Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 120 of 128
Found at i:39772479 original size:19 final size:19
Alignment explanation
Indices: 39772435--39772471 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39772425 GTGTAAATGG
*
39772435 GCCCAAGGCCCATTATTCA
1 GCCCAAGGCCCATTACTCA
39772454 GCCCAAGGCCCATTACTC
1 GCCCAAGGCCCATTACTC
39772472 GACCCAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (19 bp):
GCCCAAGGCCCATTACTCA
Found at i:39780236 original size:18 final size:19
Alignment explanation
Indices: 39780202--39780237 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39780192 ATTTTGGGTT
39780202 AGAAAAGAAAATGGGAAAA
1 AGAAAAGAAAATGGGAAAA
*
39780221 AGAAAA-AAAATTGGAAA
1 AGAAAAGAAAATGGGAAA
39780238 TGGATCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (19 bp):
AGAAAAGAAAATGGGAAAA
Found at i:39784331 original size:105 final size:106
Alignment explanation
Indices: 39783982--39784400 Score: 596
Period size: 106 Copynumber: 4.0 Consensus size: 106
39783972 AGGAAAAAGT
*
39783982 TTTCAAA-TAAGGCAATATTTCGCGTTTGAAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTGAAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
* * *
39784046 CGATTTCTCGTTTGACC-AA-AGCAAAATATCTTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
* * * * *
39784085 TTTCAAAGTAAGGCAATATTTTGCGTTTGAAAATTTGGGAGAACGTGCTCTAACGAGCTAGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTGAAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
* *
39784150 CGATTTCTCATTCGACCAAATAGCCAAATATCTTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
* * *
39784191 TTTCAAAGTAAGGTAATATTTTGCGTTTGAAAATTCGAGAGAACATGCCCTAACGTGCTGGGTTC
1 TTTCAAAGTAAGGCAATATTTTGCGTTTGAAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
*
39784256 CGATTTCTCGTTCGACCAAA-AGCCAAATATCCTTTTAAAA
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
* * * *
39784296 TTTCAAAGTGAGCCAATATTTTGCGTTT-AGAAATTCGAGAAAACGTGCCCTAACGTGCTGAGTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTGA-AAATTCGAGAGAACGTGCCCTAACGTGCTGGGTT
* * *
39784360 TCGATTTCTCGTTCAACTAAATAGCCAAATATCCTCTTAAA
65 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAA
39784401 TCTCAATCAA
Statistics
Matches: 281, Mismatches: 30, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
103 7 0.02
104 67 0.24
105 94 0.33
106 113 0.40
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (106 bp):
TTTCAAAGTAAGGCAATATTTTGCGTTTGAAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
Found at i:39784386 original size:211 final size:209
Alignment explanation
Indices: 39783982--39784392 Score: 610
Period size: 211 Copynumber: 2.0 Consensus size: 209
39783972 AGGAAAAAGT
* *
39783982 TTTCAAATAAGGCAATATTTCGCGTTTGAAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTTC
1 TTTCAAATAAGGCAATATTTCGCGTTTGAAAATTCGAGAGAACATGCCCTAACGTGCTGGGTTCC
* * * *
39784047 GATTTCTCGTTTGACCAAAGCAAAATATCTTTTTAAACTTTCAAAGTAAGGCAATATTTTGCGTT
66 GATTTCTCGTTCGACCAAAGCAAAATATCCTTTTAAAATTTCAAAGTAAGCCAATATTTTGCGTT
* * * * *
39784112 TGAAAATTTGGGAGAACGTGCTCTAACGAGCTAGGTTTCGATTTCTCATTCGACCAAATAGCCAA
131 TGAAAATTCGAGAAAACGTGCCCTAACGAGCTAGGTTTCGATTTCTCATTCAACCAAATAGCCAA
39784177 ATATCTTTTTAAAC
196 ATATCTTTTTAAAC
* *
39784191 TTTCAAAGTAAGGTAATATTTTGCGTTTGAAAATTCGAGAGAACATGCCCTAACGTGCTGGGTTC
1 TTTCAAA-TAAGGCAATATTTCGCGTTTGAAAATTCGAGAGAACATGCCCTAACGTGCTGGGTTC
* *
39784256 CGATTTCTCGTTCGACCAAAAGCCAAATATCCTTTTAAAATTTCAAAGTGAGCCAATATTTTGCG
65 CGATTTCTCGTTCGACC-AAAGCAAAATATCCTTTTAAAATTTCAAAGTAAGCCAATATTTTGCG
* * *
39784321 TTT-AGAAATTCGAGAAAACGTGCCCTAACGTGCT-GAGTTTCGATTTCTCGTTCAACTAAATAG
129 TTTGA-AAATTCGAGAAAACGTGCCCTAACGAGCTAG-GTTTCGATTTCTCATTCAACCAAATAG
39784384 CCAAATATC
192 CCAAATATC
39784393 CTCTTAAATC
Statistics
Matches: 180, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
209 7 0.04
210 71 0.39
211 102 0.57
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (209 bp):
TTTCAAATAAGGCAATATTTCGCGTTTGAAAATTCGAGAGAACATGCCCTAACGTGCTGGGTTCC
GATTTCTCGTTCGACCAAAGCAAAATATCCTTTTAAAATTTCAAAGTAAGCCAATATTTTGCGTT
TGAAAATTCGAGAAAACGTGCCCTAACGAGCTAGGTTTCGATTTCTCATTCAACCAAATAGCCAA
ATATCTTTTTAAAC
Found at i:39786622 original size:488 final size:488
Alignment explanation
Indices: 39785706--39786682 Score: 1954
Period size: 488 Copynumber: 2.0 Consensus size: 488
39785696 AGAGGAATAT
39785706 ACAACCTTGCTATGGTGTCCGAGGATCCAAGTTGACAAAGTCTACTCGAGAGCAGCTAATGTTCC
1 ACAACCTTGCTATGGTGTCCGAGGATCCAAGTTGACAAAGTCTACTCGAGAGCAGCTAATGTTCC
39785771 GACATTCTTGAAGAAATTAATGTGCATCACCGGAATGAGCGAGCAATGGGTTGCAGCCCGGATTA
66 GACATTCTTGAAGAAATTAATGTGCATCACCGGAATGAGCGAGCAATGGGTTGCAGCCCGGATTA
39785836 AGCAAAATGGGGACAGTAAATGCATACCTTGGAAAAACTTGCAAGATCTGATCTTGACACGTCCG
131 AGCAAAATGGGGACAGTAAATGCATACCTTGGAAAAACTTGCAAGATCTGATCTTGACACGTCCG
39785901 GATATAAAGAAGAGGGTTGATATCTTTACATTAAGCATTTATGGCTTAGTTGTCTTCCCTAAGGC
196 GATATAAAGAAGAGGGTTGATATCTTTACATTAAGCATTTATGGCTTAGTTGTCTTCCCTAAGGC
39785966 ATTAGGCCATGTGGATGAAGCAGTTTCAGATTTATTTGATAGGCTTGACAAGGGAGTCACACCGG
261 ATTAGGCCATGTGGATGAAGCAGTTTCAGATTTATTTGATAGGCTTGACAAGGGAGTCACACCGG
39786031 TCCCAACAATTTTGGCTGAAACCTTCAGGTCCCTAAATGCGTCTAGAAGGGCGGATGAAGGAAGG
326 TCCCAACAATTTTGGCTGAAACCTTCAGGTCCCTAAATGCGTCTAGAAGGGCGGATGAAGGAAGG
39786096 TTCATCGGATGCGTGCAGTTGCTATTGGTGTGGTTCCATAGTCACTTTTGGAAGGTGGAAAAGGT
391 TTCATCGGATGCGTGCAGTTGCTATTGGTGTGGTTCCATAGTCACTTTTGGAAGGTGGAAAAGGT
39786161 CTCATATCGGGTCTTCTCAGAAAATTACTCCCC
456 CTCATATCGGGTCTTCTCAGAAAATTACTCCCC
39786194 ACAACCTTGCTATGGTGTCCGAGGATCCAAGTTGACAAAGTCTACTCGAGAGCAGCTAATGTTCC
1 ACAACCTTGCTATGGTGTCCGAGGATCCAAGTTGACAAAGTCTACTCGAGAGCAGCTAATGTTCC
39786259 GACATTCTTGAAGAAATTAATGTGCATCACCGGAATGAGCGAGCAATGGGTTGCAGCCCGGATTA
66 GACATTCTTGAAGAAATTAATGTGCATCACCGGAATGAGCGAGCAATGGGTTGCAGCCCGGATTA
39786324 AGCAAAATGGGGACAGTAAATGCATACCTTGGAAAAACTTGCAAGATCTGATCTTGACACGTCCG
131 AGCAAAATGGGGACAGTAAATGCATACCTTGGAAAAACTTGCAAGATCTGATCTTGACACGTCCG
39786389 GATATAAAGAAGAGGGTTGATATCTTTACATTAAGCATTTATGGCTTAGTTGTCTTCCCTAAGGC
196 GATATAAAGAAGAGGGTTGATATCTTTACATTAAGCATTTATGGCTTAGTTGTCTTCCCTAAGGC
39786454 ATTAGGCCATGTGGATGAAGCAGTTTCAGATTTATTTGATAGGCTTGACAAGGGAGTCACACCGG
261 ATTAGGCCATGTGGATGAAGCAGTTTCAGATTTATTTGATAGGCTTGACAAGGGAGTCACACCGG
39786519 TCCCAACAATTTTGGCTGAAACCTTCAGGTCCCTAAATGCGTCTAGAAGGGCGGATGAAGGAAGG
326 TCCCAACAATTTTGGCTGAAACCTTCAGGTCCCTAAATGCGTCTAGAAGGGCGGATGAAGGAAGG
39786584 TTCATCGGATGCGTGCAGTTGCTATTGGTGTGGTTCCATAGTCACTTTTGGAAGGTGGAAAAGGT
391 TTCATCGGATGCGTGCAGTTGCTATTGGTGTGGTTCCATAGTCACTTTTGGAAGGTGGAAAAGGT
39786649 CTCATATCGGGTCTTCTCAGAAAATTACTCCCC
456 CTCATATCGGGTCTTCTCAGAAAATTACTCCCC
39786682 A
1 A
39786683 TTAAAAGAGC
Statistics
Matches: 489, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
488 489 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (488 bp):
ACAACCTTGCTATGGTGTCCGAGGATCCAAGTTGACAAAGTCTACTCGAGAGCAGCTAATGTTCC
GACATTCTTGAAGAAATTAATGTGCATCACCGGAATGAGCGAGCAATGGGTTGCAGCCCGGATTA
AGCAAAATGGGGACAGTAAATGCATACCTTGGAAAAACTTGCAAGATCTGATCTTGACACGTCCG
GATATAAAGAAGAGGGTTGATATCTTTACATTAAGCATTTATGGCTTAGTTGTCTTCCCTAAGGC
ATTAGGCCATGTGGATGAAGCAGTTTCAGATTTATTTGATAGGCTTGACAAGGGAGTCACACCGG
TCCCAACAATTTTGGCTGAAACCTTCAGGTCCCTAAATGCGTCTAGAAGGGCGGATGAAGGAAGG
TTCATCGGATGCGTGCAGTTGCTATTGGTGTGGTTCCATAGTCACTTTTGGAAGGTGGAAAAGGT
CTCATATCGGGTCTTCTCAGAAAATTACTCCCC
Found at i:39789442 original size:41 final size:41
Alignment explanation
Indices: 39789373--39789459 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
39789363 GCACTTAGCC
* * *
39789373 TGCTAGACATATAGTCTGAAATATTTCACCGGCATTAAGCA
1 TGCTAGACATATAGTCTGAAATACTTCACCAGCAATAAGCA
* * *
39789414 TGCTAGACATATAGTCTGAAGTGCTTCACCAGCAATAAGCC
1 TGCTAGACATATAGTCTGAAATACTTCACCAGCAATAAGCA
39789455 TGCTA
1 TGCTA
39789460 AGCGCTATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCTAGACATATAGTCTGAAATACTTCACCAGCAATAAGCA
Found at i:39812653 original size:106 final size:106
Alignment explanation
Indices: 39812461--39812876 Score: 692
Period size: 106 Copynumber: 3.9 Consensus size: 106
39812451 AGGAAAAAGT
* *
39812461 TTTCAAA-TAAGGTAATATTTCGCGTTTAGAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
39812525 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
* *
39812566 TTTCAAAGTAAGGCAATATTTTGCATTTGGAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
39812631 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
* * * *
39812672 TTTCAAAGTAAGGCAATATTTTGTGTTTGGAAATTCGAGAGAACGTGCCCCAACGTGTTGGGTTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
*
39812737 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAA
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
* *
39812778 TTTCAAAGTGAGGCAATATTTTGCGTTTAGAAATTCGAGA-ACACGTGCCCTAACGTGTTGGGTT
1 TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAGA-ACGTGCCCTAACGTGCTGGGTT
* *
39812842 TCGATTTCTCGTTCAACTAAATAGCCAAATATCCT
65 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCT
39812877 NNNNNNNNNN
Statistics
Matches: 294, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
105 8 0.03
106 286 0.97
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (106 bp):
TTTCAAAGTAAGGCAATATTTTGCGTTTAGAAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAC
Found at i:39824748 original size:24 final size:24
Alignment explanation
Indices: 39824732--39824784 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
39824722 TAATCAAAGT
39824732 TAAATATATTATGCTAATAAATGC
1 TAAATATATTATGCTAATAAATGC
* * *
39824756 TAAATATATTATACTCATAAATAC
1 TAAATATATTATGCTAATAAATGC
39824780 TAAAT
1 TAAAT
39824785 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAATATATTATGCTAATAAATGC
Found at i:39828224 original size:9 final size:9
Alignment explanation
Indices: 39828210--39828268 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
39828200 CCTCTATTTA
*
39828210 ATAATTGTT
1 ATAATTTTT
39828219 ATAATTTTT
1 ATAATTTTT
* *
39828228 ATGATTTTA
1 ATAATTTTT
39828237 ATAATTTTT
1 ATAATTTTT
*
39828246 ATGATTTTT
1 ATAATTTTT
*
39828255 ATTAGTTTTT
1 A-TAATTTTT
39828265 ATAA
1 ATAA
39828269 CATTTTAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
9 33 0.82
10 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:39828650 original size:20 final size:19
Alignment explanation
Indices: 39828627--39828692 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
39828617 TATTCCTTCC
39828627 TAATTTTGGGTATGCTTTCA
1 TAATTTTGGGTAT-CTTTCA
* *
39828647 TAATTATTGGTTATCCTT-A
1 TAATT-TTGGGTATCTTTCA
** *
39828666 TAATTTTTAGTATTCTCTCA
1 TAATTTTGGGTA-TCTTTCA
39828686 TAATTTT
1 TAATTTT
39828693 TAGCATGCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 4 0.11
19 9 0.25
20 16 0.44
21 7 0.19
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (19 bp):
TAATTTTGGGTATCTTTCA
Found at i:39828760 original size:20 final size:20
Alignment explanation
Indices: 39828735--39828800 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
39828725 TTTAAAAATT
39828735 TATTTTTAATATAAAATAAA
1 TATTTTTAATATAAAATAAA
* *
39828755 TATTTTT-GTATACTAATAAA
1 TATTTTTAATATA-AAATAAA
* *
39828775 -ATTTGTTATATATACAATTAA
1 TATTT-TTA-ATATAAAATAAA
39828796 TATTT
1 TATTT
39828801 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 8 0.22
20 15 0.42
21 5 0.14
22 8 0.22
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTTTAATATAAAATAAA
Found at i:39833616 original size:38 final size:38
Alignment explanation
Indices: 39833560--39833632 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
39833550 CTCAATAGCC
39833560 AGATTCTAATTGTTTCAAATCGTAACCGTTTAAAAGCT
1 AGATTCTAATTGTTTCAAATCGTAACCGTTTAAAAGCT
*
39833598 AGATTCTAATT-TTGTCAAATCGTAACTGTTTAAAA
1 AGATTCTAATTGTT-TCAAATCGTAACCGTTTAAAA
39833633 ATATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 2 0.06
38 31 0.94
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (38 bp):
AGATTCTAATTGTTTCAAATCGTAACCGTTTAAAAGCT
Found at i:39836411 original size:14 final size:14
Alignment explanation
Indices: 39836389--39836422 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39836379 CCTAACCTCG
*
39836389 TTTCTAAACCTCCA
1 TTTCGAAACCTCCA
39836403 TTTCGAAACCTCCA
1 TTTCGAAACCTCCA
39836417 TTTCGA
1 TTTCGA
39836423 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (14 bp):
TTTCGAAACCTCCA
Found at i:39844668 original size:5 final size:5
Alignment explanation
Indices: 39844658--39844689 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
39844648 TTCTCTCAAC
39844658 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
39844690 CATTCCAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:39849950 original size:40 final size:40
Alignment explanation
Indices: 39849901--39850017 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
39849891 TATGTGATTC
* * *
39849901 GAGACAGCTTCGGCTATTTATGGCACTTAGTGTGCG-ATT
1 GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAACT
* *
39849940 GGGAATAGCTTCGGTTATATATGGCACTTAGTGTGCGAAACT
1 GAG-ATAGCTTCGGCTATATATGGCACTTAGTGTGCG-AACT
* * *
39849982 GAGATAGCTTCAGCTATGTAAGGCACTTAGTGTGCG
1 GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCG
39850018 GGATTATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.03
40 30 0.46
41 29 0.45
42 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (40 bp):
GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAACT
Found at i:39850007 original size:41 final size:39
Alignment explanation
Indices: 39849883--39850017 Score: 135
Period size: 40 Copynumber: 3.4 Consensus size: 39
39849873 ACTATGTTTA
* * * * *
39849883 GCACTTAGTATGTGATTCGAGACAGCTTCGGCTATTTATG
1 GCACTTAGTGTGCGACT-GAGATAGCTTCGGCTATATATG
* * *
39849923 GCACTTAGTGTGCGATTGGGAATAGCTTCGGTTATATATG
1 GCACTTAGTGTGCGACTGAG-ATAGCTTCGGCTATATATG
* * *
39849963 GCACTTAGTGTGCGAAACTGAGATAGCTTCAGCTATGTAAG
1 GCACTTAGTGTGCG--ACTGAGATAGCTTCGGCTATATATG
39850004 GCACTTAGTGTGCG
1 GCACTTAGTGTGCG
39850018 GGATTATAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.03
40 45 0.56
41 29 0.36
42 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (39 bp):
GCACTTAGTGTGCGACTGAGATAGCTTCGGCTATATATG
Found at i:39850789 original size:23 final size:23
Alignment explanation
Indices: 39850759--39851051 Score: 412
Period size: 23 Copynumber: 12.8 Consensus size: 23
39850749 CTGTTTTTAC
*
39850759 ATGTATAAATGCTGTCCAATTTA
1 ATGTATAAATGCTGTCCAATTTG
*
39850782 ATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTG
*
39850805 ATGTATAAATGCTGTCCAATTTA
1 ATGTATAAATGCTGTCCAATTTG
*
39850828 ATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTG
*
39850851 ATGTATAAATGCTGTCCAATTTA
1 ATGTATAAATGCTGTCCAATTTG
*
39850874 ATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTG
*
39850897 ATGTATAAATGCTGTCCAATTTA
1 ATGTATAAATGCTGTCCAATTTG
*
39850920 ATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTG
*
39850943 GTGTAT--ATGCTG-CCTAATTTG
1 ATGTATAAATGCTGTCC-AATTTG
* *
39850964 ATGTATAAATGTTGCCCAATTTG
1 ATGTATAAATGCTGTCCAATTTG
* *
39850987 ATGTATAAATACTGTCTAATTTG
1 ATGTATAAATGCTGTCCAATTTG
* *
39851010 GTGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTG
*
39851033 ATGTATAAAAGCTGTCCAA
1 ATGTATAAATGCTGTCCAA
39851052 AACAGGGTAG
Statistics
Matches: 237, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
20 2 0.01
21 16 0.07
23 217 0.92
24 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (23 bp):
ATGTATAAATGCTGTCCAATTTG
Found at i:39850811 original size:46 final size:46
Alignment explanation
Indices: 39850759--39851051 Score: 484
Period size: 46 Copynumber: 6.4 Consensus size: 46
39850749 CTGTTTTTAC
39850759 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
39850805 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
39850851 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
39850897 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
* * *
39850943 GTGTAT--ATGCTG-CCTAATTTGATGTATAAATGTTGCCCAATTTG
1 ATGTATAAATGCTGTCC-AATTTAATGTATAAATGTTGTCCAATTTG
* * **
39850987 ATGTATAAATACTGTCTAATTTGGTGTATAAATGTTGTCCAATTTG
1 ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
*
39851033 ATGTATAAAAGCTGTCCAA
1 ATGTATAAATGCTGTCCAA
39851052 AACAGGGTAG
Statistics
Matches: 232, Mismatches: 11, Indels: 8
0.92 0.04 0.03
Matches are distributed among these distances:
43 2 0.01
44 38 0.16
46 191 0.82
47 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (46 bp):
ATGTATAAATGCTGTCCAATTTAATGTATAAATGTTGTCCAATTTG
Found at i:39854071 original size:14 final size:16
Alignment explanation
Indices: 39854038--39854071 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
39854028 CTATAATGGC
39854038 AAAAGAATGAAGAGTA
1 AAAAGAATGAAGAGTA
39854054 AAAAG-ATGAAGA-TA
1 AAAAGAATGAAGAGTA
39854068 AAAA
1 AAAA
39854072 CTAAACCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 7 0.39
16 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAAGAATGAAGAGTA
Found at i:39855871 original size:8 final size:8
Alignment explanation
Indices: 39855858--39855882 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39855848 AAATAGCGAA
39855858 AGAAATTG
1 AGAAATTG
39855866 AGAAATTG
1 AGAAATTG
39855874 AGAAATTG
1 AGAAATTG
39855882 A
1 A
39855883 ACATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:39858897 original size:20 final size:20
Alignment explanation
Indices: 39858864--39858904 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39858854 AATTCTAAAA
*
39858864 AAAATATTAAAAAATTCTTT
1 AAAATATTAAAAAATTATTT
* *
39858884 AAAATTTTATAAAATTATTT
1 AAAATATTAAAAAATTATTT
39858904 A
1 A
39858905 TTTACTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATATTAAAAAATTATTT
Found at i:39860123 original size:29 final size:28
Alignment explanation
Indices: 39860091--39860145 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
39860081 TTATATTAGA
** *
39860091 TAAATATAATTAATATTGTATGCAATATT
1 TAAATATAAAAAATATTATAT-CAATATT
39860120 TAAATATAAAAAATATTATATCAATA
1 TAAATATAAAAAATATTATATCAATA
39860146 ATTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAATATAAAAAATATTATATCAATATT
Found at i:39861239 original size:23 final size:22
Alignment explanation
Indices: 39861213--39861263 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
39861203 TTTTTTAAAA
39861213 AAAATCACTTTAATATTTTTATC
1 AAAAT-ACTTTAATATTTTTATC
*
39861236 AAAATGCTTTAATATTTTTATC
1 AAAATACTTTAATATTTTTATC
39861258 AAAATA
1 AAAATA
39861264 AATGTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATACTTTAATATTTTTATC
Found at i:39861248 original size:22 final size:22
Alignment explanation
Indices: 39861220--39861262 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
39861210 AAAAAAATCA
39861220 CTTTAATATTTTTATCAAAATG
1 CTTTAATATTTTTATCAAAATG
39861242 CTTTAATATTTTTATCAAAAT
1 CTTTAATATTTTTATCAAAAT
39861263 AAATGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
CTTTAATATTTTTATCAAAATG
Found at i:39863536 original size:5 final size:5
Alignment explanation
Indices: 39863526--39863604 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
39863516 AAAAAAATAT
* *
39863526 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
39863572 -A-TA TATTA TATTA TATTA TATATA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT
39863605 ATCTNNNNNN
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
3 4 0.06
4 4 0.06
5 32 0.51
6 22 0.35
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:39863578 original size:19 final size:19
Alignment explanation
Indices: 39863554--39863606 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
39863544 ATTATGTTTT
39863554 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
39863573 TATATTATATTATATTATA
1 TATATTATATTATATTATA
39863592 TATA-TATATATATAT
1 TATATTATAT-TATAT
39863607 CTNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:39863593 original size:2 final size:2
Alignment explanation
Indices: 39863554--39863606 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
39863544 ATTATGTTTT
39863554 TA TA T- TA TA T- TA T- TA T- TA -A TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39863588 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
39863607 CTNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 8 0.19
2 35 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:39867794 original size:43 final size:44
Alignment explanation
Indices: 39867728--39868197 Score: 300
Period size: 44 Copynumber: 10.8 Consensus size: 44
39867718 CCTTTATTTT
* * * *
39867728 AATCCGCTCCACTGTAA-CTTCAGGGAGATAGGAT-AGTGTCTTC
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCACTGGCTTC
* * * *
39867771 GATTTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTGGCTTC
* *
39867815 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATC---ACTGGCTTC
* * * * *
39867861 AGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTGGCTTC
* * ** * *** *
39867902 GATCTACTGTACTGTAA-CTTCAGAGAGATAAGATC-CTTTATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCAC-TGGCTTC
* * * * **
39867946 AATCCGCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGA-TAAGATCACTGGCTTC
* *
39867991 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTGGCTTC
* * *
39868035 AATCTGCTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTGGCTTC
* * ** * *** *
39868076 GATCTACTGTACTGTAA-CTTCAGAGAGATAAGATC-CTTTATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCAC-TGGCTTC
* * * * **
39868120 AATCCGCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGA-TAAGATCACTGGCTTC
*
39868165 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA
39868198 NNNNNNNNNN
Statistics
Matches: 327, Mismatches: 81, Indels: 37
0.73 0.18 0.08
Matches are distributed among these distances:
40 2 0.01
41 58 0.18
42 6 0.02
43 30 0.09
44 127 0.39
45 67 0.20
46 36 0.11
47 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTGGCTTC
Found at i:39867895 original size:218 final size:220
Alignment explanation
Indices: 39867650--39868072 Score: 717
Period size: 218 Copynumber: 1.9 Consensus size: 220
39867640 TTTCGTCTGG
*
39867650 TCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
* * * * * *
39867715 GATCCTTTATTTTAATCCGCTCCACTGTAACT-TCAGGGAGA-TAGGA-TAGTGTCTTCGATTTG
66 GATCCTTTATTTTAATCCGCTCCACTATAA-TATCAGGGAGATTAAGATTACTATCTTCAATCTG
*
39867777 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAG
130 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
*
39867842 ATAAGATCTGAAATTCTTCAGTCTAC
195 ATAAGACCTGAAATTCTTCAGTCTAC
* *
39867868 TCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTGTACTGTAACTTCAGAGAGATAA
1 TCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
39867933 GATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGC
66 GATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGC
39867998 TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
131 TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
39868063 TAAGACCTGA
196 TAAGACCTGA
39868073 TGCGATCTAC
Statistics
Matches: 191, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
217 1 0.01
218 100 0.52
219 4 0.02
220 86 0.45
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (220 bp):
TCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
GATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
TAAGACCTGAAATTCTTCAGTCTAC
Found at i:39867918 original size:131 final size:130
Alignment explanation
Indices: 39867782--39868023 Score: 294
Period size: 131 Copynumber: 1.9 Consensus size: 130
39867772 ATTTGCTCCG
* * * * *
39867782 CTGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAGA-T
1 CTGTAACT-TCAGAGAGATAAGATCCT-TGACTTCAATCCGCTCCACTATAATATCAGGGAGATT
*
39867844 AAGATCTGAA-ATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
64 AAGAT-T-AATA-TCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
39867908 CTGTA
126 CTGTA
* * *
39867913 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAA
1 CTGTAACTTCAGAGAGATAAGATCCTTGACTTCAATCCGCTCCACTATAATATCAGGGAGATTAA
* * * *
39867978 GATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
66 GATTAATATCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGA
39868024 TCTCTGGCTT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
130 35 0.37
131 50 0.53
132 9 0.10
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (130 bp):
CTGTAACTTCAGAGAGATAAGATCCTTGACTTCAATCCGCTCCACTATAATATCAGGGAGATTAA
GATTAATATCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTGTA
Found at i:39868025 original size:89 final size:89
Alignment explanation
Indices: 39867913--39868197 Score: 325
Period size: 89 Copynumber: 3.2 Consensus size: 89
39867903 ATCTACTGTA
39867913 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAA
1 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAA
39867978 GATTACTATCTTCAATCTGCTCCG
66 GATTACTATCTTCAATCTGCTCCG
* *** * * * **
39868002 CTGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA-T
1 CTGTAACT-TCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTATAATATCAGGGAGATT
* * * * ***
39868064 AAGA--CCTGA--TGCGATCTACTGTA
64 AAGATTACT-ATCTTCAATCTGCTCCG
39868087 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAA
1 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAA
39868152 GATTACTATCTTCAATCTGCTCCG
66 GATTACTATCTTCAATCTGCTCCG
*
39868176 CTGTAA-TCTCAGGGAGATAAGA
1 CTGTAACT-TCAGAGAGATAAGA
39868198 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
85 55 0.36
86 10 0.07
87 2 0.01
88 11 0.07
89 74 0.49
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (89 bp):
CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATATCAGGGAGATTAA
GATTACTATCTTCAATCTGCTCCG
Found at i:39868066 original size:174 final size:174
Alignment explanation
Indices: 39867776--39868197 Score: 697
Period size: 174 Copynumber: 2.4 Consensus size: 174
39867766 TCTTCGATTT
* * * ** *
39867776 GCTCCGCTGTAATCTCAGGGAGA-TAAGATCT-CTGGCTTCAATCTGCTCCACTGTAATCTCAGG
1 GCTCCACTATAATATCAGGGAGATTAAGAT-TACTATCTTCAATCTGCTCCGCTGTAATCTCAGG
* *
39867839 GAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGA
65 GAGATAAGATCT--AATGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGA
39867904 TCTACTGTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
128 TCTACTGTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
39867951 GCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
1 GCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
* *
39868016 AGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATC
66 AGATAAGATCTAAT-GCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATC
39868080 TACTGTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
130 TACTGTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
39868125 GCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
1 GCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
39868190 AGATAAGA
66 AGATAAGA
39868198 NNNNNNNNNN
Statistics
Matches: 234, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
173 1 0.00
174 165 0.71
175 21 0.09
176 47 0.20
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (174 bp):
GCTCCACTATAATATCAGGGAGATTAAGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
AGATAAGATCTAATGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
ACTGTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
Found at i:39868129 original size:85 final size:86
Alignment explanation
Indices: 39867867--39868153 Score: 314
Period size: 85 Copynumber: 3.3 Consensus size: 86
39867857 CTTCAGTCTA
* *
39867867 CTCCACTGTAACCTCAGGGAGA-TAAGACCTGATGCGATCTACTGTACTGTAACTTCAGAGAGAT
1 CTCCACTATAACATCAGGGAGATTAAGACCTGATGCGATCTACTGTACTGTAACTTCAGAGAGAT
39867931 AAGATCCTTTATTTTAATCCG
66 AAGATCCTTTATTTTAATCCG
* * * * * *** *
39867952 CTCCACTATAATATCAGGGAGATTAAGATTACT-ATCTTCAATCTGCTCCGCTGTAA-TCTCAGG
1 CTCCACTATAACATCAGGGAGATTAAGA--CCTGA--TGCGATCTACTGTACTGTAACT-TCAGA
*** * *
39868015 GAGATAAGAT-CTCTGGCTTCAATCTG
61 GAGATAAGATCCT-TTATTTTAATCCG
* *
39868041 CTCCACTGTAACCTCAGGGAGA-TAAGACCTGATGCGATCTACTGTACTGTAACTTCAGAGAGAT
1 CTCCACTATAACATCAGGGAGATTAAGACCTGATGCGATCTACTGTACTGTAACTTCAGAGAGAT
39868105 AAGATCCTTTATTTTAATCCG
66 AAGATCCTTTATTTTAATCCG
*
39868126 CTCCACTATAATATCAGGGAGATTAAGA
1 CTCCACTATAACATCAGGGAGATTAAGA
39868154 TTACTATCTT
Statistics
Matches: 156, Mismatches: 35, Indels: 21
0.74 0.17 0.10
Matches are distributed among these distances:
85 74 0.47
86 15 0.10
87 2 0.01
88 10 0.06
89 55 0.35
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (86 bp):
CTCCACTATAACATCAGGGAGATTAAGACCTGATGCGATCTACTGTACTGTAACTTCAGAGAGAT
AAGATCCTTTATTTTAATCCG
Found at i:39870981 original size:7 final size:7
Alignment explanation
Indices: 39870963--39871006 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
39870953 NNNNCTCTCT
39870963 ATTTTTC
1 ATTTTTC
39870970 A-TTTTC
1 ATTTTTC
39870976 ATTTTTC
1 ATTTTTC
39870983 ATTTTTC
1 ATTTTTC
*
39870990 A-TTCTC
1 ATTTTTC
39870996 ATTTTTC
1 ATTTTTC
39871003 ATTT
1 ATTT
39871007 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 11 0.33
7 22 0.67
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTTTC
Found at i:39870981 original size:13 final size:13
Alignment explanation
Indices: 39870965--39871006 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
39870955 NNCTCTCTAT
39870965 TTTTCA-TTTTCA
1 TTTTCATTTTTCA
39870977 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
*
39870991 TTCTCATTTTTCA
1 TTTTCATTTTTCA
39871004 TTT
1 TTT
39871007 ATTTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:39870988 original size:20 final size:20
Alignment explanation
Indices: 39870963--39871006 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
39870953 NNNNCTCTCT
*
39870963 ATTTTTCATTTTCATTTTTC
1 ATTTTTCATTCTCATTTTTC
39870983 ATTTTTCATTCTCATTTTTC
1 ATTTTTCATTCTCATTTTTC
39871003 ATTT
1 ATTT
39871007 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTTCATTCTCATTTTTC
Found at i:39874167 original size:17 final size:16
Alignment explanation
Indices: 39874145--39874176 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
39874135 ATATAGTTTT
39874145 TAAAAATAAAAGAAAAA
1 TAAAAAT-AAAGAAAAA
39874162 TAAAAATAAAGAAAA
1 TAAAAATAAAGAAAA
39874177 CAAACAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
TAAAAATAAAGAAAAA
Found at i:39874222 original size:20 final size:21
Alignment explanation
Indices: 39874197--39874235 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39874187 CAAAAGGAAG
*
39874197 AAAAAAAT-GAAGGGAAAAAT
1 AAAAAAATAAAAGGGAAAAAT
39874217 AAAAAAATAAAAGGGAAAA
1 AAAAAAATAAAAGGGAAAA
39874236 TAGAGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (21 bp):
AAAAAAATAAAAGGGAAAAAT
Found at i:39874579 original size:16 final size:16
Alignment explanation
Indices: 39874558--39874594 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
39874548 AGGGGGCTAG
* *
39874558 GTTTTTTTCTTTTGTT
1 GTTTTTTTCTGTTATT
39874574 GTTTTTTTCTGTTATT
1 GTTTTTTTCTGTTATT
39874590 GTTTT
1 GTTTT
39874595 CTGATTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.05, G:0.14, T:0.78
Consensus pattern (16 bp):
GTTTTTTTCTGTTATT
Found at i:39875602 original size:20 final size:20
Alignment explanation
Indices: 39875551--39875602 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
39875541 AACGAAGAAC
*
39875551 AAAATAAGAACAAGCCACAG
1 AAAATAAGAACGAGCCACAG
39875571 AAAATAAGAACGAGCCACAG
1 AAAATAAGAACGAGCCACAG
39875591 AAAATAAGAACG
1 AAAATAAGAACG
39875603 CAAGAGAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.60, C:0.17, G:0.17, T:0.06
Consensus pattern (20 bp):
AAAATAAGAACGAGCCACAG
Found at i:39879202 original size:7 final size:7
Alignment explanation
Indices: 39879190--39879232 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
39879180 AAGGGAGCCC
39879190 CTTATTT
1 CTTATTT
39879197 CTTATTT
1 CTTATTT
* *
39879204 TTTGTTT
1 CTTATTT
39879211 ACTTATTT
1 -CTTATTT
39879219 CTTATTT
1 CTTATTT
*
39879226 ATTATTT
1 CTTATTT
39879233 AAAGGAGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.72
Consensus pattern (7 bp):
CTTATTT
Found at i:39879217 original size:15 final size:15
Alignment explanation
Indices: 39879190--39879232 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
39879180 AAGGGAGCCC
39879190 CTTATTT-CTTATTT
1 CTTATTTACTTATTT
* *
39879204 TTTGTTTACTTATTT
1 CTTATTTACTTATTT
39879219 CTTATTTA-TTATTT
1 CTTATTTACTTATTT
39879233 AAAGGAGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.72
Consensus pattern (15 bp):
CTTATTTACTTATTT
Found at i:39879233 original size:22 final size:22
Alignment explanation
Indices: 39879190--39879233 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39879180 AAGGGAGCCC
* *
39879190 CTTATTTCTTATTTTTTGTTTA
1 CTTATTTCTTATTTATTATTTA
39879212 CTTATTTCTTATTTATTATTTA
1 CTTATTTCTTATTTATTATTTA
39879234 AAGGAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.70
Consensus pattern (22 bp):
CTTATTTCTTATTTATTATTTA
Found at i:39901533 original size:61 final size:61
Alignment explanation
Indices: 39901397--39901525 Score: 213
Period size: 61 Copynumber: 2.1 Consensus size: 61
39901387 ATTTTTGGCC
* ** *
39901397 CACACGCCCATGTGGATTAACACGGTCTAGGTAGCTGGCCTGTGTGGTCCACGTGGCCTTA
1 CACATGCCCATGTGGATTAACACGACCTAGGTAGCTGGCCTGTGTGGTCCACATGGCCTTA
*
39901458 CACATGCCCATGTGGATTAACACGACCTAGGTAGCTGGCCTGTGTGGTCCACATGGCCTTG
1 CACATGCCCATGTGGATTAACACGACCTAGGTAGCTGGCCTGTGTGGTCCACATGGCCTTA
39901519 CACATGC
1 CACATGC
39901526 TCGTGTGGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (61 bp):
CACATGCCCATGTGGATTAACACGACCTAGGTAGCTGGCCTGTGTGGTCCACATGGCCTTA
Found at i:39907371 original size:19 final size:20
Alignment explanation
Indices: 39907344--39907389 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
39907334 TAATTTTATT
* *
39907344 TAAAAATTATATAA-AAAGA
1 TAAATATTATAAAACAAAGA
39907363 TAAATATTATAAAACAAAGA
1 TAAATATTATAAAACAAAGA
*
39907383 GAAATAT
1 TAAATAT
39907390 AGAATGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAATATTATAAAACAAAGA
Found at i:39907387 original size:20 final size:19
Alignment explanation
Indices: 39907349--39907408 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
39907339 TTATTTAAAA
* *
39907349 ATTATATAAAAAGATAAAT
1 ATTATAAAAAAAGAGAAAT
39907368 ATTATAAAACAAAGAGAAAT
1 ATTATAAAA-AAAGAGAAAT
*
39907388 ATAGAATGAAAAAAAGAGAAA
1 AT--TAT-AAAAAAAGAGAAA
39907409 AAATAGATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.24
20 11 0.32
22 11 0.32
23 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.20
Consensus pattern (19 bp):
ATTATAAAAAAAGAGAAAT
Found at i:39911180 original size:11 final size:13
Alignment explanation
Indices: 39911160--39911191 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39911150 AATAAATTAA
39911160 TAAAATATCAT-T
1 TAAAATATCATAT
39911172 TAAAA-ATCATAT
1 TAAAATATCATAT
39911184 TAAAATAT
1 TAAAATAT
39911192 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:39912906 original size:20 final size:20
Alignment explanation
Indices: 39912881--39912918 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39912871 TAGCATTGGG
39912881 CTCATTTACTAATACTACAA
1 CTCATTTACTAATACTACAA
*
39912901 CTCATTTACTATTACTAC
1 CTCATTTACTAATACTAC
39912919 TGATGGGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (20 bp):
CTCATTTACTAATACTACAA
Found at i:39918160 original size:126 final size:127
Alignment explanation
Indices: 39917934--39918188 Score: 503
Period size: 126 Copynumber: 2.0 Consensus size: 127
39917924 TTTTGAGATT
39917934 TATCGCTAAAAAATAAAAAATATATAAAAATATATATATATAATTCAAAAATATTAAAAAAATCA
1 TATCGCTAAAAAATAAAAAATATATAAAAATATATATATATAATTCAAAAATATTAAAAAAATCA
39917999 CAAAGAAAAAATGAATGGAAATTTCAATTTAATCTCCTGCCCCCTTCGCCTTATCGTCTATA
66 CAAAGAAAAAATGAATGGAAATTTCAATTTAATCTCCTGCCCCCTTCGCCTTATCGTCTATA
39918061 TATCGCT-AAAAATAAAAAATATATAAAAATATATATATATAATTCAAAAATATTAAAAAAATCA
1 TATCGCTAAAAAATAAAAAATATATAAAAATATATATATATAATTCAAAAATATTAAAAAAATCA
39918125 CAAAGAAAAAATGAATGGAAATTTCAATTTAATCTCCTGCCCCCTTCGCCTTATCGTCTATA
66 CAAAGAAAAAATGAATGGAAATTTCAATTTAATCTCCTGCCCCCTTCGCCTTATCGTCTATA
39918187 TA
1 TA
39918189 ATCTTGGACC
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 121 0.95
127 7 0.05
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (127 bp):
TATCGCTAAAAAATAAAAAATATATAAAAATATATATATATAATTCAAAAATATTAAAAAAATCA
CAAAGAAAAAATGAATGGAAATTTCAATTTAATCTCCTGCCCCCTTCGCCTTATCGTCTATA
Found at i:39920725 original size:17 final size:17
Alignment explanation
Indices: 39920705--39920803 Score: 72
Period size: 17 Copynumber: 5.8 Consensus size: 17
39920695 TGTTCATATG
*
39920705 AAATAACAGTTCTTACC
1 AAATAACAGTTCATACC
* * * *
39920722 AAATGACAGCTCATGCA
1 AAATAACAGTTCATACC
* **
39920739 AAATAATAGTTCATATG
1 AAATAACAGTTCATACC
*
39920756 AAATATCAGTTCATACC
1 AAATAACAGTTCATACC
* * * *
39920773 GAATAACACTTCATGCG
1 AAATAACAGTTCATACC
*
39920790 AAATAAAAGTTCAT
1 AAATAACAGTTCAT
39920804 GCTCTATCAG
Statistics
Matches: 59, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (17 bp):
AAATAACAGTTCATACC
Found at i:39920787 original size:51 final size:51
Alignment explanation
Indices: 39920696--39920803 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
39920686 CCAAACATCT
* * *
39920696 GTTCATATGAAATAACAGTTCTTACCAAATGACAGCTCATGCAAAATAATA
1 GTTCATATGAAATAACAGTTCATACCAAATAACAGCTCATGCAAAATAAAA
* * *
39920747 GTTCATATGAAATATCAGTTCATACCGAATAACA-CTTCATGCGAAATAAAA
1 GTTCATATGAAATAACAGTTCATACCAAATAACAGC-TCATGCAAAATAAAA
39920798 GTTCAT
1 GTTCAT
39920804 GCTCTATCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 49 0.98
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (51 bp):
GTTCATATGAAATAACAGTTCATACCAAATAACAGCTCATGCAAAATAAAA
Found at i:39921488 original size:18 final size:18
Alignment explanation
Indices: 39921447--39921494 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
39921437 ACAATTTGAA
* * *
39921447 AAATTAATGCAGTTTGCC
1 AAATTAATACAGATTACC
*
39921465 ATATTAATACAGATTACC
1 AAATTAATACAGATTACC
*
39921483 AAATTAACACAG
1 AAATTAATACAG
39921495 TTCGCCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (18 bp):
AAATTAATACAGATTACC
Found at i:39921520 original size:36 final size:36
Alignment explanation
Indices: 39921447--39921527 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
39921437 ACAATTTGAA
** * *
39921447 AAATTAATGCAGTTTGCCATATTAATACAGATTACC
1 AAATTAACACAGTTCGCCATAATAATACAGATTACC
*
39921483 AAATTAACACAGTTCGCCATAATAATATA-ATTCACC
1 AAATTAACACAGTTCGCCATAATAATACAGATT-ACC
*
39921519 AAGTTAACA
1 AAATTAACA
39921528 TGGTTCACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 3 0.08
36 35 0.92
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (36 bp):
AAATTAACACAGTTCGCCATAATAATACAGATTACC
Found at i:39925485 original size:14 final size:15
Alignment explanation
Indices: 39925462--39925491 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39925452 CTTGATATAA
39925462 ATAATAATATATATG
1 ATAATAATATATATG
39925477 ATAATATATATATAT
1 ATAATA-ATATATAT
39925492 ATATAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATAATAATATATATG
Found at i:39925729 original size:3 final size:3
Alignment explanation
Indices: 39925721--39925780 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
39925711 TAACAAGATC
* * * * *
39925721 AAT AAT AAT ATT AGT AAT AAT AAC ACT GAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
39925768 ATT AATT AAT AAT
1 AAT AA-T AAT AAT
39925781 CTAATTAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.91
4 3 0.07
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:39927831 original size:41 final size:40
Alignment explanation
Indices: 39927734--39927889 Score: 152
Period size: 41 Copynumber: 3.8 Consensus size: 40
39927724 TATGAAATTC
* * * **
39927734 GAGATAGCTTGGGCTATTTATGGCACTTAGTGTGCAATTT
1 GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGAT
* *
39927774 G-GAATAGCTTCAGCTATATATGACACTTAGTGTGCGAGACT
1 GAG-ATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA-T
* *
39927815 GAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGAT
1 GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGAT
* * * *
39927855 TATAATAGCTTCGGCTATACGATGGCAATTAGTGT
1 GA-GATAGCTTCGGCTATA-TATGGCACTTAGTGT
39927890 ATGAAACATT
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 32 0.34
41 48 0.51
42 13 0.14
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (40 bp):
GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGAT
Found at i:39928591 original size:24 final size:24
Alignment explanation
Indices: 39928564--39928673 Score: 109
Period size: 24 Copynumber: 4.7 Consensus size: 24
39928554 TAGATGTATA
39928564 ATGCTGTCCATTTTGAGCATATTG
1 ATGCTGTCCATTTTGAGCATATTG
*
39928588 ATGCTGTCCATTTAGAGCATATTG
1 ATGCTGTCCATTTTGAGCATATTG
* * *
39928612 ATGCTGTCCACTTT-A--ATGTATA
1 ATGCTGTCCATTTTGAGCATAT-TG
* * *
39928634 ATGTTGTCCAGTTTGAGCATATCG
1 ATGCTGTCCATTTTGAGCATATTG
* *
39928658 ATGTTGTCCAATTTGA
1 ATGCTGTCCATTTTGA
39928674 TGTATAAATG
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.04
22 13 0.18
23 2 0.03
24 50 0.70
25 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
ATGCTGTCCATTTTGAGCATATTG
Found at i:39928642 original size:46 final size:47
Alignment explanation
Indices: 39928588--39928690 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 47
39928578 GAGCATATTG
* *
39928588 ATGCTGTCCA-TTTAGAGCATATTGATGCTGTCCACTTTAATGTAT-A
1 ATGCTGTCCAGTTT-GAGCATATCGATGCTGTCCAATTTAATGTATAA
* * *
39928634 ATGTTGTCCAGTTTGAGCATATCGATGTTGTCCAATTTGATGTATAA
1 ATGCTGTCCAGTTTGAGCATATCGATGCTGTCCAATTTAATGTATAA
39928681 ATGCTGTCCA
1 ATGCTGTCCA
39928691 AAACAGGGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
46 36 0.73
47 13 0.27
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (47 bp):
ATGCTGTCCAGTTTGAGCATATCGATGCTGTCCAATTTAATGTATAA
Found at i:39928691 original size:23 final size:22
Alignment explanation
Indices: 39928556--39928691 Score: 64
Period size: 24 Copynumber: 5.9 Consensus size: 22
39928546 GTTGTTTTTA
*
39928556 GATGTATAATGCTGTCCATTTT
1 GATGTATAATGCTGTCCAATTT
*
39928578 GA-GCATATTGATGCTGTCC-ATTT
1 GATG--TA-TAATGCTGTCCAATTT
* *
39928601 AGA-GCATATTGATGCTGTCCACTTT
1 -GATG--TA-TAATGCTGTCCAATTT
* * *
39928626 AATGTATAATGTTGTCCAGTTT
1 GATGTATAATGCTGTCCAATTT
* *
39928648 GA-GCATATCGATGTTGTCCAATTT
1 GATG--TAT-AATGCTGTCCAATTT
39928672 GATGTATAAATGCTGTCCAA
1 GATGTAT-AATGCTGTCCAA
39928692 AACAGGGTAG
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
21 2 0.02
22 16 0.18
23 23 0.25
24 45 0.49
25 5 0.05
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (22 bp):
GATGTATAATGCTGTCCAATTT
Found at i:39933183 original size:9 final size:9
Alignment explanation
Indices: 39933164--39933230 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
39933154 TTTGGTTAAA
*
39933164 AATTAATCG
1 AATTAACCG
*
39933173 AATTACCCG
1 AATTAACCG
39933182 AATTAACCG
1 AATTAACCG
39933191 AATTAACCG
1 AATTAACCG
*
39933200 GATT-ACTCG
1 AATTAAC-CG
39933209 AATTAACCG
1 AATTAACCG
39933218 AATTAACCG
1 AATTAACCG
39933227 AATT
1 AATT
39933231 GAATCACTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
8 2 0.04
9 47 0.92
10 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:39933196 original size:27 final size:27
Alignment explanation
Indices: 39933164--39933230 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
39933154 TTTGGTTAAA
*
39933164 AATTAATCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
* *
39933191 AATTAACCGGATTACTCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
39933218 AATTAACCGAATT
1 AATTAACCGAATT
39933231 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACCG
Found at i:39933427 original size:84 final size:84
Alignment explanation
Indices: 39933319--39933492 Score: 332
Period size: 84 Copynumber: 2.1 Consensus size: 84
39933309 TTATTTGTAA
39933319 TTTTTATGATTGGGTTGGGTTGAATACTTGGCTTTGGATTTGGTTTAGGTGAATAGTGGACCTAT
1 TTTTTATGATTGGGTTGGGTTGAATACTTGGCTTTGGATTTGGTTTAGGTGAATAGTGGACCTAT
39933384 TTATATATTATAATTTTAT
66 TTATATATTATAATTTTAT
39933403 TTTTGTATGATT-GGTTGGGTTGAATACTTGGCTTTGGATTTGGTTTAGGTGAATAGTGGACCTA
1 TTTT-TATGATTGGGTTGGGTTGAATACTTGGCTTTGGATTTGGTTTAGGTGAATAGTGGACCTA
39933467 TTTATATATTATAATTTTAT
65 TTTATATATTATAATTTTAT
39933487 TTTTTA
1 TTTTTA
39933493 ATTTTTTCGG
Statistics
Matches: 89, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
83 2 0.02
84 80 0.90
85 7 0.08
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (84 bp):
TTTTTATGATTGGGTTGGGTTGAATACTTGGCTTTGGATTTGGTTTAGGTGAATAGTGGACCTAT
TTATATATTATAATTTTAT
Found at i:39939816 original size:22 final size:23
Alignment explanation
Indices: 39939789--39939831 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39939779 ATTCTTCCAT
39939789 TTGTG-AATATT-TTTCTCCATTG
1 TTGTGAAATATTATTT-TCCATTG
39939811 TTGTGAAATATTATTTTCCAT
1 TTGTGAAATATTATTTTCCAT
39939832 CCTGAACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (23 bp):
TTGTGAAATATTATTTTCCATTG
Found at i:39945355 original size:26 final size:26
Alignment explanation
Indices: 39945319--39945378 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
39945309 GATTGAGAAG
* *
39945319 GCTACATTAGCCACCGAAATGGCTAA
1 GCTATATTAGCCACCGAAATGACTAA
* *
39945345 GCTATATTAGCCATCGAAATGACTAG
1 GCTATATTAGCCACCGAAATGACTAA
39945371 GCTATATT
1 GCTATATT
39945379 GGGGGGTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (26 bp):
GCTATATTAGCCACCGAAATGACTAA
Found at i:39945842 original size:23 final size:23
Alignment explanation
Indices: 39945794--39945844 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
39945784 CGGAAAATTC
** *
39945794 TGCCAGTAAAAATGCAGCCAAGT
1 TGCCAGTAAAAATGCAGAAAAAT
39945817 TGCCAGTAAAAATGC-GAAAAAAT
1 TGCCAGTAAAAATGCAG-AAAAAT
39945840 TGCCA
1 TGCCA
39945845 TTCCCCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (23 bp):
TGCCAGTAAAAATGCAGAAAAAT
Found at i:39953328 original size:51 final size:51
Alignment explanation
Indices: 39953237--39953344 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
39953227 CCAAACATCT
* * *
39953237 GTTCATATGAAATAACAGTTCTTACCAAACGACAACTCATGCAAAATAATA
1 GTTCATATGAAATAACAGTTCATACCAAACAACAACTCATGCAAAATAAAA
* * * * *
39953288 GTTCATATGAAATATCAGTTCATATCGAATAAC-ACTTCATGCGAAATAAAA
1 GTTCATATGAAATAACAGTTCATACCAAACAACAAC-TCATGCAAAATAAAA
39953339 GTTCAT
1 GTTCAT
39953345 GCTCCATCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.04
51 46 0.96
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (51 bp):
GTTCATATGAAATAACAGTTCATACCAAACAACAACTCATGCAAAATAAAA
Found at i:39953345 original size:17 final size:17
Alignment explanation
Indices: 39953273--39953346 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
39953263 AAACGACAAC
* *
39953273 TCATGCAAAATAATAGT
1 TCATGCGAAATAACAGT
** *
39953290 TCATATGAAATATCAGT
1 TCATGCGAAATAACAGT
* *
39953307 TCATATCG-AATAACACT
1 TCAT-GCGAAATAACAGT
*
39953324 TCATGCGAAATAAAAGT
1 TCATGCGAAATAACAGT
39953341 TCATGC
1 TCATGC
39953347 TCCATCATAA
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
16 2 0.05
17 40 0.93
18 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (17 bp):
TCATGCGAAATAACAGT
Found at i:39954031 original size:18 final size:18
Alignment explanation
Indices: 39953989--39954037 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
39953979 CACATTTTGA
* * *
39953989 CAAATTAATGCAGTTTGC
1 CAAATTAATACAGATTAC
*
39954007 CATATTAATACAGATTAC
1 CAAATTAATACAGATTAC
*
39954025 CAAATTAACACAG
1 CAAATTAATACAG
39954038 TTCGTTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (18 bp):
CAAATTAATACAGATTAC
Found at i:39954386 original size:5 final size:5
Alignment explanation
Indices: 39954376--39954414 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
39954366 ACCATGCGTA
39954376 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
39954415 ATACCAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:39954485 original size:28 final size:28
Alignment explanation
Indices: 39954431--39954502 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
39954421 AAATCCATTA
**
39954431 ATATATATTAGGTAAAATAAAGACATGC
1 ATATATATTATATAAAATAAAGACATGC
* * *
39954459 ATATATATTATATAAGATGAAGTCATGC
1 ATATATATTATATAAAATAAAGACATGC
*
39954487 ACATATATATATATAA
1 ATATATAT-TATATAA
39954503 TATATGTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 30 0.81
29 7 0.19
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (28 bp):
ATATATATTATATAAAATAAAGACATGC
Found at i:39954562 original size:2 final size:2
Alignment explanation
Indices: 39954550--39954579 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
39954540 CAACCAACAC
39954550 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39954580 ATTACTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39962464 original size:21 final size:22
Alignment explanation
Indices: 39962428--39962474 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
39962418 ATTCAATTTT
*
39962428 AAAATTTGAAATATAAAAATAA
1 AAAATTTGAAATATAAAAAAAA
*
39962450 AAAATTTTAAA-ATAAAAAAAA
1 AAAATTTGAAATATAAAAAAAA
39962471 AAAA
1 AAAA
39962475 GGAGGAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAAAAA
Found at i:39969620 original size:26 final size:26
Alignment explanation
Indices: 39969580--39969634 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39969570 AGAAGGCTAC
39969580 ATTAGCCACCAAAATGGCTAAACTAT
1 ATTAGCCACCAAAATGGCTAAACTAT
** **
39969606 ATTAGCCACTGAAATGGCTAGGCTAT
1 ATTAGCCACCAAAATGGCTAAACTAT
39969632 ATT
1 ATT
39969635 GGGGGTGAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (26 bp):
ATTAGCCACCAAAATGGCTAAACTAT
Found at i:39970079 original size:22 final size:23
Alignment explanation
Indices: 39970034--39970081 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39970024 GAAAATTCTT
*
39970034 CCAGTAAAAATGCAGACAAGTTG
1 CCAGTAAAAATGCAGACAAATTG
* *
39970057 CCAGTAAAAATG-TGATAAATTG
1 CCAGTAAAAATGCAGACAAATTG
39970079 CCA
1 CCA
39970082 TTCCTTTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.21
Consensus pattern (23 bp):
CCAGTAAAAATGCAGACAAATTG
Found at i:39977434 original size:22 final size:23
Alignment explanation
Indices: 39977407--39977449 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39977397 ATTATTCCAT
39977407 TTGTG-AATATT-TTTCTCCATTG
1 TTGTGAAATATTATTT-TCCATTG
39977429 TTGTGAAATATTATTTTCCAT
1 TTGTGAAATATTATTTTCCAT
39977450 CTCGAACCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (23 bp):
TTGTGAAATATTATTTTCCATTG
Found at i:39994670 original size:26 final size:25
Alignment explanation
Indices: 39994634--39994693 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 25
39994624 GATTGAGAAG
*
39994634 GCTACATTAGCCACTGAAATGGCTAA
1 GCTATATTAGCCACTGAAATGGCT-A
39994660 GCTATATTAGCCACTGAAATGGCTA
1 GCTATATTAGCCACTGAAATGGCTA
39994685 GTCTATATT
1 G-CTATATT
39994694 GGGGGTGAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (25 bp):
GCTATATTAGCCACTGAAATGGCTA
Found at i:39995155 original size:22 final size:23
Alignment explanation
Indices: 39995110--39995157 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
39995100 GAAAATTCTT
*
39995110 CCAATAAAAATGCAGACTAGTTG
1 CCAATAAAAATGCAGACTAATTG
39995133 CCAATAAAAATGC-GA-TAAATTG
1 CCAATAAAAATGCAGACT-AATTG
39995155 CCA
1 CCA
39995158 TTCCCCTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 9 0.39
23 13 0.57
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (23 bp):
CCAATAAAAATGCAGACTAATTG
Found at i:39998267 original size:47 final size:47
Alignment explanation
Indices: 39998198--39998291 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
39998188 TCTTAAAATG
39998198 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
1 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
39998245 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
1 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
39998292 AAGTATCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (47 bp):
TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
Found at i:40001932 original size:6 final size:6
Alignment explanation
Indices: 40001923--40001952 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
40001913 TCACAAGTAC
40001923 AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
40001953 TGTTCGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:40021555 original size:22 final size:22
Alignment explanation
Indices: 40021530--40021576 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
40021520 GTGCCACAAA
40021530 GAGAGTAAAGTTAAGAACAACC
1 GAGAGTAAAGTTAAGAACAACC
*
40021552 GAGAGTAAAGTTAAGAACAATC
1 GAGAGTAAAGTTAAGAACAACC
40021574 GAG
1 GAG
40021577 GGCAAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.11, G:0.26, T:0.15
Consensus pattern (22 bp):
GAGAGTAAAGTTAAGAACAACC
Found at i:40021583 original size:22 final size:22
Alignment explanation
Indices: 40021530--40021583 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
40021520 GTGCCACAAA
*
40021530 GAGAGTAAAGTTAAGAACAACC
1 GAGAGCAAAGTTAAGAACAACC
* *
40021552 GAGAGTAAAGTTAAGAACAATC
1 GAGAGCAAAGTTAAGAACAACC
*
40021574 GAGGGCAAAG
1 GAGAGCAAAG
40021584 AAGTTGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.28, T:0.13
Consensus pattern (22 bp):
GAGAGCAAAGTTAAGAACAACC
Found at i:40028386 original size:21 final size:20
Alignment explanation
Indices: 40028356--40028395 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
40028346 TTTAAGGGGT
40028356 TTTTTAGTTCAAC-AGCTGAA
1 TTTTTAGTTC-ACGAGCTGAA
40028376 TTTTTAGGTTCACGAGCTGA
1 TTTTTA-GTTCACGAGCTGA
40028396 TTCATCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
TTTTTAGTTCACGAGCTGAA
Found at i:40030422 original size:17 final size:17
Alignment explanation
Indices: 40030396--40030428 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
40030386 TATTTTTAAT
40030396 AAAAATTAT-AATTTTA
1 AAAAATTATAAATTTTA
40030412 AAAAATATATAAATTTT
1 AAAAAT-TATAAATTTT
40030429 TCTTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAATTATAAATTTTA
Found at i:40048305 original size:10 final size:11
Alignment explanation
Indices: 40048287--40048351 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
40048277 AATTTAGCAA
40048287 TTTATTTTTAT
1 TTTATTTTTAT
40048298 TTTA-TTTTATT
1 TTTATTTTTA-T
*
40048309 TTTGTTTTTAGT
1 TTTATTTTTA-T
* *
40048321 TTAATTTTTTT
1 TTTATTTTTAT
*
40048332 TTCTAATTTTTCT
1 TT-T-ATTTTTAT
40048345 TTTATTT
1 TTTATTT
40048352 GCTTCTGGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 5 0.12
11 15 0.35
12 14 0.33
13 9 0.21
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:40048316 original size:22 final size:22
Alignment explanation
Indices: 40048291--40048333 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40048281 TAGCAATTTA
*
40048291 TTTTTA-TTTTATTTTATTTTTG
1 TTTTTAGTTTAATTTT-TTTTTG
40048313 TTTTTAGTTTAATTTTTTTTT
1 TTTTTAGTTTAATTTTTTTTT
40048334 CTAATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTAGTTTAATTTTTTTTTG
Found at i:40054679 original size:4 final size:4
Alignment explanation
Indices: 40054665--40054696 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
40054655 CACCCCTTCC
*
40054665 CTTT TTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
40054697 ATTTGTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
CTTT
Found at i:40054719 original size:22 final size:23
Alignment explanation
Indices: 40054694--40054738 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
40054684 TCTTTCTTTC
40054694 TTTATTTGTCTTTA-ATTATTTT
1 TTTATTTGTCTTTAGATTATTTT
* *
40054716 TTTATTTGTTTTTAGTTTATTTT
1 TTTATTTGTCTTTAGATTATTTT
40054739 CTTTTGGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTATTTGTCTTTAGATTATTTT
Found at i:40057001 original size:26 final size:26
Alignment explanation
Indices: 40056972--40057043 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
40056962 ACCAATATCA
* * *
40056972 CAGCAAAGGTGCTAGTAATAGTGATG
1 CAGCAAAGCTGCTAGTAACAGTAATG
*
40056998 CAGCAAAGCTGCCAGTAACAGTAATG
1 CAGCAAAGCTGCTAGTAACAGTAATG
*
40057024 CAACAAAGCTGCTAGTAACA
1 CAGCAAAGCTGCTAGTAACA
40057044 ATATATGTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (26 bp):
CAGCAAAGCTGCTAGTAACAGTAATG
Found at i:40057252 original size:27 final size:27
Alignment explanation
Indices: 40057222--40057335 Score: 156
Period size: 27 Copynumber: 4.2 Consensus size: 27
40057212 AGTATAACAG
* *
40057222 TCATTTTCCCCTTCGAGGGTAATTCGA
1 TCATTTTACCCTTCAAGGGTAATTCGA
* *
40057249 TCATTTTGCCCTTCAAGGGTAATTCAA
1 TCATTTTACCCTTCAAGGGTAATTCGA
*
40057276 TCATTTTACCCTTCAAGGATAATTCGA
1 TCATTTTACCCTTCAAGGGTAATTCGA
** *
40057303 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCAAGGGTAATTCGA
40057330 TCATTT
1 TCATTT
40057336 GAGGCCTCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCTTCAAGGGTAATTCGA
Found at i:40063127 original size:6 final size:6
Alignment explanation
Indices: 40063116--40063144 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40063106 ACCCCAATAT
40063116 AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAAT
40063145 TAAGCACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:40069505 original size:26 final size:25
Alignment explanation
Indices: 40069460--40069525 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
40069450 TTTTAAGTGT
** * *
40069460 TTTCAGTATAGGCTATCTATAGTAA
1 TTTCAGTATATACTACCTATAGCAA
40069485 TTCTCAGTATATACTACCTATAGCAA
1 TT-TCAGTATATACTACCTATAGCAA
*
40069511 TTTCAGGATATACTA
1 TTTCAGTATATACTA
40069526 TCAAGGATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 14 0.40
26 21 0.60
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (25 bp):
TTTCAGTATATACTACCTATAGCAA
Found at i:40069522 original size:25 final size:26
Alignment explanation
Indices: 40069476--40069525 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
40069466 TATAGGCTAT
* *
40069476 CTATAGTAATTCTCAGTATATACTAC
1 CTATAGCAATTCTCAGGATATACTAC
40069502 CTATAGCAATT-TCAGGATATACTA
1 CTATAGCAATTCTCAGGATATACTA
40069526 TCAAGGATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (26 bp):
CTATAGCAATTCTCAGGATATACTAC
Found at i:40074232 original size:6 final size:6
Alignment explanation
Indices: 40074221--40074282 Score: 99
Period size: 6 Copynumber: 10.3 Consensus size: 6
40074211 ATTGATTTAA
40074221 AAAAAG AAAAAG AAAAATG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-
1 AAAAAG AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
40074269 AGAAAG AAAAAG AA
1 AAAAAG AAAAAG AA
40074283 CTAGAATTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.08
6 42 0.81
7 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:40074245 original size:19 final size:18
Alignment explanation
Indices: 40074221--40074282 Score: 99
Period size: 19 Copynumber: 3.4 Consensus size: 18
40074211 ATTGATTTAA
40074221 AAAAAGAAAAAGAAAAATG
1 AAAAAGAAAAAGAAAAA-G
40074240 AAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAAGAAAAAG
*
40074258 AAAAAGAAAAA-AGAAAG
1 AAAAAGAAAAAGAAAAAG
40074275 AAAAAGAA
1 AAAAAGAA
40074283 CTAGAATTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
17 13 0.31
18 12 0.29
19 17 0.40
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:40076310 original size:38 final size:38
Alignment explanation
Indices: 40076255--40076562 Score: 305
Period size: 38 Copynumber: 8.1 Consensus size: 38
40076245 GACACAAAGA
* *
40076255 CCGAATATCATTGGCACAAAGCCTGCTAGGCATAGAGC
1 CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
** * * * *
40076293 CCGAATATCACCAGCACAGAGCTTTCTAGGCACAGAAC
1 CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
* * *
40076331 CCGAATATCA-TCAGCACAAAGCCTACTAGGCACAAAGC
1 CCGAATATCACT-GGCACAAAGCCTGCTAGGCACAGAGC
** * * * * *
40076369 CTAAATATCA-TAGGCAAAAAGGCTACTAGGCATAGAAC
1 CCGAATATCACT-GGCACAAAGCCTGCTAGGCACAGAGC
** * *
40076407 CATAATATCACCGGTACAAAGCCTGCTAGGCACAGAGC
1 CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
* *
40076445 CCGAATATCACTGGCACAAAGCCTGCTAGGTACACAGC
1 CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
** *
40076483 CTAAATATCACTGGCACAAAGCCTGCTAGGCACAAAGC
1 CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
** * *
40076521 CTAAATATCACTGGCACAAAGCCTGCTAAGCACGGAGC
1 CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
40076559 CCGA
1 CCGA
40076563 GTAACGTTAC
Statistics
Matches: 221, Mismatches: 47, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
38 221 1.00
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.16
Consensus pattern (38 bp):
CCGAATATCACTGGCACAAAGCCTGCTAGGCACAGAGC
Found at i:40076448 original size:114 final size:112
Alignment explanation
Indices: 40076258--40076562 Score: 353
Period size: 114 Copynumber: 2.7 Consensus size: 112
40076248 ACAAAGACCG
* * * * * *
40076258 AATATCATTGGCACAAAGCCTGCTAGGCATAGAGCCCGAATATCACCAGCACAGAGCTTTCTAGG
1 AATATCA-TGGCACAAAGCCTGCTAGGCATAGA-ACCTAATATCACCGGCACAAAGCCTGCTAGG
*
40076323 CACAGAACCCGAATATCA-TCAGCACAAAGCCTACTAGGCACAAAGCCTA
64 CACAGAGCCCGAATATCACT-AGCACAAAGCCTACTAGGCACAAAGCCTA
* * * *
40076372 AATATCATAGGCAAAAAGGCTACTAGGCATAGAACCATAATATCACCGGTACAAAGCCTGCTAGG
1 AATATCAT-GGCACAAAGCCTGCTAGGCATAGAACC-TAATATCACCGGCACAAAGCCTGCTAGG
* * * *
40076437 CACAGAGCCCGAATATCACTGGCACAAAGCCTGCTAGGTACACAGCCTA
64 CACAGAGCCCGAATATCACTAGCACAAAGCCTACTAGGCACAAAGCCTA
* * *
40076486 AATATCACTGGCACAAAGCCTGCTAGGCACA-AAGCCTAAATATCACTGGCACAAAGCCTGCTAA
1 AATATCA-TGGCACAAAGCCTGCTAGGCATAGAA-CCT-AATATCACCGGCACAAAGCCTGCTAG
*
40076550 GCACGGAGCCCGA
63 GCACAGAGCCCGA
40076563 GTAACGTTAC
Statistics
Matches: 162, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
113 6 0.04
114 154 0.95
115 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (112 bp):
AATATCATGGCACAAAGCCTGCTAGGCATAGAACCTAATATCACCGGCACAAAGCCTGCTAGGCA
CAGAGCCCGAATATCACTAGCACAAAGCCTACTAGGCACAAAGCCTA
Found at i:40076505 original size:22 final size:22
Alignment explanation
Indices: 40076480--40076544 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
40076470 CTAGGTACAC
40076480 AGCCTAAATATCACTGGCACAA
1 AGCCTAAATATCACTGGCACAA
**
40076502 AGCCT---GCT-A--GGCACAA
1 AGCCTAAATATCACTGGCACAA
40076518 AGCCTAAATATCACTGGCACAA
1 AGCCTAAATATCACTGGCACAA
40076540 AGCCT
1 AGCCT
40076545 GCTAAGCACG
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 12 0.36
18 1 0.03
19 2 0.06
20 1 0.03
22 17 0.52
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (22 bp):
AGCCTAAATATCACTGGCACAA
Found at i:40078242 original size:25 final size:25
Alignment explanation
Indices: 40078188--40078236 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40078178 AAAATCACCA
*
40078188 CTAAGCTTTAAACAACGAAGATCTC
1 CTAAACTTTAAACAACGAAGATCTC
40078213 CTAAACTTTAAACAACGAAGATCT
1 CTAAACTTTAAACAACGAAGATCT
40078237 TTTAAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (25 bp):
CTAAACTTTAAACAACGAAGATCTC
Found at i:40081447 original size:34 final size:35
Alignment explanation
Indices: 40081403--40081469 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
40081393 CAGTAAAATA
* * *
40081403 TTTTCCGTAAAAT-GATTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAAATTACTGGAAAATATTTTAC
*
40081437 TTTTCTGTAAAATAAATTACTGGAAAATATTTT
1 TTTTCCGTAAAATAAATTACTGGAAAATATTTT
40081470 CTAGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 12 0.43
35 16 0.57
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATAAATTACTGGAAAATATTTTAC
Found at i:40082942 original size:44 final size:44
Alignment explanation
Indices: 40082892--40082982 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
40082882 GTAATTGTAA
* *
40082892 ATTAAATTATAAATATTTTTAAATGTAAAATTATCACAACTTCT
1 ATTAAATTATAAATATTCTTAAATGTAAAATTATCACAAATTCT
* * *
40082936 ATTAAATTATAATTATTCTTAAATGTATAATTATCATAAATTCT
1 ATTAAATTATAAATATTCTTAAATGTAAAATTATCACAAATTCT
40082980 ATT
1 ATT
40082983 TTTTATTAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (44 bp):
ATTAAATTATAAATATTCTTAAATGTAAAATTATCACAAATTCT
Found at i:40082975 original size:17 final size:17
Alignment explanation
Indices: 40082938--40082977 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40082928 CAACTTCTAT
*
40082938 TAAATTATAATTATTCT
1 TAAATTATAATTATTCA
40082955 TAAATGTATAATTA-TCA
1 TAAAT-TATAATTATTCA
40082972 TAAATT
1 TAAATT
40082978 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.57
18 8 0.38
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATTATAATTATTCA
Found at i:40084544 original size:14 final size:14
Alignment explanation
Indices: 40084527--40084565 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
40084517 TATAATTTGG
40084527 ATTTTGATTTTGAA
1 ATTTTGATTTTGAA
* *
40084541 ATTTTGGTTTTGAC
1 ATTTTGATTTTGAA
40084555 ATTTTGGATTT
1 ATTTT-GATTT
40084566 GGCCGGATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (14 bp):
ATTTTGATTTTGAA
Found at i:40085353 original size:25 final size:25
Alignment explanation
Indices: 40085325--40085379 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
40085315 AAAATCACCA
* *
40085325 CTAAGCTTTAAACAGCAAAGATCTC
1 CTAAACTTTAAACAACAAAGATCTC
*
40085350 CTAAACTTTAAACAACGAAGATCTC
1 CTAAACTTTAAACAACAAAGATCTC
40085375 CTAAA
1 CTAAA
40085380 ACTTACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (25 bp):
CTAAACTTTAAACAACAAAGATCTC
Found at i:40089211 original size:43 final size:42
Alignment explanation
Indices: 40089147--40089289 Score: 151
Period size: 43 Copynumber: 3.4 Consensus size: 42
40089137 TTATGTGAAA
* *
40089147 AAACGCCGCTAAAGATAATGACCTTTAGCAGCGCTTCTACCAC
1 AAACGCCGCTAAAAATAATGACTTTTAGCAGCGCTT-TACCAC
* ** *
40089190 AAACGCCGCTAAAAATCATGACTTTTAGCAATGCTATTACTAC
1 AAACGCCGCTAAAAATAATGACTTTTAGCAGCGCT-TTACCAC
* * * * * **
40089233 AAACACCACTATAAAGAATGACTTTTAGCGGCGCTTTTTCAC
1 AAACGCCGCTAAAAATAATGACTTTTAGCAGCGCTTTACCAC
40089275 AAACGCCGCTAAAAA
1 AAACGCCGCTAAAAA
40089290 CATAACTTTT
Statistics
Matches: 79, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
42 16 0.20
43 62 0.78
44 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAAATAATGACTTTTAGCAGCGCTTTACCAC
Found at i:40099484 original size:9 final size:9
Alignment explanation
Indices: 40099452--40099486 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
40099442 AAATTCACAT
*
40099452 ATTTTAATA
1 ATTTAAATA
40099461 ATTTTAAATA
1 A-TTTAAATA
40099471 ATTTAAATA
1 ATTTAAATA
40099480 ATTTAAA
1 ATTTAAA
40099487 AAACTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
ATTTAAATA
Found at i:40099622 original size:21 final size:21
Alignment explanation
Indices: 40099598--40099647 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
40099588 CACTGTTTCT
*
40099598 AATCTCACTGCTACAGTATCC
1 AATCTCACTGCTACAGTAACC
*
40099619 AATCTCACTGCTACAGTAACT
1 AATCTCACTGCTACAGTAACC
40099640 AATCTCAC
1 AATCTCAC
40099648 CGCCACCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (21 bp):
AATCTCACTGCTACAGTAACC
Found at i:40100465 original size:40 final size:40
Alignment explanation
Indices: 40100402--40100486 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
40100392 TAGCTTGAAT
* *
40100402 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGTAAGAAATTAACAAAA
*
40100442 ATCAACATTTCAATAATTT-ATATGTAAGAAATTAACAAAA
1 ATCAACACTTCAAT-ATTTAATATGTAAGAAATTAACAAAA
40100482 ATCAA
1 ATCAA
40100487 TCTTACAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.32
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGTAAGAAATTAACAAAA
Found at i:40100502 original size:40 final size:40
Alignment explanation
Indices: 40100416--40100527 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 40
40100406 ACACTTCAAT
* * * *
40100416 ATTTAATATGTAAGGAATTATCAAAAATCAACATTTCAATA
1 ATTT-ATATGTAAGAAATTAACAAAAATCAACATTACAACA
40100457 ATTTATATGTAAGAAATTAACAAAAATCAATC-TTACAACA
1 ATTTATATGTAAGAAATTAACAAAAATCAA-CATTACAACA
* * * * * *
40100497 GTTTATGTGAAACAAATTAGCACAAATCAAC
1 ATTTATATGTAAGAAATTAACAAAAATCAAC
40100528 TATTCATAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 54 0.90
41 5 0.08
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.30
Consensus pattern (40 bp):
ATTTATATGTAAGAAATTAACAAAAATCAACATTACAACA
Found at i:40101220 original size:40 final size:40
Alignment explanation
Indices: 40101176--40101303 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
40101166 GGGAAATTGG
40101176 GGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
1 GGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
* * ** * *
40101216 GGGAAAAATAAAAGGG-CTGCCGAATTGGGGA-AATTGG---
1 GGGAAAAAT-AAAGGGAAT-CGGGGTAGGGGAGAAATGGTTT
**
40101253 GGG-GGAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
1 GGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
40101292 GGGAAAAATAAA
1 GGGAAAAATAAA
40101304 ATGCGGAAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 16
0.67 0.17 0.17
Matches are distributed among these distances:
35 14 0.22
36 9 0.14
37 3 0.05
39 3 0.05
40 21 0.33
41 14 0.22
ACGTcount: A:0.38, C:0.04, G:0.41, T:0.16
Consensus pattern (40 bp):
GGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
Found at i:40101284 original size:76 final size:77
Alignment explanation
Indices: 40101151--40101304 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 77
40101141 GGAGATGCAG
*
40101151 AGGGCTGCCGATTTGGGGAAATTGGGGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
1 AGGGCTGCCGAATTGGGGAAATTGGGGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
40101216 GGGAAAAATAAA
66 GGGAAAAATAAA
**
40101228 AGGGCTGCCGAATTGGGGAAATTGGGGG-GGAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
1 AGGGCTGCCGAATTGGGGAAATTGGGGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
40101292 GGGAAAAATAAA
66 GGGAAAAATAAA
40101304 A
1 A
40101305 TGCGGAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 47 0.64
77 27 0.36
ACGTcount: A:0.36, C:0.05, G:0.42, T:0.18
Consensus pattern (77 bp):
AGGGCTGCCGAATTGGGGAAATTGGGGGAAAAATAAAGGGAATCGGGGTAGGGGAGAAATGGTTT
GGGAAAAATAAA
Found at i:40102114 original size:15 final size:15
Alignment explanation
Indices: 40102094--40102167 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
40102084 GAGTACCCCT
40102094 AACCCCTAAACCTTA
1 AACCCCTAAACCTTA
40102109 AACCCC--AACCTTTA
1 AACCCCTAAACC-TTA
* *
40102123 AA-CCATAAACCAT-
1 AACCCCTAAACCTTA
* *
40102136 AATCCCTAAACC-CA
1 AACCCCTAAACCTTA
*
40102150 TAATCCCTAAACCTTA
1 -AACCCCTAAACCTTA
40102166 AA
1 AA
40102168 TAGTAACTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
13 8 0.17
14 14 0.30
15 24 0.51
16 1 0.02
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.20
Consensus pattern (15 bp):
AACCCCTAAACCTTA
Found at i:40102145 original size:14 final size:14
Alignment explanation
Indices: 40102128--40102162 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
40102118 CTTTAAACCA
40102128 TAAACCATAATCCC
1 TAAACCATAATCCC
40102142 TAAACCCATAATCCC
1 TAAA-CCATAATCCC
40102157 TAAACC
1 TAAACC
40102163 TTAAATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:40102167 original size:22 final size:21
Alignment explanation
Indices: 40102115--40102167 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
40102105 CTTAAACCCC
40102115 AACCTTTAAACCATAAACCATA
1 AACC-TTAAACCATAAACCATA
* * * *
40102137 ATCCCTAAACCCATAATCCCTA
1 AACCTTAAA-CCATAAACCATA
40102159 AACCTTAAA
1 AACCTTAAA
40102168 TAGTAACTCC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCTTAAACCATAAACCATA
Found at i:40102307 original size:7 final size:7
Alignment explanation
Indices: 40102295--40102382 Score: 52
Period size: 7 Copynumber: 11.9 Consensus size: 7
40102285 ACTAATTAAT
40102295 CTAAACC
1 CTAAACC
40102302 CTAAACCC
1 CTAAA-CC
*
40102310 CTAACCC
1 CTAAACC
40102317 CTAAACC
1 CTAAACC
* *
40102324 ATAAATC
1 CTAAACC
*
40102331 ATAAACC
1 CTAAACC
*
40102338 CTTAACCC
1 C-TAAACC
40102346 CT-AACC
1 CTAAACC
40102352 CTTAAGTACC
1 C-TAA--ACC
*
40102362 CTTAACCC
1 C-TAAACC
40102370 CTAAACC
1 CTAAACC
*
40102377 TTAAAC
1 CTAAAC
40102383 TCCAACCTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
6 4 0.06
7 36 0.56
8 16 0.25
10 8 0.12
ACGTcount: A:0.39, C:0.40, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:40102318 original size:15 final size:15
Alignment explanation
Indices: 40102295--40102382 Score: 63
Period size: 15 Copynumber: 5.9 Consensus size: 15
40102285 ACTAATTAAT
40102295 CTAAACCCTAAACCC
1 CTAAACCCTAAACCC
*
40102310 CTAACCCCTAAA-CC
1 CTAAACCCTAAACCC
* * *
40102324 ATAAATCATAAACCC
1 CTAAACCCTAAACCC
* *
40102339 TTAACCCCT-AACCC
1 CTAAACCCTAAACCC
* *
40102353 TTAAGTACCCTTAACCC
1 CTAA--ACCCTAAACCC
*
40102370 CTAAACCTTAAAC
1 CTAAACCCTAAAC
40102383 TCCAACCTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
14 19 0.34
15 25 0.45
16 4 0.07
17 8 0.14
ACGTcount: A:0.39, C:0.40, G:0.01, T:0.20
Consensus pattern (15 bp):
CTAAACCCTAAACCC
Found at i:40102362 original size:24 final size:24
Alignment explanation
Indices: 40102335--40102380 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
40102325 TAAATCATAA
*
40102335 ACCCTTAACCCCTAACCCTTAAGT
1 ACCCTTAACCCCTAAACCTTAAGT
40102359 ACCCTTAACCCCTAAACCTTAA
1 ACCCTTAACCCCTAAACCTTAA
40102381 ACTCCAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.41, G:0.02, T:0.24
Consensus pattern (24 bp):
ACCCTTAACCCCTAAACCTTAAGT
Found at i:40102423 original size:15 final size:15
Alignment explanation
Indices: 40102386--40102434 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
40102376 CTTAAACTCC
* *
40102386 AACCTTTAAACCATA
1 AACCTATAATCCATA
*
40102401 AACC-ATAATCCTTA
1 AACCTATAATCCATA
40102415 AACCTATAATCCATA
1 AACCTATAATCCATA
40102430 AACCT
1 AACCT
40102435 TAAATAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.27
Consensus pattern (15 bp):
AACCTATAATCCATA
Found at i:40102514 original size:271 final size:268
Alignment explanation
Indices: 40101980--40102825 Score: 1293
Period size: 271 Copynumber: 3.2 Consensus size: 268
40101970 TTAATATTAC
* *
40101980 CTCTTTTACAATTATATAAAAAATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
1 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
*
40102045 CTAAACCCCTAA--CC----CC-TAAATCATAAACCTTTAA---CT---CTTGAGTACCCCTAAC
66 CTAAACCCCTAACCCCTAAACCATAAATCATAAACCCTTAACCCCTAACCTT-AGTA-CCCTAAC
*
40102097 CCCTAAACCTTAAACCCCAACCTTTAAACCATAAACCATAATCCCTAAACCCATAATCCCTAAAC
129 CCCTAAACCTTAAACCCCAACCTTTAAACCATAAACCATAATCCCTAAACCCATAATCCATAAAC
**
40102162 CTTAAATAGTAACTCCTAAACTTTAAACCCTAAACTATAATGATAACCAATTCAATATTTTAAAA
194 CTTAAATAGTAACTCCTAAACTTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAA
*
40102227 TTAATATCAT
259 TTAATACCAT
* *
40102237 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTCAAAAATACTAATTAATCTAAACC
1 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
40102302 CTAAACCCCTAACCCCTAAACCATAAATCATAAACCCTTAACCCCTAACCCTTAAGTACCCTTAA
66 CTAAACCCCTAACCCCTAAACCATAAATCATAAACCCTTAACCCCTAA-CCTT-AGTACCC-TAA
* * *
40102367 CCCCTAAACCTTAAACTCCAACCTTTAAACCATAAACCATAATCCTTAAACCTATAATCCATAAA
128 CCCCTAAACCTTAAACCCCAACCTTTAAACCATAAACCATAATCCCTAAACCCATAATCCATAAA
*
40102432 CCTTAAATAGTAACTCCTAAACTTTAAACCCTAAACTATATTGATAATTAATTCAATATTTTAAA
193 CCTTAAATAGTAACTCCTAAACTTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAA
40102497 ATTAATACCAT
258 ATTAATACCAT
*
40102508 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTCAAAAACACTAATTAATCTAAACC
1 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
*
40102573 CTAAATCCCTAACCCCTAAACCATAAATCATAAACCCTTAACCCCTAA-C------CCCTAACCC
66 CTAAACCCCTAACCCCTAAACCATAAATCATAAACCCTTAACCCCTAACCTTAGTACCCTAACCC
40102631 CTAAACCTTAAACCCCAATCC-TTAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACC
131 CTAAACCTTAAACCCCAA-CCTTTAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACC
* *
40102695 TTAAAATAGTAACTCTTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAA
195 TT-AAATAGTAACTCCTAAACTTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAA
*
40102760 TTAATACTAT
259 TTAATACCAT
* *
40102770 ATCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAATCAGTAATT
1 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAA-CACTAATT
40102826 TACCCAAAAA
Statistics
Matches: 545, Mismatches: 26, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
257 73 0.13
259 2 0.00
261 66 0.12
262 118 0.22
263 9 0.02
264 17 0.03
267 2 0.00
269 1 0.00
270 3 0.01
271 254 0.47
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30
Consensus pattern (268 bp):
CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
CTAAACCCCTAACCCCTAAACCATAAATCATAAACCCTTAACCCCTAACCTTAGTACCCTAACCC
CTAAACCTTAAACCCCAACCTTTAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACCT
TAAATAGTAACTCCTAAACTTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATT
AATACCAT
Found at i:40102584 original size:8 final size:7
Alignment explanation
Indices: 40102566--40102699 Score: 88
Period size: 7 Copynumber: 18.7 Consensus size: 7
40102556 ACTAATTAAT
40102566 CTAAACC
1 CTAAACC
40102573 CTAAATCC
1 CTAAA-CC
*
40102581 CTAACCC
1 CTAAACC
40102588 CTAAACC
1 CTAAACC
* *
40102595 ATAAATC
1 CTAAACC
*
40102602 ATAAACC
1 CTAAACC
*
40102609 CTTAACCC
1 C-TAAACC
*
40102617 CTAACCC
1 CTAAACC
*
40102624 CTAACCC
1 CTAAACC
40102631 CTAAACC
1 CTAAACC
*
40102638 TTAAACC
1 CTAAACC
* *
40102645 CCAATCC
1 CTAAACC
*
40102652 TTAAACC
1 CTAAACC
*
40102659 ATAAACC
1 CTAAACC
* *
40102666 ATAATCC
1 CTAAACC
40102673 CTAAACC
1 CTAAACC
*
40102680 CATAATCC
1 C-TAAACC
*
40102688 ATAAACC
1 CTAAACC
*
40102695 TTAAA
1 CTAAA
40102700 ATAGTAACTC
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
7 84 0.83
8 17 0.17
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:40102619 original size:36 final size:35
Alignment explanation
Indices: 40102563--40102645 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
40102553 AACACTAATT
*
40102563 AATCTAAACCCTAAATCCCTAACCCCTAAACCATA
1 AATCTAAACCCTAAACCCCTAACCCCTAAACCATA
* * *
40102598 AATCATAAACCCTTAACCCCTAACCCCTAACCCCTA
1 AATC-TAAACCCTAAACCCCTAACCCCTAAACCATA
*
40102634 AACCTTAAACCC
1 AATC-TAAACCC
40102646 CAATCCTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.40, C:0.41, G:0.00, T:0.19
Consensus pattern (35 bp):
AATCTAAACCCTAAACCCCTAACCCCTAAACCATA
Done.