Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 10 of 193
Found at i:3631956 original size:3 final size:3
Alignment explanation
Indices: 3631950--3631999 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
3631940 AATAATAATA
3631950 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3631998 AT
1 AT
3632000 AAGAGGAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3638733 original size:23 final size:24
Alignment explanation
Indices: 3638705--3638749 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3638695 AATAAGTAAT
*
3638705 TTGAATTTTA-AGTTCGAATAAAG
1 TTGAATTTTATAATTCGAATAAAG
3638728 TTGAATTTTATAATTCGAATAA
1 TTGAATTTTATAATTCGAATAA
3638750 TAAATTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (24 bp):
TTGAATTTTATAATTCGAATAAAG
Found at i:3646085 original size:28 final size:27
Alignment explanation
Indices: 3646050--3646107 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
3646040 AACCCCCCTA
*
3646050 AAATGTAATATATAAAGA-AAGGACAAT
1 AAATGTAA-ACATAAAGAGAAGGACAAT
* *
3646077 AAATAGTAAACATACAGAGAAGGGCAAT
1 AAAT-GTAAACATAAAGAGAAGGACAAT
3646105 AAA
1 AAA
3646108 AAAAGTGAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.59, C:0.07, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGTAAACATAAAGAGAAGGACAAT
Found at i:3646790 original size:27 final size:28
Alignment explanation
Indices: 3646760--3646814 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
3646750 AATTAAGGAA
*
3646760 TTATATCAT-ATTAAATATATTA-TTATT
1 TTATACCATGATTAAA-ATATTACTTATT
*
3646787 TTATACCATGTTTAAAATATTACTTATT
1 TTATACCATGATTAAAATATTACTTATT
3646815 AATAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (28 bp):
TTATACCATGATTAAAATATTACTTATT
Found at i:3647808 original size:6 final size:6
Alignment explanation
Indices: 3647800--3647842 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
3647790 ATGGCATTCT
*
3647800 ATCTCT ATCTCC ATCTCC ATCTCC ATCTCC ATCTCC ATCTCC A
1 ATCTCC ATCTCC ATCTCC ATCTCC ATCTCC ATCTCC ATCTCC A
3647843 ACCTTGATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.35
Consensus pattern (6 bp):
ATCTCC
Found at i:3654092 original size:18 final size:17
Alignment explanation
Indices: 3654035--3654111 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
3654025 AATAAAGATA
*
3654035 TAAATTTAGTTTTAAA-T
1 TAAATTTA-TTATAAATT
*
3654052 TAAATTTATTATGAATT
1 TAAATTTATTATAAATT
3654069 TAAATTTGCATTA-AAATT
1 TAAATTT--ATTATAAATT
*
3654087 TGAATTTATTATAAATT
1 TAAATTTATTATAAATT
3654104 TAAATTTA
1 TAAATTTA
3654112 AAACTAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.18
17 28 0.55
18 10 0.20
19 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAATTTATTATAAATT
Found at i:3654170 original size:46 final size:46
Alignment explanation
Indices: 3654119--3654210 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
3654109 TTAAAACTAA
* * *
3654119 ATTAAATGTCCAAAGTCCATTTATAAGCTCGATTGGGCCAAATTTG
1 ATTAAATGTCCAAAGTCCATTTACAAGCCCAATTGGGCCAAATTTG
* * *
3654165 ATTAAATGTTCAAAGTTCATTTACAAGCCCAATTGGGCTAAATTTG
1 ATTAAATGTCCAAAGTCCATTTACAAGCCCAATTGGGCCAAATTTG
3654211 GCTAGCCCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (46 bp):
ATTAAATGTCCAAAGTCCATTTACAAGCCCAATTGGGCCAAATTTG
Found at i:3654234 original size:11 final size:12
Alignment explanation
Indices: 3654218--3654246 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3654208 TTGGCTAGCC
3654218 CAAATTCAATG-
1 CAAATTCAATGA
3654229 CAAATTCAATGA
1 CAAATTCAATGA
3654241 CAAATT
1 CAAATT
3654247 GAGCCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (12 bp):
CAAATTCAATGA
Found at i:3654941 original size:15 final size:16
Alignment explanation
Indices: 3654916--3654954 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
3654906 TTGATAATTT
3654916 TATTAAATATTTATAA
1 TATTAAATATTTATAA
*
3654932 TATTAATATTTTTAATAA
1 TATTAA-ATATTT-ATAA
3654950 TATTA
1 TATTA
3654955 TTATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTAAATATTTATAA
Found at i:3656093 original size:29 final size:29
Alignment explanation
Indices: 3656061--3656153 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
3656051 CCTAAACTTC
3656061 CCAAAATCTCATTTTCAACCCCAATTTTA
1 CCAAAATCTCATTTTCAACCCCAATTTTA
* * *
3656090 CCAAAAT-TACCGTTTT-ACCCCCGAA-TTTC
1 CCAAAATCT--CATTTTCAACCCC-AATTTTA
* * *
3656119 CCAAAATCCCATTTTCAACCCTAATTTCA
1 CCAAAATCTCATTTTCAACCCCAATTTTA
3656148 CCAAAA
1 CCAAAA
3656154 ATTACCATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 8 0.16
29 34 0.69
30 7 0.14
ACGTcount: A:0.34, C:0.33, G:0.02, T:0.30
Consensus pattern (29 bp):
CCAAAATCTCATTTTCAACCCCAATTTTA
Found at i:3656120 original size:58 final size:58
Alignment explanation
Indices: 3655973--3656227 Score: 307
Period size: 59 Copynumber: 4.3 Consensus size: 58
3655963 CTGAACTATT
* * *
3655973 CAAAATTTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACTCCGATTTCAC
1 CAAAA-TTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTCAACCCCAATTTCAC
* * *
3656032 CAAAAATTACCATTTTACCCCTAAACTTCCCAAAATCTCATTTTCAACCCCAATTTTAC
1 C-AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTCAACCCCAATTTCAC
* ** *
3656091 CAAAATTACCGTTTTACCCCCGAA-TTTCCCAAAATCCCATTTTCAACCCTAATTTCAC
1 CAAAATTACCATTTTACCCCTAAACTTT-CCAAAATCCCATTTTCAACCCCAATTTCAC
* * * * * *
3656149 CAAAAATTACCATTTTACCCCTAAACATTCTAAAATCCTATTTTTAACCTCGATTTCAC
1 C-AAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTCAACCCCAATTTCAC
3656208 CAAAATTA-CATTTTTACCCC
1 CAAAATTACCA-TTTTACCCC
3656228 CGAAAGTCAA
Statistics
Matches: 168, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
57 4 0.02
58 64 0.38
59 94 0.56
60 6 0.04
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.34
Consensus pattern (58 bp):
CAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTCAACCCCAATTTCAC
Found at i:3656168 original size:29 final size:28
Alignment explanation
Indices: 3656025--3656168 Score: 100
Period size: 28 Copynumber: 4.9 Consensus size: 28
3656015 TTTAACTCCG
3656025 ATTTCACCAAAAATTACCATTTTACCCCTAA
1 ATTTCACC-AAAATTACCATTTTA-CCCT-A
* *
3656056 ACTTC-CCAAAA-T-CTCATTTTCAACCCCA
1 ATTTCACCAAAATTAC-CATTTT--ACCCTA
* * *
3656084 ATTTTACCAAAATTACCGTTTTACCCCCGA
1 ATTTCACCAAAATTACCATTTTA--CCCTA
*
3656114 ATTTC-CCAAAA-TCCCATTTTCAACCCTA
1 ATTTCACCAAAATTACCATTTT--ACCCTA
3656142 ATTTCACCAAAAATTACCATTTTACCC
1 ATTTCACC-AAAATTACCATTTTACCC
3656169 CTAAACATTC
Statistics
Matches: 89, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
27 1 0.01
28 28 0.31
29 25 0.28
30 22 0.25
31 13 0.15
ACGTcount: A:0.34, C:0.33, G:0.01, T:0.32
Consensus pattern (28 bp):
ATTTCACCAAAATTACCATTTTACCCTA
Found at i:3656185 original size:117 final size:117
Alignment explanation
Indices: 3655973--3656231 Score: 339
Period size: 117 Copynumber: 2.2 Consensus size: 117
3655963 CTGAACTATT
** * *
3655973 CAAAATTTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACTCCGATTTCACCAAAAA
1 CAAAA-TTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTCAACTCCAATTTCACCAAAAA
*
3656038 TTACCATTTTACCCCTAAACTTCCCAAAAT-CTCATTTTCAACCCCAATTTTAC
65 TTACCATTTTACCCCTAAACTTCCCAAAATCCT-ATTTTCAACCCCAATTTCAC
*
3656091 CAAAATTACCGTTTTACCCCCGAA-TTTCCCAAAATCCCATTTTCAAC-CCTAATTTCACCAAAA
1 CAAAATTACCATTTTACCCCCGAACTTT-CCAAAATCCCATTTTCAACTCC-AATTTCACCAAAA
* * * *
3656154 ATTACCATTTTACCCCTAAACATT-CTAAAATCCTATTTTTAACCTCGATTTCAC
64 ATTACCATTTTACCCCTAAAC-TTCCCAAAATCCTATTTTCAACCCCAATTTCAC
3656208 CAAAATTA-CATTTTTACCCCCGAA
1 CAAAATTACCA-TTTTACCCCCGAA
3656232 AGTCAAAAAT
Statistics
Matches: 125, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
116 6 0.05
117 110 0.88
118 9 0.07
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (117 bp):
CAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTCAACTCCAATTTCACCAAAAAT
TACCATTTTACCCCTAAACTTCCCAAAATCCTATTTTCAACCCCAATTTCAC
Found at i:3661962 original size:17 final size:17
Alignment explanation
Indices: 3661940--3661973 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3661930 TTGTTTGGTT
*
3661940 GTAAATGATTTTTCAAA
1 GTAAATGATTTTACAAA
*
3661957 GTAAATTATTTTACAAA
1 GTAAATGATTTTACAAA
3661974 CACGAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (17 bp):
GTAAATGATTTTACAAA
Found at i:3662131 original size:6 final size:6
Alignment explanation
Indices: 3662090--3662128 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3662080 GGTAAATGCT
* *
3662090 TTCTCT TTCTCC TTCTCC TTCTCC TTCTCC TTCCCC TTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTC
3662129 CCCCTTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TTCTCC
Found at i:3672326 original size:30 final size:28
Alignment explanation
Indices: 3672290--3672390 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 28
3672280 CCTAGGGGGC
3672290 AAAATGGTAATTTTGGTGTAATCGAGGTTA
1 AAAATGG-AATTTTGGTG-AATCGAGGTTA
* * *
3672320 AAAATGGAATTTT-GAGACTTC-AGGGGT-
1 AAAATGGAATTTTGGTGA-ATCGA-GGTTA
3672347 AAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGG-AA-TTTTGGTG-AATCGAGGTTA
3672378 AAAATGGAATTTT
1 AAAATGGAATTTT
3672391 AGGAGGTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
27 9 0.16
28 9 0.16
29 14 0.25
30 16 0.28
31 9 0.16
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAATCGAGGTTA
Found at i:3672502 original size:59 final size:58
Alignment explanation
Indices: 3672285--3672653 Score: 448
Period size: 59 Copynumber: 6.4 Consensus size: 58
3672275 GGATACCTAG
* * *
3672285 GGGGCAAAATGGTAA-TTTTGGTGTAATCGAGGTTAAAAATGGAATTTT-G-AGACTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAG-GTTC
*
3672341 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGG-AGGTTT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-GGAAGGTTC
* * *
3672400 AGGG---AATGGTAATTTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAGGTTC
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTC
* * * *
3672456 GGGAGTAAAATGGTAATTTTTGGTGAAATCGAAGTCAAAAATGGAATTTTAGAAGGTTTG
1 GGG-GTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGG-TTC
* * * *
3672516 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTC
* * *
3672574 AGGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATAGAATTTTGGAA-GTTT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTC
*
3672632 GGGGTAAAATGATAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
3672654 AAGTTTCGAG
Statistics
Matches: 273, Mismatches: 28, Indels: 22
0.85 0.09 0.07
Matches are distributed among these distances:
55 10 0.04
56 39 0.14
57 35 0.13
58 40 0.15
59 133 0.49
60 16 0.06
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTC
Found at i:3672563 original size:30 final size:30
Alignment explanation
Indices: 3672342--3672564 Score: 91
Period size: 30 Copynumber: 7.7 Consensus size: 30
3672332 TGAGACTTCA
*
3672342 GGGGT-AAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAAATGGTAATTTTTGGTGAAATT
* * * **
3672371 GAGGTTAAAAATGG-AATTTTAGGAG-GTTT
1 G-GGGTAAAAATGGTAATTTTTGGTGAAATT
* **
3672400 AGGG----AATGGTAATTTTTTGGTGAAACC
1 GGGGTAAAAATGGTAA-TTTTTGGTGAAATT
*
3672427 GGGGTTAAAAATGG-AA-TTTT-G-GAAGGTT
1 GGGG-TAAAAATGGTAATTTTTGGTGAA-ATT
*
3672455 CGGGAGT-AAAATGGTAATTTTTGGTGAAATC
1 -GGG-GTAAAAATGGTAATTTTTGGTGAAATT
** * ** **
3672486 GAAGTCAAAAATGG-AATTTTAGAAG-GTTT
1 GGGGT-AAAAATGGTAATTTTTGGTGAAATT
3672515 GGGGGT-AAAATGGTAATTTTTGGTGAAATT
1 -GGGGTAAAAATGGTAATTTTTGGTGAAATT
3672545 GGGGTCAAAAATGG-AATTTT
1 GGGGT-AAAAATGGTAATTTT
3672565 AGAAGGTTCA
Statistics
Matches: 135, Mismatches: 35, Indels: 47
0.62 0.16 0.22
Matches are distributed among these distances:
24 5 0.04
25 2 0.01
26 7 0.05
27 6 0.04
28 17 0.13
29 28 0.21
30 37 0.27
31 25 0.19
32 8 0.06
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (30 bp):
GGGGTAAAAATGGTAATTTTTGGTGAAATT
Found at i:3672579 original size:30 final size:27
Alignment explanation
Indices: 3672493--3672593 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 27
3672483 ATCGAAGTCA
3672493 AAAATGG-AATTTTAGAAGGTTTGGGGGT
1 AAAATGGTAATTTTAGAAGG-TT-GGGGT
* *
3672521 AAAATGGTAATTTTTGGTGAA-ATTGGGGT
1 AAAATGGTAA-TTTT--AGAAGGTTGGGGT
3672550 CAAAAATGG-AATTTTAGAAGGTTCAGGGGT
1 --AAAATGGTAATTTTAGAAGGTT--GGGGT
3672580 AAAATGGTAATTTT
1 AAAATGGTAATTTT
3672594 TAGTGAAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
27 3 0.05
28 16 0.27
29 17 0.29
30 13 0.22
31 7 0.12
32 3 0.05
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.34
Consensus pattern (27 bp):
AAAATGGTAATTTTAGAAGGTTGGGGT
Found at i:3672588 original size:118 final size:116
Alignment explanation
Indices: 3672285--3672653 Score: 500
Period size: 118 Copynumber: 3.2 Consensus size: 116
3672275 GGATACCTAG
* * * *
3672285 GGGGCAAAATGGTAA-TTTTGGTGTAATCGAGGTTAAAAATGGAATTTTG-AGACTTCAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAG-GTTCAGGGGTA
*
3672348 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGGAGGTTT
65 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTT
* *
3672400 AGGG---AATGGTAATTTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAGGTTC-GGGAG
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAGGTTCAGGG-G
* *
3672461 TAAAATGGTAATTTTTGGTGAAATCGAAGTCAAAAATGGAATTTTAGAAGGTTT
63 TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTT
* *
3672515 GGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTAGAAGGTTCAGGGGT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAGGTTCAGGGGT
* * *
3672580 AAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATAGAATTTTGGAA-GTTT
64 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTT
*
3672632 GGGGTAAAATGATAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
3672654 AAGTTTCGAG
Statistics
Matches: 225, Mismatches: 19, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
112 8 0.04
114 33 0.15
115 59 0.26
116 26 0.12
117 4 0.02
118 84 0.37
119 11 0.05
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.33
Consensus pattern (116 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAGGTTCAGGGGTAA
AATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGGTTT
Found at i:3672658 original size:28 final size:29
Alignment explanation
Indices: 3672620--3672678 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
3672610 AAAAATAGAA
*
3672620 TTTTGGAAGTTT-GGGGT-AAAATGATAAT
1 TTTTGGAAGTTTCGAGGTCAAAATG-TAAT
3672648 TTTTGGAAGTTTCGAGGTCAAAATGTAAT
1 TTTTGGAAGTTTCGAGGTCAAAATGTAAT
3672677 TT
1 TT
3672679 CCTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.43
29 10 0.36
30 6 0.21
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.41
Consensus pattern (29 bp):
TTTTGGAAGTTTCGAGGTCAAAATGTAAT
Found at i:3673746 original size:3 final size:3
Alignment explanation
Indices: 3673738--3673778 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
3673728 TATTAAATAT
*
3673738 TTA TTA TTA TTA TTA ATA TTTA TTA TTA GTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
3673779 AATATTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.85
4 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3673762 original size:16 final size:16
Alignment explanation
Indices: 3673739--3673778 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3673729 ATTAAATATT
3673739 TATTATTATTA-TTAA
1 TATTATTATTAGTTAA
*
3673754 TATTTATTATTAGTTAT
1 TA-TTATTATTAGTTAA
3673771 TATTATTA
1 TATTATTA
3673779 AATATTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 15 0.68
17 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTATTATTAGTTAA
Found at i:3673785 original size:13 final size:13
Alignment explanation
Indices: 3673742--3673785 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3673732 AAATATTTAT
3673742 TATTATTATT-AA
1 TATTATTATTAAA
**
3673754 TATTTATTATTAGT
1 TA-TTATTATTAAA
3673768 TATTATTATTAAA
1 TATTATTATTAAA
3673781 TATTA
1 TATTA
3673786 ATGGATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TATTATTATTAAA
Found at i:3675091 original size:38 final size:37
Alignment explanation
Indices: 3674973--3675389 Score: 173
Period size: 38 Copynumber: 11.4 Consensus size: 37
3674963 GTCTAATTCT
* *
3674973 TACTTCAATTTCAGAGATAAAGACTTGCTATCCAACTC
1 TACTTCAATTTCAGAGAT-AAGACATGTTATCCAACTC
* * * * *
3675011 TACTTCAATTTCAAGAGGATAGGAAATGATTTTGC-TCT-
1 TACTTCAATTTC-AGA-GATAAGACATG-TTATCCAACTC
*
3675049 TACTTCAATTTCAGAGATACAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATA-AGACATGTTATCCAACTC
* * *
3675087 TACTTCAATTTCAAGCGGAT--GAC--G-T-TGC-TCT-
1 TACTTCAATTTC-AG-AGATAAGACATGTTATCCAACTC
* *
3675118 TACTTCAATTGCAGAGATGAAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGAT-AAGACATGTTATCCAACTC
* * * *
3675156 TACTTTAATTTCAAGCGGAT--GA-A-G-T-TGC-TCT-
1 TACTTCAATTTC-AG-AGATAAGACATGTTATCCAACTC
*
3675187 TACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTC
1 TACTTCAATTTCAGAGAT-AAGACATGTTATCCAACTC
* * * *
3675224 TACTTCAATTTCAAGAGGATAGGAAATGATGT-TGCTA-T-
1 TACTTCAATTTC-AGA-GATAAGACATG-T-TATCCAACTC
* * * * *
3675262 TACTTCAATTTCGGAGATAAAGACTTGATATCCAGCTT
1 TACTTCAATTTCAGAGAT-AAGACATGTTATCCAACTC
* * ***
3675300 TACTTCAATTTTCAAGAGGATAGGAAAATG--ATCTTGCTCC
1 TACTTCAA-TTTC-AGA-GATAAG-ACATGTTATCCAACT-C
3675340 TACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTC
1 TACTTCAATTTCAGAGAT-AAGACATGTTATCCAACTC
3675377 TACTTCAATTTCA
1 TACTTCAATTTCA
3675390 AGCGGACAGA
Statistics
Matches: 281, Mismatches: 54, Indels: 89
0.66 0.13 0.21
Matches are distributed among these distances:
29 6 0.02
30 4 0.01
31 22 0.08
32 9 0.03
33 4 0.01
34 4 0.01
35 5 0.02
36 19 0.07
37 57 0.20
38 81 0.29
39 38 0.14
40 26 0.09
41 6 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (37 bp):
TACTTCAATTTCAGAGATAAGACATGTTATCCAACTC
Found at i:3675125 original size:31 final size:31
Alignment explanation
Indices: 3675087--3675199 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 31
3675077 TATCCAACTC
3675087 TACTTCAATTTCAAGCGGATGACGTTGCTCT
1 TACTTCAATTTCAAGCGGATGACGTTGCTCT
* ** * * *
3675118 TACTTCAATTGCAGAGATGAAGACGTGTTATCCAACT
1 TACTTCAATTTCA-AGCGGATGAC--G-T-TGC-TCT
* *
3675155 CTACTTTAATTTCAAGCGGATGAAGTTGCTCT
1 -TACTTCAATTTCAAGCGGATGACGTTGCTCT
3675187 TACTTCAATTTCA
1 TACTTCAATTTCA
3675200 GAGATGAAGA
Statistics
Matches: 60, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
31 24 0.40
32 9 0.15
33 2 0.03
34 2 0.03
35 2 0.03
36 2 0.03
37 8 0.13
38 11 0.18
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (31 bp):
TACTTCAATTTCAAGCGGATGACGTTGCTCT
Found at i:3675307 original size:138 final size:135
Alignment explanation
Indices: 3675042--3675391 Score: 328
Period size: 153 Copynumber: 2.4 Consensus size: 135
3675032 GGAAATGATT
*
3675042 TTGCTCTTACTTCAATTTCAGAGATACAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATACAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
* * * *
3675107 GACGTTGCTCTTACTTCAATTGCAGAGATGAAGACGTGTTATCCAACTCTACTTTAATTTCAAGC
66 GACGTTGCTATTACTTCAATTGCAGAGATAAAGACGTGATATCCAA--C-ACTTTAACTTCAAGC
3675172 GGATGAAG
128 GGATGAAG
3675180 TTGCTCTTACTTCAATTTCAGAGATGA-AGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGAT-ACAGACGTGTTATCCAACTCTACTTCAATTTC-A-A-G-
* * * * * *
3675243 TAGGAAATGATGTTGCTATTACTTCAATTTCGGAGATAAAGACTTGATATCCAGCTTTACTTCAA
61 -AGG--ATGACGTTGCTATTACTTCAATTGCAGAGATAAAGACGTGATATCCAAC---ACTTTAA
* *
3675308 TTTTCAAGAGGATAGGAAAATG
120 -CTTCAAGCGGAT--G--AA-G
* * *
3675330 ATCTTGCTCCTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAG
1 ---TTGCTCTTACTTCAATTTCAGAGATACAGACGTGTTATCCAACTCTACTTCAATTTCAAG
3675392 CGGACAGAAA
Statistics
Matches: 179, Mismatches: 13, Indels: 28
0.81 0.06 0.13
Matches are distributed among these distances:
137 16 0.09
138 39 0.22
139 2 0.01
140 1 0.01
142 3 0.02
144 47 0.26
145 11 0.06
147 1 0.01
149 2 0.01
150 2 0.01
151 1 0.01
152 2 0.01
153 52 0.29
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (135 bp):
TTGCTCTTACTTCAATTTCAGAGATACAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACGTTGCTATTACTTCAATTGCAGAGATAAAGACGTGATATCCAACACTTTAACTTCAAGCGGA
TGAAG
Found at i:3675348 original size:78 final size:75
Alignment explanation
Indices: 3674970--3675391 Score: 503
Period size: 69 Copynumber: 5.7 Consensus size: 75
3674960 TTTGTCTAAT
* *
3674970 TCTTACTTCAATTTCAGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGA
*
3675035 AATGATTTTGC
65 AATGATCTTGC
* * *
3675046 TCTTACTTCAATTTCAGAGATACAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGAT--G-
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGA
*
3675108 -ACG---TTGC
65 AATGATCTTGC
* * * * *
3675115 TCTTACTTCAATTGCAGAGATGAAGACGTGTTATCCAACTCTACTTTAATTTCAAGCGGAT--G-
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGA
3675177 AA-G---TTGC
65 AATGATCTTGC
* *
3675184 TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGGAA
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATAGGAA
*
3675249 ATGATGTTGC
66 ATGATCTTGC
* * * * *
3675259 TATTACTTCAATTTCGGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTTCAAGAGGATAGG
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCA-CTCTACTTCAA-TTTCAAGAGGATAGG
3675324 AAAATGATCTTGC
64 -AAATGATCTTGC
*
3675337 TCCTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAG
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAG
3675392 CGGACAGAAA
Statistics
Matches: 310, Mismatches: 25, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
68 22 0.07
69 102 0.33
70 2 0.01
71 2 0.01
72 3 0.01
74 1 0.00
75 36 0.12
76 74 0.24
77 25 0.08
78 43 0.14
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (75 bp):
TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATAGGAA
ATGATCTTGC
Found at i:3687528 original size:29 final size:28
Alignment explanation
Indices: 3687496--3687712 Score: 113
Period size: 29 Copynumber: 7.5 Consensus size: 28
3687486 CCCAAAGGTC
*
3687496 AAAATGGTAATTTTGGTGTAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
* **
3687525 AAAAATGGAATTTT-GAGACTTCAGGGG-T
1 -AAAATGGAATTTTGGTGAAATC-GGGGTT
*
3687553 AAAATAGTAATTTTTGGTGAAATCGGGGTT
1 AAAAT-GGAA-TTTTGGTGAAATCGGGGTT
* *** *
3687583 AAAATGGAATTTTAGGAGGTTTAGGGG-T
1 AAAATGGAATTTT-GGTGAAATCGGGGTT
* *
3687611 AAAATGGTAATTTTTGGTAAAATC-GAGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
* * *
3687640 AAAAATGGAATTTT--AGAAGGTTCGGGGGT
1 -AAAATGGAATTTTGGTGAA--ATCGGGGTT
* *
3687669 AAAATAGTAATTTTCGGTGAAATCGGAGTT
1 AAAAT-GGAATTTT-GGTGAAATCGGGGTT
3687699 AAAAATGGAATTTT
1 -AAAATGGAATTTT
3687713 AGAAAGTTTA
Statistics
Matches: 137, Mismatches: 32, Indels: 36
0.67 0.16 0.18
Matches are distributed among these distances:
26 2 0.01
27 5 0.04
28 33 0.24
29 47 0.34
30 42 0.31
31 5 0.04
32 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGGGGTT
Found at i:3687727 original size:59 final size:59
Alignment explanation
Indices: 3687496--3687861 Score: 424
Period size: 58 Copynumber: 6.3 Consensus size: 59
3687486 CCCAAAGGTC
* * * *
3687496 AAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTT-GAGACTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
* * * * *
3687553 AAAATAGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGGAGGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
* * *
3687611 AAAATGGTAATTTTTGGTAAAATC-GAGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
* * *
3687669 AAAATAGTAATTTTCGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
* * * *
3687728 -AAATGGTAATTTTTAGTGAAA-CCGAGGTTTAAAATGGAATTTTAG-AAGATTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGA-GTTAAAAATGGAATTTTAGAAAG-TTCAGGGGT
* * * * **
3687786 AAAATGGTAATTTTTAGTGAAATTAGG-GTTAAAAATAGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAA-TCGGAGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
3687845 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
3687862 AAGTTTCGAG
Statistics
Matches: 266, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
57 32 0.12
58 138 0.52
59 92 0.35
60 3 0.01
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
Found at i:3687781 original size:117 final size:117
Alignment explanation
Indices: 3687496--3687861 Score: 501
Period size: 117 Copynumber: 3.1 Consensus size: 117
3687486 CCCAAAGGTC
* * *
3687496 AAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTT-G-AGACTTCAGGGGTAAAAT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGA-TTCGGGGGTAAAAT
* *
3687558 AGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGGAGGTTTAGGGGT
65 AGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
* *
3687611 AAAATGGTAATTTTTGGTAAAATCGA-GTTAAAAATGGAATTTTAGAAGGTTCGGGGGTAAAATA
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATA
*
3687675 GTAATTTTCGGTGAAATCGGAGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
66 GTAATTTTTGGTGAAATCGG-GTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * * *
3687728 -AAATGGTAATTTTTAGTGAAACCGAGGTTTAAAATGGAATTTTAGAAGATTCGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATA
* * * * *
3687792 GTAATTTTTAGTGAAATTAGGGTTAAAAATAGAATTTTGGAAAGTTTGGGGGT
66 GTAATTTTTGGTGAAA-TCGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
3687845 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
3687862 AAGTTTCGAG
Statistics
Matches: 222, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
115 29 0.13
116 69 0.31
117 106 0.48
118 18 0.08
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATA
GTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGT
Found at i:3688955 original size:3 final size:3
Alignment explanation
Indices: 3688947--3688987 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
3688937 TATTAAATAT
*
3688947 TTA TTA TTA TTA TTA ATA TTTA TTA TTA GTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
3688988 AATATTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.85
4 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3688971 original size:16 final size:16
Alignment explanation
Indices: 3688948--3688987 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3688938 ATTAAATATT
3688948 TATTATTATTA-TTAA
1 TATTATTATTAGTTAA
*
3688963 TATTTATTATTAGTTAT
1 TA-TTATTATTAGTTAA
3688980 TATTATTA
1 TATTATTA
3688988 AATATTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 15 0.68
17 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTATTATTAGTTAA
Found at i:3688994 original size:13 final size:13
Alignment explanation
Indices: 3688951--3688994 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3688941 AAATATTTAT
3688951 TATTATTATT-AA
1 TATTATTATTAAA
**
3688963 TATTTATTATTAGT
1 TA-TTATTATTAAA
3688977 TATTATTATTAAA
1 TATTATTATTAAA
3688990 TATTA
1 TATTA
3688995 ATGGATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TATTATTATTAAA
Found at i:3689764 original size:6 final size:6
Alignment explanation
Indices: 3689755--3689842 Score: 51
Period size: 6 Copynumber: 15.0 Consensus size: 6
3689745 TTAATATTAT
* * * * *
3689755 TTTAAA TTT--A TTCAAA TTTAAA TTTAAA -ATAAA CTTAAA TAAGTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* *
3689802 TTTAAA TTTTAAA TTTAAA -ATAAA TTTAAA ATT-AA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3689843 CTCAAAGCTA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
4 3 0.05
5 12 0.20
6 36 0.59
7 6 0.10
8 4 0.07
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:3689827 original size:11 final size:11
Alignment explanation
Indices: 3689773--3689842 Score: 59
Period size: 11 Copynumber: 5.9 Consensus size: 11
3689763 TATTCAAATT
3689773 TAAATTTAAAA
1 TAAATTTAAAA
*
3689784 TAAACTTAAATAA
1 TAAA-TTTAA-AA
* *
3689797 GTAATTTTAAATTT
1 -TAAATTTAAA--A
3689811 TAAATTTAAAA
1 TAAATTTAAAA
3689822 TAAATTTAAAA
1 TAAATTTAAAA
*
3689833 TTAATTTAAA
1 TAAATTTAAA
3689843 CTCAAAGCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 24 0.51
12 5 0.11
13 15 0.32
14 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:3690056 original size:2 final size:2
Alignment explanation
Indices: 3690049--3690096 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
3690039 TTTAATTCAT
*
3690049 TA TA TA TA TA TA TA TA TA TA -A TGA -A T- TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
3690089 TA TA TA TA
1 TA TA TA TA
3690097 ATGAATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 36 0.90
3 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3690090 original size:28 final size:28
Alignment explanation
Indices: 3690050--3690103 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3690040 TTAATTCATT
3690050 ATATATATATATATATATAATGAATTAA
1 ATATATATATATATATATAATGAATTAA
3690078 ATATATATATATATATATAATGAATT
1 ATATATATATATATATATAATGAATT
3690104 TTTGTGCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
ATATATATATATATATATAATGAATTAA
Found at i:3701302 original size:97 final size:94
Alignment explanation
Indices: 3701047--3701323 Score: 247
Period size: 92 Copynumber: 2.9 Consensus size: 94
3701037 ATATTAATAC
* * *
3701047 TATAATTGATTTGATTTCTAGTGTTAAAATACAAAACATAGTCTTCATTTATTCTTATGCTGTTC
1 TATAATTGATTTGATTT-AAGAG-T-AAATAC-AAACATAGTCTTCATTTATTCTTATGCAGTTC
* *
3701112 TTAACATTACACGTGTTTTGCGAAGATCGATAT
62 TTAATATTACACGTGTTTTGTGAAGATCGATAT
* * * * * *** * * * *
3701145 TATAATTTAATTAATTTACGAG-ATATA-AGTTATTGTCATCATTTATTCATATGTAGTTCTTAA
1 TATAATTGATTTGATTTAAGAGTAAATACAAACATAGTCTTCATTTATTCTTATGCAGTTCTTAA
3701208 TATTACACGTG-TTTGTGAAGATCGATCA-
66 TATTACACGTGTTTTGTGAAGATCGAT-AT
* *
3701236 TATAATTGATTTGAGTTTAAGAGTCCAAATACGAACCATCGTCTTCATTTATTCTTATGCAGTTC
1 TATAATTGATTTGA-TTTAAGAGT--AAATAC-AAACATAGTCTTCATTTATTCTTATGCAGTTC
* * *
3701301 TTATTATTAAATGTGTTTTGTGA
62 TTAATATTACACGTGTTTTGTGA
3701324 TTATCAATCT
Statistics
Matches: 139, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
91 25 0.18
92 46 0.33
94 4 0.03
95 4 0.03
97 39 0.28
98 21 0.15
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (94 bp):
TATAATTGATTTGATTTAAGAGTAAATACAAACATAGTCTTCATTTATTCTTATGCAGTTCTTAA
TATTACACGTGTTTTGTGAAGATCGATAT
Found at i:3704793 original size:195 final size:195
Alignment explanation
Indices: 3704347--3704795 Score: 505
Period size: 195 Copynumber: 2.3 Consensus size: 195
3704337 AATATATTGG
* ** *
3704347 AATATAAATTATTGT-GTTCATTCATTAATATGCAGTTCTTTATGTTACACGTATTTGTGAAGAT
1 AATATAAATTATTGTCG-TCATTCATTAATATGTAGTTCTTTAAATTACACGTGTTTGTGAAGAT
* *
3704411 TGATCCGATAATTGATTTGATTTCTAGTGTTAAAATACAAACCATAGTCTTCTTTTATTCTTATG
65 TGATCCGATAATTGATTTGATTTCTAGAGTTAAAATACAAACCATAGTCTTCATTTATTCTTATG
* *
3704476 CAATTTTTAATATAACACGTGCTTTGCAAAGATCAATATTATAATTTATTTAATTTACGAGATTC
130 CAATTCTTAATATAACACGTGCTTTGCAAAGATCAATATTATAATTTATTTAATTTAAGAGATTC
3704541 A
195 A
* * ** * * * *
3704542 AACATAAATTATTGCCACCATTTATTCATATGTAGTT-ATCAATATTACACGTGTTTGTGAAGAT
1 AATATAAATTATTGTCGTCATTCATTAATATGTAGTTCTTTAA-ATTACACGTGTTTGTGAAGAT
* * * * *
3704606 TGAT-CGTTTAATTGATTTGATTTTTAGAGTTCAAGTACAAACGATCA-TCTTCATTTATTCTTA
65 TGATCCG-ATAATTGATTTGATTTCTAGAGTTAAAATACAAACCAT-AGTCTTCATTTATTCTTA
* * * * * * *
3704669 TGTACTTCTTAATATTACACGTGTTTTGTC-AATATCAATCTTATAGTTTATTTAATTTATAG-G
128 TGCAATTCTTAATATAACACGTGCTTTG-CAAAGATCAATATTATAATTTATTTAATTTA-AGAG
3704732 ATTCA
191 ATTCA
* * * * *
3704737 AATAGAAATTATCGTCGTCATTCATTTATACGTAGTTCTTTAAATTACATGTGTTTGTG
1 AATATAAATTATTGTCGTCATTCATTAATATGTAGTTCTTTAAATTACACGTGTTTGTG
3704796 CAAACAAATT
Statistics
Matches: 207, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
194 4 0.02
195 197 0.95
196 6 0.03
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (195 bp):
AATATAAATTATTGTCGTCATTCATTAATATGTAGTTCTTTAAATTACACGTGTTTGTGAAGATT
GATCCGATAATTGATTTGATTTCTAGAGTTAAAATACAAACCATAGTCTTCATTTATTCTTATGC
AATTCTTAATATAACACGTGCTTTGCAAAGATCAATATTATAATTTATTTAATTTAAGAGATTCA
Found at i:3710377 original size:16 final size:16
Alignment explanation
Indices: 3710358--3710388 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3710348 ATTAATAAGA
3710358 AAAAAATTACAATTCC
1 AAAAAATTACAATTCC
3710374 AAAAAATTACAATTC
1 AAAAAATTACAATTC
3710389 TTTTTACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAATTACAATTCC
Found at i:3710882 original size:16 final size:16
Alignment explanation
Indices: 3710862--3710903 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3710852 TAATTTTTTT
3710862 ATTTTAATATTAAATA
1 ATTTTAATATTAAATA
* *
3710878 TTTTTAAAATTAAATA
1 ATTTTAATATTAAATA
*
3710894 AATTTAATAT
1 ATTTTAATAT
3710904 AACTTATTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATATTAAATA
Found at i:3710974 original size:14 final size:14
Alignment explanation
Indices: 3710949--3710984 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3710939 ATTTCATTGC
3710949 AAAAAAAA-TACAA
1 AAAAAAAATTACAA
*
3710962 AAGAAAAATTACAA
1 AAAAAAAATTACAA
3710976 AAAAAAAAT
1 AAAAAAAAT
3710985 GCTTTAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.11
Consensus pattern (14 bp):
AAAAAAAATTACAA
Found at i:3723869 original size:29 final size:30
Alignment explanation
Indices: 3723837--3723895 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3723827 TTTGGGTTAA
*
3723837 TGTGCAATTATATATAT-AAATTTTAATTT
1 TGTGCAATTATATACATCAAATTTTAATTT
* * *
3723866 TGTGTAATTTTATACATCAAATTTTCATTT
1 TGTGCAATTATATACATCAAATTTTAATTT
3723896 GATCAAAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.53
Consensus pattern (30 bp):
TGTGCAATTATATACATCAAATTTTAATTT
Found at i:3725537 original size:14 final size:13
Alignment explanation
Indices: 3725518--3725553 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
3725508 TTCCTAAAGC
3725518 ATTTTTTTTTTGT
1 ATTTTTTTTTTGT
*
3725531 AATTTTTCTTTTGT
1 -ATTTTTTTTTTGT
3725545 ATTTTTTTT
1 ATTTTTTTT
3725554 GCAATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (13 bp):
ATTTTTTTTTTGT
Found at i:3725628 original size:16 final size:16
Alignment explanation
Indices: 3725599--3725639 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3725589 AGAATAAGTT
**
3725599 ATATTAAATTTATTTA
1 ATATTAAAAATATTTA
*
3725615 ATTTTAAAAATATTTA
1 ATATTAAAAATATTTA
3725631 ATATTAAAA
1 ATATTAAAA
3725640 TAAAAAAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTAAAAATATTTA
Found at i:3726135 original size:16 final size:16
Alignment explanation
Indices: 3726114--3726144 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3726104 TGTGTAAAAA
3726114 GAATTGTAATTTTTTG
1 GAATTGTAATTTTTTG
3726130 GAATTGTAATTTTTT
1 GAATTGTAATTTTTT
3726145 TTCTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (16 bp):
GAATTGTAATTTTTTG
Found at i:3737137 original size:9 final size:9
Alignment explanation
Indices: 3737123--3737153 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3737113 GAAGTCAAAA
3737123 TCATTGAAG
1 TCATTGAAG
3737132 TCATTGAAG
1 TCATTGAAG
*
3737141 TCATTAAAG
1 TCATTGAAG
3737150 TCAT
1 TCAT
3737154 ATAAGGGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (9 bp):
TCATTGAAG
Found at i:3745306 original size:30 final size:30
Alignment explanation
Indices: 3745270--3745328 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3745260 GTATTGGTAT
*
3745270 TGGCATTGGCAATGTGGATGGATCTCTCTG
1 TGGCATTGGCAATATGGATGGATCTCTCTG
*
3745300 TGGCATTGGCAATATGGATGGTTCTCTCT
1 TGGCATTGGCAATATGGATGGATCTCTCT
3745329 ATGATTGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.36
Consensus pattern (30 bp):
TGGCATTGGCAATATGGATGGATCTCTCTG
Found at i:3747664 original size:99 final size:99
Alignment explanation
Indices: 3747531--3747785 Score: 334
Period size: 99 Copynumber: 2.6 Consensus size: 99
3747521 CTTGAACTGG
* * * *
3747531 GTTAACCCTACGCTCCAAGTACATCGGTTCAGCTGTATAAACTCCATTTTCTGGGAGGCTACTTC
1 GTTAACCCTACGCTCCGAGTAAACCGGTTCAGCTGTATAAACTCCATCTTCTGGGAGGCTACTTC
* * *
3747596 CAGTATGACTATTGAGATT-CTTGGCTTCAACTAA
66 CAATATGACTATT-AAATTGATTGGCTTCAACTAA
* *
3747630 GTTAACCCTACGTTCCGAGTAAACCGGTTGAGCTGTATAAACTCCATCTTCTGGGAGGCTACTTC
1 GTTAACCCTACGCTCCGAGTAAACCGGTTCAGCTGTATAAACTCCATCTTCTGGGAGGCTACTTC
* * *
3747695 CAATATGACTATTAAATTGATTTGCTTGAACTGA
66 CAATATGACTATTAAATTGATTGGCTTCAACTAA
* * * *
3747729 GTTAACCCTACGCTCCGAGTAAACTGGTTCA-ATCCTATAAACTCCATCTTTTGGGAG
1 GTTAACCCTACGCTCCGAGTAAACCGGTTCAGCT-GTATAAACTCCATCTTCTGGGAG
3747786 CATCTCTTCC
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
98 5 0.04
99 131 0.96
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (99 bp):
GTTAACCCTACGCTCCGAGTAAACCGGTTCAGCTGTATAAACTCCATCTTCTGGGAGGCTACTTC
CAATATGACTATTAAATTGATTGGCTTCAACTAA
Found at i:3748323 original size:72 final size:72
Alignment explanation
Indices: 3748234--3748881 Score: 982
Period size: 72 Copynumber: 9.0 Consensus size: 72
3748224 TCGGCGCTCA
* *
3748234 TTGGAT-GGAGTTGAGTCTGATCATTTGTTCTTGCTAATGGAGGTGGAAGTTCCACTCCTACATC
1 TTGGATCGG-GTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATC
3748298 CACCTGAG
65 CACCTGAG
* * *
3748306 TTGGATCGGGTTGAGTCTGTTCACTTGTTGTGGCTAATGGAGGTGGAAGTTCCACTCCTGCATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATCC
*
3748371 ATCTGAG
66 ACCTGAG
* * * *
3748378 TTGGATAGGGTTGAGTCTGCTCATTTGTTGTTCCTAATGGAGGTGGAAGTTCCACTCCTGCATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATCC
3748443 ACCTGAG
66 ACCTGAG
* * *
3748450 TTAGATCGGGTTGAGTCTGCTCATTTGTTGTTCCTAATGGAGGTGGAAGTTCCACTCCTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATCC
3748515 ACCTGAG
66 ACCTGAG
* *
3748522 TTGGATCGGGTTGAGTCTGTTCATTTGTTGCTGCCAATGGAGGTGGAAGTTCCACTCCTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATCC
3748587 ACCTGAG
66 ACCTGAG
* * *
3748594 TTGAATCGGGTTGAGTCTGCTCATTTGTT-TCTGCCAATGGAGGTGGAAGTTCCACTCCTACATC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGT-TGCTAATGGAGGTGGAAGTTCCACTCCTACATC
3748658 CACCTGAG
65 CACCTGAG
*
3748666 TTGGATCGGGTTGAGTCTGTTCATTTGTT-TCTGCCAATGGAGGTGGAAG-TCTCACTCCTACAT
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGT-TGCTAATGGAGGTGGAAGTTC-CACTCCTACAT
3748729 CCACCTGAG
64 CCACCTGAG
* * * *
3748738 CTGGATTGGGTTGAGTCTGTTCATTTGTT-TCTGCCAATGGAGGTGGAAGTTCCACTCTTACATC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGT-TGCTAATGGAGGTGGAAGTTCCACTCCTACATC
*
3748802 GACCTGAG
65 CACCTGAG
* *
3748810 TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTTCTAATGGAGGTGGAAGTTCCCCTCCTACATCC
1 TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATCC
3748875 ACCTGAG
66 ACCTGAG
3748882 ATGGTTTAGG
Statistics
Matches: 535, Mismatches: 36, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
71 2 0.00
72 528 0.99
73 5 0.01
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (72 bp):
TTGGATCGGGTTGAGTCTGTTCATTTGTTGTTGCTAATGGAGGTGGAAGTTCCACTCCTACATCC
ACCTGAG
Found at i:3758710 original size:36 final size:36
Alignment explanation
Indices: 3758634--3758818 Score: 205
Period size: 30 Copynumber: 5.3 Consensus size: 36
3758624 GTATTGACGT
3758634 TGGCATTGGCATTGGCAATGTGGATGGATCTCTC--
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
*
3758668 T-G---TGGCATTGGCAATATGGATGGATCTCTCTG
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
*
3758700 TGGCATTGGCAATGGCATTGGTAATGTGGATGGATCTCTCTG
1 TGGCA-T-----TGGCATTGGCAATGTGGATGGATCTCTCTG
*
3758742 TGGCATTGGCATTGACAATGTGGATGGATCTCTC--
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
3758776 T-G---TGGCATTGGCAATGTGGATGGATCTCTCTG
1 TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
3758808 TGGCATTGGCA
1 TGGCATTGGCA
3758819 ATGTGGACGG
Statistics
Matches: 127, Mismatches: 6, Indels: 34
0.76 0.04 0.20
Matches are distributed among these distances:
30 54 0.43
32 2 0.02
33 4 0.03
34 2 0.02
36 31 0.24
41 1 0.01
42 33 0.26
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.33
Consensus pattern (36 bp):
TGGCATTGGCATTGGCAATGTGGATGGATCTCTCTG
Found at i:3758716 original size:42 final size:42
Alignment explanation
Indices: 3758670--3758791 Score: 175
Period size: 42 Copynumber: 3.0 Consensus size: 42
3758660 GATCTCTCTG
*
3758670 TGGCATTGGCAATATGGATGGATCTCTCTGTGGCATTGGCAA
1 TGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGCAA
*
3758712 TGGCATTGGTAATGTGGATGGATCTCTCTGTGGCA-T-----
1 TGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGCAA
*
3758748 TGGCATTGACAATGTGGATGGATCTCTCTGTGGCATTGGCAA
1 TGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGCAA
3758790 TG
1 TG
3758792 TGGATGGATC
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
36 33 0.47
37 1 0.01
41 1 0.01
42 35 0.50
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.33
Consensus pattern (42 bp):
TGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGCAA
Found at i:3758745 original size:72 final size:75
Alignment explanation
Indices: 3758633--3758791 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 75
3758623 GGTATTGACG
*
3758633 TTGGCATTGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATT-G-G-CAATATGGATGGATCT
1 TTGGCAATGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGTGACAATATGGATGGATCT
3758695 CTCTGTGGCA
66 CTCTGTGGCA
* *
3758705 TTGGCAATGGCATTGGTAATGTGGATGGATCTCTCTGTGGCATTGGCATTGACAATGTGGATGGA
1 TTGGCAATGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGG---TGACAATATGGATGGA
3758770 TCTCTCTGTGGCA
63 TCTCTCTGTGGCA
3758783 TTGGCAATG
1 TTGGCAATG
3758792 TGGATGGATC
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
72 42 0.54
73 1 0.01
77 1 0.01
78 34 0.44
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.33
Consensus pattern (75 bp):
TTGGCAATGGCATTGGCAATGTGGATGGATCTCTCTGTGGCATTGGTGACAATATGGATGGATCT
CTCTGTGGCA
Found at i:3765491 original size:20 final size:20
Alignment explanation
Indices: 3765465--3765509 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3765455 AATGTGAGAT
*
3765465 TTTTTTATAATTTTAATATTA
1 TTTTTAATAATTTTAAT-TTA
* *
3765486 TTTTTAATGATTTTGATTTA
1 TTTTTAATAATTTTAATTTA
3765506 TTTT
1 TTTT
3765510 ACTTGAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTAATAATTTTAATTTA
Found at i:3768794 original size:335 final size:334
Alignment explanation
Indices: 3768116--3768893 Score: 990
Period size: 335 Copynumber: 2.3 Consensus size: 334
3768106 ACTTTTTTTC
* * * * *
3768116 CCTTTAAAGAAGAGGGAGAGAATCTATCCCCAATTGAATTAAAATTAAAGTGAAAGTTACAATTG
1 CCTTTAGAGAAGAGGGAGAGAATCTGTCCCCAATTGAATTAAAATTAAGGTGAAA-TTACGATCG
* * * * *
3768181 TATCTATAACGAATGAATGATACGC-TT-TTAGATCTGAAAAACATAATCATTGTTTCAGATAAA
65 TATCTATATCGAATGAATG--ACGCGTTCTTAGATCTGAAAGACATAATCATTATTTCAAACAAA
* * *
3768244 GTATGACATATAGAGAAAGAAAGATTGAATTAACTACATCGAATCACCCATAACTTTTTTTTCAC
128 GTAAGACATATAGAGAAAGAAAGATTGAATTAACTACATCGAATCACCCAAAAC-TTCTTTTCAC
* * * *
3768309 TTTCCTCAACAGAACCAGAATCAGTAATGGGTACAACAATTGTCTCACTATCCAACAAATGACAC
192 TTACCTCAACAGAACCAAAATCAATAATGGGGACAACAATTGTCTCACTATCCAACAAATGACAC
* *
3768374 GTTCTCGGATATGAGCAATATAATTGTAATTTTGTACAGATACATCATACATCGATCATCTTTCT
257 GTTCTCAGATATGAGCAATATAATCGTAATTTTGTACAGATACATCATACATCGATCATCTTTCT
3768439 TGTTTTAAATCAT
322 TGTTTTAAATCAT
* * * * *
3768452 TCTTTAGATAAGAGGGAGAGGATTTGTCCCCAATTAAATTAAAATTAAGGTGAATATTACGATCG
1 CCTTTAGAGAAGAGGGAGAGAATCTGTCCCCAATTGAATTAAAATTAAGGTGAA-ATTACGATCG
* *
3768517 TATCTATATCGAATGAATGGCGCGTTCTTAGATCTGAAAGACATGATCATTATTTCAAACAAAGT
65 TATCTATATCGAATGAATGACGCGTTCTTAGATCTGAAAGACATAATCATTATTTCAAACAAAGT
*
3768582 AAGACATATAGAGAAAGAAAGATTTGAATTAACTACATCGAATCACTCAAAAC-TCTTTTCACTT
130 AAGACATATAGAGAAAGAAAGA-TTGAATTAACTACATCGAATCACCCAAAACTTCTTTTCACTT
* ** * * *
3768646 ACCTCAACTA-AACCAAAATCAATACTGGGGACAATGATT-TTTCCACTATCCAACACATGACAT
194 ACCTCAAC-AGAACCAAAATCAATAATGGGGACAACAATTGTCT-CACTATCCAACAAATGACAC
* * * * * *
3768709 GTTTTCAGATATGAGCTATGTAATCGTAATTTTGTATAGATACATCATACATTGATTATCTTTCT
257 GTTCTCAGATATGAGCAATATAATCGTAATTTTGTACAGATACATCATACATCGATCATCTTTCT
3768774 TGTTTTAAATCAT
322 TGTTTTAAATCAT
* ** * * * *
3768787 CCTTTAGAGAAGAGGAAGTTAATCTGACTCCAATTGAATTAAAATTAAGCTGAAGGGTTACGATC
1 CCTTTAGAGAAGAGGGAGAGAATCTGTCCCCAATTGAATTAAAATTAAGGTGAA--ATTACGATC
* * *
3768852 GTATCTATATCGAACGAATGACACGTTCTTAGATGTGAAAGA
64 GTATCTATATCGAATGAATGACGCGTTCTTAGATCTGAAAGA
3768894 GAACTGTTAT
Statistics
Matches: 379, Mismatches: 56, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
334 5 0.01
335 173 0.46
336 172 0.45
337 29 0.08
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (334 bp):
CCTTTAGAGAAGAGGGAGAGAATCTGTCCCCAATTGAATTAAAATTAAGGTGAAATTACGATCGT
ATCTATATCGAATGAATGACGCGTTCTTAGATCTGAAAGACATAATCATTATTTCAAACAAAGTA
AGACATATAGAGAAAGAAAGATTGAATTAACTACATCGAATCACCCAAAACTTCTTTTCACTTAC
CTCAACAGAACCAAAATCAATAATGGGGACAACAATTGTCTCACTATCCAACAAATGACACGTTC
TCAGATATGAGCAATATAATCGTAATTTTGTACAGATACATCATACATCGATCATCTTTCTTGTT
TTAAATCAT
Found at i:3771323 original size:24 final size:25
Alignment explanation
Indices: 3771271--3771328 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
3771261 TGGGGTACAC
* * *
3771271 TTCAAGTCAGAGTCCAAAGTTTGAG
1 TTCAAGTCAGAATCCAAAGTTTAAA
*
3771296 TTCAAGTCAGAATTC-AAGTTTAAA
1 TTCAAGTCAGAATCCAAAGTTTAAA
3771320 TTCAAGTCA
1 TTCAAGTCA
3771329 AAGGAGACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (25 bp):
TTCAAGTCAGAATCCAAAGTTTAAA
Found at i:3771894 original size:31 final size:32
Alignment explanation
Indices: 3771795--3771894 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 32
3771785 GATTAAATCA
* *
3771795 AAATTAAAATTTCAAATATAC-TTTTCA-ATC
1 AAATTAAAATTTCAAATATACAATTACACATC
** * *
3771825 ACAATTAAAATTTCACGTGTATAATTACAC-T-
1 A-AATTAAAATTTCAAATATACAATTACACATC
*
3771856 AAATTAAAATTT-ATATATACAATTACACATC
1 AAATTAAAATTTCAAATATACAATTACACATC
3771887 AAATTAAA
1 AAATTAAA
3771895 GTTAATGTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
29 12 0.22
30 13 0.24
31 25 0.45
32 5 0.09
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (32 bp):
AAATTAAAATTTCAAATATACAATTACACATC
Found at i:3777984 original size:13 final size:14
Alignment explanation
Indices: 3777966--3777997 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3777956 AGTTTAGGCT
3777966 TTAAATTT-TTTAA
1 TTAAATTTATTTAA
3777979 TTAAATTTATTTAA
1 TTAAATTTATTTAA
3777993 TTAAA
1 TTAAA
3777998 AATCTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAATTTATTTAA
Found at i:3779564 original size:3 final size:3
Alignment explanation
Indices: 3779556--3779584 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3779546 AGATTTGCAA
3779556 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
3779585 ACGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:3784106 original size:29 final size:29
Alignment explanation
Indices: 3784073--3784339 Score: 152
Period size: 29 Copynumber: 9.3 Consensus size: 29
3784063 TTAAAAATGC
*
3784073 AATTTTTGGATGCTCGGGGGTAAAATGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* * * ** *
3784102 AA-TTTTGAAAGTTCAGGGAAAAAAT-GC
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* * * *
3784129 AATTTTTAGATGCTCGGGGGCAAAAGGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* * * * * *
3784158 GATTTTGGGATGTCCAGGGGTAAAACGAT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* * **
3784187 AATTTTTGGAAGTTTGAGGGCAAAAAT-GT
1 AATTTTTGGATGTTCG-GGGGTAAAATGGT
* *
3784216 GA-TTTTGGATGTTCGGAGGTAAAATGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* * *
3784244 AATTTTTGAAAAGTTC-GAGGTCAAAAT-GT
1 AATTTTTG-GATGTTCGGGGGT-AAAATGGT
* **
3784273 AATTCTTGGAAT-TTTAGGGGTAAAATGGT
1 AATTTTTGG-ATGTTCGGGGGTAAAATGGT
* * * *
3784302 AATTTTTAGATGTTTGAGGGTAAATTGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
3784331 AATTTTTGG
1 AATTTTTGG
3784340 TAAGTATAAA
Statistics
Matches: 172, Mismatches: 55, Indels: 22
0.69 0.22 0.09
Matches are distributed among these distances:
27 10 0.06
28 55 0.32
29 90 0.52
30 17 0.10
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (29 bp):
AATTTTTGGATGTTCGGGGGTAAAATGGT
Found at i:3784208 original size:58 final size:57
Alignment explanation
Indices: 3784146--3784321 Score: 178
Period size: 58 Copynumber: 3.1 Consensus size: 57
3784136 AGATGCTCGG
* * * *
3784146 GGGCAAAAGGGTGATTTTGGGATGTCCAGGGGTAAAACGATAATTTTTGGAAGTTTGA
1 GGGCAAAA-TGTGATTTTGGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTGA
* *
3784204 GGGCAAAAATGTGATTTT-GGATGTTC-GGAGGTAAAATGGTAATTTTTGAAAAGTTCGA
1 GGGC-AAAATGTGATTTTGGGATGTTCAGG-GGTAAAATGGTAATTTTTG-GAAGTTTGA
* * * * * *
3784262 GGTCAAAATGTAATTCTTGGAAT-TTTAGGGGTAAAATGGTAATTTTTAGATGTTTGA
1 GGGCAAAATGTGATT-TTGGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTGA
3784319 GGG
1 GGG
3784322 TAAATTGGTA
Statistics
Matches: 97, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.02
57 42 0.43
58 44 0.45
59 9 0.09
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.34
Consensus pattern (57 bp):
GGGCAAAATGTGATTTTGGGATGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTGA
Found at i:3784333 original size:58 final size:55
Alignment explanation
Indices: 3784159--3784336 Score: 160
Period size: 57 Copynumber: 3.1 Consensus size: 55
3784149 CAAAAGGGTG
* * * * * *
3784159 ATTTTGGGATGTCCAGGGGTAAAACGATAATTTTTGGAAGTTTGAGGGCAAAAATGTG
1 ATTTT-GGATGT-TAGGGGTAAAATGGTAATTTTTAGAAGTTTGAGGG-TAAAATGTA
* * *
3784217 ATTTTGGATGTTCGGAGGTAAAATGGTAATTTTTGAAAAGTTCGA-GGTCAAAATGTA
1 ATTTTGGATGTTAGG-GGTAAAATGGTAATTTTT-AGAAGTTTGAGGGT-AAAATGTA
* * *
3784274 ATTCTTGGAATTTTAGGGGTAAAATGGTAATTTTTAGATGTTTGAGGGTAAATTGGTA
1 ATT-TTGG-ATGTTAGGGGTAAAATGGTAATTTTTAGAAGTTTGAGGGTAAAAT-GTA
3784332 ATTTT
1 ATTTT
3784337 TGGTAAGTAT
Statistics
Matches: 98, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
56 2 0.02
57 47 0.48
58 43 0.44
59 6 0.06
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (55 bp):
ATTTTGGATGTTAGGGGTAAAATGGTAATTTTTAGAAGTTTGAGGGTAAAATGTA
Found at i:3784392 original size:29 final size:29
Alignment explanation
Indices: 3784243--3784456 Score: 116
Period size: 30 Copynumber: 7.3 Consensus size: 29
3784233 GGTAAAATGG
* * *
3784243 TAATTTTTGAAAAGTTCGA-GGTCAAAATG
1 TAATTTTTG-AAAGTTTGAGGGTTAAAATA
* * * * *
3784272 TAATTCTTGGAA-TTTTAGGGGTAAAATGG
1 TAATTTTTGAAAGTTTGAGGGTTAAAAT-A
* * *
3784301 TAATTTTT-AGATGTTTGAGGG-TAAATTGG
1 TAATTTTTGA-AAGTTTGAGGGTTAAAAT-A
* * * * *
3784330 TAATTTTTGGTAAGTATAAAGGTCT-AAATG
1 TAATTTTT-GAAAGTTTGAGGGT-TAAAATA
*
3784360 TAATTTTTGAAAGTTTGAGGGTTAAGATA
1 TAATTTTTGAAAGTTTGAGGGTTAAAATA
*
3784389 TAATTTTTGGAAAGTTTGAGGGTAAAAATA
1 TAATTTTT-GAAAGTTTGAGGGTTAAAATA
* * *
3784419 TAATCTTTAGAAAG-TTCAGGGGTTAAAATG
1 TAAT-TTTTGAAAGTTTGA-GGGTTAAAATA
3784449 TAATTTTT
1 TAATTTTT
3784457 AAAAAATTTA
Statistics
Matches: 143, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.02
28 10 0.07
29 59 0.41
30 64 0.45
31 6 0.04
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.40
Consensus pattern (29 bp):
TAATTTTTGAAAGTTTGAGGGTTAAAATA
Found at i:3786233 original size:12 final size:11
Alignment explanation
Indices: 3786218--3786266 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
3786208 AGAATAAAAA
*
3786218 TAAATTTAAACT
1 TAAA-TTAAATT
3786230 TAAATTAAATT
1 TAAATTAAATT
*
3786241 TAAAATAAATT
1 TAAATTAAATT
*
3786252 TAAAAATAAATT
1 T-AAATTAAATT
3786264 TAA
1 TAA
3786267 TCTTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 19 0.56
12 15 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:3786254 original size:17 final size:17
Alignment explanation
Indices: 3786200--3786281 Score: 61
Period size: 17 Copynumber: 5.1 Consensus size: 17
3786190 TAGACTCTTA
* *
3786200 TTAAATTTAGAATAAAA
1 TTAAATTTAAAATAAAT
* *
3786217 ATAAATTTAAACTTAAA-
1 TTAAATTTAAA-ATAAAT
3786234 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
3786251 TT--A---AAAATAAAT
1 TTAAATTTAAAATAAAT
3786263 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
3786280 TT
1 TT
3786282 TAAAAAAGAG
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
12 11 0.21
13 1 0.02
15 1 0.02
16 4 0.08
17 32 0.60
18 4 0.08
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:3787009 original size:209 final size:209
Alignment explanation
Indices: 3786650--3787325 Score: 908
Period size: 209 Copynumber: 3.2 Consensus size: 209
3786640 TTCATTTCTC
* * * * * *
3786650 GGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGTATCACCTGTTTTGATACGCTTCTTTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTA
* * *
3786715 TCT-ATTAGGAAGACGGATTTGGTCCACTTCTCTATATCTCATCAGGAAGACGATCGCTTTATTG
66 TCTCATCAGGAAGACGAATTTGGTCCACTTTTCTATATCTCATCAGGAAGACGATCGCTTTATTG
* * * *
3786779 CTTCGACCTGCTTCTCAATATCTCATTAGGAAGCT-GAGATTCGAAGTTTTGCTCGCATTGAGCT
131 CTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAG-GGTTCGAAGTTTCGCTCACATTGAGCT
3786843 TTGTTTCATTGATTA
195 TTGTTTCATTGATTA
* * * *
3786858 GGTCTACTTCTCAATATCTCATCAGGAAGATGACCGCATTACTTGCTTTGATCCGCTTCGCTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTA
* * * * * *
3786923 TCTCATCAAGAAGACGAATTTGATCTACTTTTTTGTATCTCATCAGGAAGACGATCACTTTATTG
66 TCTCATCAGGAAGACGAATTTGGTCCACTTTTCTATATCTCATCAGGAAGACGATCGCTTTATTG
* * *
3786988 CTTCGACCTGCTTTTCAATATCTCATCAGGAAGTTAGGGTTCGAAGTTTCACTCACATTGAGCTT
131 CTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTT
3787053 TGTTTCATTGATTA
196 TGTTTCATTGATTA
** *
3787067 GGTCTACTTCTCAGTATCTCATCAGGAAGACAATCGCATCACTTGTTTTGATCCGCTTCTCTGTA
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTA
* * * *
3787132 TCTCATCAGGTAGAC-AGATTTGGTCCGCTTTTCTATATCTCATCAGGAATACGACCGCTTTATT
66 TCTCATCAGGAAGACGA-ATTTGGTCCACTTTTCTATATCTCATCAGGAAGACGATCGCTTTATT
* * * * * *
3787196 ACTTCGACTTGATTCTCAGTATCTCATCAGGAAGCTAGGGCTCGAAGTTTCGCACACATTGAGCT
130 GCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCT
*
3787261 TTGTTTCATTGATTT
195 TTGTTTCATTGATTA
* ** * *
3787276 GGTATACTTCTTTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTTG
1 GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
3787326 GATAACTGCA
Statistics
Matches: 404, Mismatches: 61, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
208 59 0.15
209 344 0.85
210 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
GGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCGCTTCTCTGTA
TCTCATCAGGAAGACGAATTTGGTCCACTTTTCTATATCTCATCAGGAAGACGATCGCTTTATTG
CTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTT
TGTTTCATTGATTA
Found at i:3799506 original size:27 final size:29
Alignment explanation
Indices: 3799476--3799540 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
3799466 TCAAAAATGC
* *
3799476 AATTTTTGGATGCCCG-GGG-AAAAGGGT
1 AATTTTTGGACGCCCGAGGGTAAAACGGT
* *
3799503 AATTTTGGGACGTCCGAGGGTAAAACGGT
1 AATTTTTGGACGCCCGAGGGTAAAACGGT
3799532 AATTTTTGG
1 AATTTTTGG
3799541 CAATATGGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 13 0.42
28 3 0.10
29 15 0.48
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (29 bp):
AATTTTTGGACGCCCGAGGGTAAAACGGT
Found at i:3799582 original size:29 final size:28
Alignment explanation
Indices: 3799520--3799744 Score: 115
Period size: 29 Copynumber: 7.7 Consensus size: 28
3799510 GGACGTCCGA
* *
3799520 GGGTAAAACGGTAATTTTTGGCAAT-AT-G
1 GGGTAAAATGGTAATTTTT-G-AATGTTAG
3799548 GTGGTAAAATGGTAATTTTTGAATGCTTAG
1 G-GGTAAAATGGTAATTTTTGAATG-TTAG
* *
3799578 GGGTAAAATGGTAATTTTTAAAAGTTTAAG
1 GGGTAAAATGGTAATTTTTGAATG-TT-AG
* ** * *
3799608 AGCAAAAAT-GTAATTTTGGATAT-TGAG
1 GGGTAAAATGGTAATTTTTGA-ATGTTAG
* *
3799635 GGGTAAAATGGTAACTTTTTGGAAAGTTCG
1 GGGTAAAATGGTAA-TTTTT-GAATGTTAG
*
3799665 GGGTACAAAAT-GTAATTCTTAGACAT-TTAG
1 GGGT--AAAATGGTAATT-TTTGA-ATGTTAG
* *
3799695 GGGTAAAATGGTAATGTTTAGGAA-GTTTG
1 GGGTAAAATGGTAAT-TTT-TGAATGTTAG
3799724 GAGGTCAAAAT-GTAATTTTTG
1 G-GGT-AAAATGGTAATTTTTG
3799745 GAAAATTTAG
Statistics
Matches: 152, Mismatches: 25, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
27 11 0.07
28 13 0.09
29 70 0.46
30 41 0.27
31 12 0.08
32 5 0.03
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGAATGTTAG
Found at i:3799657 original size:30 final size:28
Alignment explanation
Indices: 3799520--3799836 Score: 141
Period size: 30 Copynumber: 10.8 Consensus size: 28
3799510 GGACGTCCGA
* *
3799520 GGGTAAAACGGTAATTTTTGGCAA-TATG
1 GGGTAAAATGGTAATTTTTGGAAATTA-G
*
3799548 GTGGTAAAATGGTAATTTTT-GAATGCTTAG
1 G-GGTAAAATGGTAATTTTTGGAA--ATTAG
*
3799578 GGGTAAAATGGTAATTTTT-AAAAGTTTAAG
1 GGGTAAAATGGTAATTTTTGGAAA--TT-AG
* ** *
3799608 AGCAAAAAT-GTAA-TTTTGGATATTGAG
1 GGGTAAAATGGTAATTTTTGGAAATT-AG
*
3799635 GGGTAAAATGGTAACTTTTTGGAAAGTTCG
1 GGGTAAAATGGTAA-TTTTTGGAAA-TTAG
* * *
3799665 GGGTACAAAAT-GTAATTCTTAGACATTTAG
1 GGGT--AAAATGGTAATTTTTGGA-AATTAG
* * *
3799695 GGGTAAAATGGTAATGTTTAGGAAGTTTG
1 GGGTAAAATGGTAAT-TTTTGGAAATTAG
3799724 GAGGTCAAAAT-GTAATTTTTGGAAAATTTAG
1 G-GGT-AAAATGGTAATTTTTGG-AAA-TTAG
* * * *
3799755 CGATCAAAAT-ATAATTTTTGGAAAGTTTAA
1 GGGT-AAAATGGTAATTTTTGGAAA--TTAG
*
3799785 GGGTCAAAAT-ATAATTTTTGGAAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGAAA--TTAG
*
3799815 GGGTTCAAAAT-ATAATTTTTGG
1 GGG-T-AAAATGGTAATTTTTGG
3799837 GTAATTCAGA
Statistics
Matches: 231, Mismatches: 35, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
27 10 0.04
28 16 0.07
29 63 0.27
30 102 0.44
31 35 0.15
32 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGAAATTAG
Found at i:3799704 original size:60 final size:58
Alignment explanation
Indices: 3799520--3799802 Score: 183
Period size: 60 Copynumber: 4.8 Consensus size: 58
3799510 GGACGTCCGA
* * *
3799520 GGGTAAAACGGTAATTTTTGGCAA--TATGGTGGT--AAAATGGTAATTTTTGA-ATGCTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTA-GG-GGTACAAAAT-GTAATTTTAGACAT--TTAG
* * * * * * *
3799578 GGGTAAAATGGTAATTTTT-AAAAGTTTAAGAGCA-AAAATGTAATTTTGGATATTGAG
1 GGGTAAAATGGTAATTTTTGGAAAG-TTAGGGGTACAAAATGTAATTTTAGACATTTAG
*
3799635 GGGTAAAATGGTAACTTTTTGGAAAGTTCGGGGTACAAAATGTAATTCTTAGACATTTAG
1 GGGTAAAATGGTAA-TTTTTGGAAAGTTAGGGGTACAAAATGTAATT-TTAGACATTTAG
* * * *
3799695 GGGTAAAATGGTAATGTTTAGG-AAGTTTGGAGGT-CAAAATGTAATTTTTGGAAAATTTAG
1 GGGTAAAATGGTAAT-TTTTGGAAAGTTAGG-GGTACAAAATGTAA-TTTTAG-ACATTTAG
* * * * *
3799755 CGATCAAAAT-ATAATTTTTGGAAAGTTTAAGGGT-CAAAATATAATTTT
1 GGGT-AAAATGGTAATTTTTGGAAAG-TTAGGGGTACAAAATGTAATTTT
3799803 TGGAAAGTTT
Statistics
Matches: 182, Mismatches: 27, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
57 19 0.10
58 39 0.21
59 53 0.29
60 63 0.35
61 8 0.04
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTAGGGGTACAAAATGTAATTTTAGACATTTAG
Found at i:3799733 original size:59 final size:57
Alignment explanation
Indices: 3799520--3799742 Score: 181
Period size: 59 Copynumber: 3.8 Consensus size: 57
3799510 GGACGTCCGA
* * * * *
3799520 GGGTAAAACGGTAATTTTTGGCAA-TATGGTGGT-AAAATGGTAATTTTTGA-ATGCTTAG
1 GGGTAAAATGGTAATTTTAGG-AAGTTTGGAGGTCAAAAT-GTAATTTTAGACAT--TTAG
* * * * *
3799578 GGGTAAAATGGTAATTTTTA-AAAGTTT-AAGAG-CAAAAATGTAATTTTGGATATTGAG
1 GGGTAAAATGGTAA-TTTTAGGAAGTTTGGAG-GTC-AAAATGTAATTTTAGACATTTAG
* *
3799635 GGGTAAAATGGTAACTTTTTGGAAAGTTCGG-GGTACAAAATGTAATTCTTAGACATTTAG
1 GGGTAAAATGGTAA-TTTTAGG-AAGTTTGGAGGT-CAAAATGTAATT-TTAGACATTTAG
3799695 GGGTAAAATGGTAATGTTTAGGAAGTTTGGAGGTCAAAATGTAATTTT
1 GGGTAAAATGGTAAT-TTTAGGAAGTTTGGAGGTCAAAATGTAATTTT
3799743 TGGAAAATTT
Statistics
Matches: 133, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
57 24 0.18
58 29 0.22
59 48 0.36
60 32 0.24
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTAGGAAGTTTGGAGGTCAAAATGTAATTTTAGACATTTAG
Found at i:3799826 original size:31 final size:30
Alignment explanation
Indices: 3799560--3799836 Score: 191
Period size: 30 Copynumber: 9.3 Consensus size: 30
3799550 GGTAAAATGG
* * *
3799560 TAATTTTT-GAATGCTTAGGGGT-AAAATGG
1 TAATTTTTGGAAAGTTTAGGGGTCAAAAT-A
* * * *
3799589 TAATTTTT-AAAAGTTTAAGAG-CAAAAATG
1 TAATTTTTGGAAAGTTTAGGGGTC-AAAATA
* * *
3799618 TAA-TTTTGGATA-TTGAGGGGT-AAAATGG
1 TAATTTTTGGAAAGTTTAGGGGTCAAAAT-A
* *
3799646 TAACTTTTTGGAAAG-TTCGGGGTACAAAATG
1 TAA-TTTTTGGAAAGTTTAGGGGT-CAAAATA
* * * *
3799677 TAATTCTTAGACA-TTTAGGGGT-AAAATGG
1 TAATTTTTGGAAAGTTTAGGGGTCAAAAT-A
* *
3799706 TAATGTTTAGG-AAGTTT-GGAGGTCAAAATG
1 TAAT-TTTTGGAAAGTTTAGG-GGTCAAAATA
* * *
3799736 TAATTTTTGGAAAATTTAGCGATCAAAATA
1 TAATTTTTGGAAAGTTTAGGGGTCAAAATA
*
3799766 TAATTTTTGGAAAGTTTAAGGGTCAAAATA
1 TAATTTTTGGAAAGTTTAGGGGTCAAAATA
3799796 TAATTTTTGGAAAGTTTAGGGGTTCAAAATA
1 TAATTTTTGGAAAGTTTAGGGG-TCAAAATA
3799827 TAATTTTTGG
1 TAATTTTTGG
3799837 GTAATTCAGA
Statistics
Matches: 198, Mismatches: 31, Indels: 36
0.75 0.12 0.14
Matches are distributed among these distances:
27 5 0.03
28 18 0.09
29 35 0.18
30 107 0.54
31 28 0.14
32 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (30 bp):
TAATTTTTGGAAAGTTTAGGGGTCAAAATA
Found at i:3799981 original size:12 final size:12
Alignment explanation
Indices: 3799964--3799989 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3799954 AAAATAAAAC
3799964 AAAACTTGATTT
1 AAAACTTGATTT
3799976 AAAACTTGATTT
1 AAAACTTGATTT
3799988 AA
1 AA
3799990 GGACGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AAAACTTGATTT
Found at i:3800782 original size:28 final size:27
Alignment explanation
Indices: 3800733--3800787 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
3800723 TGTCAGTGAT
* *
3800733 GGTGGTGCAACTTGGTGGTGACAGTGGC
1 GGTGGTGCAACGTGGTGCTGAC-GTGGC
3800761 GGTGGTGCAA-GTGGTTGCTGACGTGGC
1 GGTGGTGCAACGTGG-TGCTGACGTGGC
3800788 ACCCTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (27 bp):
GGTGGTGCAACGTGGTGCTGACGTGGC
Found at i:3800999 original size:17 final size:17
Alignment explanation
Indices: 3800977--3801054 Score: 104
Period size: 17 Copynumber: 4.6 Consensus size: 17
3800967 GGAGTCTTAT
*
3800977 TAAATTTAGAA-TAAAAA
1 TAAATTTA-AATTTAAAA
* *
3800994 TAAATTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
3801011 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
3801028 CAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
3801045 TAAATTTAAA
1 TAAATTTAAA
3801055 AATAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
16 2 0.04
17 52 0.96
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:3801003 original size:6 final size:6
Alignment explanation
Indices: 3800994--3801066 Score: 71
Period size: 6 Copynumber: 12.7 Consensus size: 6
3800984 AGAATAAAAA
* * *
3800994 TAAATT TAAACT TAAA-T TAAATT TAAATT TAAA-A CAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* **
3801040 TAAA-A TAAATT TAAAAA TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAA
3801067 AAAAAGAGTG
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
5 12 0.23
6 41 0.77
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATT
Found at i:3801014 original size:23 final size:23
Alignment explanation
Indices: 3800988--3801068 Score: 63
Period size: 28 Copynumber: 3.3 Consensus size: 23
3800978 AAATTTAGAA
3800988 TAAAAATAAATTTAAACTTAAAT
1 TAAAAATAAATTTAAACTTAAAT
**
3801011 TAAATTTAAATTTAAAACAAATTTAAAT
1 TAAAAATAAATTT-AAAC----TTAAAT
* **
3801039 TTAAAATAAATTTAAAAATAAATT
1 TAAAAATAAATTTAAACTTAAA-T
3801063 TAAAAA
1 TAAAAA
3801069 AAAGAGTGGG
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
23 15 0.34
24 10 0.23
27 3 0.07
28 16 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAAATAAATTTAAACTTAAAT
Found at i:3801067 original size:11 final size:11
Alignment explanation
Indices: 3800990--3801067 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
3800980 ATTTAGAATA
3800990 AAAATAAATTT
1 AAAATAAATTT
*
3801001 AAACTTAAA-TT
1 AAA-ATAAATTT
*
3801012 AAATTTAAATTT
1 AAA-ATAAATTT
*
3801024 AAAACAAA-TT
1 AAAATAAATTT
3801034 ----TAAATTT
1 AAAATAAATTT
3801041 AAAATAAATTT
1 AAAATAAATTT
3801052 AAAAATAAATTT
1 -AAAATAAATTT
3801064 AAAA
1 AAAA
3801068 AAAAGAGTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
6 3 0.06
7 2 0.04
10 2 0.04
11 27 0.50
12 20 0.37
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:3802599 original size:28 final size:30
Alignment explanation
Indices: 3802559--3802629 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 30
3802549 CAAATGATTT
3802559 TAAAATTATTAAAATTA-TTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAATAA
* *
3802587 TAAATTTATTAAAATTATTTTTTTAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAATAA
3802617 TAAAATTATTAAA
1 TAAAATTATTAAA
3802630 TAATTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 16 0.42
29 9 0.24
30 13 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAATAA
Found at i:3802612 original size:30 final size:28
Alignment explanation
Indices: 3802559--3802629 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 28
3802549 CAAATGATTT
3802559 TAAAATTATTAAAATTATTTTTAAA-ATA
1 TAAAATTATTAAAATTATTTTTAAATA-A
*
3802587 TAAATTTATTAAAATTATTTTTTTAAATAA
1 TAAAATTATTAAAATTA--TTTTTAAATAA
3802617 TAAAATTATTAAA
1 TAAAATTATTAAA
3802630 TAATTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 16 0.42
30 21 0.55
31 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAATAA
Found at i:3808505 original size:16 final size:16
Alignment explanation
Indices: 3808484--3808517 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3808474 TGCCTCAAAG
3808484 GATACTCCCATGATTT
1 GATACTCCCATGATTT
3808500 GATACTCCCATGATTT
1 GATACTCCCATGATTT
3808516 GA
1 GA
3808518 CTGAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (16 bp):
GATACTCCCATGATTT
Found at i:3811338 original size:2 final size:2
Alignment explanation
Indices: 3811331--3811377 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3811321 CCACTTCATT
3811331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3811373 TA TA T
1 TA TA T
3811378 TTTTAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3816614 original size:21 final size:20
Alignment explanation
Indices: 3816566--3816616 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
3816556 AGAAAATCAA
*
3816566 CAAAGAAAAGGGCAGATATG
1 CAAAGAAAAGGGCAGAGATG
*
3816586 CAGA-AAAAGGAAGCAGAGAT-
1 CAAAGAAAAGG--GCAGAGATG
3816606 CAAAGAAAAGG
1 CAAAGAAAAGG
3816617 TGTGAGACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.24
20 6 0.24
21 13 0.52
ACGTcount: A:0.55, C:0.10, G:0.29, T:0.06
Consensus pattern (20 bp):
CAAAGAAAAGGGCAGAGATG
Found at i:3829230 original size:4 final size:4
Alignment explanation
Indices: 3829207--3829288 Score: 65
Period size: 4 Copynumber: 20.5 Consensus size: 4
3829197 CTCCCTCAAG
* * * * * * *
3829207 ATAT ATAT TTAC ATAC ATAT ATAT ATGT ATAT GTAT ATAT ACAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
3829255 ATAT ATAT ACAT ACAT ATAC ATAT GTAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
3829289 TCCAATATAA
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:3829237 original size:6 final size:6
Alignment explanation
Indices: 3829207--3829288 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
3829197 CTCCCTCAAG
* * * * * * *
3829207 ATATAT ATTTAC ATACAT ATATAT ATGTAT ATGTAT ATATAC ATATGT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
3829255 ATATAT ATACAT ACATAT ACATAT GTATAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
3829289 TCCAATATAA
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:3829243 original size:14 final size:14
Alignment explanation
Indices: 3829235--3829287 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
3829225 ATATATATGT
3829235 ATATGTATATATAC
1 ATATGTATATATAC
3829249 ATATGTATATAT--
1 ATATGTATATATAC
** *
3829261 ATACATACATATAC
1 ATATGTATATATAC
3829275 ATATGTATATATA
1 ATATGTATATATA
3829288 TTCCAATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 9 0.29
14 22 0.71
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (14 bp):
ATATGTATATATAC
Found at i:3829248 original size:26 final size:26
Alignment explanation
Indices: 3829219--3829288 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
3829209 ATATATTTAC
* * ** *
3829219 ATACATATATATATGTATATGTATAT
1 ATACATATGTATATATATACATACAT
3829245 ATACATATGTATATATATACATACAT
1 ATACATATGTATATATATACATACAT
3829271 ATACATATGTATATATAT
1 ATACATATGTATATATAT
3829289 TCCAATATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (26 bp):
ATACATATGTATATATATACATACAT
Found at i:3829378 original size:21 final size:21
Alignment explanation
Indices: 3829336--3829383 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3829326 ATGTGACACA
**
3829336 CACGTGATAGACCCTTACAAG
1 CACGTGATAGACCCCAACAAG
* *
3829357 CACGTGATAGGCCCCAAGAAG
1 CACGTGATAGACCCCAACAAG
3829378 CACGTG
1 CACGTG
3829384 CACAGCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (21 bp):
CACGTGATAGACCCCAACAAG
Found at i:3833931 original size:31 final size:30
Alignment explanation
Indices: 3833896--3833958 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
3833886 TTTTGACCAC
*
3833896 TGAACTATTCGAAAGTTTTCATTTAAGTCAT
1 TGAACTATTCAAAAGTTTTCATTTAAG-CAT
* *
3833927 TGAACTATTTAAAAGTTTTTATTTAAGCAT
1 TGAACTATTCAAAAGTTTTCATTTAAGCAT
3833957 TG
1 TG
3833959 GATTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (30 bp):
TGAACTATTCAAAAGTTTTCATTTAAGCAT
Found at i:3855569 original size:31 final size:29
Alignment explanation
Indices: 3855500--3855569 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
3855490 GTCCCAGGTT
* * *
3855500 ATATTTTAGTCACTTATGTTTGAAATGTT
1 ATATTTTAGTCACTTACGTTTCAAATGTA
* *
3855529 ACATTTTAGTCACTTACGTTATCATATTGTA
1 ATATTTTAGTCACTTACGTT-TCA-AATGTA
3855560 ATATTTTAGT
1 ATATTTTAGT
3855570 TACTGAGCCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 18 0.55
30 2 0.06
31 13 0.39
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (29 bp):
ATATTTTAGTCACTTACGTTTCAAATGTA
Found at i:3860095 original size:17 final size:18
Alignment explanation
Indices: 3860058--3860095 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3860048 TTTCCATAAC
*
3860058 TTTATAATATAAATTTTT
1 TTTATAATATAAATCTTT
3860076 TTTATAATAT-AATCTTT
1 TTTATAATATAAATCTTT
3860093 TTT
1 TTT
3860096 CCATAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATAATATAAATCTTT
Found at i:3860099 original size:45 final size:47
Alignment explanation
Indices: 3860036--3860142 Score: 141
Period size: 50 Copynumber: 2.3 Consensus size: 47
3860026 CTCCTTATGA
*
3860036 ATAATATAA-TTTTTTCCATAACTTT-AT-AATAT-AAATTTTTTTT
1 ATAATATAATTTTTTTCCATAACTTTCATAAATATAAAATTATTTTT
3860079 ATAATATAATCTTTTTTCCATAACTTTCATAAAATATACAAATTATTTTT
1 ATAATATAAT-TTTTTTCCATAACTTTCAT-AAATATA-AAATTATTTTT
*
3860129 ATAATGTAATTTTT
1 ATAATATAATTTTT
3860143 AGGATTTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
43 9 0.16
45 16 0.29
46 2 0.04
48 5 0.09
49 4 0.07
50 19 0.35
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.52
Consensus pattern (47 bp):
ATAATATAATTTTTTTCCATAACTTTCATAAATATAAAATTATTTTT
Found at i:3862075 original size:269 final size:269
Alignment explanation
Indices: 3861596--3862137 Score: 1030
Period size: 269 Copynumber: 2.0 Consensus size: 269
3861586 TTGTAATTTT
3861596 GGAGCAATTTAAGAGCATGAGTTGAATGTAAAAGTTGAGTTCCTTGTATTTTCAGTTCATGATAT
1 GGAGCAATTTAAGAGCATGAGTTGAATGTAAAAGTTGAGTTCCTTGTATTTTCAGTTCATGATAT
*
3861661 GTTTACTTGACTCTGTATATGGTTATCAGTTGATGAAGTTGACTCTCTGCACGTAGATTTCTCTG
66 GTTTACTTGACTCTGTATATGGTTATCAGTTGATGAAGTTGACTCTCTGCACATAGATTTCTCTG
3861726 TCGGCAATGTTATTGAGAAACTAGGTTCATATTTTAATGGCTTTGATTCCTTGTTTTGGCCAATA
131 TCGGCAATGTTATTGAGAAACTAGGTTCATATTTTAATGGCTTTGATTCCTTGTTTTGGCCAATA
*
3861791 TACAGATTTCATTGCCTTTGAAGAAAACATGAAACCTTAATATGACAACGTTATTTGTATCGAGT
196 TACAGATTTCATTGCCTTTGAAGAAAACATGAAACCTTAATATGACAACGTTATTTGTATAGAGT
3861856 ACTAGGAAA
261 ACTAGGAAA
*
3861865 GGAGCAATTTAAGAGCATGAGTTGAATTTAAAAGTTGAGTTCCTTGTATTTTCAGTTCATGATAT
1 GGAGCAATTTAAGAGCATGAGTTGAATGTAAAAGTTGAGTTCCTTGTATTTTCAGTTCATGATAT
3861930 GTTTACTTGACTCTGTATATGGTTATCAGTTGATGAAGTTGACTCTCTGCACATAGATTTCTCTG
66 GTTTACTTGACTCTGTATATGGTTATCAGTTGATGAAGTTGACTCTCTGCACATAGATTTCTCTG
* *
3861995 TCGGCAATGTTATTGAGAAACTAGGTTCATATTTTAATGGTTTTGATTCCTTGTTTTGGCCAATT
131 TCGGCAATGTTATTGAGAAACTAGGTTCATATTTTAATGGCTTTGATTCCTTGTTTTGGCCAATA
*
3862060 TACAGATTTCATTGCCTTTGAAGAGAACATGAAACCTTAATATGACAACGTTATTTGTATAGAGT
196 TACAGATTTCATTGCCTTTGAAGAAAACATGAAACCTTAATATGACAACGTTATTTGTATAGAGT
3862125 ACTAGGAAA
261 ACTAGGAAA
3862134 GGAG
1 GGAG
3862138 GGATGCTATT
Statistics
Matches: 267, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
269 267 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (269 bp):
GGAGCAATTTAAGAGCATGAGTTGAATGTAAAAGTTGAGTTCCTTGTATTTTCAGTTCATGATAT
GTTTACTTGACTCTGTATATGGTTATCAGTTGATGAAGTTGACTCTCTGCACATAGATTTCTCTG
TCGGCAATGTTATTGAGAAACTAGGTTCATATTTTAATGGCTTTGATTCCTTGTTTTGGCCAATA
TACAGATTTCATTGCCTTTGAAGAAAACATGAAACCTTAATATGACAACGTTATTTGTATAGAGT
ACTAGGAAA
Found at i:3874523 original size:13 final size:13
Alignment explanation
Indices: 3874507--3874553 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
3874497 TTATATAATT
*
3874507 TTTTTAATATTAA
1 TTTTTATTATTAA
*
3874520 -TTTTATTATAAA
1 TTTTTATTATTAA
3874532 TTTTTATTATATATA
1 TTTTTATTAT-TA-A
3874547 TTTTTAT
1 TTTTTAT
3874554 AAAATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 10 0.36
13 9 0.32
14 1 0.04
15 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTATTATTAA
Found at i:3874524 original size:25 final size:27
Alignment explanation
Indices: 3874496--3874574 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 27
3874486 AATTGGGCCA
3874496 TTTATAT-AATTTTT-TTA-ATATTAAT
1 TTTATATAAATTTTTATTATATA-TAAT
*
3874521 TTTATTATAAATTTTTATTATATATATT
1 TTTA-TATAAATTTTTATTATATATAAT
* *
3874549 TTTATA-AAATATTTATT-TTTATAAT
1 TTTATATAAATTTTTATTATATATAAT
3874574 T
1 T
3874575 ATTCATAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 11 0.24
26 13 0.28
27 9 0.20
28 10 0.22
29 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTATATAAATTTTTATTATATATAAT
Found at i:3874528 original size:28 final size:28
Alignment explanation
Indices: 3874497--3874574 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
3874487 ATTGGGCCAT
3874497 TTATATAATTTTT-TTA-ATATTAATTTTA
1 TTATA-AATTTTTATTATATA-TAATTTTA
*
3874525 TTATAAATTTTTATTATATATATTTTTA
1 TTATAAATTTTTATTATATATAATTTTA
* *
3874553 -TA-AAATATTTATT-TTTATAATT
1 TTATAAATTTTTATTATATATAATT
3874575 ATTCATAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
25 7 0.16
26 10 0.23
27 9 0.20
28 15 0.34
29 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATAAATTTTTATTATATATAATTTTA
Found at i:3874549 original size:15 final size:14
Alignment explanation
Indices: 3874497--3874553 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
3874487 ATTGGGCCAT
3874497 TTATATAATTTTT-
1 TTATATAATTTTTA
3874510 TTAATATTAA-TTTTA
1 TT-ATA-TAATTTTTA
3874525 TTATA-AATTTTTA
1 TTATATAATTTTTA
3874538 TTATATATATTTTTA
1 TTATATA-ATTTTTA
3874553 T
1 T
3874554 AAAATATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.05
13 12 0.32
14 11 0.29
15 13 0.34
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATATAATTTTTA
Found at i:3874558 original size:26 final size:26
Alignment explanation
Indices: 3874496--3874565 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
3874486 AATTGGGCCA
*
3874496 TTTATATAATTTTT-TTAATATTAAT
1 TTTATAAAATTTTTATTAATATTAAT
*
3874521 TTTATTATAAATTTTTATT-ATATATATT
1 TTTA-TA-AAATTTTTATTAATAT-TAAT
*
3874549 TTTATAAAATATTTATT
1 TTTATAAAATTTTTATT
3874566 TTTATAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.11
26 12 0.32
27 13 0.34
28 9 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTATAAAATTTTTATTAATATTAAT
Found at i:3874560 original size:15 final size:16
Alignment explanation
Indices: 3874531--3874572 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3874521 TTTATTATAA
* *
3874531 ATTTTTATTATATA-T
1 ATTTTTATAAAATATT
3874546 ATTTTTATAAAATATTT
1 ATTTTTATAAAATA-TT
3874563 ATTTTTATAA
1 ATTTTTATAA
3874573 TTATTCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
17 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTATAAAATATT
Found at i:3874560 original size:17 final size:17
Alignment explanation
Indices: 3874540--3874572 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3874530 AATTTTTATT
3874540 ATATATATTTTTATAAA
1 ATATATATTTTTATAAA
*
3874557 ATATTTATTTTTATAA
1 ATATATATTTTTATAA
3874573 TTATTCATAA
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:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATATTTTTATAAA
Found at i:3875552 original size:14 final size:14
Alignment explanation
Indices: 3875530--3875559 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3875520 TAAATTAAAA
*
3875530 AATATTATATATTT
1 AATACTATATATTT
3875544 AATACTATATATTT
1 AATACTATATATTT
3875558 AA
1 AA
3875560 ACGTTGAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
AATACTATATATTT
Found at i:3880551 original size:13 final size:13
Alignment explanation
Indices: 3880533--3880557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3880523 ATTCTAGTTT
3880533 AAAAATATTTTTC
1 AAAAATATTTTTC
3880546 AAAAATATTTTT
1 AAAAATATTTTT
3880558 GAGGAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATATTTTTC
Found at i:3893985 original size:22 final size:24
Alignment explanation
Indices: 3893960--3894012 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
3893950 CACTATCTCA
3893960 TAGTGAATTTGCA-CTTAAGG-CT
1 TAGTGAATTTGCATCTTAAGGACT
* *
3893982 TAGTTAATTTGCATGTTAAGGACT
1 TAGTGAATTTGCATCTTAAGGACT
3894006 TAGTGAA
1 TAGTGAA
3894013 GTTCTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 12 0.46
23 6 0.23
24 8 0.31
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (24 bp):
TAGTGAATTTGCATCTTAAGGACT
Found at i:3894628 original size:19 final size:20
Alignment explanation
Indices: 3894599--3894637 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3894589 GCAGTTAGAA
*
3894599 AAAATTTCTTTGAGAAATTC
1 AAAATTTCTTTGACAAATTC
3894619 AAAA-TTCTTTGACAAATTC
1 AAAATTTCTTTGACAAATTC
3894638 GGATTGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (20 bp):
AAAATTTCTTTGACAAATTC
Found at i:3899346 original size:3 final size:3
Alignment explanation
Indices: 3899338--3899366 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3899328 ACTGCACCAG
3899338 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3899367 AGCTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3904653 original size:30 final size:30
Alignment explanation
Indices: 3904619--3904680 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3904609 TGAGATGATT
* *
3904619 TAATAAAAAAT-ATAAATTTAAAAGCTAAAA
1 TAATAAAAAATAATAAA-TAAAAAACTAAAA
*
3904649 TAATAATAAATAATAAATAAAAAACTAAAA
1 TAATAAAAAATAATAAATAAAAAACTAAAA
3904679 TA
1 TA
3904681 TTTTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (30 bp):
TAATAAAAAATAATAAATAAAAAACTAAAA
Found at i:3923064 original size:6 final size:6
Alignment explanation
Indices: 3923053--3923088 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3923043 TACCCCTTTT
* *
3923053 TTCTTC TTCTTC TTCTCC TTCTCC TTCTCC TTCTCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
3923089 ATTCATCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCTCC
Found at i:3925208 original size:33 final size:33
Alignment explanation
Indices: 3925166--3925236 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3925156 AACCCCCCCC
*
3925166 CCCCTATGCTAGCACTAGGATGCCTAACATCGA
1 CCCCTATGCTAGCACTAGGATGCCTAACATCAA
*
3925199 CCCCTATGCTAGTACTAGGATGCCTAACATCAA
1 CCCCTATGCTAGCACTAGGATGCCTAACATCAA
3925232 CCCCT
1 CCCCT
3925237 TCCCATTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (33 bp):
CCCCTATGCTAGCACTAGGATGCCTAACATCAA
Found at i:3944083 original size:23 final size:23
Alignment explanation
Indices: 3944040--3944084 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3944030 AATAATCTAA
*
3944040 ATTTAAAAATATACATCAAAATG
1 ATTTAAAAATATACATAAAAATG
*
3944063 ATTTAAAATTA-ACAGTAAAAAT
1 ATTTAAAAATATACA-TAAAAAT
3944085 TGATATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTTAAAAATATACATAAAAATG
Found at i:3945230 original size:13 final size:13
Alignment explanation
Indices: 3945200--3945236 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3945190 ATTATCGATA
3945200 AATTAAAAAT-AT
1 AATTAAAAATAAT
3945212 -ATTAAAAATAAT
1 AATTAAAAATAAT
*
3945224 AATTAAAATTAAT
1 AATTAAAAATAAT
3945237 TTTAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:3948437 original size:86 final size:85
Alignment explanation
Indices: 3948309--3948524 Score: 312
Period size: 86 Copynumber: 2.5 Consensus size: 85
3948299 AATTTAAGAT
*
3948309 TATTTAAATAAAAAATATTATTATTATATTTC-AATTTATATCAAATAAT-ATATTGATTTGATA
1 TATTTAAATAAAAAA-ATTATTATTATATTTCAAATTT-TATCAAATAATGA-ATTGATTTGACA
*
3948372 ATACATTATTTATCAAATTTTAA
63 ATACATTATTTACCAAATTTTAA
* *
3948395 TATTTAAATAAAAAAGATTATTATTATATTACAAATTTTATCAAATAATGAGTTGATTTGACAAT
1 TATTTAAATAAAAAA-ATTATTATTATATTTCAAATTTTATCAAATAATGAATTGATTTGACAAT
3948460 ACATTATTTACCAAATTTTAA
65 ACATTATTTACCAAATTTTAA
* * *
3948481 TATTTAAAT-TAAAAATTATTATTATATTTTAATTTTTATCAAAT
1 TATTTAAATAAAAAAATTATTATTATATTTCAAATTTTATCAAAT
3948525 TTTAAATTTA
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
84 27 0.23
85 4 0.03
86 82 0.69
87 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (85 bp):
TATTTAAATAAAAAAATTATTATTATATTTCAAATTTTATCAAATAATGAATTGATTTGACAATA
CATTATTTACCAAATTTTAA
Found at i:3948645 original size:22 final size:22
Alignment explanation
Indices: 3948620--3948678 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
3948610 TGGATCACCC
3948620 AAATTCTAGCTCACCT-AAACCA
1 AAATT-TAGCTCACCTAAAACCA
*
3948642 AAATTTTAGCTCA-CTAAAATCA
1 AAA-TTTAGCTCACCTAAAACCA
3948664 AAATTTCAGCTCACC
1 AAATTT-AGCTCACC
3948679 AACACCCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.16
22 24 0.75
23 3 0.09
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (22 bp):
AAATTTAGCTCACCTAAAACCA
Found at i:3949553 original size:15 final size:15
Alignment explanation
Indices: 3949533--3949562 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3949523 CGATGTCTCG
3949533 ATTCTAATTATTTTT
1 ATTCTAATTATTTTT
3949548 ATTCTAATTATTTTT
1 ATTCTAATTATTTTT
3949563 CAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTCTAATTATTTTT
Found at i:3949698 original size:20 final size:19
Alignment explanation
Indices: 3949675--3949719 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3949665 ATTTTCGAAT
*
3949675 TTTTTATAATATTTTTTCTA
1 TTTTTA-AATATTTTTTATA
*
3949695 TTTTCGAAATATTTTTTATA
1 TTTT-TAAATATTTTTTATA
3949715 TTTTT
1 TTTTT
3949720 GAATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTAAATATTTTTTATA
Found at i:3949715 original size:29 final size:29
Alignment explanation
Indices: 3949664--3949719 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
3949654 ATGTAAGATA
3949664 TATTTTCGAATTTTTTATAATATTTTTTC
1 TATTTTCGAATTTTTTATAATATTTTTTC
3949693 TATTTTCGAAATATTTTT-T-ATATTTTT
1 TATTTTCG-AAT-TTTTTATAATATTTTT
3949720 GAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 16 0.64
30 4 0.16
31 5 0.20
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (29 bp):
TATTTTCGAATTTTTTATAATATTTTTTC
Found at i:3949791 original size:22 final size:22
Alignment explanation
Indices: 3949766--3949825 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
3949756 AAATGTTTTT
3949766 TACATTTTCGAAATATAAAAAA
1 TACATTTTCGAAATATAAAAAA
*
3949788 TACATTTTCAAAATATAAAAAA
1 TACATTTTCGAAATATAAAAAA
*
3949810 TACATTTTTGAAATAT
1 TACATTTTCGAAATAT
3949826 TTTTTTTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (22 bp):
TACATTTTCGAAATATAAAAAA
Found at i:3950957 original size:30 final size:30
Alignment explanation
Indices: 3950923--3951024 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
3950913 TCTGATTTTT
*
3950923 TTTCGTTTACT-TTTTAAATTTAATTTGTAA
1 TTTCGTTTA-TATTTTAAATTTAATTTCTAA
*
3950953 TTTCGTTT-TATTTTAAATTTAATTTTTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* * *
3950982 TTTCCTGTATATTTTAATTTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* *
3951012 TTTCCTGTATATT
1 TTTCGTTTATATT
3951025 CTAATTATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.02
29 24 0.37
30 40 0.62
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:3950966 original size:29 final size:30
Alignment explanation
Indices: 3950934--3951024 Score: 130
Period size: 30 Copynumber: 3.1 Consensus size: 30
3950924 TTCGTTTACT
* * *
3950934 TTTTAAATTTAATTTGTAATTTCGT-TTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
*
3950963 TTTTAAATTTAATTTTTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
*
3950993 TTTTAATTTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
3951023 TT
1 TT
3951025 CTAATTATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 23 0.41
30 33 0.59
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:3950996 original size:17 final size:17
Alignment explanation
Indices: 3950976--3951030 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
3950966 TAAATTTAAT
3950976 TTTTAATTTCCTGTATA
1 TTTTAATTTCCTGTATA
3950993 TTTTAA-TT--T-TA-A
1 TTTTAATTTCCTGTATA
3951005 TTTCTAATTTCCTGTATA
1 TTT-TAATTTCCTGTATA
*
3951023 TTCTAATT
1 TTTTAATT
3951031 ATTATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
12 4 0.13
13 5 0.16
14 3 0.10
16 3 0.10
17 13 0.42
18 3 0.10
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (17 bp):
TTTTAATTTCCTGTATA
Done.