Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 38 of 52
Found at i:6240335 original size:16 final size:15
Alignment explanation
Indices: 6240296--6240343 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 15
6240286 TTATTAAATA
6240296 AAAAT-TATTTATAT
1 AAAATATATTTATAT
6240310 -AAATATATTTATAT
1 AAAATATATTTATAT
*
6240324 AAAATCTAATTTATAT
1 AAAATAT-ATTTATAT
6240340 AAAA
1 AAAA
6240344 AAATAATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
15 5 0.17
16 12 0.40
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATATATTTATAT
Found at i:6241080 original size:14 final size:14
Alignment explanation
Indices: 6241061--6241088 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6241051 TGCATTATTG
6241061 ATTTATTTTATTTT
1 ATTTATTTTATTTT
6241075 ATTTATTTTATTTT
1 ATTTATTTTATTTT
6241089 TTGCATGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:6242061 original size:2 final size:2
Alignment explanation
Indices: 6242054--6242102 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6242044 TTAGACACTC
6242054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6242096 AT AT AT A
1 AT AT AT A
6242103 ATCATTTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6242515 original size:29 final size:30
Alignment explanation
Indices: 6242476--6242542 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
6242466 TTTTTCACTC
* *
6242476 AAATAAGTTTTTAATTTTTAATTTAT-TTT
1 AAATAAATTTTTAATTTTTAAATTATATTT
*
6242505 AATTAAATTTTTAATTTTTAAATTATATTT
1 AAATAAATTTTTAATTTTTAAATTATATTT
6242535 AAATAAAT
1 AAATAAAT
6242543 CATTAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
AAATAAATTTTTAATTTTTAAATTATATTT
Found at i:6242549 original size:30 final size:29
Alignment explanation
Indices: 6242486--6242549 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
6242476 AAATAAGTTT
* * **
6242486 TTAATTTTTAATTTATTTTAATTAAATTT
1 TTAATTTTTAAATTATTTTAAATAAATCA
6242515 TTAATTTTTAAATTATATTTAAATAAATCA
1 TTAATTTTTAAATTAT-TTTAAATAAATCA
6242545 TTAAT
1 TTAAT
6242550 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTAATTTTTAAATTATTTTAAATAAATCA
Found at i:6244083 original size:23 final size:23
Alignment explanation
Indices: 6244037--6244106 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
6244027 AGCTCACAAC
*
6244037 ATTTAAATAAA--TAACTTA-AT
1 ATTTAAATAAATTTAATTTATAT
6244057 -TTTAAATAAATTTAATTTATAT
1 ATTTAAATAAATTTAATTTATAT
* *
6244079 ATTTAATTATAATTT-TTTTATAT
1 ATTTAAATA-AATTTAATTTATAT
*
6244102 TTTTA
1 ATTTA
6244107 TACGAAATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.24
21 6 0.15
22 2 0.05
23 18 0.44
24 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAATTTAATTTATAT
Found at i:6247399 original size:2 final size:2
Alignment explanation
Indices: 6247386--6247431 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
6247376 ATCGATTATC
*
6247386 AT AT AA AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6247427 AT AT A
1 AT AT A
6247432 AAGAGATGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6250052 original size:15 final size:16
Alignment explanation
Indices: 6250026--6250055 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6250016 GTTTTGGTGG
6250026 AGGTGAGGGTGGAGAA
1 AGGTGAGGGTGGAGAA
6250042 AGGTG-GGGTGGAGA
1 AGGTGAGGGTGGAGA
6250056 TTGAGGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.60, T:0.13
Consensus pattern (16 bp):
AGGTGAGGGTGGAGAA
Found at i:6263384 original size:21 final size:21
Alignment explanation
Indices: 6263360--6263456 Score: 59
Period size: 23 Copynumber: 4.1 Consensus size: 21
6263350 ATTTAAAAAA
6263360 ATAAATTATTTATATTATTAT
1 ATAAATTATTTATATTATTAT
*
6263381 ATAAAAATTATTGTATATTATATAGC
1 AT--AAATTATT-TATATTAT-TA-T
6263407 ATAAATTATATGTTATATTTATTAT
1 ATAAA-T-TAT-TTATA-TTATTAT
* * *
6263432 ATTACATAATTTTAAATTATTAT
1 A-TAAATTA-TTTATATTATTAT
6263455 AT
1 AT
6263457 GAATGCATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
21 2 0.03
22 1 0.02
23 16 0.27
24 16 0.27
25 6 0.10
26 14 0.23
27 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (21 bp):
ATAAATTATTTATATTATTAT
Found at i:6263410 original size:26 final size:23
Alignment explanation
Indices: 6263362--6263411 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
6263352 TTAAAAAAAT
*
6263362 AAATTATTTATATTATTATATAA
1 AAATTATTTATATTATTACATAA
6263385 AAATTATTGTATATTATATAGCATAA
1 AAATTATT-TATATTAT-TA-CATAA
6263411 A
1 A
6263412 TTATATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 8 0.35
25 2 0.09
26 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATTATTTATATTATTACATAA
Found at i:6263634 original size:29 final size:29
Alignment explanation
Indices: 6263580--6263635 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
6263570 TACTTAACTT
* *
6263580 TTTAATTTTACTCAAATAAGCTCTTAACC
1 TTTAATTTTACTCAAAAAAACTCTTAACC
*
6263609 TTTAATTTTTACTTAAAAAAAC-CTTAA
1 TTTAA-TTTTACTCAAAAAAACTCTTAA
6263636 ATTAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTAATTTTACTCAAAAAAACTCTTAACC
Found at i:6263738 original size:29 final size:29
Alignment explanation
Indices: 6263697--6263762 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
6263687 GATGAGTTTT
* *
6263697 TTTAGATATAATCAAAGTATAGGAACTTA
1 TTTAAATACAATCAAAGTATAGGAACTTA
*
6263726 TTTAAATACAATCAAAGTATAGGAATTTA
1 TTTAAATACAATCAAAGTATAGGAACTTA
*
6263755 CTTAAATA
1 TTTAAATA
6263763 AAATTGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (29 bp):
TTTAAATACAATCAAAGTATAGGAACTTA
Found at i:6264955 original size:16 final size:15
Alignment explanation
Indices: 6264902--6264956 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
6264892 TAATTTAATA
*
6264902 TAATTTTATAATCAT
1 TAATTTTATAATTAT
6264917 T-ATTTTATAATT-T
1 TAATTTTATAATTAT
6264930 TAATTTTTTATAATTAT
1 TAA--TTTTATAATTAT
6264947 TAATATTTAT
1 TAAT-TTTAT
6264957 TTTAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 2 0.06
14 11 0.32
15 2 0.06
16 15 0.44
17 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTTATAATTAT
Found at i:6265507 original size:17 final size:17
Alignment explanation
Indices: 6265480--6265513 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6265470 TATATTAAAA
6265480 TAAATTTATTTAATAATT
1 TAAATTTATTTAA-AATT
6265498 TAAA-TTATTTAAAATT
1 TAAATTTATTTAAAATT
6265514 ATTAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTATTTAAAATT
Found at i:6265518 original size:18 final size:18
Alignment explanation
Indices: 6265461--6265513 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
6265451 TTTTAAACTA
* * *
6265461 TTAAATTTATATATTAAA
1 TTAAATTTATTTAATAAT
*
6265479 ATAAATTTATTTAATAAT
1 TTAAATTTATTTAATAAT
6265497 TTAAA-TTATTTAA-AAT
1 TTAAATTTATTTAATAAT
6265513 T
1 T
6265514 ATTAATCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
18 18 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAATTTATTTAATAAT
Found at i:6268627 original size:2 final size:2
Alignment explanation
Indices: 6268620--6268652 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6268610 GCAGTGGTAG
6268620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6268653 GCTTGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6268934 original size:3 final size:3
Alignment explanation
Indices: 6268926--6268967 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
6268916 TATAGAATGG
*
6268926 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6268968 AGAAGACTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6269748 original size:29 final size:30
Alignment explanation
Indices: 6269684--6269752 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
6269674 TTATTTTTAT
* * *
6269684 TATTT-ATAATTAAATTAAATACAAATATT
1 TATTTAATAATTAAATTAAATAAAAAAATA
* *
6269713 TTTTTAATTATTAAATT-AATAAAAAAATA
1 TATTTAATAATTAAATTAAATAAAAAAATA
6269742 TATTTAA-AATT
1 TATTTAATAATT
6269753 TGTTTTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 3 0.09
29 19 0.59
30 10 0.31
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
TATTTAATAATTAAATTAAATAAAAAAATA
Found at i:6269898 original size:22 final size:22
Alignment explanation
Indices: 6269873--6269924 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
6269863 TAGACATTTG
*
6269873 TTTTATATATATTTGAATT-TTA
1 TTTTAT-TATATTTAAATTATTA
*
6269895 TTTTATTTTATTTAAATTATTA
1 TTTTATTATATTTAAATTATTA
*
6269917 TTTAATTA
1 TTTTATTA
6269925 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTATTATATTTAAATTATTA
Found at i:6269929 original size:19 final size:18
Alignment explanation
Indices: 6269907--6269951 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
6269897 TTATTTTATT
* *
6269907 TAAATTATTATTTAATTAA
1 TAAAATATT-TTTAAATAA
6269926 TAAAAATATTTTTAAATAA
1 T-AAAATATTTTTAAATAA
6269945 TAAAATA
1 TAAAATA
6269952 AATTTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATTTTTAAATAA
Found at i:6269961 original size:20 final size:19
Alignment explanation
Indices: 6269923--6269962 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
6269913 ATTATTTAAT
* *
6269923 TAATAAAAATATTTTTAAA
1 TAATAAAAAAATTTATAAA
6269942 TAATAAAATAAATTTATAAA
1 TAATAAAA-AAATTTATAAA
6269962 T
1 T
6269963 CAAATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAAAAAAATTTATAAA
Found at i:6270884 original size:26 final size:25
Alignment explanation
Indices: 6270855--6270916 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
6270845 TACAATAAGT
* * *
6270855 AAAAATTTATCTAAAGTAATTGGATA
1 AAAAATTTAACCAAA-TAATTAGATA
*
6270881 AAAAATTTTAACCGAATAATTAGATA
1 AAAAA-TTTAACCAAATAATTAGATA
6270907 AAAAATTTAA
1 AAAAATTTAA
6270917 AAAATATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 5 0.16
26 19 0.61
27 7 0.23
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (25 bp):
AAAAATTTAACCAAATAATTAGATA
Found at i:6275558 original size:42 final size:42
Alignment explanation
Indices: 6275506--6275599 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
6275496 TTTGGTTGTT
* * * * *
6275506 AATAATGATTGAATAGTAATAAATTAAGTATGCTAAGAAGTC
1 AATATTGATTGAATAATAATAAATTAAGGATGCTAAAAAGCC
*
6275548 AATATTGATTGAATAATAATAAATTAAGGATGTTAAAAAGCC
1 AATATTGATTGAATAATAATAAATTAAGGATGCTAAAAAGCC
*
6275590 ACTATTGATT
1 AATATTGATT
6275600 CAAAATTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (42 bp):
AATATTGATTGAATAATAATAAATTAAGGATGCTAAAAAGCC
Found at i:6284489 original size:3 final size:3
Alignment explanation
Indices: 6284481--6284520 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
6284471 CAGTTCGTCT
*
6284481 TTC TTC TTC TTC TTC TTC GTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6284521 CTGTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:6288201 original size:16 final size:16
Alignment explanation
Indices: 6288182--6288237 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
6288172 TTTGTTTCGT
6288182 TAAATAGTTATTTCAC
1 TAAATAGTTATTTCAC
* *
6288198 TAAATAGTTTGTTTC-T
1 TAAATAG-TTATTTCAC
6288214 TAAATAGTTATTTCAC
1 TAAATAGTTATTTCAC
6288230 TAAATAGT
1 TAAATAGT
6288238 CGATTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 22 0.65
17 6 0.18
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (16 bp):
TAAATAGTTATTTCAC
Found at i:6288220 original size:32 final size:33
Alignment explanation
Indices: 6288172--6288237 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
6288162 TGTGACGTCA
6288172 TTTGTTTCGTTAAATAGTTATTTCACTAAATAG
1 TTTGTTTCGTTAAATAGTTATTTCACTAAATAG
6288205 TTTGTTTC-TTAAATAGTTATTTCACTAAATAG
1 TTTGTTTCGTTAAATAGTTATTTCACTAAATAG
6288237 T
1 T
6288238 CGATTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (33 bp):
TTTGTTTCGTTAAATAGTTATTTCACTAAATAG
Found at i:6290515 original size:21 final size:19
Alignment explanation
Indices: 6290491--6290544 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
6290481 TACTTATATT
*
6290491 TATATTTAATATATATTTAAA
1 TATATATAA-ATAT-TTTAAA
6290512 TATAAATATAAATATTTTAAA
1 TAT--ATATAAATATTTTAAA
6290533 TATATATAAATA
1 TATATATAAATA
6290545 AATAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.30
21 12 0.40
22 4 0.13
23 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATATAAATATTTTAAA
Found at i:6290536 original size:31 final size:33
Alignment explanation
Indices: 6290495--6290560 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
6290485 TATATTTATA
* *
6290495 TTTAATATATATTTAAAT-ATAAATATAAATAT
1 TTTAATATATATATAAATAATAAATAAAAATAT
6290527 TTTAA-ATATATATAAATAAATAAATAAAAATAT
1 TTTAATATATATATAAAT-AATAAATAAAAATAT
6290560 T
1 T
6290561 CACAGTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 11 0.37
32 5 0.17
33 14 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TTTAATATATATATAAATAATAAATAAAAATAT
Found at i:6295848 original size:19 final size:19
Alignment explanation
Indices: 6295824--6295862 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6295814 TAGTCTAACC
6295824 TATATTATTTTTAAT-TTTA
1 TATATT-TTTTTAATATTTA
6295843 TATATTTTTTTAATATTTA
1 TATATTTTTTTAATATTTA
6295862 T
1 T
6295863 GTTTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATATTTTTTTAATATTTA
Found at i:6297302 original size:3 final size:3
Alignment explanation
Indices: 6297294--6297324 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6297284 CTGGTCTTAC
6297294 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6297325 TGTTGAACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6299622 original size:21 final size:20
Alignment explanation
Indices: 6299598--6299636 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6299588 ATAATATATC
6299598 TAATACATAATATTTTAAATT
1 TAAT-CATAATATTTTAAATT
* *
6299619 TAATTATAATTTTTTAAA
1 TAATCATAATATTTTAAA
6299637 AAATATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATCATAATATTTTAAATT
Found at i:6300916 original size:21 final size:20
Alignment explanation
Indices: 6300885--6300926 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6300875 ATAATAAAAA
* *
6300885 ATATATTTATATTTATATTT
1 ATATATTTATAATTAAATTT
6300905 ATATATTTTATAATTAAATTT
1 ATATA-TTTATAATTAAATTT
6300926 A
1 A
6300927 AATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTTATAATTAAATTT
Found at i:6302820 original size:17 final size:17
Alignment explanation
Indices: 6302798--6302831 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6302788 AAAAAAAATT
6302798 GAAGTCATCACAATATC
1 GAAGTCATCACAATATC
6302815 GAAGTCATCACAATATC
1 GAAGTCATCACAATATC
6302832 ATAAACTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
GAAGTCATCACAATATC
Found at i:6303053 original size:20 final size:20
Alignment explanation
Indices: 6302998--6303053 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
6302988 GTTATAAAAA
* *
6302998 AATAAAAAATTTAGTAAATC
1 AATAAAAAATTAATTAAATC
* *
6303018 AATAAAAAATCAAATTAAATT
1 AATAAAAAAT-TAATTAAATC
6303039 AATAAAAAATTAATT
1 AATAAAAAATTAATT
6303054 TTATATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAAAAATTAATTAAATC
Found at i:6305557 original size:2 final size:2
Alignment explanation
Indices: 6305550--6305604 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
6305540 GAAATTGATG
*
6305550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
6305592 AC AT AC AT AT AT A
1 AT AT AT AT AT AT A
6305605 GGACACGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6306316 original size:2 final size:2
Alignment explanation
Indices: 6306309--6306343 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6306299 TCTTTGTATT
6306309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6306344 GTATTTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6308243 original size:15 final size:15
Alignment explanation
Indices: 6308183--6308245 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
6308173 ATATTTTTAG
*
6308183 TATATATT-AGATATA
1 TATATATTAAAAT-TA
* * *
6308198 TATGTACTAAAATCA
1 TATATATTAAAATTA
6308213 TATATATTGAATAATTA
1 TATATATT-AA-AATTA
6308230 TATATATTAAAATTA
1 TATATATTAAAATTA
6308245 T
1 T
6308246 GTTAAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
15 19 0.50
16 7 0.18
17 12 0.32
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (15 bp):
TATATATTAAAATTA
Found at i:6309483 original size:9 final size:10
Alignment explanation
Indices: 6309459--6309496 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
6309449 AAATAAAATT
* *
6309459 ATTTTTATTT
1 ATTTTTAATA
6309469 ATTTTTAATA
1 ATTTTTAATA
6309479 ATTTTTAATA
1 ATTTTTAATA
6309489 ATTTTTAA
1 ATTTTTAA
6309497 CAAGATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:6310149 original size:17 final size:18
Alignment explanation
Indices: 6310129--6310171 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
6310119 ATTGGTATCC
6310129 TATTATTATTATTAA-AA
1 TATTATTATTATTAATAA
*
6310146 TATTATTATTTTTAATAA
1 TATTATTATTATTAATAA
6310164 TATTATTA
1 TATTATTA
6310172 AGGTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTATTATTAATAA
Found at i:6310622 original size:31 final size:30
Alignment explanation
Indices: 6310555--6310615 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
6310545 AAATTAAAAT
* *
6310555 TTTAAAATAATTAGATGATTATAACCCTTAA
1 TTTAAAATAA-TAGATGATTACAACCATTAA
*
6310586 TTTAAAATAA-AGATGATTACAATCATTAA
1 TTTAAAATAATAGATGATTACAACCATTAA
6310615 T
1 T
6310616 AATTAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTAAAATAATAGATGATTACAACCATTAA
Found at i:6310747 original size:14 final size:13
Alignment explanation
Indices: 6310705--6310748 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
6310695 ATTGTAACTA
6310705 AAATTAAAATTTT
1 AAATTAAAATTTT
**
6310718 AAATTAAACAAATT
1 AAATTAAA-ATTTT
6310732 AAATTAAATATTTT
1 AAATTAAA-ATTTT
6310746 AAA
1 AAA
6310749 ATAATAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:6310975 original size:40 final size:39
Alignment explanation
Indices: 6310899--6310971 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
6310889 AATATTAACA
6310899 TAATAATATAATTAAAAAATATGAACATAATAATAACTT
1 TAATAATATAATTAAAAAATATGAACATAATAATAACTT
* *
6310938 TAATAATATTATTAAAAAAT-T-AACATTATAATAA
1 TAATAATATAATTAAAAAATATGAACATAATAATAA
6310972 TAACAGTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 12 0.38
38 1 0.03
39 19 0.59
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (39 bp):
TAATAATATAATTAAAAAATATGAACATAATAATAACTT
Found at i:6312281 original size:15 final size:15
Alignment explanation
Indices: 6312257--6312292 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6312247 ATTGCCTGGT
*
6312257 GGTGGTGGAGGTGGA
1 GGTGGAGGAGGTGGA
*
6312272 GGTGGAGGAGGTGGC
1 GGTGGAGGAGGTGGA
6312287 GGTGGA
1 GGTGGA
6312293 AATGAAGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.03, G:0.67, T:0.17
Consensus pattern (15 bp):
GGTGGAGGAGGTGGA
Found at i:6313903 original size:15 final size:15
Alignment explanation
Indices: 6313883--6313915 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6313873 AGAAACCTAC
6313883 TTTGTTTTT-TTGTTT
1 TTTGTTTTTGTT-TTT
6313898 TTTGTTTTTGTTTTT
1 TTTGTTTTTGTTTTT
6313913 TTT
1 TTT
6313916 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTGTTTTTGTTTTT
Found at i:6313907 original size:13 final size:13
Alignment explanation
Indices: 6313889--6313913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6313879 CTACTTTGTT
6313889 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
6313902 TTTTTGTTTTTT
1 TTTTTGTTTTTT
6313914 TTTAAAAAAT
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:6315961 original size:2 final size:2
Alignment explanation
Indices: 6315954--6315999 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6315944 TGATTCGATC
6315954 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
6315996 TA TA
1 TA TA
6316000 ATTATTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6322782 original size:2 final size:2
Alignment explanation
Indices: 6322775--6322801 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6322765 AATCACATTT
6322775 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6322802 ATGACCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6323165 original size:11 final size:11
Alignment explanation
Indices: 6323149--6323173 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6323139 GTAGCCAGCC
6323149 GTTGGAGAAAA
1 GTTGGAGAAAA
6323160 GTTGGAGAAAA
1 GTTGGAGAAAA
6323171 GTT
1 GTT
6323174 AGGTTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (11 bp):
GTTGGAGAAAA
Found at i:6323501 original size:16 final size:17
Alignment explanation
Indices: 6323476--6323518 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
6323466 ACATAAATAA
* *
6323476 ATATTTTAAA-ATTTAT
1 ATATTATAAATATTAAT
6323492 ATATTATAAATTATTAAT
1 ATATTATAAA-TATTAAT
6323510 ATATTATAA
1 ATATTATAA
6323519 TTATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATAAATATTAAT
Found at i:6325870 original size:31 final size:33
Alignment explanation
Indices: 6325807--6325871 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
6325797 TTTAAATATA
* * *
6325807 AATATAAAAAAATTTTAAATTATTAAATTATTT
1 AATATAAAAAAATTTAAAATTATAAAAATATTT
6325840 AATAT-AAAAAATTTAAAATT-TAAAAATATTT
1 AATATAAAAAAATTTAAAATTATAAAAATATTT
6325871 A
1 A
6325872 TATCAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 10 0.34
32 14 0.48
33 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATAAAAAAATTTAAAATTATAAAAATATTT
Found at i:6326797 original size:18 final size:17
Alignment explanation
Indices: 6326768--6326806 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6326758 TTAAAAAATC
6326768 TAATTTTTATTAATT-TT
1 TAATTTTTATT-ATTATT
6326785 TAATTTATTATTATTATT
1 TAATTT-TTATTATTATT
6326803 TAAT
1 TAAT
6326807 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTATTATTATT
Found at i:6327797 original size:2 final size:2
Alignment explanation
Indices: 6327790--6327818 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6327780 TGAACATGAA
6327790 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6327819 TTTGGAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6328708 original size:78 final size:83
Alignment explanation
Indices: 6328556--6328717 Score: 217
Period size: 78 Copynumber: 2.0 Consensus size: 83
6328546 TTAATAGTAA
* * * * *
6328556 TAAATTTTAATAGTAATTATTTTTTATAAAAAAATTAAATTTATCTTTTTGAAGTATTTAAAGTA
1 TAAATTTTAATAGTAATTAATTTTTATAAAAAAATCAAATTTATC--TTTAAAATATGTAAAGTA
6328621 ATTTTAAATTAGATATCATT
64 ATTTTAAATTAGATATCATT
6328641 TAAA-TTTAATAGT-ATTAATTTTTATAAAAAAATCAAA-TT-TC-TTAAAATATGTAAAGTAAT
1 TAAATTTTAATAGTAATTAATTTTTATAAAAAAATCAAATTTATCTTTAAAATATGTAAAGTAAT
*
6328701 TTTAAATTATATATCAT
66 TTTAAATTAGATATCAT
6328718 GAATAATTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
78 32 0.45
81 2 0.03
82 2 0.03
83 22 0.31
84 9 0.13
85 4 0.06
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (83 bp):
TAAATTTTAATAGTAATTAATTTTTATAAAAAAATCAAATTTATCTTTAAAATATGTAAAGTAAT
TTTAAATTAGATATCATT
Found at i:6330122 original size:35 final size:36
Alignment explanation
Indices: 6330055--6330129 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
6330045 TTATAAATAT
**
6330055 TAAAAAATATATTAAATTATTTTTATTAAAATTTAA
1 TAAAAAATATATTAAATTATTACTATTAAAATTTAA
*
6330091 TAAAAAA-ATTTTAAATTATTAACTATT-AAATTTAA
1 TAAAAAATATATTAAATTATT-ACTATTAAAATTTAA
6330126 -AAAA
1 TAAAA
6330130 TATTTACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 4 0.11
35 20 0.57
36 11 0.31
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
TAAAAAATATATTAAATTATTACTATTAAAATTTAA
Found at i:6334792 original size:12 final size:12
Alignment explanation
Indices: 6334775--6334813 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
6334765 TTAAAATATT
6334775 ATTTTATATTAA
1 ATTTTATATTAA
6334787 ATTTTATA-T-A
1 ATTTTATATTAA
6334797 ATTTTATAATTAA
1 ATTTTAT-ATTAA
6334810 ATTT
1 ATTT
6334814 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 9 0.38
13 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTATATTAA
Found at i:6334800 original size:22 final size:23
Alignment explanation
Indices: 6334770--6334813 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
6334760 TATTATTAAA
*
6334770 ATATTATTTTAT-ATTAAATTTT
1 ATATAATTTTATAATTAAATTTT
6334792 ATATAATTTTATAATTAAATTT
1 ATATAATTTTATAATTAAATTT
6334814 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATAATTTTATAATTAAATTTT
Found at i:6334819 original size:22 final size:22
Alignment explanation
Indices: 6334775--6334819 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6334765 TTAAAATATT
*
6334775 ATTTTATATTAAATTTTATATA
1 ATTTTATATTAAATTTTAAATA
6334797 ATTTTATAATTAAA-TTTAAATA
1 ATTTTAT-ATTAAATTTTAAATA
6334819 A
1 A
6334820 AAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTATATTAAATTTTAAATA
Found at i:6335335 original size:21 final size:21
Alignment explanation
Indices: 6335311--6335362 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6335301 TTATTAAAAA
6335311 TTAT-TTAAAATTAAATTAATT
1 TTATATTAAAATTAAA-TAATT
*
6335332 TTATATTAAAATTTAATAATT
1 TTATATTAAAATTAAATAATT
* *
6335353 TAAAATTAAA
1 TTATATTAAA
6335363 TAAATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATTAAAATTAAATAATT
Found at i:6335357 original size:15 final size:15
Alignment explanation
Indices: 6335336--6335380 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
6335326 TTAATTTTAT
*
6335336 ATTAAAATTTAATAA
1 ATTAAAATTAAATAA
*
6335351 TTTAAAATTAAATAA
1 ATTAAAATTAAATAA
6335366 ATT-AAATATAAATAA
1 ATTAAAAT-TAAATAA
6335381 TTTTAATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATTAAATAA
Found at i:6335850 original size:48 final size:49
Alignment explanation
Indices: 6335759--6335851 Score: 129
Period size: 48 Copynumber: 1.9 Consensus size: 49
6335749 AATAATTTTT
*
6335759 AATTTATATATATATTATAATTATATGTAAAATATTTTATATTTATATA
1 AATTTATATATATATTATAATTATATGTAAAATATATTATATTTATATA
*
6335808 AATTT-TAT-TATATTAATAATT-TATGTAAATTAATATTATATTTA
1 AATTTATATATATATT-ATAATTATATGTAAAAT-ATATTATATTTA
6335852 ATTATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 15 0.38
48 20 0.50
49 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (49 bp):
AATTTATATATATATTATAATTATATGTAAAATATATTATATTTATATA
Found at i:6335865 original size:28 final size:28
Alignment explanation
Indices: 6335790--6335876 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 28
6335780 TATATGTAAA
* * *
6335790 ATATTTTAT-ATTTATATAAATTTTATT
1 ATATTTAATAATTTATGTAAATTATATT
6335817 ATA-TTAATAATTTATGTAAATTAATATT
1 ATATTTAATAATTTATGTAAATT-ATATT
*
6335845 ATATTTAATTATTT-T-TAAAATTATATTT
1 ATATTTAATAATTTATGT-AAATTATA-TT
6335873 ATAT
1 ATAT
6335877 AAATGTGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.08
27 19 0.37
28 19 0.37
29 9 0.18
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATATTTAATAATTTATGTAAATTATATT
Found at i:6336023 original size:4 final size:4
Alignment explanation
Indices: 6336014--6336047 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
6336004 ATCCTCCCTA
6336014 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
6336048 TTTGAGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:6336636 original size:20 final size:20
Alignment explanation
Indices: 6336611--6336655 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
6336601 TTTTATGCTC
6336611 TAAAAGCATAAATAATGAAA
1 TAAAAGCATAAATAATGAAA
*
6336631 TAAAAGCATAAATAATTAAA
1 TAAAAGCATAAATAATGAAA
6336651 TAAAA
1 TAAAA
6336656 AAAAAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (20 bp):
TAAAAGCATAAATAATGAAA
Found at i:6339970 original size:204 final size:204
Alignment explanation
Indices: 6339620--6340031 Score: 718
Period size: 204 Copynumber: 2.0 Consensus size: 204
6339610 AAGGACAGCT
*
6339620 CACATGGGAACACTACCAAACATGCACCACATGCCCATGAAACTGAAGTGAATATGCCCACTGTC
1 CACATGGGAACACTACCAAACATGCACCACATACCCATGAAACTGAAGTGAATATGCCCACTGTC
* * *
6339685 AAGGAAAGTGGTAATGGACCAAATGTTCCCACTAAGGAAAATGGTTCAACACAGGAACCTTCAAC
66 AAGGAAAGTGGCAATGGACCAAATGTTCCCACTAAAGAAAATGGCTCAACACAGGAACCTTCAAC
*
6339750 TTCAGTGAGACCAAGAAGGTCTCAAGGCATCCAACAAAATAGAGAATATGTCTCCGAGAGGTTGA
131 TTCAGTGAGACCAAGAAGGTCTCAAGGCATCCAACAAAATAGAGAAGATGTCTCCGAGAGGTTGA
6339815 ATATTCCAA
196 ATATTCCAA
* *
6339824 CACATGGGAACACTACCAAACATGCACCACATACCCATGACAA-TGAAGTGACTATGCCTACTGT
1 CACATGGGAACACTACCAAACATGCACCACATACCCATGA-AACTGAAGTGAATATGCCCACTGT
*
6339888 CAAGGAAAGTGGCAATGGACCAAATGTTCCCAGTAAAGAAAATGGCTCAACACAGGAACCTTCAA
65 CAAGGAAAGTGGCAATGGACCAAATGTTCCCACTAAAGAAAATGGCTCAACACAGGAACCTTCAA
*
6339953 CTTCAGTGAGACCAAGAAGGTCTCAAGGCATCCAACAAAATAGAGAAGCTGTCTCCGAGAGGTTG
130 CTTCAGTGAGACCAAGAAGGTCTCAAGGCATCCAACAAAATAGAGAAGATGTCTCCGAGAGGTTG
*
6340018 AATATTCCAG
195 AATATTCCAA
6340028 CACA
1 CACA
6340032 AGCTGTGGTT
Statistics
Matches: 197, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
204 195 0.99
205 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (204 bp):
CACATGGGAACACTACCAAACATGCACCACATACCCATGAAACTGAAGTGAATATGCCCACTGTC
AAGGAAAGTGGCAATGGACCAAATGTTCCCACTAAAGAAAATGGCTCAACACAGGAACCTTCAAC
TTCAGTGAGACCAAGAAGGTCTCAAGGCATCCAACAAAATAGAGAAGATGTCTCCGAGAGGTTGA
ATATTCCAA
Found at i:6340499 original size:2 final size:2
Alignment explanation
Indices: 6340492--6340532 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6340482 TATCTGTTTC
6340492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6340533 TATTTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6342652 original size:80 final size:80
Alignment explanation
Indices: 6342519--6342673 Score: 258
Period size: 80 Copynumber: 1.9 Consensus size: 80
6342509 CAGTTGTGAA
* * *
6342519 CCGAAAATGAATTCATAATCATAATTTAAATTTTGATGAGTTCATAATTGCAATTTAAATTCTGA
1 CCGAAAATGAATTCATAATCACAATTTAAATTCTGATGAGTTCATAATTGCAATTTAAATTCTAA
6342584 CTAATCATGAAGACC
66 CTAATCATGAAGACC
*
6342599 CCGAAAATGAATTCATAA-CTACAATTTAAATTCTGATTAGTTCATAATTGCAATTTAAATTCTA
1 CCGAAAATGAATTCATAATC-ACAATTTAAATTCTGATGAGTTCATAATTGCAATTTAAATTCTA
6342663 ACTAATCATGA
65 ACTAATCATGA
6342674 TGGAGATTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 1 0.01
80 69 0.99
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (80 bp):
CCGAAAATGAATTCATAATCACAATTTAAATTCTGATGAGTTCATAATTGCAATTTAAATTCTAA
CTAATCATGAAGACC
Found at i:6343784 original size:12 final size:12
Alignment explanation
Indices: 6343767--6343796 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6343757 AGAGGTTTCT
6343767 TAATTATTATTA
1 TAATTATTATTA
6343779 TAATTATTATTA
1 TAATTATTATTA
*
6343791 TTATTA
1 TAATTA
6343797 ATGATCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATTATTATTA
Found at i:6344116 original size:16 final size:17
Alignment explanation
Indices: 6344091--6344130 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
6344081 AAATTATAAA
6344091 AAATAATAAAT-AATTT
1 AAATAATAAATAAATTT
*
6344107 AAATATTAAATAAATTT
1 AAATAATAAATAAATTT
6344124 AAATAAT
1 AAATAAT
6344131 TTTAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAAATAAATTT
Found at i:6345714 original size:27 final size:26
Alignment explanation
Indices: 6345684--6345738 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
6345674 AAATAAGTTT
*
6345684 ATATTTATATTAAATAATAAAATAAAA
1 ATATATATATTAAATAAT-AAATAAAA
* *
6345711 ATATATATGTTAAATAATAATTAAAA
1 ATATATATATTAAATAATAAATAAAA
6345737 AT
1 AT
6345739 TATTCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATATATATATTAAATAATAAATAAAA
Found at i:6346618 original size:89 final size:91
Alignment explanation
Indices: 6346438--6346622 Score: 211
Period size: 89 Copynumber: 2.0 Consensus size: 91
6346428 TGAATAATTA
* * *
6346438 AAATTATTAAATTTAAATTTATATTAAATAATAAAATATAAATAAATTATTTTTATTTTGAATAA
1 AAATTATTAAATTTAAATTTATATTAAATAATAAAATATAAATAAATTATATTTATGTTAAATAA
*
6346503 TATTTATTCAATAATTTATATTAAAAAT
66 TA--TATTAAATAATTTATATTAAAAAT
* *
6346531 AAATTATTATAA-TTATATTTATATT-AAT-AT-ATATATAAA-AAATTATATTTATGTTAAATA
1 AAATTATTA-AATTTAAATTTATATTAAATAATAAAATATAAATAAATTATATTTATGTTAAATA
*
6346591 ATA-ATTAAATATTATTTATGTTAAAAAAT
65 ATATATTAAATA--ATTTATATT-AAAAAT
6346620 AAA
1 AAA
6346623 ATAAATAATT
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
86 7 0.09
88 8 0.10
89 30 0.37
90 8 0.10
91 2 0.02
92 3 0.04
93 21 0.26
94 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (91 bp):
AAATTATTAAATTTAAATTTATATTAAATAATAAAATATAAATAAATTATATTTATGTTAAATAA
TATATTAAATAATTTATATTAAAAAT
Found at i:6349376 original size:6 final size:6
Alignment explanation
Indices: 6349367--6349412 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
6349357 TTTTTTAAAA
6349367 ATATTT ATATTT GATATTT ATATTT AATATTT ATATATGT ATATTT
1 ATATTT ATATTT -ATATTT ATATTT -ATATTT ATAT-T-T ATATTT
6349413 TAAATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 17 0.47
7 14 0.39
8 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (6 bp):
ATATTT
Found at i:6349385 original size:13 final size:13
Alignment explanation
Indices: 6349367--6349412 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
6349357 TTTTTTAAAA
6349367 ATATTTATATTTG
1 ATATTTATATTTG
*
6349380 ATATTTATATTTA
1 ATATTTATATTTG
*
6349393 ATATTTATATATG
1 ATATTTATATTTG
6349406 TATATTT
1 -ATATTT
6349413 TAAATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:6352014 original size:2 final size:2
Alignment explanation
Indices: 6352009--6352036 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6351999 TTAGACACAC
6352009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6352037 TGAAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6352454 original size:13 final size:13
Alignment explanation
Indices: 6352428--6352461 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6352418 AAGGGATATA
*
6352428 AGAGAGGATGCTTG
1 AGAG-GGATACTTG
6352442 AGAGGGATACTTG
1 AGAGGGATACTTG
6352455 AGAGGGA
1 AGAGGGA
6352462 GGAGGGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.32, C:0.06, G:0.44, T:0.18
Consensus pattern (13 bp):
AGAGGGATACTTG
Found at i:6356436 original size:13 final size:13
Alignment explanation
Indices: 6356404--6356448 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6356394 AAAGAATTGA
**
6356404 AGAGGGATACAAG
1 AGAGGGATACTTG
*
6356417 AGA-GGATGCTTG
1 AGAGGGATACTTG
6356429 AGAGGGATACTTG
1 AGAGGGATACTTG
6356442 AGAGGGA
1 AGAGGGA
6356449 GGAGGGAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.36, C:0.07, G:0.42, T:0.16
Consensus pattern (13 bp):
AGAGGGATACTTG
Found at i:6356735 original size:11 final size:12
Alignment explanation
Indices: 6356719--6356747 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6356709 ACAATTTTAA
6356719 AAAATAAAA-TT
1 AAAATAAAATTT
6356730 AAAATAAAATTT
1 AAAATAAAATTT
6356742 AAAATA
1 AAAATA
6356748 TTAATTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATAAAATTT
Found at i:6356742 original size:25 final size:24
Alignment explanation
Indices: 6356683--6356745 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
6356673 GATAGCATTT
6356683 AATAAAATTT-AAAAATAAAAATA
1 AATAAAATTTAAAAAATAAAAATA
** * *
6356706 TGTACAATTTTAAAAAATAAAATTAA
1 AATA-AAATTTAAAAAATAAAAAT-A
6356732 AATAAAATTTAAAA
1 AATAAAATTTAAAA
6356746 TATTAATTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 2 0.07
24 5 0.17
25 20 0.67
26 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAAAATTTAAAAAATAAAAATA
Found at i:6360577 original size:21 final size:21
Alignment explanation
Indices: 6360531--6360577 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
6360521 TCAAATATAT
6360531 TTAAATTATTATTTATTAACA
1 TTAAATTATTATTTATTAACA
*
6360552 ATAAA-TATTATTTTATTTAA-A
1 TTAAATTATTA-TTTA-TTAACA
6360573 TTAAA
1 TTAAA
6360578 ATATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATTATTATTTATTAACA
Found at i:6361406 original size:50 final size:50
Alignment explanation
Indices: 6361277--6361509 Score: 376
Period size: 50 Copynumber: 4.6 Consensus size: 50
6361267 ATGGCCACAT
* *
6361277 TTGTCAAAGGTTGGTGAAGAATCGTCAACAACAATGGCCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
6361327 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
6361378 TTGTCAAAGGTTGGTGAAGAATCATCAACAATAATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* * *
6361428 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGACCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
6361478 TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
6361510 GGCAACAACT
Statistics
Matches: 171, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 124 0.73
51 47 0.27
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
Found at i:6366017 original size:50 final size:50
Alignment explanation
Indices: 6365888--6366121 Score: 360
Period size: 50 Copynumber: 4.7 Consensus size: 50
6365878 ATGGCCACAT
*
6365888 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
6365938 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
6365989 TTGTCAAAGGTTGGTGAAGAATCATCAACAATAATGGTCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* * * *
6366039 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGACCACCTTTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* * *
6366089 TTGTCAAAGGTTAGTGAAGGATAGTCAACAATA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATA
6366122 GCAACAACTT
Statistics
Matches: 168, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 120 0.71
51 48 0.29
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
Found at i:6370700 original size:20 final size:20
Alignment explanation
Indices: 6370666--6370711 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6370656 AAGAATTGAA
*
6370666 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
** *
6370686 GAGGGATACTTGAGATGGAG
1 GAGGGATACAAGAGAGGGAG
6370706 GAGGGA
1 GAGGGA
6370712 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.48, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:6375259 original size:20 final size:20
Alignment explanation
Indices: 6375225--6375270 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6375215 AAGAATTGAA
*
6375225 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
** *
6375245 GAGGGATACTTGAGATGGAG
1 GAGGGATACAAGAGAGGGAG
6375265 GAGGGA
1 GAGGGA
6375271 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.48, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:6375915 original size:26 final size:26
Alignment explanation
Indices: 6375886--6375941 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
6375876 ATTTGTCTAG
*
6375886 AATCCCATAATAAA-TTAAACTTTATC
1 AATCCCA-AATAAAGTTAAACTTCATC
6375912 AATCCCAAATAAAGTTAAACTTCATC
1 AATCCCAAATAAAGTTAAACTTCATC
6375938 AATC
1 AATC
6375942 ATATCTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.30
Consensus pattern (26 bp):
AATCCCAAATAAAGTTAAACTTCATC
Found at i:6382414 original size:13 final size:13
Alignment explanation
Indices: 6382396--6382425 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6382386 ATATATATTT
6382396 TATGTATTCTTTA
1 TATGTATTCTTTA
*
6382409 TATGTATTTTTTA
1 TATGTATTCTTTA
6382422 TATG
1 TATG
6382426 AAGTTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.63
Consensus pattern (13 bp):
TATGTATTCTTTA
Found at i:6383020 original size:23 final size:24
Alignment explanation
Indices: 6382982--6383035 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 24
6382972 TGATTATTTT
6382982 TTAT-TTTAAAATAATAATAATAA
1 TTATATTTAAAATAATAATAATAA
6383005 TTATATTTAAAA-AATAATAATAA
1 TTATATTTAAAATAATAATAATAA
6383028 -TATATTTA
1 TTATATTTA
6383036 CACATCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.27
23 15 0.50
24 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTATATTTAAAATAATAATAATAA
Found at i:6383083 original size:29 final size:28
Alignment explanation
Indices: 6383051--6383117 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
6383041 CTTAAATTAA
*
6383051 AAATAATTAATAATAATTAA-ATATCATAT
1 AAATAATTAATAA-AAATAATA-ATCATAT
* *
6383080 AAATAATTTGATAAAAATAATAATTATAT
1 AAATAA-TTAATAAAAATAATAATCATAT
6383109 AAATAATTA
1 AAATAATTA
6383118 GAAAGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.06
29 23 0.72
30 7 0.22
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
AAATAATTAATAAAAATAATAATCATAT
Found at i:6385254 original size:18 final size:19
Alignment explanation
Indices: 6385233--6385278 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
6385223 TATTTGCGTG
*
6385233 ATTTATATTATTTT-AATT
1 ATTTATATTATTTTAAAGT
*
6385251 ATTT-TATTTTTTTTAAAGT
1 ATTTATA-TTATTTTAAAGT
6385270 ATTTATATT
1 ATTTATATT
6385279 TGACATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 10 0.43
19 9 0.39
20 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATATTATTTTAAAGT
Found at i:6387646 original size:2 final size:2
Alignment explanation
Indices: 6387639--6387671 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6387629 AATGATGCAA
6387639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6387672 ATGATGATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6388015 original size:2 final size:2
Alignment explanation
Indices: 6388008--6388049 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6387998 TGTTTATGAC
6388008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6388050 GATGGAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6389335 original size:16 final size:18
Alignment explanation
Indices: 6389314--6389353 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
6389304 TTAGTTACTA
6389314 TATATTTAT-TTAA-AAT
1 TATATTTATATTAAGAAT
6389330 TATA-TTATATTAAGAAT
1 TATATTTATATTAAGAAT
6389347 TA-ATTTA
1 TATATTTA
6389354 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATATTTATATTAAGAAT
Found at i:6391526 original size:31 final size:31
Alignment explanation
Indices: 6391488--6391554 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
6391478 AATCAAATTC
* *
6391488 ATTTGGCTAGTGGCTAGTAAATTCAATTTTG
1 ATTTGGCTAGCGGCTAGCAAATTCAATTTTG
* *
6391519 ATTTGGCTGGCGGTTAGCAAATTCAATTTTG
1 ATTTGGCTAGCGGCTAGCAAATTCAATTTTG
6391550 ATTTG
1 ATTTG
6391555 ACTGACAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (31 bp):
ATTTGGCTAGCGGCTAGCAAATTCAATTTTG
Found at i:6391622 original size:31 final size:31
Alignment explanation
Indices: 6391561--6391622 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
6391551 TTTGACTGAC
* * *
6391561 AGCTGACGGTTAAAAAATTCAATTTGGAATT
1 AGCTGACGGCTAAAAAATTCAATATCGAATT
*
6391592 AGCTGGCGGCTAAAAAATTTCAA-ATCGAATT
1 AGCTGACGGCTAAAAAA-TTCAATATCGAATT
6391623 CTATTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (31 bp):
AGCTGACGGCTAAAAAATTCAATATCGAATT
Found at i:6394819 original size:2 final size:2
Alignment explanation
Indices: 6394814--6394850 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6394804 TGTGTGTGAA
6394814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6394851 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6394855 original size:2 final size:2
Alignment explanation
Indices: 6394850--6394880 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6394840 ATATATATAT
6394850 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6394881 AACAGAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6398885 original size:13 final size:13
Alignment explanation
Indices: 6398867--6398891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6398857 ATTATATGTT
6398867 AAATATAAATATC
1 AAATATAAATATC
6398880 AAATATAAATAT
1 AAATATAAATAT
6398892 TTAAAAAAAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:6399717 original size:17 final size:18
Alignment explanation
Indices: 6399695--6399729 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6399685 GTCATACAGT
6399695 AATTTTT-ATTCTAAAAC
1 AATTTTTCATTCTAAAAC
6399712 AATTTTTCATTCTAAAAC
1 AATTTTTCATTCTAAAAC
6399730 GCAGACATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTTCATTCTAAAAC
Found at i:6405008 original size:17 final size:17
Alignment explanation
Indices: 6404986--6405018 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6404976 ACCTCATTTA
*
6404986 AAATTTATTTTAAAAAT
1 AAATTTAATTTAAAAAT
6405003 AAATTTAATTTAAAAA
1 AAATTTAATTTAAAAA
6405019 ATATATCTTT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAATTTAAAAAT
Found at i:6405013 original size:18 final size:17
Alignment explanation
Indices: 6404986--6405021 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6404976 ACCTCATTTA
*
6404986 AAATTTATTTTAAAAAT
1 AAATTTATTTAAAAAAT
6405003 AAATTTAATTTAAAAAAT
1 AAATTT-ATTTAAAAAAT
6405021 A
1 A
6405022 TATCTTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTATTTAAAAAAT
Found at i:6406340 original size:21 final size:21
Alignment explanation
Indices: 6406314--6406355 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6406304 CTAACCATAC
*
6406314 ATAAAGTTACCTTTATTAAGT
1 ATAAAGTTACCTTTACTAAGT
6406335 ATAAAGTTACCTTTACTAAGT
1 ATAAAGTTACCTTTACTAAGT
6406356 GCATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
ATAAAGTTACCTTTACTAAGT
Found at i:6411824 original size:30 final size:30
Alignment explanation
Indices: 6411788--6411898 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
6411778 ATTTTATTGC
*
6411788 ACTCAAATAAATTATTAATTTTTAATTTAT
1 ACTCAAATAAATTTTTAATTTTTAATTTAT
* * *
6411818 ACTCAAATAAATTTTTAACTATTAATTTGT
1 ACTCAAATAAATTTTTAATTTTTAATTTAT
** *
6411848 AC-CTAAATAAATTTTTAAACTTCAATTTAT
1 ACTC-AAATAAATTTTTAATTTTTAATTTAT
* * * *
6411878 ATTTAAATAAACTGTTAATTT
1 ACTCAAATAAATTTTTAATTT
6411899 AAATCAATCT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 1 0.02
30 63 0.98
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (30 bp):
ACTCAAATAAATTTTTAATTTTTAATTTAT
Found at i:6417354 original size:2 final size:2
Alignment explanation
Indices: 6417342--6417388 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
6417332 ATTAATAAAT
*
6417342 TA TA T- TA TA TA TA T- TA -A TA TA TT TA TA TCA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
6417382 TA TA TA T
1 TA TA TA T
6417389 TATTTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 34 0.87
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6417386 original size:25 final size:23
Alignment explanation
Indices: 6417330--6417389 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
6417320 AAATTTTAAA
* *
6417330 ATATTAATA-AATTATATTATAT
1 ATATTAATATATTTATATCATAT
6417352 ATATTAATATATTTATATCATAT
1 ATATTAATATATTTATATCATAT
6417375 ATATATATATATATT
1 ATAT-TA-ATATATT
6417390 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 9 0.27
23 15 0.45
24 2 0.06
25 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTAATATATTTATATCATAT
Found at i:6417840 original size:21 final size:21
Alignment explanation
Indices: 6417814--6417879 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
6417804 AAATATTTTA
6417814 AAATTATTAAAAATAAATATT
1 AAATTATTAAAAATAAATATT
* *
6417835 AAATTA-TATAAATATAATATAA
1 AAATTATTAAAAATA-AATAT-T
*
6417857 AAATAATTAAAAATAATATATT
1 AAATTATTAAAAATAA-ATATT
6417879 A
1 A
6417880 TAAATAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 7 0.19
23 11 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTATTAAAAATAAATATT
Found at i:6417871 original size:10 final size:10
Alignment explanation
Indices: 6417813--6417873 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 10
6417803 TAAATATTTT
*
6417813 AAAATTATTA
1 AAAATAATTA
*
6417823 AAAATAAATA
1 AAAATAATTA
* *
6417833 TTAAATTATATA
1 -AAAATAAT-TA
*
6417845 AATATAATATA
1 AAAATAAT-TA
6417856 AAAATAATTA
1 AAAATAATTA
6417866 AAAATAAT
1 AAAATAAT
6417874 ATATTATAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 18 0.45
11 20 0.50
12 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATAATTA
Found at i:6417896 original size:21 final size:20
Alignment explanation
Indices: 6417824--6417896 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 20
6417814 AAATTATTAA
* * *
6417824 AAATAAATATTAAATTATAT
1 AAATATATATTAAAATAAAT
* *
6417844 AAATATAATATAAAAATAATTAA
1 AAATAT-ATATTAAAATAA--AT
6417867 AAATAATATATTATAAATAAAT
1 AAAT-ATATATTA-AAATAAAT
6417889 AAATATAT
1 AAATATAT
6417897 TAAATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.12
21 13 0.32
22 5 0.12
23 10 0.24
24 8 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATATATTAAAATAAAT
Found at i:6417909 original size:33 final size:33
Alignment explanation
Indices: 6417821--6417917 Score: 94
Period size: 33 Copynumber: 3.0 Consensus size: 33
6417811 TTAAAATTAT
*
6417821 TAAAAATAAATATTAAATTATATA-AATAT-AATA
1 TAAAAAT--ATATTAAATTTTATATAATATAAATA
** * *
6417854 TAAAAATA-ATTAAAAATAATATATTATAAATA
1 TAAAAATATATTAAATTTTATATAATATAAATA
6417886 -AATAAATATATTAAATTTTATATAATATAAAT
1 TAA-AAATATATTAAATTTTATATAATATAAAT
6417918 TATTAATTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
30 9 0.18
31 7 0.14
32 9 0.18
33 26 0.51
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAATATATTAAATTTTATATAATATAAATA
Found at i:6417931 original size:25 final size:24
Alignment explanation
Indices: 6417883--6417936 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
6417873 TATATTATAA
6417883 ATAAATAAATATATTAAATTTTAT
1 ATAAATAAATATATTAAATTTTAT
*
6417907 ATAATATAAAT-TATTAATTTATTAT
1 ATAA-ATAAATATATTAAATT-TTAT
6417932 ATAAA
1 ATAAA
6417937 ATATCTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATAAATATATTAAATTTTAT
Found at i:6417966 original size:26 final size:22
Alignment explanation
Indices: 6417920--6417964 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
6417910 ATATAAATTA
6417920 TTAATTTATTATATAAAATATC
1 TTAATTTATTATATAAAATATC
6417942 TTAATTATATTATACTAAAATAT
1 TTAATT-TATTATA-TAAAATAT
6417965 ATAAATCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
24 8 0.38
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATTTATTATATAAAATATC
Found at i:6420970 original size:67 final size:66
Alignment explanation
Indices: 6420892--6421022 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
6420882 AATTATTATT
6420892 ATATCTAAATTTTTATAAATATAAAATATCTTAAATCACAATTATAAAAAAACGAAATACACGAA
1 ATATCTAAATTTTTATAAATATAAAATATCTT-AATCACAATTATAAAAAAACGAAATACACGAA
6420957 TC
65 TC
6420959 ATATCTAAATTTTTATAAATATAAAATATCTTAATCACAATTATAAAAAAACGAAATACACGAA
1 ATATCTAAATTTTTATAAATATAAAATATCTTAATCACAATTATAAAAAAACGAAATACACGAA
6421023 CAAGATAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
66 32 0.50
67 32 0.50
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.31
Consensus pattern (66 bp):
ATATCTAAATTTTTATAAATATAAAATATCTTAATCACAATTATAAAAAAACGAAATACACGAAT
C
Found at i:6423152 original size:20 final size:21
Alignment explanation
Indices: 6423118--6423158 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
6423108 AAAATGGTCA
6423118 TTATTATTTATTAAA-ATTTT
1 TTATTATTTATTAAATATTTT
6423138 TTATTATTT-TATAAATATTTT
1 TTATTATTTAT-TAAATATTTT
6423159 AATTTATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 13 0.68
21 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTATTTATTAAATATTTT
Found at i:6435039 original size:2 final size:2
Alignment explanation
Indices: 6435032--6435061 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6435022 TCAATTGTAC
6435032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6435062 TTTCTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6441182 original size:19 final size:18
Alignment explanation
Indices: 6441155--6441190 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6441145 ATTTTCTTTA
*
6441155 TATTTTTTTAATGTTATTT
1 TATTATTTTAAT-TTATTT
6441174 TATTATTTTAATTTATT
1 TATTATTTTAATTTATT
6441191 GAAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TATTATTTTAATTTATTT
Found at i:6442512 original size:23 final size:23
Alignment explanation
Indices: 6442480--6442549 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 23
6442470 TTGAAAAAGG
6442480 TTTTA-ATTTTAAAATAATTATA
1 TTTTATATTTTAAAATAATTATA
* *
6442502 TTTTATATTTTAAAATTAAATAATT
1 TTTTATATTTTAAAA-T-AATTATA
*
6442527 TTTTATTAATTTAATAATAATTA
1 TTTTA-TATTTTAA-AATAATTA
6442550 ATGTCGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.13
23 9 0.23
24 1 0.03
25 14 0.36
26 8 0.21
27 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATATTTTAAAATAATTATA
Found at i:6442785 original size:24 final size:24
Alignment explanation
Indices: 6442740--6442785 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6442730 TTATATGTAT
*
6442740 AATATTAATTATATTTAAATATAA
1 AATATTAATTATATTAAAATATAA
*
6442764 AATATTTATT-TATTAAAGATAT
1 AATATTAATTATATTAAA-ATAT
6442786 TTTATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATATTAATTATATTAAAATATAA
Found at i:6442787 original size:17 final size:17
Alignment explanation
Indices: 6442761--6442793 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6442751 TATTTAAATA
6442761 TAAAATA-TTTATTTAT
1 TAAAATATTTTATTTAT
6442777 TAAAGATATTTTATTTA
1 TAAA-ATATTTTATTTA
6442794 AATTACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 3 0.20
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TAAAATATTTTATTTAT
Found at i:6443607 original size:22 final size:21
Alignment explanation
Indices: 6443561--6443604 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
6443551 AATTTATTCA
6443561 TTAATTTTTAAAATATAATAT
1 TTAATTTTTAAAATATAATAT
*
6443582 TTAATATTTTAAAATTTAA-AT
1 TTAAT-TTTTAAAATATAATAT
6443603 TT
1 TT
6443605 TAACATACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATTTTTAAAATATAATAT
Found at i:6443866 original size:25 final size:25
Alignment explanation
Indices: 6443838--6443908 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
6443828 TAAATTTGAT
* *
6443838 AATTTTAAATATAATATGATAAAAA
1 AATTTAAAATATAATATAATAAAAA
*
6443863 AATTTAAAATATAATATAATATAAA
1 AATTTAAAATATAATATAATAAAAA
* *
6443888 AATAATATTAATATAATATAA
1 AAT-TTA-AAATATAATATAA
6443909 ATTATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 25 0.64
26 2 0.05
27 12 0.31
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (25 bp):
AATTTAAAATATAATATAATAAAAA
Found at i:6443880 original size:5 final size:5
Alignment explanation
Indices: 6443870--6443920 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
6443860 AAAAATTTAA
* *
6443870 AATAT AATAT AATAT AAAAAT AATATT AATAT AATAT AA-AT TAT-T AATAT
1 AATAT AATAT AATAT -AATAT AATA-T AATAT AATAT AATAT AATAT AATAT
6443920 A
1 A
6443921 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.16
5 23 0.61
6 9 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:6443887 original size:17 final size:17
Alignment explanation
Indices: 6443867--6443903 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6443857 TAAAAAAATT
6443867 TAAAATATAATA-TAATA
1 TAAAA-ATAATATTAATA
6443884 TAAAAATAATATTAATA
1 TAAAAATAATATTAATA
6443901 TAA
1 TAA
6443904 TATAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATAATATTAATA
Found at i:6443916 original size:18 final size:18
Alignment explanation
Indices: 6443874--6443934 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
6443864 ATTTAAAATA
6443874 TAATATAATATAAAAATAATAT
1 TAATATAATAT--AAAT--TAT
6443896 TAATATAATATAAATTAT
1 TAATATAATATAAATTAT
*
6443914 TAATATATTA-AAATTTAT
1 TAATATAATATAAA-TTAT
6443932 TAA
1 TAA
6443935 AAATATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 3 0.08
18 19 0.51
20 4 0.11
22 11 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAATATAAATTAT
Done.