Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 102 of 106
Found at i:38989153 original size:16 final size:16
Alignment explanation
Indices: 38989128--38989162 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38989118 TGATAAAGTC
38989128 AATTTATTATTT-TTT
1 AATTTATTATTTATTT
38989143 AATTGTATTATTTATTT
1 AATT-TATTATTTATTT
38989160 AAT
1 AAT
38989163 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 8 0.44
17 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
AATTTATTATTTATTT
Found at i:39003298 original size:23 final size:23
Alignment explanation
Indices: 39003263--39003308 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
39003253 AAAGTCATAC
39003263 TCTTCCTTCTTCTCAAAATATTCT
1 TCTTCCTTCTTCTCAAAAT-TTCT
39003287 TCTT-CTTCTTCTCAAAATTTCT
1 TCTTCCTTCTTCTCAAAATTTCT
39003309 AACAGGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.18
23 14 0.64
24 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.52
Consensus pattern (23 bp):
TCTTCCTTCTTCTCAAAATTTCT
Found at i:39004391 original size:2 final size:2
Alignment explanation
Indices: 39004384--39004422 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39004374 AAAGTTGTAA
39004384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39004423 TNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39004474 original size:2 final size:2
Alignment explanation
Indices: 39004467--39004516 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
39004457 AAAGTTAGTA
* *
39004467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39004509 AA AT AT AT
1 AT AT AT AT
39004517 TTTCATGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:39013743 original size:18 final size:18
Alignment explanation
Indices: 39013729--39013765 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39013719 TTATTTTCTT
39013729 TTTACCTT-ATATTTTTC
1 TTTACCTTCATATTTTTC
*
39013746 TTTATCTTCATATTTTTC
1 TTTACCTTCATATTTTTC
39013764 TT
1 TT
39013766 GAACCAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTACCTTCATATTTTTC
Found at i:39024918 original size:19 final size:19
Alignment explanation
Indices: 39024896--39024938 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
39024886 TATTATAATA
*
39024896 TTTATCAAATATAACAAAT
1 TTTATCAAATATAAAAAAT
* * *
39024915 TTTAACCATTATAAAAAAT
1 TTTATCAAATATAAAAAAT
39024934 TTTAT
1 TTTAT
39024939 AATTTCATAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTATCAAATATAAAAAAT
Found at i:39027969 original size:22 final size:23
Alignment explanation
Indices: 39027931--39027979 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
39027921 AAGTAAACAA
* *
39027931 AAAATAAAATTATAATTCAAGT-
1 AAAATAAAAGTATAATTAAAGTG
39027953 AAAATAAATAGTA-AATTAAAGTG
1 AAAATAAA-AGTATAATTAAAGTG
39027976 AAAA
1 AAAA
39027980 ATCTATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (23 bp):
AAAATAAAAGTATAATTAAAGTG
Found at i:39037656 original size:13 final size:13
Alignment explanation
Indices: 39037624--39037665 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
39037614 CAAACGGCTC
* *
39037624 TTTCTCTTTCTCT
1 TTTCTTTTTCTTT
*
39037637 TTCCTTTTTCTTT
1 TTTCTTTTTCTTT
39037650 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
39037663 TTT
1 TTT
39037666 GGAGGGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:39051965 original size:23 final size:24
Alignment explanation
Indices: 39051946--39051991 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
39051936 TACTTTTTAT
39051946 AAAATC-AAAAAATAATTTTTAAA
1 AAAATCAAAAAAATAATTTTTAAA
*
39051969 AAAATCAAAAAAATGATTTTTAA
1 AAAATCAAAAAAATAATTTTTAA
39051992 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATCAAAAAAATAATTTTTAAA
Found at i:39058147 original size:56 final size:55
Alignment explanation
Indices: 39058073--39058225 Score: 182
Period size: 56 Copynumber: 2.7 Consensus size: 55
39058063 CAGCCGCTGG
**
39058073 AAGAATCAAAGACAAAACATAGATACACCTGCTCCTTTATTTAGAGTTAAACTCTT
1 AAGAATCAAAGAC-AAACATAGATACACCTGCTCCTTTATTTAGAGAAAAACTCTT
* * * * *
39058129 AAGAATAAAAAACTAAACATAGGTATACCTACTCCTTTATTTAGAGAAAAACTCTT
1 AAGAATCAAAGAC-AAACATAGATACACCTGCTCCTTTATTTAGAGAAAAACTCTT
* *
39058185 AAGAATCAAAGACAAA-ATAGAGGTTCACCTGCTCCATTATT
1 AAGAATCAAAGACAAACATAGA--TACACCTGCTCCTTTATT
39058226 AGTAACAACA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 4 0.05
55 3 0.04
56 73 0.91
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (55 bp):
AAGAATCAAAGACAAACATAGATACACCTGCTCCTTTATTTAGAGAAAAACTCTT
Found at i:39066289 original size:2 final size:2
Alignment explanation
Indices: 39066282--39066314 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39066272 AATTATTTAC
39066282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39066315 AAGTTTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39066467 original size:2 final size:2
Alignment explanation
Indices: 39066460--39066493 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39066450 ACTTAATGTA
39066460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39066494 ACTAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39067116 original size:6 final size:6
Alignment explanation
Indices: 39067101--39067146 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
39067091 AGCACCAACA
* *
39067101 ACCC-C ACCATC ACCATC ACCCTC ACCCTC ACCCTC ACCCTC ACCCT
1 ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ACCCT
39067147 GTTTGCCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.22, C:0.63, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCCTC
Found at i:39068745 original size:3 final size:3
Alignment explanation
Indices: 39068737--39068761 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39068727 TTAAATACAT
39068737 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
39068762 ATACAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39069476 original size:19 final size:19
Alignment explanation
Indices: 39069441--39069479 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
39069431 CATGATATAA
39069441 TATTTAAAAAATCTTTAAAT
1 TATTTAAAAAA-CTTTAAAT
39069461 TATTTAAAAAGA-TTTAAAT
1 TATTTAAAAA-ACTTTAAAT
39069480 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 10 0.56
21 1 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
TATTTAAAAAACTTTAAAT
Found at i:39069548 original size:30 final size:30
Alignment explanation
Indices: 39069514--39069580 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
39069504 TAATCGAGTC
* * *
39069514 TTTATACTTTTAATTTGAGTTAAATAAATT
1 TTTATAATTTTAATTTGAGTCAAATAAATA
**
39069544 TTTATAATTTTGTTTTGAGTCAAATAAATA
1 TTTATAATTTTAATTTGAGTCAAATAAATA
39069574 TTTATAA
1 TTTATAA
39069581 CTAATAATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTAATTTGAGTCAAATAAATA
Found at i:39069907 original size:30 final size:30
Alignment explanation
Indices: 39069836--39069907 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
39069826 TATATTTAAT
* *
39069836 TAAATTTTTATATTTTTATTTTAAGTCAAA
1 TAAATATTTATATTTTCATTTTAAGTCAAA
39069866 TAAATCA-TTATATTTTCATTTTGAA-TCAAA
1 TAAAT-ATTTATATTTTCATTTT-AAGTCAAA
39069896 TAAATATTTATA
1 TAAATATTTATA
39069908 ATTAATGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 1 0.03
30 34 0.92
31 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (30 bp):
TAAATATTTATATTTTCATTTTAAGTCAAA
Found at i:39072274 original size:2 final size:2
Alignment explanation
Indices: 39072267--39072302 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
39072257 GTACTACTGC
* *
39072267 AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39072303 TTTAACTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:39086973 original size:19 final size:19
Alignment explanation
Indices: 39086949--39086986 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39086939 ATTGACAAAC
39086949 ACAACAAATAAGTAAAGAT
1 ACAACAAATAAGTAAAGAT
39086968 ACAACAAATAAGTAAAGAT
1 ACAACAAATAAGTAAAGAT
39086987 TGCGCATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (19 bp):
ACAACAAATAAGTAAAGAT
Found at i:39088412 original size:14 final size:14
Alignment explanation
Indices: 39088376--39088468 Score: 52
Period size: 14 Copynumber: 6.6 Consensus size: 14
39088366 ATTAACTACT
39088376 AATTAAATTAATAAA
1 AATTAAA-TAATAAA
*
39088391 AATAAAATAATAAA
1 AATTAAATAATAAA
* *
39088405 ATTTAAAT-TTAAA
1 AATTAAATAATAAA
*
39088418 TAATCAAA-AATAAA
1 -AATTAAATAATAAA
*
39088432 GATCTTAAAT-AT-AA
1 -A-ATTAAATAATAAA
*
39088446 ACTTAAATAATTAAA
1 AATTAAATAA-TAAA
39088461 AA-TAAATA
1 AATTAAATA
39088469 TCCATACAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
12 7 0.12
13 6 0.10
14 32 0.53
15 15 0.25
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (14 bp):
AATTAAATAATAAA
Found at i:39088427 original size:35 final size:34
Alignment explanation
Indices: 39088378--39088466 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 34
39088368 TAACTACTAA
* *
39088378 TTAAATTAATAAAAATAAA-ATAATAAAATTTAAAT
1 TTAAA-TAATAAAAATAAAGAT-ATAAAATATAAAC
* *
39088413 TTAAATAATCAAAAATAAAGATCTTAAATATAAAC
1 TTAAATAAT-AAAAATAAAGATATAAAATATAAAC
39088448 TTAAATAATTAAAAATAAA
1 TTAAATAA-TAAAAATAAA
39088467 TATCCATACA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 4 0.09
35 40 0.85
36 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (34 bp):
TTAAATAATAAAAATAAAGATATAAAATATAAAC
Found at i:39088485 original size:40 final size:40
Alignment explanation
Indices: 39088442--39088585 Score: 144
Period size: 40 Copynumber: 3.6 Consensus size: 40
39088432 GATCTTAAAT
* * ** *
39088442 ATAAACTTAAATAATTAAAAATAAATATCCATACAACGAT
1 ATAAACTTAAATAACTAAAAATAAATATCCAAACAATAAC
* * * ** *
39088482 ATAAACTTATATAATTATACCTAAATATCCAAATAATAAC
1 ATAAACTTAAATAACTAAAAATAAATATCCAAACAATAAC
* * *
39088522 ATAAGCTTAAATAACTAAATACAAATATCCAAACAAATAAC
1 ATAAACTTAAATAACTAAAAATAAATATCCAAAC-AATAAC
*
39088563 ATAAACTTAAATAACAAAAAATA
1 ATAAACTTAAATAACTAAAAATA
39088586 TAATTTTTAT
Statistics
Matches: 82, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
40 57 0.70
41 25 0.30
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.26
Consensus pattern (40 bp):
ATAAACTTAAATAACTAAAAATAAATATCCAAACAATAAC
Found at i:39089322 original size:26 final size:26
Alignment explanation
Indices: 39089292--39089363 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
39089282 TACTATTTAG
39089292 ATTA-TAATTATTTTAAAAATTTATAA
1 ATTATTAA-TATTTTAAAAATTTATAA
39089318 ATTATTAATATTTTAAAAATTTATAA
1 ATTATTAATATTTTAAAAATTTATAA
*
39089344 ATTATTAATATTTAAAAAAT
1 ATTATTAATATTTTAAAAAT
39089364 AAAATAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 41 0.93
27 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTATTAATATTTTAAAAATTTATAA
Found at i:39089902 original size:14 final size:14
Alignment explanation
Indices: 39089883--39089910 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39089873 GTTTGGTAAA
39089883 TTTTTTTATAAGTT
1 TTTTTTTATAAGTT
39089897 TTTTTTTATAAGTT
1 TTTTTTTATAAGTT
39089911 ATAATTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
TTTTTTTATAAGTT
Found at i:39108503 original size:22 final size:21
Alignment explanation
Indices: 39108452--39108509 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
39108442 ATACTCAAAA
39108452 TTAAAATAATTTAGTCCTTTAAT
1 TTAAAA-AATTTAGTCCTTT-AT
*
39108475 TTTAAAAATTTAGTCCCTCTT-T
1 TTAAAAAATTTAGT-CCT-TTAT
39108497 TTAAAAAAATTTA
1 TT-AAAAAATTTA
39108510 ATTTTACCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 11 0.37
23 17 0.57
24 2 0.07
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAAAAAATTTAGTCCTTTAT
Found at i:39108632 original size:32 final size:32
Alignment explanation
Indices: 39108595--39108657 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
39108585 GCATACCATG
* *
39108595 TGGCATCGACATGATGACGTGACAATATCACA
1 TGGCATCGACATGATAACATGACAATATCACA
*
39108627 TGGCATCGACATGATAACATGACAATGTCAC
1 TGGCATCGACATGATAACATGACAATATCAC
39108658 GTGATACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (32 bp):
TGGCATCGACATGATAACATGACAATATCACA
Found at i:39110193 original size:2 final size:2
Alignment explanation
Indices: 39110180--39110255 Score: 77
Period size: 2 Copynumber: 38.5 Consensus size: 2
39110170 AATGCTTATG
* * * *
39110180 TA TA TG TA TA TA TA -A TA TA TC TA TA CA GT- TA TC TA TA TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
39110221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39110256 TCATACCACT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
1 3 0.05
2 57 0.93
3 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39110374 original size:21 final size:20
Alignment explanation
Indices: 39110337--39110375 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39110327 CTATTATATA
*
39110337 TTATAATATTAACATATAAC
1 TTATAATATTAAAATATAAC
*
39110357 TTATATTATTTAAAATATA
1 TTATAATA-TTAAAATATA
39110376 TAACTTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATAATATTAAAATATAAC
Found at i:39115155 original size:2 final size:2
Alignment explanation
Indices: 39115150--39115181 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39115140 TTTTTTTATT
39115150 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39115182 TTACAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:39115567 original size:114 final size:114
Alignment explanation
Indices: 39115365--39115595 Score: 446
Period size: 114 Copynumber: 2.0 Consensus size: 114
39115355 TATGACTATC
39115365 ATTGTTTTTTTATTTTTTTGTTATTTCTATTCTTATTCATTTATTGATTTTTTTAGACCAAACCT
1 ATTGTTTTTTTATTTTTTTGTTATTTCTATTCTTATTCATTTATTGATTTTTTTAGACCAAACCT
39115430 AAGAACTCTCATAAATATGAATATTGATCCCAATATATATATATATACAT
66 AAGAACTCTCATAAATATGAATATTGATCCCAATATATATATATATAC-T
39115480 ATTGTTTTTTTATTTTTTTGTTATTTCTATTCTTATTCATTTATTGA-TTTTTTAGACCAAACCT
1 ATTGTTTTTTTATTTTTTTGTTATTTCTATTCTTATTCATTTATTGATTTTTTTAGACCAAACCT
39115544 AAGAACTCTCATAAATATGAATATTGATCCCAATATATATATATATACT
66 AAGAACTCTCATAAATATGAATATTGATCCCAATATATATATATATACT
39115593 ATT
1 ATT
39115596 ACAACCATTA
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
113 4 0.03
114 65 0.56
115 47 0.41
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (114 bp):
ATTGTTTTTTTATTTTTTTGTTATTTCTATTCTTATTCATTTATTGATTTTTTTAGACCAAACCT
AAGAACTCTCATAAATATGAATATTGATCCCAATATATATATATATACT
Found at i:39116098 original size:11 final size:11
Alignment explanation
Indices: 39116068--39116106 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
39116058 CCCCGTCGAC
39116068 TTCTTCTTTCTTT
1 TTCTT-TTT-TTT
39116081 TTC-TTTTTTT
1 TTCTTTTTTTT
39116091 TTCTTTTTTTT
1 TTCTTTTTTTT
39116102 TTCTT
1 TTCTT
39116107 CTCTTCCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.24
11 15 0.60
12 1 0.04
13 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:39116102 original size:10 final size:10
Alignment explanation
Indices: 39116071--39116102 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
39116061 CGTCGACTTC
*
39116071 TTCTTTCTTT
1 TTCTTTTTTT
39116081 TTCTTTTTTT
1 TTCTTTTTTT
39116091 TTCTTTTTTT
1 TTCTTTTTTT
39116101 TT
1 TT
39116103 TCTTCTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:39116111 original size:16 final size:16
Alignment explanation
Indices: 39116071--39116111 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
39116061 CGTCGACTTC
39116071 TTCTTTCTTTTTCTTT
1 TTCTTTCTTTTTCTTT
*
39116087 TTTTTTCTTTTT-TTT
1 TTCTTTCTTTTTCTTT
39116102 TTCTTCTCTT
1 TTCTT-TCTT
39116112 CCTCTCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTCTTTCTTTTTCTTT
Found at i:39116165 original size:13 final size:13
Alignment explanation
Indices: 39116147--39116188 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
39116137 GCTGGCTTCT
*
39116147 TCTTTCTTTTTCC
1 TCTTTCTTTCTCC
39116160 TCTTTCTTTCTCC
1 TCTTTCTTTCTCC
*
39116173 T-TCTCTTTCT-C
1 TCTTTCTTTCTCC
39116184 TCTTT
1 TCTTT
39116189 TCTCCCTGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTTTCTTTCTCC
Found at i:39116193 original size:75 final size:75
Alignment explanation
Indices: 39116007--39116187 Score: 205
Period size: 75 Copynumber: 2.5 Consensus size: 75
39115997 TCTCCTTTTT
* *
39116007 TTTTTTTCTTTCTTTCTC-TCCCTTAT-TTC-CTT-CT-TCCTTTCCTTTCTCTCTCCCCGTCGA
1 TTTTTCTCTTTCTTTCTCTTCTCTT-TCTTCTCTTCCTCTCCTTTCCTTTCTCTCTCCCCGTCGA
39116067 CTTCTTCTTTC
65 CTTCTTCTTTC
* * * * * *
39116078 TTTTTCTTTTTTTTTCTTTTTTTTTTCTTCTCTTCCTCTCCTTTCCTTTCTCTCTCCCCG-CTGG
1 TTTTTCTCTTTCTTTCTCTTCTCTTTCTTCTCTTCCTCTCCTTTCCTTTCTCTCTCCCCGTC-GA
39116142 CTTCTTCTTTC
65 CTTCTTCTTTC
39116153 TTTTTCCTCTTTCTTTCTCCTTCTCTTTC-TCTCTT
1 TTTTT-CTCTTTCTTTCT-CTTCTCTTTCTTCTCTT
39116188 TTCTCCCTGC
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
71 15 0.17
72 6 0.07
73 3 0.03
74 3 0.03
75 39 0.44
76 16 0.18
77 7 0.08
ACGTcount: A:0.01, C:0.34, G:0.03, T:0.62
Consensus pattern (75 bp):
TTTTTCTCTTTCTTTCTCTTCTCTTTCTTCTCTTCCTCTCCTTTCCTTTCTCTCTCCCCGTCGAC
TTCTTCTTTC
Found at i:39116232 original size:13 final size:14
Alignment explanation
Indices: 39116214--39116249 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
39116204 CACACCCTTC
39116214 TCCTCTTCTCTCT-
1 TCCTCTTCTCTCTA
39116227 TCCTCTTCTCTCTA
1 TCCTCTTCTCTCTA
*
39116241 TCGTCTTCT
1 TCCTCTTCT
39116250 TCCTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.03, C:0.42, G:0.03, T:0.53
Consensus pattern (14 bp):
TCCTCTTCTCTCTA
Found at i:39122812 original size:32 final size:32
Alignment explanation
Indices: 39122766--39122843 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
39122756 TAAAATGATG
* *
39122766 ATGTGAC-ATGTCACATGATATCGACATAATA
1 ATGTGACAATGTCACATGACACCGACATAATA
*
39122797 ATGTGACAATGTCACATGACACCGACATGATA
1 ATGTGACAATGTCACATGACACCGACATAATA
* *
39122829 ATATGACAATATCAC
1 ATGTGACAATGTCAC
39122844 GTGTCACTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 7 0.17
32 34 0.83
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (32 bp):
ATGTGACAATGTCACATGACACCGACATAATA
Found at i:39124075 original size:12 final size:12
Alignment explanation
Indices: 39124041--39124078 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39124031 AATATATGTA
39124041 TATATATATAA-
1 TATATATATAAT
*
39124052 TATATTACATAAT
1 TATA-TATATAAT
39124065 TATATATATAAT
1 TATATATATAAT
39124077 TA
1 TA
39124079 ATGATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 15 0.65
13 4 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATATAAT
Found at i:39124203 original size:134 final size:136
Alignment explanation
Indices: 39123983--39124249 Score: 346
Period size: 134 Copynumber: 2.0 Consensus size: 136
39123973 AATGTAATCG
*
39123983 TATAAATAAAGTTTATTATAAGTTATAGTAATGCTTAGGTATAAATTAAATATATGTATATATAT
1 TATAAATAAAGTCTATTATAAGTTATAGTAATGCTTAGGTATAAATTAAATATATGTATATATAT
* *
39124048 ATAATATATTACATAATTATAT-ATAT-AATTAATGATACAAATTTTATGTTAAAATATTTTATA
66 ATAATATATTACATAATTATATAATATAAATTAATGACACAAATTATATGTTAAAATATTTTATA
39124111 TGATCA
131 TGATCA
* *
39124117 TATAAATAAAGTCTATTATAAGTTATAGTAATGTTTATGTATAAATTAAATATATGTATATATA-
1 TATAAATAAAGTCTATTATAAGTTATAGTAATGCTTAGGTATAAATTAAATATATGTATATATAT
** * * * * *
39124181 AT-ATATGACTT-TGTTATATATATACATATAAAATTAATGACATAACTTATATGTTATAATGTT
66 ATAATAT-A-TTACATAAT-TATATA-ATAT-AAATTAATGACACAAATTATATGTTAAAATATT
39124244 TTATAT
126 TTATAT
39124250 CAAAGTTTAT
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
132 4 0.04
133 6 0.05
134 68 0.60
136 4 0.04
138 32 0.28
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (136 bp):
TATAAATAAAGTCTATTATAAGTTATAGTAATGCTTAGGTATAAATTAAATATATGTATATATAT
ATAATATATTACATAATTATATAATATAAATTAATGACACAAATTATATGTTAAAATATTTTATA
TGATCA
Found at i:39124415 original size:22 final size:23
Alignment explanation
Indices: 39124379--39124430 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
39124369 TATGTATATG
*
39124379 TATATATAATATATTTATACAAT
1 TATATATAATATATTCATACAAT
*
39124402 TATATAT-ATATATTCATACCAT
1 TATATATAATATATTCATACAAT
*
39124424 TTTATAT
1 TATATAT
39124431 TACGAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATATAATATATTCATACAAT
Found at i:39136545 original size:41 final size:41
Alignment explanation
Indices: 39136500--39136580 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
39136490 ACATATTAAG
39136500 TTATTAGATTAAACTATTAAAATATAATATGTTATGATAGA
1 TTATTAGATTAAACTATTAAAATATAATATGTTATGATAGA
* * *
39136541 TTATTAGATTGAACTGTTAAGATATAATATGTTATGATAG
1 TTATTAGATTAAACTATTAAAATATAATATGTTATGATAG
39136581 GTTTAGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (41 bp):
TTATTAGATTAAACTATTAAAATATAATATGTTATGATAGA
Found at i:39137187 original size:18 final size:19
Alignment explanation
Indices: 39137157--39137196 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
39137147 AATATATGAG
39137157 TAAATAGAATAAA-AATAAA
1 TAAATAGAATAAACAA-AAA
39137176 TAAATA-AATAAACAAAAA
1 TAAATAGAATAAACAAAAA
39137194 TAA
1 TAA
39137197 TACTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (19 bp):
TAAATAGAATAAACAAAAA
Found at i:39145567 original size:16 final size:16
Alignment explanation
Indices: 39145545--39145585 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39145535 TTTAAAATCT
* *
39145545 AAAATGATCTGAATTT
1 AAAATGATCAGAATTC
*
39145561 GAAATGATCAGAATTC
1 AAAATGATCAGAATTC
39145577 AAAATGATC
1 AAAATGATC
39145586 CAAACCATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (16 bp):
AAAATGATCAGAATTC
Found at i:39151823 original size:21 final size:21
Alignment explanation
Indices: 39151797--39151839 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39151787 TTAGTGGCGG
39151797 CGGCGACGGC-AGCGGAAGCGA
1 CGGCGACGGCGA-CGGAAGCGA
*
39151818 CGGCGACTGCGACGGAAGCGA
1 CGGCGACGGCGACGGAAGCGA
39151839 C
1 C
39151840 TGTGACGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.30, G:0.44, T:0.02
Consensus pattern (21 bp):
CGGCGACGGCGACGGAAGCGA
Found at i:39152120 original size:10 final size:10
Alignment explanation
Indices: 39152105--39152135 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
39152095 ACCGGCCATG
39152105 AAAAAAA-AA
1 AAAAAAAGAA
39152114 AAAAAAAGAA
1 AAAAAAAGAA
39152124 AAAAAAAGAA
1 AAAAAAAGAA
39152134 AA
1 AA
39152136 GGGTAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:39152127 original size:15 final size:15
Alignment explanation
Indices: 39152107--39152136 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39152097 CGGCCATGAA
39152107 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
39152122 AAAAAAAAAGAAAAG
1 AAAAAAAAAAAAAAG
39152137 GGTAAAGTAN
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:39153045 original size:15 final size:14
Alignment explanation
Indices: 39153025--39153060 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
39153015 AATTATTTTG
39153025 AAATAATGAAAAAAT
1 AAATAAT-AAAAAAT
39153040 AAATAATAAAAAAT
1 AAATAATAAAAAAT
39153054 AAA-AATA
1 AAATAATA
39153061 TCTTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 10 0.48
15 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAATAAAAAAT
Found at i:39153175 original size:17 final size:17
Alignment explanation
Indices: 39153153--39153186 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39153143 AATATTATCT
39153153 TTATAATTAAAATATTA
1 TTATAATTAAAATATTA
39153170 TTATAATTAAAATATTA
1 TTATAATTAAAATATTA
39153187 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAATTAAAATATTA
Found at i:39153810 original size:20 final size:19
Alignment explanation
Indices: 39153768--39153810 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
39153758 TCGTTATATT
39153768 TAATATTATATCAATAAAA
1 TAATATTATATCAATAAAA
*
39153787 -AATATTTTATCAATATAAA
1 TAATATTATATCAATA-AAA
39153806 TAATA
1 TAATA
39153811 AAAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.67
19 3 0.14
20 4 0.19
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATTATATCAATAAAA
Found at i:39153833 original size:26 final size:27
Alignment explanation
Indices: 39153766--39153835 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
39153756 TATCGTTATA
39153766 TTTAATATTA-T-ATCAATAAAAAATAT
1 TTTAATATTATTAAT-AATAAAAAATAT
* *
39153792 TTT-ATCAATATAAATAATAAAAAA-AT
1 TTTAAT-ATTATTAATAATAAAAAATAT
39153818 TTTAATATTATTAATAAT
1 TTTAATATTATTAATAAT
39153836 TGAATTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
25 2 0.06
26 21 0.58
27 11 0.31
28 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAATATTATTAATAATAAAAAATAT
Found at i:39156320 original size:22 final size:22
Alignment explanation
Indices: 39156278--39156332 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
39156268 ATTTTTGAAA
39156278 ATTATGTGACTAGTTTTTAGGT
1 ATTATGTGACTAGTTTTTAGGT
*
39156300 ATTATGTTACTAGTTTTTAGGT
1 ATTATGTGACTAGTTTTTAGGT
*
39156322 ATTACGTGACT
1 ATTATGTGACT
39156333 GACTTTGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (22 bp):
ATTATGTGACTAGTTTTTAGGT
Found at i:39156371 original size:26 final size:26
Alignment explanation
Indices: 39156342--39156409 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
39156332 TGACTTTGAA
*
39156342 CATTGCGTGATTAGTTTTTGATAAGG
1 CATTACGTGATTAGTTTTTGATAAGG
* **
39156368 CATTACGTGATTAGTTTTTTATATTG
1 CATTACGTGATTAGTTTTTGATAAGG
*
39156394 TATTACGTGATTAGTT
1 CATTACGTGATTAGTT
39156410 GATAGGTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.49
Consensus pattern (26 bp):
CATTACGTGATTAGTTTTTGATAAGG
Found at i:39156444 original size:23 final size:23
Alignment explanation
Indices: 39156417--39156488 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
39156407 GTTGATAGGT
*
39156417 ATTGCGTGACTTGTTAGTAAGAC
1 ATTGCGTGACTAGTTAGTAAGAC
39156440 ATTGCGTGACTAGTTAGTAAGATC
1 ATTGCGTGACTAGTTAGTAAGA-C
* * *
39156464 -TTGTGTGACTAGTTACTAAGGC
1 ATTGCGTGACTAGTTAGTAAGAC
39156486 ATT
1 ATT
39156489 ATGTGATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 41 0.95
24 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.36
Consensus pattern (23 bp):
ATTGCGTGACTAGTTAGTAAGAC
Found at i:39157393 original size:19 final size:20
Alignment explanation
Indices: 39157359--39157396 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39157349 AGTCATGTCA
*
39157359 AAAATTAATTAAAAATAATT
1 AAAATTAATAAAAAATAATT
39157379 AAAATT-ATAAAAAATAAT
1 AAAATTAATAAAAAATAAT
39157397 ATTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTAATAAAAAATAATT
Found at i:39159734 original size:101 final size:101
Alignment explanation
Indices: 39159559--39159760 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
39159549 TACAATGGAA
39159559 ATCTTGCTGGACTCAACGTTCCTTTAGATGAGTCTAATGTTCAGCCTTCTCCTGCACCATTCAAA
1 ATCTTGCTGGACTCAACGTTCCTTTAGATGAGTCTAATGTTCAGCCTTCTCCTGCACCATTCAAA
39159624 AAGTCAAAGAAAGGATTACAAAAGCAGATTAAGTAC
66 AAGTCAAAGAAAGGATTACAAAAGCAGATTAAGTAC
39159660 ATCTTGCTGGACTCAACGTTCCTTTAGATGAGTCTAATGTTCAGCCTTCTCCTGCACCATTCAAA
1 ATCTTGCTGGACTCAACGTTCCTTTAGATGAGTCTAATGTTCAGCCTTCTCCTGCACCATTCAAA
39159725 AAGTCAAAGAAAGGATTACAAAAGCAGATTAAGTAC
66 AAGTCAAAGAAAGGATTACAAAAGCAGATTAAGTAC
39159761 TCACTTAGTG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (101 bp):
ATCTTGCTGGACTCAACGTTCCTTTAGATGAGTCTAATGTTCAGCCTTCTCCTGCACCATTCAAA
AAGTCAAAGAAAGGATTACAAAAGCAGATTAAGTAC
Found at i:39161924 original size:36 final size:36
Alignment explanation
Indices: 39161878--39162029 Score: 164
Period size: 36 Copynumber: 4.2 Consensus size: 36
39161868 AATTGTTTAA
* * *
39161878 TTTAATCAATTAGATCTAATAACTTAATTAAACAAT
1 TTTAATCAATTAGACCCAACAACTTAATTAAACAAT
* ** *
39161914 TTTAATCAATTAGGCCCAATGACTTAATTAAATAAT
1 TTTAATCAATTAGACCCAACAACTTAATTAAACAAT
* * *
39161950 TTTAATCAATTAGACCCAACGACTTAAGTAAATAA-
1 TTTAATCAATTAGACCCAACAACTTAATTAAACAAT
* * *
39161985 TTTAATTACTTA-AGTCCAACAACTTAATTAAACAAT
1 TTTAATCAATTAGA-CCCAACAACTTAATTAAACAAT
39162021 TTTAATCAA
1 TTTAATCAA
39162030 GTACTTGAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
34 1 0.01
35 27 0.28
36 70 0.71
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (36 bp):
TTTAATCAATTAGACCCAACAACTTAATTAAACAAT
Found at i:39169428 original size:15 final size:16
Alignment explanation
Indices: 39169403--39169432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39169393 GTATATTATA
39169403 AAAAAATTAAATTAAT
1 AAAAAATTAAATTAAT
39169419 AAAAAA-TAAATTAA
1 AAAAAATTAAATTAA
39169433 AATTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATTAAATTAAT
Found at i:39183650 original size:22 final size:22
Alignment explanation
Indices: 39183622--39183663 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
39183612 TACGAAATAG
39183622 ATAAAAATAAAATAATTATTTT
1 ATAAAAATAAAATAATTATTTT
39183644 ATAAAAATAAAATAATTATT
1 ATAAAAATAAAATAATTATT
39183664 ACATAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAATAAAATAATTATTTT
Found at i:39183669 original size:22 final size:22
Alignment explanation
Indices: 39183622--39183669 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
39183612 TACGAAATAG
**
39183622 ATAAAAATAAAATAATTATTTT
1 ATAAAAATAAAATAATTATTAC
39183644 ATAAAAATAAAATAATTATTAC
1 ATAAAAATAAAATAATTATTAC
39183666 ATAA
1 ATAA
39183670 TTTAGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAAAATAAAATAATTATTAC
Found at i:39188819 original size:15 final size:15
Alignment explanation
Indices: 39188799--39188830 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39188789 AAATATTATT
39188799 TAATTAATAAATTAA
1 TAATTAATAAATTAA
*
39188814 TAATTAATTAATTAA
1 TAATTAATAAATTAA
39188829 TA
1 TA
39188831 CATTGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTAATAAATTAA
Found at i:39193468 original size:3 final size:3
Alignment explanation
Indices: 39193462--39193487 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39193452 TCATCAAAAT
39193462 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
39193488 TAAGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:39211792 original size:2 final size:2
Alignment explanation
Indices: 39211785--39211824 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39211775 TCATGGATAC
*
39211785 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39211825 TGGTTGGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39215726 original size:30 final size:30
Alignment explanation
Indices: 39215690--39215749 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
39215680 TTCTTTCTGC
39215690 TTCTAGTTTATATTTGTTATTATACTTATA
1 TTCTAGTTTATATTTGTTATTATACTTATA
39215720 TTCTAGTTTATATTTGTTATTATACTTATA
1 TTCTAGTTTATATTTGTTATTATACTTATA
39215750 GATGATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (30 bp):
TTCTAGTTTATATTTGTTATTATACTTATA
Found at i:39217786 original size:29 final size:29
Alignment explanation
Indices: 39217746--39217803 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
39217736 ATTTTCAAAT
*
39217746 TTAAAATATT-AATTTTTTATAATATATAA
1 TTAAAATATTAAAATTTTTATAATA-ATAA
*
39217775 TTAAAA-ACTTAAAATTTTTATTATAATAA
1 TTAAAATA-TTAAAATTTTTATAATAATAA
39217804 GATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.04
29 12 0.48
30 12 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TTAAAATATTAAAATTTTTATAATAATAA
Found at i:39218028 original size:20 final size:20
Alignment explanation
Indices: 39217986--39218030 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39217976 ATTATTCTCT
* ***
39217986 ATTTTTATTTTTCATTTTTA
1 ATTTATATTTTTCATTAAAA
39218006 ATTTATATTTTTCATTAAAA
1 ATTTATATTTTTCATTAAAA
39218026 ATTTA
1 ATTTA
39218031 AAATATTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTATATTTTTCATTAAAA
Found at i:39218612 original size:17 final size:17
Alignment explanation
Indices: 39218590--39218622 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39218580 TTGGTTGATT
39218590 TTGAAGAATAGCTAATA
1 TTGAAGAATAGCTAATA
*
39218607 TTGAAGGATAGCTAAT
1 TTGAAGAATAGCTAAT
39218623 CTTTAGGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (17 bp):
TTGAAGAATAGCTAATA
Found at i:39222302 original size:21 final size:21
Alignment explanation
Indices: 39222272--39222323 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
39222262 AATTTTTAAG
39222272 TATTGCGTGACTGACTTTGGA
1 TATTGCGTGACTGACTTTGGA
* *
39222293 TATTGTGTGACTGACTTTGGG
1 TATTGCGTGACTGACTTTGGA
*
39222314 CATTGCGTGA
1 TATTGCGTGA
39222324 TTAGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.13, G:0.31, T:0.38
Consensus pattern (21 bp):
TATTGCGTGACTGACTTTGGA
Found at i:39222354 original size:26 final size:26
Alignment explanation
Indices: 39222315--39222421 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
39222305 GACTTTGGGC
* *
39222315 ATTGCGTGATTAGTTTTTTATAAAGT
1 ATTGCGTGATTAGTTTTTGATAAGGT
* *
39222341 ATTGCGTGACTAGTTTTTGATAAGGC
1 ATTGCGTGATTAGTTTTTGATAAGGT
* *
39222367 ATTGCGTGAATAGTTTCTGATAAGGT
1 ATTGCGTGATTAGTTTTTGATAAGGT
*
39222393 ATTGCGTGATTAGTTTCTGATAAGGT
1 ATTGCGTGATTAGTTTTTGATAAGGT
39222419 ATT
1 ATT
39222422 ACGCGACTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.43
Consensus pattern (26 bp):
ATTGCGTGATTAGTTTTTGATAAGGT
Found at i:39222487 original size:26 final size:26
Alignment explanation
Indices: 39222458--39222592 Score: 112
Period size: 23 Copynumber: 5.6 Consensus size: 26
39222448 GACTAACTTC
*
39222458 AGGCATTGCGTGACTAGTTTTTGATA
1 AGGCATTGCGTGACTAGTGTTTGATA
*
39222484 AGGCATTGCGTGATTAGT-TTCTGATA
1 AGGCATTGCGTGACTAGTGTT-TGATA
* * *
39222510 GGGCATTACGTGATTA--G-TTGAT-
1 AGGCATTGCGTGACTAGTGTTTGATA
*
39222532 AGGCATTGCGTGACT--TGTTAG-TA
1 AGGCATTGCGTGACTAGTGTTTGATA
* *
39222555 AGGTATTGCGTGACT--TGTTAG-TA
1 AGGCATTGCGTGACTAGTGTTTGATA
39222578 AGGCATTGCGTGACT
1 AGGCATTGCGTGACT
39222593 TAGGTATTGC
Statistics
Matches: 95, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
22 14 0.15
23 42 0.44
24 1 0.01
25 2 0.02
26 36 0.38
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (26 bp):
AGGCATTGCGTGACTAGTGTTTGATA
Found at i:39222534 original size:95 final size:95
Alignment explanation
Indices: 39222363--39222546 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 95
39222353 GTTTTTGATA
* *
39222363 AGGCATTGCGTGAATAGTTTCTGATAAGGTATTGCGTGATTAGTTTCTGATAAGGTATTACGCGA
1 AGGCATTGCGTGAATAGTTTCTGATAAGGCATTGCGTGATTAGTTTCTGATAAGGCATTACGCGA
* *
39222428 CTAATTAATAGGCGTTGTGTGACTAACTTC
66 CTAATTAATAGGCATTGCGTGACTAACTTC
* * * *
39222458 AGGCATTGCGTGACTAGTTTTTGATAAGGCATTGCGTGATTAGTTTCTGATAGGGCATTACGTGA
1 AGGCATTGCGTGAATAGTTTCTGATAAGGCATTGCGTGATTAGTTTCTGATAAGGCATTACGCGA
* * *
39222523 TTAGTTGATAGGCATTGCGTGACT
66 CTAATTAATAGGCATTGCGTGACT
39222547 TGTTAGTAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 78 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.36
Consensus pattern (95 bp):
AGGCATTGCGTGAATAGTTTCTGATAAGGCATTGCGTGATTAGTTTCTGATAAGGCATTACGCGA
CTAATTAATAGGCATTGCGTGACTAACTTC
Found at i:39222563 original size:23 final size:23
Alignment explanation
Indices: 39222532--39222593 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
39222522 ATTAGTTGAT
39222532 AGGCATTGCGTGACTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
*
39222555 AGGTATTGCGTGACTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
39222578 AGGCATTGCGTGACTT
1 AGGCATTGCGTGACTT
39222594 AGGTATTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (23 bp):
AGGCATTGCGTGACTTGTTAGTA
Found at i:39222632 original size:22 final size:22
Alignment explanation
Indices: 39222604--39222683 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
39222594 AGGTATTGCT
*
39222604 TAAAAATCAGTCACATGATGTC
1 TAAAAATCAGTCACATAATGTC
*
39222626 TAAAAATCAGTCACGTAATGTC
1 TAAAAATCAGTCACATAATGTC
* * *
39222648 T-AAAATCAATCATATAATGGC
1 TAAAAATCAGTCACATAATGTC
39222669 TAAAAA-CTAGTCACA
1 TAAAAATC-AGTCACA
39222684 CAGTGATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.38
22 30 0.62
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (22 bp):
TAAAAATCAGTCACATAATGTC
Found at i:39222723 original size:22 final size:22
Alignment explanation
Indices: 39222693--39222741 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
39222683 ACAGTGATTA
*
39222693 AATCACGCAATACCTAAAAACT
1 AATCTCGCAATACCTAAAAACT
*
39222715 AATCTCGCAATACTTAAAAACT
1 AATCTCGCAATACCTAAAAACT
39222737 AATCT
1 AATCT
39222742 AATCAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (22 bp):
AATCTCGCAATACCTAAAAACT
Found at i:39225980 original size:30 final size:28
Alignment explanation
Indices: 39225946--39226111 Score: 94
Period size: 29 Copynumber: 5.9 Consensus size: 28
39225936 ACCAAGTTAG
39225946 GTTGTTACACGCCATGTTGAAAAAAATATT
1 GTTGTTACACGCCATGTT-AAAAAAATA-T
* * *
39225976 GTTGTTACACGCTATG-TATAAAAACA-
1 GTTGTTACACGCCATGTTAAAAAAATAT
* *
39226002 --TGTTACACGTCATAGTT--AAAAA-AG
1 GTTGTTACACGCCAT-GTTAAAAAAATAT
*
39226026 GTTGTTACACACCATGTTAAACAAAAAAATACT
1 GTTGTTACACGCCATGTT----AAAAAAATA-T
* * *
39226059 GTTGTTACACGTCATATTGAAAAAATATT
1 GTTGTTACACGCCATGTTAAAAAAATA-T
* * *
39226088 ATTGTTACACGCCATATTCAAAAA
1 GTTGTTACACGCCATGTTAAAAAA
39226112 CATTTTATTA
Statistics
Matches: 107, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
23 1 0.01
24 16 0.15
25 4 0.04
26 12 0.11
28 7 0.07
29 31 0.29
30 15 0.14
31 5 0.05
32 1 0.01
33 15 0.14
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (28 bp):
GTTGTTACACGCCATGTTAAAAAAATAT
Found at i:39226122 original size:27 final size:29
Alignment explanation
Indices: 39226063--39226124 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
39226053 AATACTGTTG
* * *
39226063 TTACACGTCATATTGAAAAAATATTATTG
1 TTACACGCCATATTGAAAAAACATTATTA
*
39226092 TTACACGCCATATT-CAAAAACATT-TTA
1 TTACACGCCATATTGAAAAAACATTATTA
39226119 TTACAC
1 TTACAC
39226125 TTTAATGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.28
28 8 0.28
29 13 0.45
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.35
Consensus pattern (29 bp):
TTACACGCCATATTGAAAAAACATTATTA
Found at i:39241604 original size:23 final size:23
Alignment explanation
Indices: 39241573--39241618 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
39241563 TCGATTATTT
*
39241573 AATTTTTTTTATTTT-TTATTTTA
1 AATTATTTTTATTTTATT-TTTTA
39241596 AATTATTTTTATTTTATTTTTTA
1 AATTATTTTTATTTTATTTTTTA
39241619 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (23 bp):
AATTATTTTTATTTTATTTTTTA
Found at i:39246061 original size:19 final size:19
Alignment explanation
Indices: 39246037--39246077 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
39246027 CCCCCCCCTT
39246037 TTTTTTTTTTTGGGTTTTG
1 TTTTTTTTTTTGGGTTTTG
39246056 TTTTTTTTTTTGGGTTTTG
1 TTTTTTTTTTTGGGTTTTG
39246075 TTT
1 TTT
39246078 AACTTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTTTGGGTTTTG
Found at i:39246084 original size:19 final size:19
Alignment explanation
Indices: 39246043--39246084 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39246033 CCTTTTTTTT
***
39246043 TTTTTGGGTTTTGTTTTTT
1 TTTTTGGGTTTTGTTTAAC
39246062 TTTTTGGGTTTTGTTTAAC
1 TTTTTGGGTTTTGTTTAAC
39246081 TTTT
1 TTTT
39246085 CATGTACCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.02, G:0.19, T:0.74
Consensus pattern (19 bp):
TTTTTGGGTTTTGTTTAAC
Found at i:39250271 original size:2 final size:2
Alignment explanation
Indices: 39250264--39250304 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
39250254 CTAAATATCT
*
39250264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39250305 TTACATCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39295621 original size:49 final size:49
Alignment explanation
Indices: 39295549--39295646 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
39295539 AAGAAAATCA
39295549 GAGGTTAGCAATGAATTTCATAGTAACATTTTGTATTGTCACATGTTCT
1 GAGGTTAGCAATGAATTTCATAGTAACATTTTGTATTGTCACATGTTCT
* *
39295598 GAGGTTAGCAATGAATTTTATAGTAACATTTTGTATTTTCACATGTTCT
1 GAGGTTAGCAATGAATTTCATAGTAACATTTTGTATTGTCACATGTTCT
39295647 AACTCTATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (49 bp):
GAGGTTAGCAATGAATTTCATAGTAACATTTTGTATTGTCACATGTTCT
Found at i:39316320 original size:46 final size:46
Alignment explanation
Indices: 39316270--39316367 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 46
39316260 ATTTTCAACG
*
39316270 GAAAAA-ACAATTGGAACA-ATTCCCGTTGGAAATAGGATTTCCAATT
1 GAAAAATA-AATTGGAA-ATATTCCCGTTGGAAATAGGATTTCCAATA
* * ***
39316316 GAAAAATAAATTGGAAATTTTTCCGTTGGAAATCTTATTTCCAATA
1 GAAAAATAAATTGGAAATATTCCCGTTGGAAATAGGATTTCCAATA
39316362 GAAAAA
1 GAAAAA
39316368 CATTTAGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
45 1 0.02
46 42 0.95
47 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (46 bp):
GAAAAATAAATTGGAAATATTCCCGTTGGAAATAGGATTTCCAATA
Found at i:39321479 original size:21 final size:21
Alignment explanation
Indices: 39321453--39321517 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
39321443 CGGATTTGGG
39321453 AATTTGTTAAGCACCCCTAAA
1 AATTTGTTAAGCACCCCTAAA
* * ***
39321474 AATTTGCTAAG--TCCCTGCC
1 AATTTGTTAAGCACCCCTAAA
*
39321493 AATTTGTTAAGCACCCCCAAA
1 AATTTGTTAAGCACCCCTAAA
39321514 AATT
1 AATT
39321518 CACTACTGAG
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
19 14 0.45
21 17 0.55
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (21 bp):
AATTTGTTAAGCACCCCTAAA
Found at i:39325436 original size:3 final size:3
Alignment explanation
Indices: 39325428--39325452 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39325418 CGTAAATTAT
39325428 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
39325453 AAGTCTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39326159 original size:81 final size:81
Alignment explanation
Indices: 39326013--39326224 Score: 234
Period size: 80 Copynumber: 2.6 Consensus size: 81
39326003 ACATGTCATG
* * * * * *
39326013 GTTAAAAAAAGTTATTACACACCATATT-AAAAAAAATATTATTATTACACACCATGTACGAAAA
1 GTTAAAAAAAGTTGTTACACGCCATGTTGAAAAAAAATATTGTTGTTACACACCATGTACAAAAA
*
39326077 CAT-ATTACATGCCGT
66 CATGATTACATGACGT
* *
39326092 GATTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACA-TCCATGTACAAA
1 G-TTAAAAAAAGTTGTTACACGCCATGTTG-AAAAAAAATATTGTTGTTACACACCATGTACAAA
* * *
39326156 AACATGTTATACGTTACG-
64 AACATGAT-TACATGACGT
* * *
39326174 GTTAAAAAAGGTTGTTGCATGCCATGTTGAAAAAAAATATTGTTGTTACAC
1 GTTAAAAAAAGTTGTTACACGCCATGTTGAAAAAAAATATTGTTGTTACAC
39326225 GTTATATATA
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 44 0.40
81 39 0.35
82 21 0.19
83 6 0.05
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (81 bp):
GTTAAAAAAAGTTGTTACACGCCATGTTGAAAAAAAATATTGTTGTTACACACCATGTACAAAAA
CATGATTACATGACGT
Found at i:39326238 original size:81 final size:81
Alignment explanation
Indices: 39326094--39326245 Score: 209
Period size: 81 Copynumber: 1.9 Consensus size: 81
39326084 CATGCCGTGA
*
39326094 TTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATCCATGTACAAAAAC
1 TTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATCCATATACAAAAAC
39326159 ATGTTATACGTTACGG
66 ATGTTATACGTTACGG
** * * * *
39326175 TTAAAAAAGGTTGTTGCATGCCATGTTG-AAAAAAAATATTGTTGTTACA-CGTTATATATAAAA
1 TTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATC--CATATACAAAA
39326238 ACATGTTA
64 ACATGTTA
39326246 CACACCATGT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 1 0.02
80 21 0.34
81 40 0.65
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (81 bp):
TTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATCCATATACAAAAAC
ATGTTATACGTTACGG
Found at i:39326262 original size:81 final size:81
Alignment explanation
Indices: 39326012--39326265 Score: 203
Period size: 81 Copynumber: 3.2 Consensus size: 81
39326002 TACATGTCAT
* * * * * * * * *
39326012 GGTTAAAAAAAGTTATTACACACCATATT--AAAAAAAATATTATTATTACACACCATGTACGAA
1 GGTTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACA-TCCATATACAAA
* ** **
39326075 AACATATTACATGCCGT
65 AACATGTTACACACCAC
* *
39326092 GATTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATCCATGTACAAAA
1 GGTTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATCCATATACAAAA
* ***
39326157 ACATGTTATACGTTAC
66 ACATGTTACACACCAC
** * * * *
39326173 GGTTAAAAAAGGTTGTTGCATGCCATGTTG-AAAAAAAATATTGTTGTTACA-CGTTATATATAA
1 GGTTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATC--CATATACAA
39326236 AAACATGTTACACACCA-
64 AAACATGTTACACACCAC
*
39326253 TGTTAAAAAAAAT
1 GGTTAAAAAAAAT
39326266 ATTATTCTTA
Statistics
Matches: 139, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
79 1 0.01
80 55 0.40
81 64 0.46
82 19 0.14
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.30
Consensus pattern (81 bp):
GGTTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATATTGTTGTTACATCCATATACAAAA
ACATGTTACACACCAC
Found at i:39326488 original size:22 final size:22
Alignment explanation
Indices: 39326437--39326489 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
39326427 AGTATTTTTA
39326437 ACATATTTTTATAAATCAAAAC
1 ACATATTTTTATAAATCAAAAC
* * **
39326459 ATAAATTTTT-TTTATCTAAAAC
1 ACATATTTTTATAAATC-AAAAC
39326481 ACATATTTT
1 ACATATTTT
39326490 GACAAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (22 bp):
ACATATTTTTATAAATCAAAAC
Found at i:39330496 original size:20 final size:20
Alignment explanation
Indices: 39330448--39330496 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
39330438 AATAACAATC
*
39330448 AAATGAAGAGCAAATATGTA
1 AAATGAAGTGCAAATATGTA
39330468 AAATGAAGTGCAAATATGTA
1 AAATGAAGTGCAAATATGTA
39330488 AAATGAAGT
1 AAATGAAGT
39330497 TTATTGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (20 bp):
AAATGAAGTGCAAATATGTA
Found at i:39332517 original size:54 final size:53
Alignment explanation
Indices: 39332457--39332588 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 53
39332447 TGACCTAATT
* *
39332457 TTGATCACGAACTATACTTGACATC-TTCGTTTCAATGGACTTCACGACTTGATC
1 TTGATCACGAACTATACTTGATATCTTTC--TTCAAAGGACTTCACGACTTGATC
*
39332511 TTGATCACGAAC---ACTTGATATCATTTCTTCAAAGGTCTTCACGACTTGATC
1 TTGATCACGAACTATACTTGATATC-TTTCTTCAAAGGACTTCACGACTTGATC
39332562 TTGATCACGAACTATACTTGATATCTT
1 TTGATCACGAACTATACTTGATATCTT
39332589 AATAATGAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
51 43 0.61
53 5 0.07
54 22 0.31
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (53 bp):
TTGATCACGAACTATACTTGATATCTTTCTTCAAAGGACTTCACGACTTGATC
Found at i:39333088 original size:57 final size:57
Alignment explanation
Indices: 39332982--39333089 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
39332972 GCGTTATTCT
* * * *
39332982 TAAATTATCTTAATTTATTTAGAGATAAATTAAATAATCAAATTTAATTTTTATCTC
1 TAAATTATCATAATTTATTTAGACATAAATTAAATAATAAAATTAAATTTTTATCTC
*
39333039 TAAATTATCATAA-TTA-TTAGACATAAATTAAATGACTAATAATTAAATTTT
1 TAAATTATCATAATTTATTTAGACATAAATTAAAT-AATAA-AATTAAATTTT
39333090 GATTGGTGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
55 16 0.36
56 6 0.14
57 22 0.50
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (57 bp):
TAAATTATCATAATTTATTTAGACATAAATTAAATAATAAAATTAAATTTTTATCTC
Found at i:39333155 original size:81 final size:80
Alignment explanation
Indices: 39333032--39333285 Score: 295
Period size: 81 Copynumber: 3.2 Consensus size: 80
39333022 AATTTAATTT
* * * * *
39333032 TTATCTCTAAATTATCATAATTA-TTAGACATAAATTAAATGACTAATAATTAAATTTTGATTGG
1 TTATCTTTAAATTATCTTATTTATTTAGAAATAAATTAGATGACTAATAATTAAATTTTGATTGG
*
39333096 TGAAAAAA-ATGAATA
66 T-AAAAAATATAAATA
* * *
39333111 TTATCTTTAAATTATCTTGATTTATTTAGAGATAAATTGGATGACTAATAATTAAATTTTAATTG
1 TTATCTTTAAATTATCTT-ATTTATTTAGAAATAAATTAGATGACTAATAATTAAATTTTGATTG
*
39333176 ATAAAAAATATAAATA
65 GTAAAAAATATAAATA
*
39333192 TTAT-TTCTAAATTATCTTAATTTATTTAGAAACAAATTAGATGA-TCAATAATTAAATTTTGAT
1 TTATCTT-TAAATTATCTT-ATTTATTTAGAAATAAATTAGATGACT-AATAATTAAATTTTGAT
** *
39333255 TGGT--TTAATTTAAATA
63 TGGTAAAAAATATAAATA
39333271 TTATCTTTAAATTAT
1 TTATCTTTAAATTAT
39333286 TTTAAGGTAT
Statistics
Matches: 151, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
79 37 0.25
80 15 0.10
81 99 0.66
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (80 bp):
TTATCTTTAAATTATCTTATTTATTTAGAAATAAATTAGATGACTAATAATTAAATTTTGATTGG
TAAAAAATATAAATA
Found at i:39339481 original size:42 final size:41
Alignment explanation
Indices: 39339434--39339654 Score: 133
Period size: 42 Copynumber: 5.5 Consensus size: 41
39339424 TTTAAACATG
39339434 AATATTTTATTTATAATCTTATCATTAATATTATAAAATATT
1 AATATTTTATTTATAAT-TTATCATTAATATTATAAAATATT
* * * *
39339476 AATATTTTATTTATAATTTA--AATATTATTAT-GATTATT
1 AATATTTTATTTATAATTTATCATTAATATTATAAAATATT
* ** *
39339514 TAT-TTTTAATTTAT--TTTATTTTTAAATATTA-ATAAT-TT
1 AATATTTT-ATTTATAATTTATCATT-AATATTATAAAATATT
* * ** *
39339552 -ATAATTTATTTA-AGATACTAAAAATTGATAATT-T-AAATATT
1 AATATTTTATTTATA-AT--TTATCATTAAT-ATTATAAAATATT
* *
39339593 AATATTTTATTTATAATTTAATCATTAACATTATAAAATACT
1 AATATTTTATTTATAATTT-ATCATTAATATTATAAAATATT
* *
39339635 CATATTTAATTTATAATTTA
1 AATATTTTATTTATAATTTA
39339655 AATGTTATTA
Statistics
Matches: 134, Mismatches: 26, Indels: 39
0.67 0.13 0.20
Matches are distributed among these distances:
36 4 0.03
37 11 0.08
38 19 0.14
39 18 0.13
40 9 0.07
41 19 0.14
42 53 0.40
43 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (41 bp):
AATATTTTATTTATAATTTATCATTAATATTATAAAATATT
Found at i:39339582 original size:27 final size:26
Alignment explanation
Indices: 39339534--39339586 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
39339524 TTATTTTATT
* * *
39339534 TTTAAATATTAATAATTTATAATTTA
1 TTTAAATACTAAAAATTGATAATTTA
39339560 TTTAAGATACTAAAAATTGATAATTTA
1 TTTAA-ATACTAAAAATTGATAATTTA
39339587 AATATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTAAATACTAAAAATTGATAATTTA
Found at i:39339599 original size:159 final size:155
Alignment explanation
Indices: 39339424--39339716 Score: 453
Period size: 159 Copynumber: 1.9 Consensus size: 155
39339414 TTATTTTATT
* * *
39339424 TTTAAACATGAATATTTTATTTATAATCTT-ATCATTAATATTATAAAATATTAATATTTTATTT
1 TTTAAACATGAATATTTTATTTATAAT-TTAATCATTAACATTATAAAATACTAATATTTAATTT
*
39339488 ATAATTTAAATATTATTATGATTATTTATTTTTAATTTATTTTATTTTTAAATATTAATAATTTA
65 ATAATTTAAATATTATTATGATTATTTATTTTT-A-TT-TTAT-TTTTTAAATATTAATAATTTA
39339553 TAATTTATTTAAGATACTAAAAATTGATAA
126 TAATTTATTTAAGATACTAAAAATTGATAA
* * *
39339583 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTCATATTTAATTTA
1 TTTAAACATGAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTAATTTA
* *
39339648 TAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTTTAAATATTAATCATTTATAATT
66 TAATTTAAATATTATTATGATTATTTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATT
39339713 TATT
131 TATT
39339717 ATTTAAGTTT
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
155 29 0.23
156 3 0.02
157 2 0.02
158 3 0.02
159 87 0.70
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (155 bp):
TTTAAACATGAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTAATTTA
TAATTTAAATATTATTATGATTATTTATTTTTATTTTATTTTTTAAATATTAATAATTTATAATT
TATTTAAGATACTAAAAATTGATAA
Found at i:39342902 original size:3 final size:3
Alignment explanation
Indices: 39342894--39342919 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39342884 TGTTACAAAA
39342894 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
39342920 GATGCTGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39343705 original size:11 final size:11
Alignment explanation
Indices: 39343689--39343714 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39343679 GTCATATTCC
39343689 TTTTCTTTTCT
1 TTTTCTTTTCT
39343700 TTTTCTTTTCT
1 TTTTCTTTTCT
39343711 TTTT
1 TTTT
39343715 TAATATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:39353847 original size:6 final size:6
Alignment explanation
Indices: 39353824--39353865 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 6
39353814 ATCTCTATGC
39353824 TTTTCT TATTTC- TTTTCT TTTTCTT TTTTCCT TTTTCT TTTT
1 TTTTCT T-TTTCT TTTTCT TTTTC-T TTTT-CT TTTTCT TTTT
39353866 TTTCTTGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 13 0.41
7 14 0.44
8 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:39357116 original size:28 final size:29
Alignment explanation
Indices: 39357061--39357117 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
39357051 TTTAATTTAA
*
39357061 AATAAAAATATAAAAATTTAATTAAATAT
1 AATAAAAATATAAAAAATTAATTAAATAT
* *
39357090 AATAAAAA-ATAAAAAATTATTTGAATAT
1 AATAAAAATATAAAAAATTAATTAAATAT
39357118 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
AATAAAAATATAAAAAATTAATTAAATAT
Found at i:39363842 original size:2 final size:2
Alignment explanation
Indices: 39363835--39363872 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39363825 TCCTAGAACT
39363835 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39363873 CCCCTCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39387024 original size:5 final size:5
Alignment explanation
Indices: 39387014--39387046 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
39387004 TTATTATGTA
39387014 AAAAT AAAAT AAAAT AAAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AA
39387047 TTATTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:39387033 original size:11 final size:11
Alignment explanation
Indices: 39387014--39387043 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39387004 TTATTATGTA
39387014 AAAAT-AAAAT
1 AAAATAAAAAT
39387024 AAAATAAAAAT
1 AAAATAAAAAT
39387035 AAAATAAAA
1 AAAATAAAA
39387044 TAATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:39387033 original size:16 final size:16
Alignment explanation
Indices: 39387012--39387046 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
39387002 AATTATTATG
39387012 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
39387028 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
39387044 TAA
1 TAA
39387047 TTATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:39387156 original size:15 final size:15
Alignment explanation
Indices: 39387136--39387166 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39387126 ATAATTTTAG
39387136 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
*
39387151 AATAAAAAGATAAAA
1 AATAAAAAAATAAAA
39387166 A
1 A
39387167 CACCTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:39387235 original size:34 final size:32
Alignment explanation
Indices: 39387197--39387271 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 32
39387187 ATTATTTATT
*
39387197 TTTAATAAAATTTTTAA-ATATTAATAATCTAGAA
1 TTTAATAAAA-TATTAATA-ATTAATAATCTA-AA
*
39387231 TTTAATTAAAATATTAATAATTAATAATTTAAA
1 TTTAA-TAAAATATTAATAATTAATAATCTAAA
39387264 TATTAATA
1 T-TTAATA
39387272 TTTTATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
33 5 0.14
34 25 0.69
35 6 0.17
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (32 bp):
TTTAATAAAATATTAATAATTAATAATCTAAA
Found at i:39387287 original size:24 final size:23
Alignment explanation
Indices: 39387209--39387385 Score: 102
Period size: 27 Copynumber: 7.6 Consensus size: 23
39387199 TAATAAAATT
39387209 TTTAAATATTAATAATCTAGAATTTAA
1 TTTAAATATTAATAAT-T---ATTTAA
* *
39387236 TTAAAATATTAATAATTA-ATAA
1 TTTAAATATTAATAATTATTTAA
*
39387258 TTTAAATATTAATATTTTATTTAA
1 TTTAAATATTAATA-ATTATTTAA
* *
39387282 TTTAAATATT-ATGATGA-TTAA
1 TTTAAATATTAATAATTATTTAA
** * *
39387303 TTTTTAT-TTTAT-TTTATTT--
1 TTTAAATATTAATAATTATTTAA
*
39387322 TTTAAAATATTAATAATTGATAATTTA
1 TTT-AAATATTAATAATT-AT--TTAA
39387349 TTTAAAATATTAATAATTGA--TAA
1 TTT-AAATATTAATAATT-ATTTAA
39387372 TTTAAATATTAATA
1 TTTAAATATTAATA
39387386 TTTTATTTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 29
0.72 0.10 0.17
Matches are distributed among these distances:
19 3 0.02
20 6 0.05
21 17 0.14
22 31 0.26
23 13 0.11
24 13 0.11
25 2 0.02
26 1 0.01
27 35 0.29
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
TTTAAATATTAATAATTATTTAA
Found at i:39387309 original size:114 final size:115
Alignment explanation
Indices: 39387180--39387407 Score: 315
Period size: 114 Copynumber: 2.0 Consensus size: 115
39387170 CTTTTATTAT
*
39387180 TTAT-ATGATT-ATTTAT-TTTTAATAAAATTTTT-AAATATTAATAATCT-AGAATTTAATTAA
1 TTATGATGATTAATTTTTATTTTAATAAAATTTTTAAAATATTAATAAT-TGAGAATTTAATTAA
39387240 AATATTAATAATTAATAATTTAAATATTAATATTTTA-TTTAATTTAAATA
65 AATATTAATAATTAATAATTTAAATATTAATATTTTATTTTAATTTAAATA
* ** * * *
39387290 TTATGATGATTAATTTTTATTTTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAA
1 TTATGATGATTAATTTTTATTTTAATAAAATTTTTAAAATATTAATAATTGAGAATTTAATTAAA
* *
39387355 ATATTAATAATTGATAATTTAAATATTAATATTTTATTTTTAATTTAATTA
66 ATATTAATAATTAATAATTTAAATATTAATATTTTA-TTTTAATTTAAATA
39387406 TT
1 TT
39387408 TATATTTTAC
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
110 4 0.04
111 6 0.06
112 5 0.05
113 13 0.13
114 60 0.59
116 14 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (115 bp):
TTATGATGATTAATTTTTATTTTAATAAAATTTTTAAAATATTAATAATTGAGAATTTAATTAAA
ATATTAATAATTAATAATTTAAATATTAATATTTTATTTTAATTTAAATA
Found at i:39387355 original size:27 final size:27
Alignment explanation
Indices: 39387318--39387375 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
39387308 ATTTTATTTT
39387318 ATTT-TTTAAAATATTAATAATTGATA
1 ATTTATTTAAAATATTAATAATTGATA
39387344 ATTTATTTAAAATATTAATAATTGATA
1 ATTTATTTAAAATATTAATAATTGATA
39387371 ATTTA
1 ATTTA
39387376 AATATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (27 bp):
ATTTATTTAAAATATTAATAATTGATA
Found at i:39387407 original size:87 final size:85
Alignment explanation
Indices: 39387236--39387408 Score: 192
Period size: 87 Copynumber: 2.0 Consensus size: 85
39387226 TAGAATTTAA
* *
39387236 TTAAAATATTAATAATTAATAATTTAAATATTAATATTTTATTTAATTTAAATATTATGATGATT
1 TTAAAATATTAATAATTAATAATTTAAATATTAATAATTGA-TTAATTTAAATATTATGAT-ATT
* *
39387301 AATTTTTATTTTATTTTATTTT
64 AATTTTTAATTTATATTATTTT
*
39387323 TTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGA-TAATTTAAATATTA--AT
1 TTAAAATATTAATAA-T--TAA-TAATTT-AAATATTAATAATTGATTAATTTAAATATTATGAT
*
39387385 ATTTTATTTTTAATTTA-ATTATTT
61 A-TTAATTTTTAATTTATATTATTT
39387409 ATATTTTACA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
87 22 0.30
88 16 0.22
90 17 0.23
91 5 0.07
92 14 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (85 bp):
TTAAAATATTAATAATTAATAATTTAAATATTAATAATTGATTAATTTAAATATTATGATATTAA
TTTTTAATTTATATTATTTT
Found at i:39387422 original size:42 final size:39
Alignment explanation
Indices: 39387358--39387444 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 39
39387348 ATTTAAAATA
39387358 TTAATAATTGATAATTTAAATATTAATATTTTATTTTTAAT
1 TTAATAATTGATAATTTAAATATTAATATTTTA--TTTAAT
* * * *
39387399 TTAATTATTTATATTTTACAATATTAGTATTTTATTTAAT
1 TTAATAATTGATAATTTA-AATATTAATATTTTATTTAAT
39387439 TTAATA
1 TTAATA
39387445 TTATTATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 11 0.28
41 15 0.38
42 14 0.35
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (39 bp):
TTAATAATTGATAATTTAAATATTAATATTTTATTTAAT
Found at i:39387447 original size:114 final size:112
Alignment explanation
Indices: 39387207--39387435 Score: 295
Period size: 114 Copynumber: 2.0 Consensus size: 112
39387197 TTTAATAAAA
39387207 TTTTTAAATATTAATAATCTAGAATTTAATTAAAATATTAATAATTAATAATTTAAATATTAATA
1 TTTTTAAATATTAATAATCTAGAATTTAATTAAAATATTAATAATTAATAATTTAAATATTAATA
* * *
39387272 TTTTATTTAATTTAAATATTATGATGATTAATTTTTATTTTATTTTAT
66 TTTTATTTAATTTAAATATTATGATGATTAAATATTA-TGTATTTTAT
* * *
39387320 TTTTTAAAATATTAATAAT-TGATAATTTATTTAAAATATTAATAATTGATAATTTAAATATTAA
1 TTTTT-AAATATTAATAATCT-AGAATTTAATTAAAATATTAATAATTAATAATTTAAATATTAA
* *
39387384 TATTTTATTTTTAATTTAATTATTTAT-AT-TTTACAATATTA-GTATTTTAT
64 TATTTTA--TTTAATTTAAATA-TTATGATGATTA-AATATTATGTATTTTAT
39387434 TT
1 TT
39387436 AATTTAATAT
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
113 6 0.06
114 70 0.69
115 3 0.03
116 19 0.19
117 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (112 bp):
TTTTTAAATATTAATAATCTAGAATTTAATTAAAATATTAATAATTAATAATTTAAATATTAATA
TTTTATTTAATTTAAATATTATGATGATTAAATATTATGTATTTTAT
Found at i:39387499 original size:24 final size:25
Alignment explanation
Indices: 39387470--39387537 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 25
39387460 ATTTTATTTT
*
39387470 TTATTTTTAAAA-ATTAATAATTGA
1 TTATTTTTAAAATATTAATAATAGA
39387494 TTATTTATTTAAAATATTAATAATAGA
1 TTA-TT-TTTAAAATATTAATAATAGA
*
39387521 -TA-ATTT-AAATATTAATA
1 TTATTTTTAAAATATTAATA
39387538 TTTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 11 0.28
23 3 0.08
24 3 0.08
25 2 0.05
26 9 0.23
27 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATTTTTAAAATATTAATAATAGA
Found at i:39387526 original size:27 final size:26
Alignment explanation
Indices: 39387475--39387527 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
39387465 ATTTTTTATT
* *
39387475 TTTAAAAATTAATAATTGATTATTTA
1 TTTAAAAATTAATAATAGATAATTTA
39387501 TTTAAAATATTAATAATAGATAATTTA
1 TTTAAAA-ATTAATAATAGATAATTTA
39387528 AATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTAAAAATTAATAATAGATAATTTA
Found at i:39387561 original size:25 final size:25
Alignment explanation
Indices: 39387531--39387621 Score: 132
Period size: 25 Copynumber: 3.6 Consensus size: 25
39387521 TAATTTAAAT
39387531 ATTAATATTTTATTTATAATTAGTC
1 ATTAATATTTTATTTATAATTAGTC
* *
39387556 ATTAATATTTTTATTTA-ATTTAAAT-
1 ATTAATA-TTTTATTTATAATT-AGTC
39387581 ATTAATATTTTATTTATAATTAGTC
1 ATTAATATTTTATTTATAATTAGTC
39387606 ATTAATATTTTATTTA
1 ATTAATATTTTATTTA
39387622 ATTTAAATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
24 11 0.19
25 36 0.62
26 11 0.19
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTAATATTTTATTTATAATTAGTC
Found at i:39387568 original size:152 final size:155
Alignment explanation
Indices: 39387244--39387566 Score: 469
Period size: 152 Copynumber: 2.1 Consensus size: 155
39387234 AATTAAAATA
* * *
39387244 TTAATAATTAATAATTTAAATATTAATATTTTATTTAATTTAAATATTATGATGATTAATTTTTA
1 TTAATCATTAATATTTTAAATATTAATATTTTATTTAATTTAAATATTATGATGATCAATTTTTA
* *
39387309 TTTTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATT
66 TATTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATT
*
39387374 TAAATATTAATATTTTATTTTTAAT
131 TAAATATTAATATTTTATTTATAAT
* * * * *
39387399 TTAATTATTTATATTTTACAATATTAGTATTTTATTTAATTT-AATATTATTATGATCCATTATT
1 TTAATCATTAATATTTTA-AATATTAATATTTTATTTAATTTAAATATTATGATGATCAATT-TT
*
39387463 T-TATT-TTTTA-TTTTTAAAA-ATTAATAATTGATTATTTATTTAAAATATTAATAATAGATAA
64 TATATTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAA
39387524 TTTAAATATTAATATTTTATTTATAA-
129 TTTAAATATTAATATTTTATTTATAAT
*
39387550 TTAGTCATTAATATTTT
1 TTAATCATTAATATTTT
39387567 TATTTAATTT
Statistics
Matches: 152, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
151 14 0.09
152 65 0.43
153 9 0.06
154 5 0.03
155 34 0.22
156 25 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (155 bp):
TTAATCATTAATATTTTAAATATTAATATTTTATTTAATTTAAATATTATGATGATCAATTTTTA
TATTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATT
TAAATATTAATATTTTATTTATAAT
Found at i:39387578 original size:50 final size:49
Alignment explanation
Indices: 39387521--39387633 Score: 217
Period size: 50 Copynumber: 2.3 Consensus size: 49
39387511 TAATAATAGA
39387521 TAATTTAAATATTAATATTTTATTTATAATTAGTCATTAATATTTTTATT
1 TAATTTAAATATTAATATTTTATTTATAATTAGTCATTAATA-TTTTATT
39387571 TAATTTAAATATTAATATTTTATTTATAATTAGTCATTAATATTTTATT
1 TAATTTAAATATTAATATTTTATTTATAATTAGTCATTAATATTTTATT
39387620 TAATTTAAATATTA
1 TAATTTAAATATTA
39387634 TTATGATTAG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 21 0.33
50 42 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (49 bp):
TAATTTAAATATTAATATTTTATTTATAATTAGTCATTAATATTTTATT
Found at i:39387615 original size:152 final size:151
Alignment explanation
Indices: 39387244--39387625 Score: 393
Period size: 152 Copynumber: 2.5 Consensus size: 151
39387234 AATTAAAATA
* * * * **
39387244 TTAATAATTAATAATTTA-AATATTAATATTTTATTTAATTTAA-ATATTATGATGATTAATTTT
1 TTAATCATTAATATTTTACAATATTAATATTATATTTAATTTAATATATTATCAT--CCAA----
*
39387307 TATTTTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAA
60 TATTTTATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAA
*
39387372 TTTAAATATTAATATTTTATTTTTAAT
125 TTTAAATATTAATATTTTATTTATAAT
* * * * * *
39387399 TTAATTATTTATATTTTACAATATTAGTATTTTATTTAATTTAATATTATTATGATCCATTATTT
1 TTAATCATTAATATTTTACAATATTAATATTATATTTAATTTAATA-TATTATCATCCAATATTT
* *
39387464 TATTTTTTATTTTTAAAA-ATTAATAATTGATTATTTATTTAAAATATTAATAATAGATAATTTA
65 TATTTTAT-TTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATTTA
39387528 AATATTAATATTTTATTTATAA-
129 AATATTAATATTTTATTTATAAT
* * * *
39387550 TTAGTCATTAATATTTTTATTTAAT-TTAAATATTAATATTTTATTT-ATA-ATTAGTCAT-TAA
1 TTAATCATTAATA-TTTTA--CAATATT-AATATT-ATATTTAATTTAATATATTA-TCATCCAA
*
39387611 TATTTTATTTAATTT
60 TATTTTATTTTATTT
39387626 AAATATTATT
Statistics
Matches: 194, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
151 12 0.06
152 98 0.51
153 14 0.07
154 11 0.06
155 24 0.12
156 25 0.13
157 1 0.01
158 9 0.05
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (151 bp):
TTAATCATTAATATTTTACAATATTAATATTATATTTAATTTAATATATTATCATCCAATATTTT
ATTTTATTTTTTAAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATTTAAA
TATTAATATTTTATTTATAAT
Found at i:39387705 original size:27 final size:26
Alignment explanation
Indices: 39387665--39387721 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
39387655 ATTTTATTTT
39387665 ATTT-TTTAAATATTAATAATTGATA
1 ATTTATTTAAATATTAATAATTGATA
*
39387690 ATTTATTTAAAATATTAATAATTGATT
1 ATTTATTT-AAATATTAATAATTGATA
39387717 ATTTA
1 ATTTA
39387722 ATTATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.10
27 22 0.76
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:39387846 original size:25 final size:26
Alignment explanation
Indices: 39387799--39387852 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
39387789 AATAGAAATA
* **
39387799 ATTTATAATTTAAATATTTATATTTT
1 ATTTACAATTTAAATATCAATATTTT
39387825 ATTTACAATTT-AATATCAATATTTT
1 ATTTACAATTTAAATATCAATATTTT
39387850 ATT
1 ATT
39387853 AAAAGTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTACAATTTAAATATCAATATTTT
Found at i:39390281 original size:6 final size:6
Alignment explanation
Indices: 39390267--39390299 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39390257 TCTACTGGTT
*
39390267 CAGGGG CAGGAG CAGGAG CAGGAG CAGGAG CAG
1 CAGGAG CAGGAG CAGGAG CAGGAG CAGGAG CAG
39390300 ATTTGGAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.52, T:0.00
Consensus pattern (6 bp):
CAGGAG
Found at i:39392365 original size:30 final size:29
Alignment explanation
Indices: 39392316--39392388 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
39392306 GATACAAATT
*
39392316 TTAAATAAA-TTTTTATTTTT-TATTATA
1 TTAAATAAATTTTTTATTTTTATATTAAA
* *
39392343 TTTAATCAAATTTTTATATTTTTATTTTAAA
1 TTAAAT-AAATTTTT-TATTTTTATATTAAA
39392374 TTAAATAAATTTTTT
1 TTAAATAAATTTTTT
39392389 TTATTAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 5 0.13
28 3 0.08
29 5 0.13
30 15 0.39
31 10 0.26
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
TTAAATAAATTTTTTATTTTTATATTAAA
Done.