTTTCGG
1 GGTCAAAATGGTAATTTTTGGATGTTCGG
** * *
4396612 GGGAAAAATGGTAATTTTTAGATGTTTGG
1 GGTCAAAATGGTAATTTTTGGATGTTCGG
* *
4396641 AGTCAAAATGGCAATTTTTGGATGTTCG
1 GGTCAAAATGGTAATTTTTGGATGTTCG
4396669 AGGGAAAAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
28 5 0.07
29 65 0.93
ACGTcount: A:0.25, C:0.06, G:0.30, T:0.38
Consensus pattern (29 bp):
GGTCAAAATGGTAATTTTTGGATGTTCGG
Found at i:4396636 original size:58 final size:57
Alignment explanation
Indices: 4396559--4396677 Score: 157
Period size: 58 Copynumber: 2.1 Consensus size: 57
4396549 TTTGAGGTCG
* * * * * * *
4396559 AAAATGTGATTTTTGGATGTTCGGGGTCAAAATGGTAATTTTTGGGTTTTCGGGGGA
1 AAAATGTAATTTTTAGATGTTCGGAGTCAAAATGGCAATTTTTGGATGTTCGAGGGA
*
4396616 AAAATGGTAATTTTTAGATGTTTGGAGTCAAAATGGCAATTTTTGGATGTTCGAGGGA
1 AAAAT-GTAATTTTTAGATGTTCGGAGTCAAAATGGCAATTTTTGGATGTTCGAGGGA
4396674 AAAA
1 AAAA
4396678 ATACAATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 5 0.09
58 48 0.91
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTTAGATGTTCGGAGTCAAAATGGCAATTTTTGGATGTTCGAGGGA
Found at i:4396740 original size:30 final size:30
Alignment explanation
Indices: 4396682--4396805 Score: 164
Period size: 30 Copynumber: 4.2 Consensus size: 30
4396672 GAAAAAATAC
*
4396682 AATTTTGGAAAAGTTTA-GGGTGAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* *
4396711 GATTTTGGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
* *
4396741 AATTTTAGAAAAGTTTAAGGGTCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT
*
4396771 AATTTTGGAGAAA--TTAGAGGTCAAAATGT
1 AATTTTGGA-AAAGTTTAGGGGTCAAAATGT
4396800 AATTTT
1 AATTTT
4396806 TAAATAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
29 36 0.43
30 45 0.54
31 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTAGGGGTCAAAATGT
Found at i:4396797 original size:59 final size:58
Alignment explanation
Indices: 4396682--4396805 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 58
4396672 GAAAAAATAC
* * * * *
4396682 AATTTTGGAAAAGTTTAGGGTGAAAATGTGATTTTGGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTGGAAAAG-TTAGAGGTCAAAATGT
4396741 AATTTTAGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAGAAA-TTAGAGGTCAAAATGT
1 AATTTTAGAAAAGTTT-AGGGTCAAAATGTAATTTTGGA-AAAGTTAGAGGTCAAAATGT
4396800 AATTTT
1 AATTTT
4396806 TAAATAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 35 0.60
60 20 0.34
61 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (58 bp):
AATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTGGAAAAGTTAGAGGTCAAAATGT
Found at i:4398536 original size:17 final size:17
Alignment explanation
Indices: 4398497--4398548 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
4398487 ACCTTATTTT
*
4398497 TAAATTTAAATTTAAAC
1 TAAATTTAAATTTAAAA
** *
4398514 CCAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
4398531 TAAATTTAGATTTAAAA
1 TAAATTTAAATTTAAAA
4398548 T
1 T
4398549 TGGGTTCAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4404201 original size:22 final size:23
Alignment explanation
Indices: 4404166--4404211 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
4404156 GGCATGGAGG
4404166 AGGAAAGATGAGAGG-CGAGAGA
1 AGGAAAGATGAGAGGTCGAGAGA
*
4404188 AGGAAA-ATGAAGAGGTGGAGAGA
1 AGGAAAGATG-AGAGGTCGAGAGA
4404211 A
1 A
4404212 AAAAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.52
23 7 0.33
ACGTcount: A:0.48, C:0.02, G:0.43, T:0.07
Consensus pattern (23 bp):
AGGAAAGATGAGAGGTCGAGAGA
Found at i:4404208 original size:21 final size:21
Alignment explanation
Indices: 4404160--4404208 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
4404150 AAGATGGGCA
*
4404160 TGGAGGAGGAAAGATGAGAGG
1 TGGAGAAGGAAAGATGAGAGG
*
4404181 CGAGAGAAGGAAA-ATGAAGAGG
1 TG-GAGAAGGAAAGATG-AGAGG
4404203 TGGAGA
1 TGGAGA
4404209 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.43, C:0.02, G:0.47, T:0.08
Consensus pattern (21 bp):
TGGAGAAGGAAAGATGAGAGG
Found at i:4405517 original size:35 final size:35
Alignment explanation
Indices: 4405478--4405546 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
4405468 TATATAACTT
4405478 AAATTAAATAAATAACTATTGTTCTTTGAATACTG
1 AAATTAAATAAATAACTATTGTTCTTTGAATACTG
*
4405513 AAATTAAATAAATAATTATTGTTCTTTGAATACT
1 AAATTAAATAAATAACTATTGTTCTTTGAATACT
4405547 CAATGATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (35 bp):
AAATTAAATAAATAACTATTGTTCTTTGAATACTG
Found at i:4410832 original size:31 final size:29
Alignment explanation
Indices: 4410796--4410862 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
4410786 CTTTTATTTT
4410796 AAAAATATGACAATAAAAAAAACAAATAATA
1 AAAAATATGA-AATAAAAAAAACAAA-AATA
* ** *
4410827 TAAAATA-GATTTAAAAAAAAGAAAAATA
1 AAAAATATGAAATAAAAAAAACAAAAATA
4410855 AAAAATAT
1 AAAAATAT
4410863 ACATAATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 10 0.33
29 12 0.40
30 2 0.07
31 6 0.20
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.19
Consensus pattern (29 bp):
AAAAATATGAAATAAAAAAAACAAAAATA
Found at i:4414563 original size:31 final size:30
Alignment explanation
Indices: 4414527--4414597 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
4414517 CTTTTATTTT
4414527 AAAAATATGACAATAAAAAAAACAAATAATA
1 AAAAATATGACAATAAAAAAAACAAA-AATA
* ** *
4414558 TAAAATA-GA-TTTAAAAAAAAGAAAAATA
1 AAAAATATGACAATAAAAAAAACAAAAATA
4414586 AAAAATAT-ACAA
1 AAAAATATGACAA
4414598 AATGCTATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
28 11 0.35
29 12 0.39
30 2 0.06
31 6 0.19
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (30 bp):
AAAAATATGACAATAAAAAAAACAAAAATA
Found at i:4418295 original size:31 final size:29
Alignment explanation
Indices: 4418259--4418325 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
4418249 CTTTTATTTT
4418259 AAAAATATGACAATAAAAAAAACAAATAATA
1 AAAAATATGA-AATAAAAAAAACAAA-AATA
* ** *
4418290 TAAAATA-GATTTAAAAAAAAGAAAAATA
1 AAAAATATGAAATAAAAAAAACAAAAATA
4418318 AAAAATAT
1 AAAAATAT
4418326 ACATAATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 10 0.33
29 12 0.40
30 2 0.07
31 6 0.20
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.19
Consensus pattern (29 bp):
AAAAATATGAAATAAAAAAAACAAAAATA
Found at i:4424004 original size:31 final size:29
Alignment explanation
Indices: 4423968--4424034 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
4423958 CTTTTATTTT
4423968 AAAAATATGACAATAAAAAAAACAAATAATA
1 AAAAATATGA-AATAAAAAAAACAAA-AATA
* ** *
4423999 TAAAATA-GATTTAAAAAAAAGAAAAATA
1 AAAAATATGAAATAAAAAAAACAAAAATA
4424027 AAAAATAT
1 AAAAATAT
4424035 ACATAATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 10 0.33
29 12 0.40
30 2 0.07
31 6 0.20
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.19
Consensus pattern (29 bp):
AAAAATATGAAATAAAAAAAACAAAAATA
Done.