Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 130 of 132
Found at i:40351934 original size:28 final size:30
Alignment explanation
Indices: 40351883--40351942 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
40351873 AGTTTATATA
*
40351883 TTTATAATTTTTAAAAGATTAAAT-TAATT
1 TTTATAATTTTTAAAAGATAAAATATAATT
* *
40351912 TTTATAA-TTTTAAGAGGTAAAATATAATT
1 TTTATAATTTTTAAAAGATAAAATATAATT
40351941 TT
1 TT
40351943 ATTTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (30 bp):
TTTATAATTTTTAAAAGATAAAATATAATT
Found at i:40352502 original size:13 final size:13
Alignment explanation
Indices: 40352484--40352510 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40352474 TAAACCCCAT
40352484 TTGTCGACCGCCA
1 TTGTCGACCGCCA
40352497 TTGTCGACCGCCA
1 TTGTCGACCGCCA
40352510 T
1 T
40352511 GGCTCATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.22, T:0.26
Consensus pattern (13 bp):
TTGTCGACCGCCA
Found at i:40358646 original size:29 final size:30
Alignment explanation
Indices: 40358614--40358677 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
40358604 TACCTAATAT
40358614 CAATCA-AAATTTACATGCTTGAAAGATAC
1 CAATCACAAATTTACATGCTTGAAAGATAC
*
40358643 CAAT-ACATATTTACATGCTTGAAAGATAC
1 CAATCACAAATTTACATGCTTGAAAGATAC
*
40358672 GAATCA
1 CAATCA
40358678 TAAGAATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (30 bp):
CAATCACAAATTTACATGCTTGAAAGATAC
Found at i:40360043 original size:18 final size:18
Alignment explanation
Indices: 40360020--40360054 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40360010 AATTCATATT
40360020 ACTTTCAATTCCAATTTC
1 ACTTTCAATTCCAATTTC
* *
40360038 ACTTTCACTTTCAATTT
1 ACTTTCAATTCCAATTT
40360055 TGATCACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
ACTTTCAATTCCAATTTC
Found at i:40360385 original size:17 final size:18
Alignment explanation
Indices: 40360351--40360386 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40360341 TGAATTTCTA
40360351 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
40360369 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
40360386 T
1 T
40360387 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:40360785 original size:15 final size:16
Alignment explanation
Indices: 40360759--40360788 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40360749 TCTATTCCTT
40360759 CTTTTGTTTCTTTTTC
1 CTTTTGTTTCTTTTTC
40360775 CTTTT-TTTCTTTTT
1 CTTTTGTTTCTTTTT
40360789 ATTTTTTATA
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:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (16 bp):
CTTTTGTTTCTTTTTC
Found at i:40372730 original size:18 final size:18
Alignment explanation
Indices: 40372707--40372759 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
40372697 TTATGTTTCC
40372707 CGTAGTTTGTGTTGTAAT
1 CGTAGTTTGTGTTGTAAT
* *
40372725 CGTAGTTTGTGTTGCATT
1 CGTAGTTTGTGTTGTAAT
*
40372743 CGTAGTTTGCGTTGTAA
1 CGTAGTTTGTGTTGTAA
40372760 GACTACTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.15, C:0.09, G:0.28, T:0.47
Consensus pattern (18 bp):
CGTAGTTTGTGTTGTAAT
Found at i:40372979 original size:20 final size:20
Alignment explanation
Indices: 40372955--40372999 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40372945 ATTTTAAATG
* *
40372955 AATTCTCTGTTTTTTGAATC
1 AATTCTCTATTGTTTGAATC
* *
40372975 GATTCTTTATTGTTTGAATC
1 AATTCTCTATTGTTTGAATC
40372995 AATTC
1 AATTC
40373000 ATTATTATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (20 bp):
AATTCTCTATTGTTTGAATC
Found at i:40373004 original size:20 final size:20
Alignment explanation
Indices: 40372967--40373005 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40372957 TTCTCTGTTT
* *
40372967 TTTGAATCGATTCTTTATTG
1 TTTGAATCAATTCATTATTG
40372987 TTTGAATCAATTCATTATT
1 TTTGAATCAATTCATTATT
40373006 ATTTTAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (20 bp):
TTTGAATCAATTCATTATTG
Found at i:40378659 original size:20 final size:21
Alignment explanation
Indices: 40378624--40378665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40378614 AAAAACGTAT
* *
40378624 AAAAATAAC-ATTTAAACAAC
1 AAAAATAACAACTAAAACAAC
40378644 AAAAATAACAACTAAAACAAC
1 AAAAATAACAACTAAAACAAC
40378665 A
1 A
40378666 GTTAAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAATAACAACTAAAACAAC
Found at i:40378676 original size:32 final size:32
Alignment explanation
Indices: 40378624--40378697 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
40378614 AAAAACGTAT
* *
40378624 AAAAATAACATTTAAACAACAAAAATAACAAC
1 AAAAACAACAGTTAAACAACAAAAATAACAAC
* * *
40378656 TAAAACAACAGTTAAACAACAAAAATAATAGC
1 AAAAACAACAGTTAAACAACAAAAATAACAAC
40378688 AAAAACAACA
1 AAAAACAACA
40378698 TCAAAACAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.68, C:0.16, G:0.03, T:0.14
Consensus pattern (32 bp):
AAAAACAACAGTTAAACAACAAAAATAACAAC
Found at i:40378705 original size:32 final size:32
Alignment explanation
Indices: 40378637--40378709 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
40378627 AATAACATTT
* *
40378637 AAACAACAAAAATAACAACTAAAACAACAGTT
1 AAACAACAAAAATAACAACAAAAACAACAGTA
* *
40378669 AAACAACAAAAATAATAGCAAAAACAACA-TCA
1 AAACAACAAAAATAACAACAAAAACAACAGT-A
40378701 AAACAACAA
1 AAACAACAA
40378710 TTAAAACAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 35 0.97
ACGTcount: A:0.68, C:0.19, G:0.03, T:0.10
Consensus pattern (32 bp):
AAACAACAAAAATAACAACAAAAACAACAGTA
Found at i:40378735 original size:20 final size:19
Alignment explanation
Indices: 40378712--40378766 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
40378702 AACAACAATT
40378712 AAAACAGCAAAAAAAGCACC
1 AAAACAGCAAAAAAA-CACC
*
40378732 AAAACAGTAAAAATAACACC
1 AAAACAGCAAAAA-AACACC
*
40378752 AAAATAGCAAAAAAA
1 AAAACAGCAAAAAAA
40378767 TAACAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.69, C:0.18, G:0.07, T:0.05
Consensus pattern (19 bp):
AAAACAGCAAAAAAACACC
Found at i:40378735 original size:44 final size:44
Alignment explanation
Indices: 40378638--40378735 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
40378628 ATAACATTTA
* * *
40378638 AACAACAAAAATAACAACTAAAACAACAGTTAAACAACAAAAAT
1 AACACCAAAAACAACAACTAAAACAACAATTAAACAACAAAAAT
* * * *
40378682 AATAGCAAAAACAACATC-AAAACAACAATTAAAACAGCAAAAA-
1 AACACCAAAAACAACAACTAAAACAACAATT-AAACAACAAAAAT
40378725 AAGCACCAAAA
1 AA-CACCAAAA
40378736 CAGTAAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
43 13 0.30
44 31 0.70
ACGTcount: A:0.67, C:0.19, G:0.04, T:0.09
Consensus pattern (44 bp):
AACACCAAAAACAACAACTAAAACAACAATTAAACAACAAAAAT
Found at i:40378800 original size:23 final size:21
Alignment explanation
Indices: 40378720--40378801 Score: 76
Period size: 23 Copynumber: 3.8 Consensus size: 21
40378710 TTAAAACAGC
* *
40378720 AAAAAAAGCACCAAAACAGT-
1 AAAAAAAACACCAAAATAGTA
* *
40378740 AAAAATAACACCAAAATAGCA
1 AAAAAAAACACCAAAATAGTA
*
40378761 AAAAAATAACAAACAAAATAGTA
1 AAAAAA-AAC-ACCAAAATAGTA
40378784 AAAAAAACAGCACCAAAA
1 AAAAAAA-A-CACCAAAA
40378802 CAATAATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 16 0.33
21 5 0.10
22 4 0.08
23 23 0.47
24 1 0.02
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.07
Consensus pattern (21 bp):
AAAAAAAACACCAAAATAGTA
Found at i:40390218 original size:28 final size:27
Alignment explanation
Indices: 40390187--40390243 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
40390177 AAACGGGACC
*
40390187 TTTGAATACTCGGGGGC-AAAATGGTAAT
1 TTTGAAT-CTCGAGGGCAAAAAT-GTAAT
*
40390215 TTTGACTCTCGAGGGCAAAAATGTAAT
1 TTTGAATCTCGAGGGCAAAAATGTAAT
40390242 TT
1 TT
40390244 CGGAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (27 bp):
TTTGAATCTCGAGGGCAAAAATGTAAT
Found at i:40390294 original size:58 final size:59
Alignment explanation
Indices: 40390232--40390419 Score: 249
Period size: 58 Copynumber: 3.2 Consensus size: 59
40390222 CTCGAGGGCA
* ** * *
40390232 AAAAT-GTAATTTCGGAAAAATTCGGGGTTAAAAATGGGATTTTGGAAGGTTCAAGGGT
1 AAAATGGTAATTTTGGTGAAATTCGGGGTCAAAAATGGAATTTTGGAAGGTTCAAGGGT
**
40390290 AAAATGGTAATTTTTGGTGAAA-TCGGGGTCAAAAATGGAATTTTGGAAGGTTCTGGGGT
1 AAAATGGTAA-TTTTGGTGAAATTCGGGGTCAAAAATGGAATTTTGGAAGGTTCAAGGGT
***
40390349 AAAATGGTAATTTTGGTGAAATT-GGGGTCAAAAATGGAATTTTGGAAGGTTTGGGGGT
1 AAAATGGTAATTTTGGTGAAATTCGGGGTCAAAAATGGAATTTTGGAAGGTTCAAGGGT
40390407 -AAATGGTAATTTT
1 AAAATGGTAATTTT
40390420 TAAAAAGTTC
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
57 13 0.11
58 49 0.42
59 48 0.41
60 8 0.07
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTGGTGAAATTCGGGGTCAAAAATGGAATTTTGGAAGGTTCAAGGGT
Found at i:40390302 original size:29 final size:27
Alignment explanation
Indices: 40390252--40390469 Score: 122
Period size: 29 Copynumber: 7.5 Consensus size: 27
40390242 TTCGGAAAAA
*
40390252 TTCGGGGTTAAAAATGGGATTTTGGAAGG
1 TTCGGGG-T-AAAATGGAATTTTGGAAGG
*
40390281 TTCAAGGGTAAAATGGTAATTTTTGGTGAA--
1 TTC-GGGGTAAAATGG-AA-TTTT-G-GAAGG
*
40390311 ATCGGGGTCAAAAATGGAATTTTGGAAGG
1 TTCGGGGT--AAAATGGAATTTTGGAAGG
*
40390340 TTCTGGGGTAAAATGGTAATTTTGGTGAA-A
1 TTC-GGGGTAAAATGG-AATTTT-G-GAAGG
40390370 TT-GGGGTCAAAAATGGAATTTTGGAAGG
1 TTCGGGGT--AAAATGGAATTTTGGAAGG
* ** *
40390398 TTTGGGGGT-AAATGGTAATTTTTAAAAAG
1 -TTCGGGGTAAAATGG-AA-TTTTGGAAGG
* *
40390427 TTCGGGGGTAAAATGTAATTTTTGGAAGT
1 TTC-GGGGTAAAATGGAA-TTTTGGAAGG
40390456 TTCGGGGTCAAAAT
1 TTCGGGGT-AAAAT
40390470 ACAATTTTTG
Statistics
Matches: 150, Mismatches: 16, Indels: 46
0.71 0.08 0.22
Matches are distributed among these distances:
27 12 0.08
28 30 0.20
29 58 0.39
30 36 0.24
31 11 0.07
32 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (27 bp):
TTCGGGGTAAAATGGAATTTTGGAAGG
Found at i:40390317 original size:59 final size:59
Alignment explanation
Indices: 40390253--40390420 Score: 259
Period size: 58 Copynumber: 2.9 Consensus size: 59
40390243 TCGGAAAAAT
* * *
40390253 TCGGGGTTAAAAATGGGATTTTGGAAGGTTCAAGGGTAAAATGGTAATTTTTGGTGAAA
1 TCGGGGTCAAAAATGGAATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTTGGTGAAA
*
40390312 TCGGGGTCAAAAATGGAATTTTGGAAGGTTCTGGGGTAAAATGGTAA-TTTTGGTGAAA
1 TCGGGGTCAAAAATGGAATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTTGGTGAAA
* **
40390370 TTGGGGTCAAAAATGGAATTTTGGAAGGTTTGGGGGT-AAATGGTAATTTTT
1 TCGGGGTCAAAAATGGAATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTT
40390421 AAAAAGTTCG
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
57 9 0.09
58 49 0.49
59 43 0.43
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (59 bp):
TCGGGGTCAAAAATGGAATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTTGGTGAAA
Found at i:40390450 original size:58 final size:55
Alignment explanation
Indices: 40390248--40390469 Score: 200
Period size: 58 Copynumber: 3.8 Consensus size: 55
40390238 TAATTTCGGA
* **
40390248 AAAATTCGGGGTTAAAAATGGGATTTTGGAAGGTTCAAGGGTAAAATGGTAATTTTTGGT
1 AAAATT-GGGG-TAAAAATGGAATTTTGGAAGGTT-TGGGGTAAAATGGTAA-TTTT-GT
* *
40390308 GAAATCGGGGTCAAAAATGGAATTTTGGAAGGTTCTGGGGTAAAATGGTAATTTTGGT
1 AAAATTGGGGT-AAAAATGGAATTTTGGAAGGTT-TGGGGTAAAATGGTAATTTT-GT
*
40390366 GAAATTGGGGTCAAAAATGGAATTTTGGAAGGTTTGGGGGT-AAATGGTAATTTT-T
1 AAAATTGGGGT-AAAAATGGAATTTTGGAAGGTTT-GGGGTAAAATGGTAATTTTGT
*
40390421 AAAAAGTTCGGGGGT-AAAATGTAATTTTTGGAA-GTTTCGGGGTCAAAAT
1 -AAAA-TT--GGGGTAAAAATGGAA-TTTTGGAAGGTTT-GGGGT-AAAAT
40390470 ACAATTTTTG
Statistics
Matches: 144, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
55 1 0.01
56 3 0.02
57 33 0.23
58 54 0.38
59 49 0.34
60 4 0.03
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.32
Consensus pattern (55 bp):
AAAATTGGGGTAAAAATGGAATTTTGGAAGGTTTGGGGTAAAATGGTAATTTTGT
Found at i:40408980 original size:16 final size:18
Alignment explanation
Indices: 40408949--40408981 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40408939 TTAAAAACAT
40408949 TAAAACAAACATTAAAAA
1 TAAAACAAACATTAAAAA
40408967 TAAAA-AAA-ATTAAAA
1 TAAAACAAACATTAAAA
40408982 TACATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (18 bp):
TAAAACAAACATTAAAAA
Found at i:40409177 original size:12 final size:12
Alignment explanation
Indices: 40409162--40409206 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
40409152 AAATAATAGT
40409162 AAAAAACAACAA
1 AAAAAACAACAA
*
40409174 AAAAAACAATAA
1 AAAAAACAACAA
* *
40409186 AAATAACAGCAA
1 AAAAAACAACAA
*
40409198 AAAATACAA
1 AAAAAACAA
40409207 AAACAGTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.78, C:0.13, G:0.02, T:0.07
Consensus pattern (12 bp):
AAAAAACAACAA
Found at i:40409193 original size:24 final size:23
Alignment explanation
Indices: 40409162--40409206 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
40409152 AAATAATAGT
40409162 AAAAAACAACAAAAAAAACAATA
1 AAAAAACAACAAAAAAAACAATA
* *
40409185 AAAATAACAGCAAAAAATACAA
1 AAAA-AACAACAAAAAAAACAA
40409207 AAACAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.78, C:0.13, G:0.02, T:0.07
Consensus pattern (23 bp):
AAAAAACAACAAAAAAAACAATA
Found at i:40409217 original size:18 final size:19
Alignment explanation
Indices: 40409176--40409221 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
40409166 AACAACAAAA
40409176 AAAACAATAAAAATAACAGC
1 AAAA-AATAAAAATAACAGC
* *
40409196 AAAAAATACAAA-AACAGT
1 AAAAAATAAAAATAACAGC
40409214 AAAAAATA
1 AAAAAATA
40409222 GTATCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 7 0.29
20 4 0.17
ACGTcount: A:0.74, C:0.11, G:0.04, T:0.11
Consensus pattern (19 bp):
AAAAAATAAAAATAACAGC
Found at i:40409263 original size:19 final size:19
Alignment explanation
Indices: 40409236--40409324 Score: 81
Period size: 19 Copynumber: 4.5 Consensus size: 19
40409226 CAAAACAGCA
* *
40409236 ACCAAAACAATAAAAAAGC
1 ACCAAAACAGTAAAAAAAC
*
40409255 ACTAAAACAGTAAAAAAAC
1 ACCAAAACAGTAAAAAAAC
40409274 ACCAAAACAGTAAAATTTAGAA-
1 ACCAAAACAGTAAAA---A-AAC
*
40409296 ATCAAAACAGTAAAAAAAGC
1 ACCAAAACAGTAAAAAAA-C
*
40409316 ACGAAAACA
1 ACCAAAACA
40409325 ACAATATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.04
19 31 0.54
20 7 0.12
22 15 0.26
23 2 0.04
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.10
Consensus pattern (19 bp):
ACCAAAACAGTAAAAAAAC
Found at i:40410452 original size:20 final size:20
Alignment explanation
Indices: 40410424--40410476 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
40410414 TTCATTGTTG
*
40410424 TTTTAAATCGATTCTTTGCT
1 TTTTGAATCGATTCTTTGCT
* *
40410444 TTTTGAATCAATTTTTTGCT
1 TTTTGAATCGATTCTTTGCT
*
40410464 GTTTGAATCGATT
1 TTTTGAATCGATT
40410477 AATTATTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTTGAATCGATTCTTTGCT
Found at i:40412280 original size:19 final size:19
Alignment explanation
Indices: 40412253--40412290 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40412243 ACGGTTTGTT
*
40412253 TTAGTGATTCTATTAAAAA
1 TTAGGGATTCTATTAAAAA
*
40412272 TTAGGGATTCTGTTAAAAA
1 TTAGGGATTCTATTAAAAA
40412291 AATTTAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
TTAGGGATTCTATTAAAAA
Found at i:40415333 original size:97 final size:98
Alignment explanation
Indices: 40415163--40415350 Score: 290
Period size: 97 Copynumber: 1.9 Consensus size: 98
40415153 CTTGAAAAAA
* * * * *
40415163 GGTATTTGATTATCCTGGTTTAAAGAAAAAGTCGCGTCTAGTAAGTTAAGGCACAAATTTTCAAA
1 GGTATTCGATTATCCCGATTTAAAGAAAAAGTCGCGCCTAGTAAGTTAAGGCAAAAATTTTCAAA
*
40415228 ACCTGAAATAAAGGAATATTGCCTCGATTTAAG
66 ACCTGAAATAAAGGAATATTACCTCGATTTAAG
*
40415261 GGTATTCGATTATCCCGATTTGAAGAAAAA-TCGCGCCTAGTAAGTTAAGGCAAAAATTTTCAAA
1 GGTATTCGATTATCCCGATTTAAAGAAAAAGTCGCGCCTAGTAAGTTAAGGCAAAAATTTTCAAA
40415325 A-CTCGAAATAAAGGAATATTACCTCG
66 ACCT-GAAATAAAGGAATATTACCTCG
40415351 TTTTTAAATA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
96 2 0.02
97 54 0.66
98 26 0.32
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (98 bp):
GGTATTCGATTATCCCGATTTAAAGAAAAAGTCGCGCCTAGTAAGTTAAGGCAAAAATTTTCAAA
ACCTGAAATAAAGGAATATTACCTCGATTTAAG
Found at i:40415700 original size:28 final size:29
Alignment explanation
Indices: 40415626--40415701 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 29
40415616 GAAGTTTCGA
* * * *
40415626 AAAGTTTGGGGGTTAAAATATATTTTTGG
1 AAAGTTTAGGGGTAAAAATACATTTTAGG
40415655 AAAGTTTTAGGGGTAAAAATACATTTTAGG
1 AAAG-TTTAGGGGTAAAAATACATTTTAGG
40415685 AAA-TTTA-GGGTAAAAAT
1 AAAGTTTAGGGGTAAAAAT
40415702 GTGATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.24
28 4 0.10
29 4 0.10
30 24 0.57
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAGTTTAGGGGTAAAAATACATTTTAGG
Found at i:40415708 original size:28 final size:28
Alignment explanation
Indices: 40415647--40416008 Score: 287
Period size: 29 Copynumber: 12.5 Consensus size: 28
40415637 GTTAAAATAT
**
40415647 ATTTTTGGAAAGTTTTAGGGGTAAAAAT-AC
1 ATTTTTGG-AAG-TTTA-GGGTAAAAATGTG
* *
40415677 ATTTTAGGAAATTTAGGGTAAAAATGTG
1 ATTTTTGGAAGTTTAGGGTAAAAATGTG
* ** *
40415705 ATTTTTGGAAGTTCAGGGGCAAAATGTA
1 ATTTTTGGAAGTTTAGGGTAAAAATGTG
** * *
40415733 ATTTTTAAAAAGTTTAGAGGCAAAAATGTA
1 ATTTTT-GGAAGTTTAG-GGTAAAAATGTG
* *
40415763 ATTTTTGGAAGATTGGGGT-AAAATGTG
1 ATTTTTGGAAGTTTAGGGTAAAAATGTG
* * *
40415790 ATTTTTGGAAGTTTGGAGGTAAAACTATG
1 ATTTTTGGAAGTTTAG-GGTAAAAATGTG
* **
40415819 ATTTTTGGAAGTTCGAGGACAAAAAATGTG
1 ATTTTTGGAAGTT-TAGG-GTAAAAATGTG
* *
40415849 ATTTTTGGAAGTTCGAGAGTAAAAATGTG
1 ATTTTTGGAAGTT-TAGGGTAAAAATGTG
* * *
40415878 ATTTTTGGAAGTTCAAGGGAAAAAATGTA
1 ATTTTTGGAAGTT-TAGGGTAAAAATGTG
* *
40415907 ATTTTTGGAAGTTTAGGGTTAAAATGTA
1 ATTTTTGGAAGTTTAGGGTAAAAATGTG
* *
40415935 ATTTTTAGAAAGTTTAGGGGTAAAAAATATG
1 ATTTTT-GGAAGTTTA-GGGT-AAAAATGTG
* * *
40415966 ATTTTTGCGAAGTTTGGGGTCAAAATATG
1 ATTTTTG-GAAGTTTAGGGTAAAAATGTG
40415995 ATTTTTGGATAGTT
1 ATTTTTGGA-AGTT
40416009 CAAGGACCTC
Statistics
Matches: 273, Mismatches: 47, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
27 32 0.12
28 57 0.21
29 109 0.40
30 57 0.21
31 18 0.07
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
ATTTTTGGAAGTTTAGGGTAAAAATGTG
Found at i:40415758 original size:58 final size:56
Alignment explanation
Indices: 40415677--40416009 Score: 262
Period size: 59 Copynumber: 5.8 Consensus size: 56
40415667 GTAAAAATAC
* * *
40415677 ATTTTAGGAAATTTAG-GGTAAAAATGTGATTTTTGGAAGTTCAGGGGCAAAATGTA
1 ATTTTTGGAAGTTTAGAGGTAAAAATGTGATTTTTGGAAGTTC-GGGACAAAATGTA
** * * ** *
40415733 ATTTTTAAAAAGTTTAGAGGCAAAAATGTAATTTTTGGAAGATT-GGGGTAAAATGTG
1 ATTTTT-GGAAGTTTAGAGGTAAAAATGTGATTTTTGGAAG-TTCGGGACAAAATGTA
* * * *
40415790 ATTTTTGGAAGTTTGGAGGTAAAACTATGATTTTTGGAAGTTCGAGGACAAAAAATGTG
1 ATTTTTGGAAGTTTAGAGGTAAAAATGTGATTTTTGGAAGTTCG-GGAC--AAAATGTA
* *
40415849 ATTTTTGGAAG-TTCGAGAGTAAAAATGTGATTTTTGGAAGTTCAAGGGAAAAAATGTA
1 ATTTTTGGAAGTTTAGAG-GTAAAAATGTGATTTTTGGAAGTTC--GGGACAAAATGTA
* * * * * * *
40415907 ATTTTTGGAAGTTTAG-GGTTAAAATGTAATTTTTAGAAAGTTTAGGGGTAAAAAATATG
1 ATTTTTGGAAGTTTAGAGGTAAAAATGTGATTTTT-GGAAG-TT-CGGG-ACAAAATGTA
* * *
40415966 ATTTTTGCGAAGTTT-GGGGTCAAAATATGATTTTTGGATAGTTC
1 ATTTTTG-GAAGTTTAGAGGTAAAAATGTGATTTTTGGA-AGTTC
40416010 AAGGACCTCT
Statistics
Matches: 225, Mismatches: 34, Indels: 34
0.77 0.12 0.12
Matches are distributed among these distances:
55 2 0.01
56 33 0.15
57 41 0.18
58 52 0.23
59 69 0.31
60 27 0.12
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (56 bp):
ATTTTTGGAAGTTTAGAGGTAAAAATGTGATTTTTGGAAGTTCGGGACAAAATGTA
Found at i:40416768 original size:27 final size:27
Alignment explanation
Indices: 40416738--40416789 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40416728 TTTCCCCTTC
* *
40416738 TTATTAA-AATATGTTTTTTATACATTA
1 TTATTAACAAT-TGTTATTGATACATTA
40416765 TTATTAACAATTGTTATTGATACAT
1 TTATTAACAATTGTTATTGATACAT
40416790 GTACATCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (27 bp):
TTATTAACAATTGTTATTGATACATTA
Found at i:40417044 original size:18 final size:19
Alignment explanation
Indices: 40417007--40417047 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
40416997 AATAATAAGT
40417007 AATAAATGGTAATATAATA
1 AATAAATGGTAATATAATA
40417026 AATAAATAGGT-AT-TAATA
1 AATAAAT-GGTAATATAATA
40417044 AATA
1 AATA
40417048 TATGCAGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 9 0.43
20 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (19 bp):
AATAAATGGTAATATAATA
Found at i:40417669 original size:6 final size:6
Alignment explanation
Indices: 40417635--40417743 Score: 61
Period size: 6 Copynumber: 19.0 Consensus size: 6
40417625 TATTTGGACT
* * *
40417635 TTTAAA GTTTAAA TTT-AA TTTAAA -ATAAA TTTAAA CTTAAA -ATAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
40417681 TTCAAA CTCAAA -ATAAG TTTAAA TTTAAA -GTAAA TTTAAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40417725 TTAAAA TTTAAA CTTTAAA
1 TTTAAA TTTAAA -TTTAAA
40417744 ATTAGATCCA
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
4 4 0.05
5 19 0.24
6 43 0.55
7 12 0.15
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:40417676 original size:17 final size:17
Alignment explanation
Indices: 40417644--40417745 Score: 102
Period size: 17 Copynumber: 6.1 Consensus size: 17
40417634 TTTTAAAGTT
*
40417644 TAAATTT-AATTTAAAA
1 TAAATTTAAACTTAAAA
40417660 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
* *
40417677 TAAATTCAAACTCAAAA
1 TAAATTTAAACTTAAAA
* * *
40417694 TAAGTTTAAATTTAAAG
1 TAAATTTAAACTTAAAA
*
40417711 TAAATTTAAA--TAAAT
1 TAAATTTAAACTTAAAA
40417726 TAAAATTTAAACTTTAAAA
1 T-AAATTTAAAC-TTAAAA
40417745 T
1 T
40417746 TAGATCCATT
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
15 5 0.07
16 16 0.23
17 44 0.63
19 5 0.07
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:40417680 original size:22 final size:23
Alignment explanation
Indices: 40417637--40417680 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
40417627 TTTGGACTTT
* **
40417637 TAAAGTTTAAATTTAATTTAAAA
1 TAAAGTTTAAACTTAAAATAAAA
40417660 TAAA-TTTAAACTTAAAATAAA
1 TAAAGTTTAAACTTAAAATAAA
40417681 TTCAAACTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAGTTTAAACTTAAAATAAAA
Found at i:40419959 original size:59 final size:60
Alignment explanation
Indices: 40419888--40420254 Score: 264
Period size: 59 Copynumber: 6.2 Consensus size: 60
40419878 ATTTTATTTA
* * * *
40419888 AAAATTATATTTTGATCTCT-AACTTTTTCAAAATTACATTTTAACCC-CTAAACTTTTCC
1 AAAATTACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTC-AAACTTTTCC
* * * * * *
40419947 ATAATTACATTTTCA-CCCTAAACTTTTCCAAAATTGCATTTTGACCCTCGAACTTCTCA
1 AAAATTACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTCC
* * *
40420006 AAAATTACATTTTGACCCCCT-AACTTTTCCAAAATTATATTTTGATCCTCAAACTTTTCC
1 AAAATTACATTTTGA-TCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTCC
* * * * * * *
40420066 AAAATCACATTTTTAT-CCTAAACTTTTCCAAAATTACATTTTTACCCCCGAA--TATCTA
1 AAAATTACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTC-C
* * *
40420124 AAAATTACCATTTT-AT-CCTCGAACTTTTCCAAAATTACCACTTT-ACCC-CGAAC--TTCC
1 AAAATTA-CATTTTGATCCCT-AAACTTTTCCAAAATTA-CATTTTGACCCTCAAACTTTTCC
* ** * *
40420181 AAAAATTACCATTTT-ACCCCCGAA--TATCTAAAAATTACCATTTTGACCC-CAAACTTTTCC
1 -AAAATTA-CATTTTGATCCCTAAACTTTTC-CAAAATTA-CATTTTGACCCTCAAACTTTTCC
40420241 AAAATTACCATTTT
1 AAAATTA-CATTTT
40420255 TCCCCCGAGT
Statistics
Matches: 253, Mismatches: 39, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
56 3 0.01
57 16 0.06
58 49 0.19
59 125 0.49
60 56 0.22
61 4 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (60 bp):
AAAATTACATTTTGATCCCTAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTTTCC
Found at i:40420013 original size:89 final size:88
Alignment explanation
Indices: 40419917--40420254 Score: 262
Period size: 89 Copynumber: 3.8 Consensus size: 88
40419907 TAACTTTTTC
*
40419917 AAAATTACATTTTAACCCCTAAACTTTTCCATAATTACATTTTCACCCT-AAACTTTTCCAAAAT
1 AAAATTACATTTTAACCCCT-AACTTTTCCAAAATTACATTTTCACCCTCAAACTTTTCCAAAAT
** *
40419981 TGCATTTTGACCCTCGAACTTCTCA
65 CACATTTTGACCCT-AAACTTCTCA
* * * *
40420006 AAAATTACATTTTGACCCCCTAACTTTTCCAAAATTATATTTTGATCCTCAAACTTTTCCAAAAT
1 AAAATTACATTTT-AACCCCTAACTTTTCCAAAATTACATTTTCACCCTCAAACTTTTCCAAAAT
* * * *
40420071 CACATTTTTATCCTAAACTTTTCC
65 CACATTTTGACCCTAAACTTCTCA
* * * * * *
40420095 AAAATTACATTTTTACCCCCGAA--TATCTAAAAATTACCATTTT-ATCCTCGAACTTTTCCAAA
1 AAAATTACA-TTTTAACCCCTAACTTTTC-CAAAATTA-CATTTTCACCCTCAAACTTTTCCAAA
* * **
40420157 ATTACCACTTT-ACCCCGAACTTC-CA
63 ATCA-CATTTTGACCCTAAACTTCTCA
* * * * *
40420182 AAAATTACCATTTTACCCCCGAA--TATCTAAAAATTACCATTTTGACCC-CAAACTTTTCCAAA
1 AAAATTA-CATTTTAACCCCTAACTTTTC-CAAAATTA-CATTTTCACCCTCAAACTTTTCCAAA
*
40420244 ATTACCATTTT
63 ATCA-CATTTT
40420255 TCCCCCGAGT
Statistics
Matches: 214, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
87 67 0.31
88 41 0.19
89 71 0.33
90 35 0.16
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (88 bp):
AAAATTACATTTTAACCCCTAACTTTTCCAAAATTACATTTTCACCCTCAAACTTTTCCAAAATC
ACATTTTGACCCTAAACTTCTCA
Found at i:40420158 original size:30 final size:29
Alignment explanation
Indices: 40419908--40420260 Score: 240
Period size: 30 Copynumber: 12.0 Consensus size: 29
40419898 TTTGATCTCT
* *
40419908 AACTTTTTCAAAATTACATTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTT-ACCCCCA
* *
40419938 AACTTTTCCATAATTACATTTT-CACCCTA
1 AACTTTTCCAAAATTACATTTTAC-CCCCA
* * *
40419967 AACTTTTCCAAAATTGCATTTTGACCCTCG
1 AACTTTTCCAAAATTACATTTT-ACCCCCA
* * *
40419997 AACTTCTCAAAAATTACATTTTGACCCCCT
1 AACTTTTCCAAAATTACATTTT-ACCCCCA
* * *
40420027 AACTTTTCCAAAATTATATTTTGATCCTCA
1 AACTTTTCCAAAATTACATTTT-ACCCCCA
* * *
40420057 AACTTTTCCAAAATCACATTTTTA-TCCTA
1 AACTTTTCCAAAATTACA-TTTTACCCCCA
*
40420086 AACTTTTCCAAAATTACATTTTTACCCCCG
1 AACTTTTCCAAAATTACA-TTTTACCCCCA
* * * * *
40420116 AA--TATCTAAAAATTACCATTTTATCCTCG
1 AACTTTTC-CAAAATTA-CATTTTACCCCCA
* *
40420145 AACTTTTCCAAAATTACCACTTTA-CCCCG
1 AACTTTTCCAAAATTA-CATTTTACCCCCA
*
40420174 AAC--TTCCAAAAATTACCATTTTACCCCCG
1 AACTTTTCC-AAAATTA-CATTTTACCCCCA
* *
40420203 AA--TATCTAAAAATTACCATTTTGA-CCCCA
1 AACTTTTC-CAAAATTA-CATTTT-ACCCCCA
*
40420232 AACTTTTCCAAAATTACCATTTTTCCCCC
1 AACTTTTCCAAAATTA-CATTTTACCCCC
40420261 GAGTATCTGA
Statistics
Matches: 264, Mismatches: 42, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.02
28 18 0.07
29 104 0.39
30 127 0.48
31 11 0.04
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTTTCCAAAATTACATTTTACCCCCA
Found at i:40420260 original size:59 final size:57
Alignment explanation
Indices: 40420123--40420298 Score: 194
Period size: 59 Copynumber: 3.0 Consensus size: 57
40420113 CCGAATATCT
* * * * * *
40420123 AAAAATTACCATTTTATCCTCGAACT-TTTCCAAAATTACCACTTTACCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAA-TATCT-AAAAATTACCATTTTACCCCAAACTTCC
40420181 AAAAATTACCATTTTACCCCCGAATATCTAAAAATTACCATTTTGACCCCAAACTTTTCC
1 AAAAATTACCATTTTACCCCCGAATATCTAAAAATTACCATTTT-ACCCCAAAC--TTCC
* * * *
40420241 -AAAATTACCATTTTTCCCCCGAGTATCTGAAAATTACCATTTTACCCTCAAATTTCC
1 AAAAATTACCATTTTACCCCCGAATATCTAAAAATTACCATTTTACCC-CAAACTTCC
40420298 A
1 A
40420299 GAAGTCACAT
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
57 18 0.18
58 36 0.35
59 44 0.43
60 4 0.04
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCCGAATATCTAAAAATTACCATTTTACCCCAAACTTCC
Found at i:40420274 original size:29 final size:29
Alignment explanation
Indices: 40420095--40420287 Score: 173
Period size: 29 Copynumber: 6.6 Consensus size: 29
40420085 AAACTTTTCC
40420095 AAAATTA-CATTTTTACCCCCGAATATCTA
1 AAAATTACCA-TTTTACCCCCGAATATCTA
* * * *
40420124 AAAATTACCATTTTATCCTCGAACT-TTTCC
1 AAAATTACCATTTTACCCCCGAA-TATCT-A
* *
40420154 AAAATTACCACTTTA-CCCCGAACT-TCCA
1 AAAATTACCATTTTACCCCCGAA-TATCTA
40420182 AAAATTACCATTTTACCCCCGAATATCTA
1 AAAATTACCATTTTACCCCCGAATATCTA
* * *
40420211 AAAATTACCATTTTGA-CCCCAAACT-TTTCC
1 AAAATTACCATTTT-ACCCCCGAA-TATCT-A
* * *
40420241 AAAATTACCATTTTTCCCCCGAGTATCTG
1 AAAATTACCATTTTACCCCCGAATATCTA
40420270 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
40420288 TCAAATTTCC
Statistics
Matches: 134, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
28 15 0.11
29 79 0.59
30 40 0.30
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATATCTA
Found at i:40430914 original size:20 final size:20
Alignment explanation
Indices: 40430886--40430923 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40430876 TTGTTTTTTA
40430886 TTTTAAATC-AGTTCTTTGCT
1 TTTTAAATCGA-TTCTTTGCT
*
40430906 TTTTGAATCGATTCTTTG
1 TTTTAAATCGATTCTTTG
40430924 TTGTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTTAAATCGATTCTTTGCT
Found at i:40437086 original size:22 final size:22
Alignment explanation
Indices: 40437048--40437090 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40437038 CTCCATAACT
*
40437048 TTAAAATATATTAATTATATTC
1 TTAAAATATAATAATTATATTC
40437070 TTAAAATATCAAT-ATTATATT
1 TTAAAATAT-AATAATTATATT
40437091 AATAAAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAATATAATAATTATATTC
Found at i:40437155 original size:13 final size:13
Alignment explanation
Indices: 40437137--40437161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40437127 TATAGTATAG
40437137 TTTAAAATAAAAT
1 TTTAAAATAAAAT
40437150 TTTAAAATAAAA
1 TTTAAAATAAAA
40437162 ATAAATATTA
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:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAAAATAAAAT
Found at i:40437176 original size:15 final size:15
Alignment explanation
Indices: 40437156--40437194 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
40437146 AAATTTTAAA
40437156 ATAAAAATAAATATT
1 ATAAAAATAAATATT
* *
40437171 ATAAAAATTAATGTT
1 ATAAAAATAAATATT
*
40437186 TTAAAAATA
1 ATAAAAATA
40437195 TTAGTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
ATAAAAATAAATATT
Found at i:40450908 original size:10 final size:9
Alignment explanation
Indices: 40450883--40450907 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40450873 TCTTTACTAA
40450883 TTTAAAATT
1 TTTAAAATT
40450892 TTTAAAATT
1 TTTAAAATT
40450901 TTTAAAA
1 TTTAAAA
40450908 ACCTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:40458986 original size:29 final size:29
Alignment explanation
Indices: 40458898--40459165 Score: 149
Period size: 29 Copynumber: 9.2 Consensus size: 29
40458888 CGAAAATGAG
* **
40458898 ATTTTGGAAAGTTCAGGGGT-AAATGGTA
1 ATTTTGGGAAGTTTGGGGGTAAAATGGTA
* * * **
40458926 ATTTTGGTGAA-ATCGGGGTTAAAAAT-AAA
1 ATTTTGG-GAAGTTTGGGGGT-AAAATGGTA
* *
40458955 ATTTTCGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTGGGAAGTTTGGGGGTAAAATGGTA
* * * **
40458984 ATTTTGGTGAA-ATCGGGGTTAAAAAT-AAA
1 ATTTTGG-GAAGTTTGGGGGT-AAAATGGTA
40459013 ATTTTGGGAAGTTTTGGGGGTAAAATGGTA
1 ATTTTGGGAAG-TTTGGGGGTAAAATGGTA
* * *
40459043 ATTTTTGGTGAA-ATCGGGGTTAAAAATGG-A
1 A-TTTTGG-GAAGTTTGGGGGT-AAAATGGTA
* *
40459073 ATTTTGGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTGGGAAGTTTGGGGGTAAAATGGTA
* * * *
40459102 ATTTTTGGTGAA-ATCGAGGTTAAAAATGG-A
1 A-TTTTGG-GAAGTTTGGGGGT-AAAATGGTA
*
40459132 ATTTTGGAAAGTTTGGGGGTAAAATGGTA
1 ATTTTGGGAAGTTTGGGGGTAAAATGGTA
40459161 ATTTT
1 ATTTT
40459166 TGAACAGTCA
Statistics
Matches: 180, Mismatches: 40, Indels: 39
0.69 0.15 0.15
Matches are distributed among these distances:
28 42 0.23
29 71 0.39
30 42 0.23
31 22 0.12
32 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
ATTTTGGGAAGTTTGGGGGTAAAATGGTA
Found at i:40459091 original size:59 final size:59
Alignment explanation
Indices: 40458859--40459167 Score: 439
Period size: 59 Copynumber: 5.3 Consensus size: 59
40458849 GCCCGGGAGC
* ** **
40458859 AAAATGGTAATTTTTGGTGAAATCGAGGTCGAAAAT-GAGATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGA-ATTTTGGAAAGTTTGGGGGT
* *
40458918 -AAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATAAAATTTTCGG-AAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTT-GGAAAGTTTGGGGGT
* *
40458975 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGGAAGTTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAG-TTTGGGGGT
* *
40459034 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTGGGGGT
* *
40459093 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTGGGGGT
40459152 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
40459168 AACAGTCAAG
Statistics
Matches: 232, Mismatches: 12, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
57 40 0.17
58 57 0.25
59 99 0.43
60 36 0.16
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTGGGGGT
Found at i:40461025 original size:6 final size:6
Alignment explanation
Indices: 40461014--40461072 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
40461004 TTAAATTTGA
* *
40461014 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AGGTAAAT TTAAAT TTACAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTA-AAT
40461063 -TAAAT TTAAA
1 TTAAAT TTAAA
40461073 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 28 0.65
7 2 0.05
8 5 0.12
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:40461035 original size:17 final size:17
Alignment explanation
Indices: 40461015--40461072 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
40461005 TAAATTTGAT
40461015 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
40461032 TAAATTTAAA--T-AGG
1 TAAATTTAAATTTAAAG
40461046 TAAATTTAAATTTACAA-
1 TAAATTTAAATTTA-AAG
40461063 TAAATTTAAA
1 TAAATTTAAA
40461073 ATCAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 20 0.57
18 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:40461940 original size:158 final size:158
Alignment explanation
Indices: 40461652--40461941 Score: 490
Period size: 158 Copynumber: 1.8 Consensus size: 158
40461642 TATCATGTAG
* *
40461652 TGCTCACACAAGCTGTGGGTCAAGATGTTAGATTACACGATGCTGCTCACATGAGCTGTGGAGAA
1 TGCTCACACAAGCTGTGGGTCAAGATGTTAAATTACACGATGCTGCTCACACGAGCTGTGGAGAA
* * *
40461717 TCCGCAACATATGCCGGATCTTAGCCATCAGTAAGACATCTAAGACCAACACCCATATAACATGT
66 TCCGCAACATATACCCGATCTCAGCCATCAGTAAGACATCTAAGACCAACACCCATATAACATGT
40461782 AATGCTCACACGAGCTATGAAGTGGGCC
131 AATGCTCACACGAGCTATGAAGTGGGCC
* *
40461810 TGCTCACACGAGCTGTGGGTCGAGATGTTAAATTACACGATGCTGCTCACACGAGCTGTGGAGAA
1 TGCTCACACAAGCTGTGGGTCAAGATGTTAAATTACACGATGCTGCTCACACGAGCTGTGGAGAA
* * *
40461875 TCCGCAACATATACCCGATCTCAGCCATCGGTAAGACATCTAAGACCAGCATCCATATAACATGT
66 TCCGCAACATATACCCGATCTCAGCCATCAGTAAGACATCTAAGACCAACACCCATATAACATGT
40461940 AA
131 AA
40461942 ATCCCGAAAT
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 122 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (158 bp):
TGCTCACACAAGCTGTGGGTCAAGATGTTAAATTACACGATGCTGCTCACACGAGCTGTGGAGAA
TCCGCAACATATACCCGATCTCAGCCATCAGTAAGACATCTAAGACCAACACCCATATAACATGT
AATGCTCACACGAGCTATGAAGTGGGCC
Found at i:40462903 original size:15 final size:15
Alignment explanation
Indices: 40462873--40462910 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40462863 TAATCCCTCC
40462873 ATTTTCTATTTCCATT
1 ATTTT-TATTTCCATT
*
40462889 ATTTTTATTTTCATT
1 ATTTTTATTTCCATT
40462904 ATTTTTA
1 ATTTTTA
40462911 ATTGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTATTTCCATT
Found at i:40464617 original size:35 final size:35
Alignment explanation
Indices: 40464548--40464618 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
40464538 GCTAAAGGTC
* * *
40464548 AGAGCATTAGCGGCACTTGTGGGAAAGCGTCGCTA
1 AGAGCATTAGCGGCACTTATGGAAAAGCGCCGCTA
* *
40464583 AGAGCATTAGCGGCGCTTATGGAAAAGTGCCGCTA
1 AGAGCATTAGCGGCACTTATGGAAAAGCGCCGCTA
40464618 A
1 A
40464619 AAGTGGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (35 bp):
AGAGCATTAGCGGCACTTATGGAAAAGCGCCGCTA
Found at i:40466002 original size:43 final size:43
Alignment explanation
Indices: 40465941--40466052 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
40465931 GGCGTTTTTC
* * * *
40465941 AAAGACCATGTTCTTTAGCGGCGTTTGTG-GTAAAAGCGCCGCT
1 AAAGAACATGATCTTTAGCGGCATTTGTGAG-AAAAGCACCGCT
*
40465984 AAAGAACATGATCTTTAGCGGCATTTGTGAGGAAAGCACCGCT
1 AAAGAACATGATCTTTAGCGGCATTTGTGAGAAAAGCACCGCT
* *
40466027 AAAGAACATGGTCTTTAGTGGCATTT
1 AAAGAACATGATCTTTAGCGGCATTT
40466053 TTCCTCATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 60 0.98
44 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
AAAGAACATGATCTTTAGCGGCATTTGTGAGAAAAGCACCGCT
Found at i:40472694 original size:17 final size:17
Alignment explanation
Indices: 40472672--40472708 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40472662 GTTTTTTCTA
*
40472672 AAATTTAAACTTAATAT
1 AAATTTAAACTTAAAAT
*
40472689 AAATTTAAATTTAAAAT
1 AAATTTAAACTTAAAAT
40472706 AAA
1 AAA
40472709 AATTAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTTAAAAT
Found at i:40472732 original size:20 final size:19
Alignment explanation
Indices: 40472702--40472747 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
40472692 TTTAAATTTA
40472702 AAATA-AAAATTAAATGTCC
1 AAATACAAAATTAAA-GTCC
40472721 AAATACAAAATTAAAGTCC
1 AAATACAAAATTAAAGTCC
*
40472740 AATTACAA
1 AAATACAA
40472748 GTCCAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (19 bp):
AAATACAAAATTAAAGTCC
Found at i:40473110 original size:27 final size:26
Alignment explanation
Indices: 40473080--40473159 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 26
40473070 TGTAAGGGGT
40473080 TACAAACCCATATTTGAAAACTCAATA
1 TACAAACCCATATTTGAAAA-TCAATA
* *
40473107 TACAAACCCTTCTTTGAAAATCAATA
1 TACAAACCCATATTTGAAAATCAATA
* *
40473133 GACAGAACCCAT-TCTGGAAAATCAATA
1 TACA-AACCCATAT-TTGAAAATCAATA
40473160 CACTATCCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.22
27 36 0.78
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (26 bp):
TACAAACCCATATTTGAAAATCAATA
Found at i:40474698 original size:30 final size:30
Alignment explanation
Indices: 40474664--40474813 Score: 84
Period size: 30 Copynumber: 5.1 Consensus size: 30
40474654 GTATTTTTGA
40474664 CCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCCGATTTCACCAAAAATTACCATTTTAC
* *
40474694 CCCCGA--ACATTCC-AAAA-TCCCATTTTTGA-
1 CCCCGATTTCA--CCAAAAATTACCA-TTTT-AC
* * * *
40474723 TCTCGATTTCACTAAAAATTATCATTTTAC
1 CCCCGATTTCACCAAAAATTACCATTTTAC
* **
40474753 CCTCGAACTTT--CC-AAAATT-CCATTTTTG
1 CCCCG-A-TTTCACCAAAAATTACCATTTTAC
* *
40474781 ACCCGATTTCATCAAAAATTACCATTTTAC
1 CCCCGATTTCACCAAAAATTACCATTTTAC
40474811 CCC
1 CCC
40474814 AAACCTTCCA
Statistics
Matches: 86, Mismatches: 19, Indels: 30
0.64 0.14 0.22
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 16 0.19
29 26 0.30
30 31 0.36
31 6 0.07
32 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (30 bp):
CCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:40474730 original size:59 final size:58
Alignment explanation
Indices: 40474656--40474841 Score: 257
Period size: 59 Copynumber: 3.2 Consensus size: 58
40474646 CAAAAATTGT
40474656 ATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
1 ATTTTTGA-CCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
* * * * * *
40474715 ATTTTTGATCTCGATTTCACTAAAAATTATCATTTTACCCTCGAACTTTCCAAAATTCC
1 ATTTTTGA-CCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
* * *
40474774 ATTTTTGACCCGATTTCATCAAAAATTACCATTTTA-CCCCAAACCTTCCAAAATCCC
1 ATTTTTGACCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
*
40474831 ATTTTTAACCC
1 ATTTTTGACCC
40474842 CAAATTTTCC
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
57 27 0.24
58 24 0.22
59 60 0.54
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (58 bp):
ATTTTTGACCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
Found at i:40474825 original size:29 final size:31
Alignment explanation
Indices: 40474736--40474931 Score: 109
Period size: 29 Copynumber: 6.7 Consensus size: 31
40474726 CGATTTCACT
* *
40474736 AAAAATTATCA-TTTT-ACCCTCGAACTTTCC
1 AAAAATTACCATTTTTAACCC-CAAACTTTCC
* *
40474766 -AAAATT-CCATTTTTGA-CCC-GA-TTTCATC
1 AAAAATTACCATTTTTAACCCCAAACTTTC--C
*
40474794 AAAAATTACCA-TTTT-ACCCCAAACCTTCC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
* *
40474823 -AAAA-TCCCATTTTTAACCCCAAATTTTCC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
* ** * *
40474852 CAAAATTA-CATTTTTGCCCCCGAACTTTTC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
* *
40474882 AAAAATTACCA-TTTT-ACACCGAACTTTCC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
*
40474911 -AAAATT-TCATTTTTTAACCCC
1 AAAAATTACCA-TTTTTAACCCC
40474932 GATTTCACCA
Statistics
Matches: 130, Mismatches: 19, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.03
27 7 0.05
28 19 0.15
29 53 0.41
30 41 0.32
31 6 0.05
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAAATTACCATTTTTAACCCCAAACTTTCC
Found at i:40474885 original size:88 final size:89
Alignment explanation
Indices: 40474792--40474954 Score: 233
Period size: 88 Copynumber: 1.8 Consensus size: 89
40474782 CCCGATTTCA
*
40474792 TCAAAAATTACCATTTTACCCCAAACCTTCCAAAATCCCA-TTTTTAACCCCAAATTTTC-CCAA
1 TCAAAAATTACCATTTTACACCAAACCTTCCAAAATCCCATTTTTTAACCCC-AA-TTTCACCAA
40474855 AATTAC-ATTTTTGCCCCCGAACTTT
64 AATTACTATTTTTGCCCCCGAACTTT
* * ** *
40474880 TCAAAAATTACCATTTTACACCGAACTTTCCAAAATTTCATTTTTTAACCCCGATTTCACCAAAA
1 TCAAAAATTACCATTTTACACCAAACCTTCCAAAATCCCATTTTTTAACCCCAATTTCACCAAAA
40474945 TTACTATTTT
66 TTACTATTTT
40474955 ACCCTCGGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
87 4 0.06
88 46 0.70
89 16 0.24
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (89 bp):
TCAAAAATTACCATTTTACACCAAACCTTCCAAAATCCCATTTTTTAACCCCAATTTCACCAAAA
TTACTATTTTTGCCCCCGAACTTT
Found at i:40474958 original size:28 final size:28
Alignment explanation
Indices: 40474737--40474958 Score: 102
Period size: 29 Copynumber: 7.6 Consensus size: 28
40474727 GATTTCACTA
40474737 AAAATTA-TCATTTTACCCTCGAACTTTCC
1 AAAATTACT-ATTTTACCC-CGAACTTTCC
*
40474766 AAAATT-CCATTTTTGA-CCCG-A-TTTCATC
1 AAAATTACTA-TTTT-ACCCCGAACTTTC--C
* * *
40474794 AAAAATTACCATTTTACCCCAAACCTTCC
1 -AAAATTACTATTTTACCCCGAACTTTCC
* * * *
40474823 AAAA-TCCCATTTTTAACCCCAAATTTTCCC
1 AAAATTACTA-TTTT-ACCCCGAACTTT-CC
* *
40474853 AAAATTAC-ATTTTTGCCCCCGAACTTTTCA
1 AAAATTACTA-TTTT-ACCCCGAAC-TTTCC
* *
40474883 AAAATTACCATTTTACACCGAACTTTCC
1 AAAATTACTATTTTACCCCGAACTTTCC
* *
40474911 AAAATTTCATTTTTTAACCCCG-A-TTTCACC
1 AAAATTAC-TATTTT-ACCCCGAACTTT--CC
40474941 AAAATTACTATTTTACCC
1 AAAATTACTATTTTACCC
40474959 TCGGGAATCC
Statistics
Matches: 152, Mismatches: 21, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 31 0.20
29 53 0.35
30 50 0.33
31 9 0.06
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTACTATTTTACCCCGAACTTTCC
Found at i:40476384 original size:31 final size:30
Alignment explanation
Indices: 40476349--40476408 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
40476339 ATCAATCAAA
* *
40476349 ATTTACATGCTTGAAATATACCAATACATAT
1 ATTTACATGCTTGAAAGATACAAAT-CATAT
40476380 ATTTACATGCTTGAAAGATACAAATCATA
1 ATTTACATGCTTGAAAGATACAAATCATA
40476409 AGAATGTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.33
Consensus pattern (30 bp):
ATTTACATGCTTGAAAGATACAAATCATAT
Found at i:40485448 original size:17 final size:17
Alignment explanation
Indices: 40485426--40485462 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40485416 GTTTTTTCTA
*
40485426 AAATTTAAACTTAATAT
1 AAATTTAAACTTAAAAT
*
40485443 AAATTTAAATTTAAAAT
1 AAATTTAAACTTAAAAT
40485460 AAA
1 AAA
40485463 AATTAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTTAAAAT
Found at i:40485486 original size:20 final size:19
Alignment explanation
Indices: 40485456--40485501 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
40485446 TTTAAATTTA
40485456 AAATA-AAAATTAAATGTCC
1 AAATACAAAATTAAA-GTCC
40485475 AAATACAAAATTAAAGTCC
1 AAATACAAAATTAAAGTCC
*
40485494 AATTACAA
1 AAATACAA
40485502 GTCCAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (19 bp):
AAATACAAAATTAAAGTCC
Found at i:40485864 original size:27 final size:26
Alignment explanation
Indices: 40485834--40485913 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 26
40485824 TGTAAGGGGT
40485834 TACAAACCCATATTTGAAAACTCAATA
1 TACAAACCCATATTTGAAAA-TCAATA
* *
40485861 TACAAACCCTTCTTTGAAAATCAATA
1 TACAAACCCATATTTGAAAATCAATA
* *
40485887 GACAGAACCCAT-TCTGGAAAATCAATA
1 TACA-AACCCATAT-TTGAAAATCAATA
40485914 CACTATCCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.22
27 36 0.78
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (26 bp):
TACAAACCCATATTTGAAAATCAATA
Found at i:40487452 original size:30 final size:30
Alignment explanation
Indices: 40487418--40487567 Score: 84
Period size: 30 Copynumber: 5.1 Consensus size: 30
40487408 GTATTTTTGA
40487418 CCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCCGATTTCACCAAAAATTACCATTTTAC
* *
40487448 CCCCGA--ACATTCC-AAAA-TCCCATTTTTGA-
1 CCCCGATTTCA--CCAAAAATTACCA-TTTT-AC
* * * *
40487477 TCTCGATTTCACTAAAAATTATCATTTTAC
1 CCCCGATTTCACCAAAAATTACCATTTTAC
* **
40487507 CCTCGAACTTT--CC-AAAATT-CCATTTTTG
1 CCCCG-A-TTTCACCAAAAATTACCATTTTAC
* *
40487535 ACCCGATTTCATCAAAAATTACCATTTTAC
1 CCCCGATTTCACCAAAAATTACCATTTTAC
40487565 CCC
1 CCC
40487568 AAACCTTCCA
Statistics
Matches: 86, Mismatches: 19, Indels: 30
0.64 0.14 0.22
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 16 0.19
29 26 0.30
30 31 0.36
31 6 0.07
32 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (30 bp):
CCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:40487484 original size:59 final size:58
Alignment explanation
Indices: 40487410--40487595 Score: 257
Period size: 59 Copynumber: 3.2 Consensus size: 58
40487400 CAAAAATTGT
40487410 ATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
1 ATTTTTGA-CCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
* * * * * *
40487469 ATTTTTGATCTCGATTTCACTAAAAATTATCATTTTACCCTCGAACTTTCCAAAATTCC
1 ATTTTTGA-CCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
* * *
40487528 ATTTTTGACCCGATTTCATCAAAAATTACCATTTTA-CCCCAAACCTTCCAAAATCCC
1 ATTTTTGACCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
*
40487585 ATTTTTAACCC
1 ATTTTTGACCC
40487596 CAAATTTTCC
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
57 27 0.24
58 24 0.22
59 60 0.54
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (58 bp):
ATTTTTGACCCGATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCC
Found at i:40487579 original size:29 final size:31
Alignment explanation
Indices: 40487490--40487685 Score: 109
Period size: 29 Copynumber: 6.7 Consensus size: 31
40487480 CGATTTCACT
* *
40487490 AAAAATTATCA-TTTT-ACCCTCGAACTTTCC
1 AAAAATTACCATTTTTAACCC-CAAACTTTCC
* *
40487520 -AAAATT-CCATTTTTGA-CCC-GA-TTTCATC
1 AAAAATTACCATTTTTAACCCCAAACTTTC--C
*
40487548 AAAAATTACCA-TTTT-ACCCCAAACCTTCC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
* *
40487577 -AAAA-TCCCATTTTTAACCCCAAATTTTCC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
* ** * *
40487606 CAAAATTA-CATTTTTGCCCCCGAACTTTTC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
* *
40487636 AAAAATTACCA-TTTT-ACACCGAACTTTCC
1 AAAAATTACCATTTTTAACCCCAAACTTTCC
*
40487665 -AAAATT-TCATTTTTTAACCCC
1 AAAAATTACCA-TTTTTAACCCC
40487686 GATTTCACCA
Statistics
Matches: 130, Mismatches: 19, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.03
27 7 0.05
28 19 0.15
29 53 0.41
30 41 0.32
31 6 0.05
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAAATTACCATTTTTAACCCCAAACTTTCC
Found at i:40487639 original size:88 final size:89
Alignment explanation
Indices: 40487546--40487708 Score: 233
Period size: 88 Copynumber: 1.8 Consensus size: 89
40487536 CCCGATTTCA
*
40487546 TCAAAAATTACCATTTTACCCCAAACCTTCCAAAATCCCA-TTTTTAACCCCAAATTTTC-CCAA
1 TCAAAAATTACCATTTTACACCAAACCTTCCAAAATCCCATTTTTTAACCCC-AA-TTTCACCAA
40487609 AATTAC-ATTTTTGCCCCCGAACTTT
64 AATTACTATTTTTGCCCCCGAACTTT
* * ** *
40487634 TCAAAAATTACCATTTTACACCGAACTTTCCAAAATTTCATTTTTTAACCCCGATTTCACCAAAA
1 TCAAAAATTACCATTTTACACCAAACCTTCCAAAATCCCATTTTTTAACCCCAATTTCACCAAAA
40487699 TTACTATTTT
66 TTACTATTTT
40487709 ACCCTCGGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
87 4 0.06
88 46 0.70
89 16 0.24
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (89 bp):
TCAAAAATTACCATTTTACACCAAACCTTCCAAAATCCCATTTTTTAACCCCAATTTCACCAAAA
TTACTATTTTTGCCCCCGAACTTT
Found at i:40487712 original size:28 final size:28
Alignment explanation
Indices: 40487491--40487712 Score: 102
Period size: 29 Copynumber: 7.6 Consensus size: 28
40487481 GATTTCACTA
40487491 AAAATTA-TCATTTTACCCTCGAACTTTCC
1 AAAATTACT-ATTTTACCC-CGAACTTTCC
*
40487520 AAAATT-CCATTTTTGA-CCCG-A-TTTCATC
1 AAAATTACTA-TTTT-ACCCCGAACTTTC--C
* * *
40487548 AAAAATTACCATTTTACCCCAAACCTTCC
1 -AAAATTACTATTTTACCCCGAACTTTCC
* * * *
40487577 AAAA-TCCCATTTTTAACCCCAAATTTTCCC
1 AAAATTACTA-TTTT-ACCCCGAACTTT-CC
* *
40487607 AAAATTAC-ATTTTTGCCCCCGAACTTTTCA
1 AAAATTACTA-TTTT-ACCCCGAAC-TTTCC
* *
40487637 AAAATTACCATTTTACACCGAACTTTCC
1 AAAATTACTATTTTACCCCGAACTTTCC
* *
40487665 AAAATTTCATTTTTTAACCCCG-A-TTTCACC
1 AAAATTAC-TATTTT-ACCCCGAACTTT--CC
40487695 AAAATTACTATTTTACCC
1 AAAATTACTATTTTACCC
40487713 TCGGGAATCC
Statistics
Matches: 152, Mismatches: 21, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 31 0.20
29 53 0.35
30 50 0.33
31 9 0.06
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTACTATTTTACCCCGAACTTTCC
Found at i:40489138 original size:31 final size:30
Alignment explanation
Indices: 40489103--40489162 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
40489093 ATCAATCAAA
* *
40489103 ATTTACATGCTTGAAATATACCAATACATAT
1 ATTTACATGCTTGAAAGATACAAAT-CATAT
40489134 ATTTACATGCTTGAAAGATACAAATCATA
1 ATTTACATGCTTGAAAGATACAAATCATA
40489163 AGAATGTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.33
Consensus pattern (30 bp):
ATTTACATGCTTGAAAGATACAAATCATAT
Found at i:40491821 original size:21 final size:21
Alignment explanation
Indices: 40491795--40491834 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40491785 GTTATCCAGG
*
40491795 ACAACATAAAAATAAAATATT
1 ACAACATAAAAAAAAAATATT
40491816 ACAACATAAAAAAAAAATA
1 ACAACATAAAAAAAAAATA
40491835 AAATTGTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (21 bp):
ACAACATAAAAAAAAAATATT
Found at i:40504613 original size:20 final size:21
Alignment explanation
Indices: 40504583--40504671 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 21
40504573 ATCACATACA
40504583 ATTATTTTTAAAAAAAATTAC
1 ATTATTTTTAAAAAAAATTAC
*
40504604 ATTA-TTTTAAAAAAAATTAT
1 ATTATTTTTAAAAAAAATTAC
*
40504624 ATCT-TTCTTAAATTTTAATCAAATTAC
1 AT-TATTTTTAAA----AA--AAATTAC
40504651 ATTATTTTTTAAAAAAAATTA
1 ATTA-TTTTTAAAAAAAATTA
40504672 TGTACAACTC
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
20 17 0.31
21 11 0.20
22 6 0.11
24 2 0.04
25 2 0.04
26 1 0.02
27 8 0.15
28 7 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTTTTAAAAAAAATTAC
Found at i:40508431 original size:15 final size:15
Alignment explanation
Indices: 40508411--40508449 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
40508401 ATTTTAAAGA
*
40508411 AAAAATGAATATTGT
1 AAAAATAAATATTGT
*
40508426 AAAAATAAATGTTGT
1 AAAAATAAATATTGT
*
40508441 AGAAATAAA
1 AAAAATAAA
40508450 AATTTTGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:40515602 original size:17 final size:16
Alignment explanation
Indices: 40515582--40515615 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40515572 TTAGAATTTG
40515582 TATATTAAAAATATTCT
1 TATATT-AAAATATTCT
*
40515599 TATATTTAAATATTCT
1 TATATTAAAATATTCT
40515615 T
1 T
40515616 TTTATTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTAAAATATTCT
Found at i:40518164 original size:27 final size:25
Alignment explanation
Indices: 40518130--40518192 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 25
40518120 ATTAAAAATT
40518130 AAAAATAATATAATATATGTTGTATAA
1 AAAAATAATATAATATAT-TT-TATAA
* *
40518157 AAAAATAATATGATATATTTTTTAA
1 AAAAATAATATAATATATTTTATAA
40518182 AAAAATAATAT
1 AAAAATAATAT
40518193 GAGAGCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 15 0.44
26 2 0.06
27 17 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
AAAAATAATATAATATATTTTATAA
Found at i:40518193 original size:25 final size:27
Alignment explanation
Indices: 40518130--40518194 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 27
40518120 ATTAAAAATT
*
40518130 AAAAATAATATAATATATGTTGTATAA
1 AAAAATAATATGATATATGTTGTATAA
*
40518157 AAAAATAATATGATATAT-TT-TTTAA
1 AAAAATAATATGATATATGTTGTATAA
40518182 AAAAATAATATGA
1 AAAAATAATATGA
40518195 GAGCTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 17 0.47
26 2 0.06
27 17 0.47
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (27 bp):
AAAAATAATATGATATATGTTGTATAA
Found at i:40523799 original size:18 final size:18
Alignment explanation
Indices: 40523776--40523817 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
40523766 GTTAGAAAGA
*
40523776 TTGAGAAAAGGGTTCTTT
1 TTGAGAAAAGGGTTCGTT
40523794 TTGAGAAAAGGGTTCGTT
1 TTGAGAAAAGGGTTCGTT
40523812 TTGAGA
1 TTGAGA
40523818 TAGTGACCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.36
Consensus pattern (18 bp):
TTGAGAAAAGGGTTCGTT
Found at i:40528502 original size:4 final size:4
Alignment explanation
Indices: 40528488--40528630 Score: 123
Period size: 4 Copynumber: 36.8 Consensus size: 4
40528478 AGGGAGGTTA
* * * *
40528488 ATAC CTAC ATAC ATAC AT-- ATAC ACAC ACAC ATAC TTAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
40528534 ATAC ACAC ACAC ACAC ACAC ATAC ATAC ATAC --AC ACAC ACAC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
40528580 ACAC ACAC ACAC ACAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
40528628 ATA
1 ATA
40528631 TCCATTGCTT
Statistics
Matches: 126, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.03
4 122 0.97
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (4 bp):
ATAC
Found at i:40530204 original size:15 final size:16
Alignment explanation
Indices: 40530184--40530225 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
40530174 AAAATTGTAC
40530184 TTTAATTTTAT-TATT
1 TTTAATTTTATATATT
*
40530199 TTTAATTTTTATATTTT
1 TTTAA-TTTTATATATT
40530216 TTTAATTTTA
1 TTTAATTTTA
40530226 AAATTCTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATTTTATATATT
Found at i:40533846 original size:14 final size:14
Alignment explanation
Indices: 40533827--40533855 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40533817 TCAAAGCTTG
40533827 AATCTTTAAAACTC
1 AATCTTTAAAACTC
40533841 AATCTTTAAAACTC
1 AATCTTTAAAACTC
40533855 A
1 A
40533856 TTAACCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
AATCTTTAAAACTC
Found at i:40535477 original size:15 final size:16
Alignment explanation
Indices: 40535451--40535480 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40535441 AAAAATAGAA
40535451 ATTTATAATATTAAAT
1 ATTTATAATATTAAAT
40535467 ATTTA-AATATTAAA
1 ATTTATAATATTAAA
40535481 AAAATATTGT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTATAATATTAAAT
Found at i:40544222 original size:33 final size:33
Alignment explanation
Indices: 40544177--40544239 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
40544167 ATTTAATATA
*
40544177 AATATATATAATTATTATCTAACAT-ATATAATT
1 AATATATATAATT-TTATATAACATAATATAATT
*
40544210 AATATA-ATTAATTTTTTATAACATAATATA
1 AATATATA-TAATTTTATATAACATAATATA
40544240 TTTGGGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (33 bp):
AATATATATAATTTTATATAACATAATATAATT
Found at i:40551482 original size:58 final size:58
Alignment explanation
Indices: 40551410--40551529 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
40551400 ACTCATCAAC
*
40551410 AAACTAAACACAAATATTTTTAAACCCAAATATAATTTTATTCTTCAAA-AACACTCAT
1 AAACTAAACACAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATAACACTCAT
*
40551468 AAACTAAATC-CAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAA-CACAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
40551526 AAAC
1 AAAC
40551530 AACTCCTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
57 3 0.05
58 54 0.93
59 1 0.02
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACACAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
Found at i:40555453 original size:60 final size:62
Alignment explanation
Indices: 40555370--40555664 Score: 290
Period size: 60 Copynumber: 4.9 Consensus size: 62
40555360 AAAAAAACAA
*
40555370 TTTGGTGTTGGCCATTGCATGGTCGACACCACTTTTCTATCTGAT-AAAAAA-TCAAATTTT
1 TTTGGTGTTGGCCATTGCATGGTCGACACCACTTTTTTATCTGATAAAAAAATTCAAATTTT
* *
40555430 TTTGGTGTTGGTCA-TGCATTGGTCGACACCACTTTTTTATCTGA-CAAAAAATTCAAATTTT
1 TTTGGTGTTGGCCATTGCA-TGGTCGACACCACTTTTTTATCTGATAAAAAAATTCAAATTTT
* * *
40555491 TTT-GTGTTGGCCATTGCATGGCCGACA-CTCTTTTTTATTTGATAAAAAAAATTCAAATTTT
1 TTTGGTGTTGGCCATTGCATGGTCGACACCACTTTTTTATCTGAT-AAAAAAATTCAAATTTT
* ** *** *
40555552 TTTAGTGTTGATCA-TGCATTGG-CTGACATTTC-TTTTTATCTGATAAAAAAA-TCAAAATTT
1 TTTGGTGTTGGCCATTGCA-TGGTC-GACACCACTTTTTTATCTGATAAAAAAATTCAAATTTT
* * * * * *
40555612 TTT-ATATTGACCATTGCATGGGCGACATC-CTCTTTTTATTTGATAAAAAAATT
1 TTTGGTGTTGGCCATTGCATGGTCGACACCACT-TTTTTATCTGATAAAAAAATT
40555665 TGATTCTTTA
Statistics
Matches: 203, Mismatches: 17, Indels: 29
0.82 0.07 0.12
Matches are distributed among these distances:
58 1 0.00
59 32 0.16
60 94 0.46
61 48 0.24
62 26 0.13
63 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (62 bp):
TTTGGTGTTGGCCATTGCATGGTCGACACCACTTTTTTATCTGATAAAAAAATTCAAATTTT
Found at i:40555663 original size:121 final size:121
Alignment explanation
Indices: 40555381--40555664 Score: 353
Period size: 121 Copynumber: 2.3 Consensus size: 121
40555371 TTGGTGTTGG
* * * * *
40555381 CCATTGCATGGTCGACACCACTTTTCTATCTGAT-AAAAAA-TCAAATTTTTTTGGTGTTGGTCA
1 CCATTGCATGGCCGACACCTCTTTT-TATTTGATAAAAAAATTCAAATTTTTTTAGTGTTGATCA
* * * * *
40555444 TGCATTGGTCGACACCACTTTTTTATCTGACAAAAAATTCAAATTTTTTTGTGTTGG
65 TGCATTGGTCGACACCACTTTTTTATCTGACAAAAAAATCAAAATTTTTTATATTGA
40555501 CCATTGCATGGCCGACA-CTCTTTTTTATTTGATAAAAAAAATTCAAATTTTTTTAGTGTTGATC
1 CCATTGCATGGCCGACACCTC-TTTTTATTTGAT-AAAAAAATTCAAATTTTTTTAGTGTTGATC
*** *
40555565 ATGCATTGG-CTGACATTTC-TTTTTATCTGATAAAAAAATCAAAATTTTTTATATTGA
64 ATGCATTGGTC-GACACCACTTTTTTATCTGACAAAAAAATCAAAATTTTTTATATTGA
*
40555622 CCATTGCATGGGCGACATCCTCTTTTTATTTGATAAAAAAATT
1 CCATTGCATGGCCGACA-CCTCTTTTTATTTGATAAAAAAATT
40555665 TGATTCTTTA
Statistics
Matches: 142, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
119 9 0.06
120 20 0.14
121 64 0.45
122 46 0.32
123 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (121 bp):
CCATTGCATGGCCGACACCTCTTTTTATTTGATAAAAAAATTCAAATTTTTTTAGTGTTGATCAT
GCATTGGTCGACACCACTTTTTTATCTGACAAAAAAATCAAAATTTTTTATATTGA
Found at i:40555905 original size:51 final size:51
Alignment explanation
Indices: 40555829--40555928 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
40555819 AAAAAATATA
*
40555829 ATTTTTTGGTGTCTAACACCAATCATTGGGATGAAATTTGATGAGGTGTAT
1 ATTTTTTGGTGTCTAACACCAATCATTGGGATGAAATCTGATGAGGTGTAT
40555880 ATTTTTTGGTGTCTAACACCAATCATTGGGATGAAATCTGATGAGGTGT
1 ATTTTTTGGTGTCTAACACCAATCATTGGGATGAAATCTGATGAGGTGT
40555929 CAGCTATTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (51 bp):
ATTTTTTGGTGTCTAACACCAATCATTGGGATGAAATCTGATGAGGTGTAT
Found at i:40556895 original size:11 final size:11
Alignment explanation
Indices: 40556848--40556896 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
40556838 AATAAATTTG
40556848 TTTAAAACTCA
1 TTTAAAACTCA
*
40556859 TTTAATAAATCA
1 TTTAA-AACTCA
** *
40556871 TTTAAAGTTTA
1 TTTAAAACTCA
40556882 TTTAAAACTCA
1 TTTAAAACTCA
40556893 TTTA
1 TTTA
40556897 TTGTTCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (11 bp):
TTTAAAACTCA
Found at i:40557085 original size:23 final size:23
Alignment explanation
Indices: 40557041--40557086 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40557031 TTGTGAATAT
* * *
40557041 TGTTCACGAATATATTCGTTTAA
1 TGTTCACAAACATATTCATTTAA
*
40557064 TGTTCACAAACATATTTATTTAA
1 TGTTCACAAACATATTCATTTAA
40557087 CTTAAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
TGTTCACAAACATATTCATTTAA
Found at i:40557907 original size:14 final size:14
Alignment explanation
Indices: 40557888--40557931 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
40557878 TTTTCACATG
40557888 TTTTGTTTT-TTTT
1 TTTTGTTTTATTTT
40557901 ATTTTGTTTTATTTT
1 -TTTTGTTTTATTTT
*
40557916 TTTAGTTTTATTTT
1 TTTTGTTTTATTTT
40557930 TT
1 TT
40557932 AAAATAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 24 0.86
15 4 0.14
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (14 bp):
TTTTGTTTTATTTT
Found at i:40557924 original size:19 final size:18
Alignment explanation
Indices: 40557894--40557929 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40557884 CATGTTTTGT
*
40557894 TTTTTTTATTTTGTTTTA
1 TTTTTTTATTTTATTTTA
40557912 TTTTTTTAGTTTTATTTT
1 TTTTTTTA-TTTTATTTT
40557930 TTAAAATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTTTTATTTTATTTTA
Found at i:40560385 original size:63 final size:63
Alignment explanation
Indices: 40560257--40560386 Score: 138
Period size: 63 Copynumber: 2.1 Consensus size: 63
40560247 TAATTGAGAC
* * * * *** *
40560257 AAAAAAAAAAGCTTAAGTATCAAATTGGACATTAAGCCAAAGTTAGATACTTGATTGAAATAA
1 AAAAAAAAAAACTTAAGTAACAAATTGAACATTAAGCCAAACTTAGATACCAAATTGAAAAAA
* *
40560320 AAAAAAAAAAACTTAAGTAACAAATTGAACATTGTAA-CTAAACTTAGGTACCAAATT-AAAAAA
1 AAAAAAAAAAACTTAAGTAACAAATTGAACA-T-TAAGCCAAACTTAGATACCAAATTGAAAAAA
40560383 AAAA
1 AAAA
40560387 CTCAGATTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
63 37 0.67
64 15 0.27
65 3 0.05
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.23
Consensus pattern (63 bp):
AAAAAAAAAAACTTAAGTAACAAATTGAACATTAAGCCAAACTTAGATACCAAATTGAAAAAA
Found at i:40595429 original size:156 final size:159
Alignment explanation
Indices: 40595141--40595455 Score: 456
Period size: 156 Copynumber: 2.0 Consensus size: 159
40595131 CAAAAATTAA
* *
40595141 AAGAAATTCATGCATATTAGTCTAAGACACCCTCTATACTTAATGGTCAATTAAAACCAATACAA
1 AAGAAATTAATGCATACTAGTCTAAGACACCCTCTATACTTAATGGTCAATTAAAACCAATACAA
* * * * *
40595206 CATCATTAAATTTTGACTAACACTTCCATCCACATTTAAAAATTAAGCAAGTAACACTATACTAA
66 CATCATTAAAATTTAACCAACACTTCCATCCACATTCAAAAATTAAGCAAGTAACACTATACCAA
*
40595271 TC-AAAAA-A-ATTACATTTGATTCAAAC
131 TCAAAAAAGAGATTACATTTAATTCAAAC
* * * * *
40595297 AAGAAATTAATGCATACTAGTCTAAGACTCCTTCTATACTTAATGGTCACTTAAAATCAATACTA
1 AAGAAATTAATGCATACTAGTCTAAGACACCCTCTATACTTAATGGTCAATTAAAACCAATACAA
* * * *
40595362 TATGATTAAAATTTAACCAACATTTCCATCCAGATTCAAAAATTAAGCAAGTAACACTATACCAA
66 CATCATTAAAATTTAACCAACACTTCCATCCACATTCAAAAATTAAGCAAGTAACACTATACCAA
40595427 TCAAAAAAGAGATTACATTTAATTCAAAC
131 TCAAAAAAGAGATTACATTTAATTCAAAC
40595456 CAAACCAACA
Statistics
Matches: 139, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
156 116 0.83
157 5 0.04
158 1 0.01
159 17 0.12
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (159 bp):
AAGAAATTAATGCATACTAGTCTAAGACACCCTCTATACTTAATGGTCAATTAAAACCAATACAA
CATCATTAAAATTTAACCAACACTTCCATCCACATTCAAAAATTAAGCAAGTAACACTATACCAA
TCAAAAAAGAGATTACATTTAATTCAAAC
Found at i:40596020 original size:17 final size:18
Alignment explanation
Indices: 40595988--40596023 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40595978 GATTACGGTG
40595988 AATAATAATAATAAAATT
1 AATAATAATAATAAAATT
*
40596006 AATAAT-ATGATAAAATT
1 AATAATAATAATAAAATT
40596023 A
1 A
40596024 TGACTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATAATAATAATAAAATT
Found at i:40598799 original size:17 final size:19
Alignment explanation
Indices: 40598779--40598820 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
40598769 TTTAATTAAA
40598779 TTTAATTATT-AATT-TTT
1 TTTAATTATTAAATTATTT
* *
40598796 TTTAAATGTTAAATTATTT
1 TTTAATTATTAAATTATTT
40598815 TTTAAT
1 TTTAAT
40598821 AAAAATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTAATTATTAAATTATTT
Found at i:40603363 original size:16 final size:16
Alignment explanation
Indices: 40603342--40603376 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40603332 GGTCAAGATT
* *
40603342 AAAAATCCAAAATTTA
1 AAAAATACAAAAATTA
40603358 AAAAATACAAAAATTA
1 AAAAATACAAAAATTA
40603374 AAA
1 AAA
40603377 TTAACCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATACAAAAATTA
Found at i:40620981 original size:29 final size:28
Alignment explanation
Indices: 40620915--40620989 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 28
40620905 AGTCCCCAAG
40620915 CTTTCCAAAATTCCATTTTAACCCCAAAA
1 CTTTCCAAAATTCCA-TTTAACCCCAAAA
* *
40620944 C-TTCTAAAAATTACCATTT-ACCCCTAAA
1 CTTTC-CAAAATT-CCATTTAACCCCAAAA
40620972 CTTTCCAAAATTCCATTT
1 CTTTCCAAAATTCCATTT
40620990 TTAACCTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 6 0.15
28 18 0.45
29 13 0.32
30 3 0.08
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.35
Consensus pattern (28 bp):
CTTTCCAAAATTCCATTTAACCCCAAAA
Found at i:40621045 original size:59 final size:59
Alignment explanation
Indices: 40620949--40621436 Score: 507
Period size: 59 Copynumber: 8.3 Consensus size: 59
40620939 CAAAACTTCT
* *
40620949 AAAAATTACCA-TTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * * *
40621007 CAAAATTACCATTTTACCCCCAAA-TCTTCCAAAATTCCATTTTTAACCCCAATTTCACC
1 AAAAATTACCATTTTACCCCCAAACT-TTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * * *
40621066 CAAAATTACCATTTTACCCTCGAA-TCTTCCAAAATCCCA-TTTTAACC-CGATTTTACC
1 AAAAATTACCATTTTACCCCCAAACT-TTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * *
40621123 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAA-CTCTGGTTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTC-GATTTCACC
* * * * *
40621182 AAAAATTACCATTTTACCCCCAAACTTTCCAAAAATTCCA-ATTTAACCCCAAAACTT--CC
1 AAAAATTACCATTTTACCCCCAAACTTTCC-AAAATCCCATTTTTAACCTC--GATTTCACC
* *
40621241 AAAAATTACCATTTTA-CCCCAGAA-TCTTCCAAAATCCCATTTTTAAACTCGGTTTCACC
1 AAAAATTACCATTTTACCCCCA-AACT-TTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * * * *
40621300 AGAAATTACCATTTTACTCCCGAACTTTCCAAAATCCCATTTTTAACCTCGGTTTCACT
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * * * * * *
40621359 AAAAGTTATCGTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACC-CTAATTTTACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTC-GATTTCACC
40621418 AAAAATTA-CATTTTTACCC
1 AAAAATTACCA-TTTTACCC
40621437 TCGAAAGTCA
Statistics
Matches: 365, Mismatches: 47, Indels: 35
0.82 0.11 0.08
Matches are distributed among these distances:
57 47 0.13
58 43 0.12
59 259 0.71
60 14 0.04
61 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
Found at i:40621050 original size:29 final size:28
Alignment explanation
Indices: 40620917--40621283 Score: 176
Period size: 29 Copynumber: 12.6 Consensus size: 28
40620907 TCCCCAAGCT
* *
40620917 TTCCAAAATTCCATTTTAACCCCAAAAC
1 TTCCAAAATTCCATTTTACCCCCAAATC
* *
40620945 TTCTAAAAATTACCA-TTTACCCCTAAA-C
1 TTC-CAAAATT-CCATTTTACCCCCAAATC
* * **
40620973 TTTCCAAAATTCCATTTTTAACCTCGATTTC
1 -TTCCAAAATTCCA-TTTT-ACCCCCAAATC
**
40621004 ACCCAAAATTACCATTTTACCCCCAAATC
1 TTCCAAAATT-CCATTTTACCCCCAAATC
* *
40621033 TTCCAAAATTCCATTTTTAACCCCAATTTC
1 TTCCAAAATTCCA-TTTTACCCCCAA-ATC
** * *
40621063 ACCCAAAATTACCATTTTACCCTCGAATC
1 TTCCAAAATT-CCATTTTACCCCCAAATC
* * * *
40621092 TTCCAAAATCCCATTTTA-ACCC-GATT
1 TTCCAAAATTCCATTTTACCCCCAAATC
* *
40621118 TTACCAAAAATTACCATTTTACCCTCGAA-C
1 TT-CC-AAAATT-CCATTTTACCCCCAAATC
* * * ***
40621148 TTTCCAAAATCCCATTTTTA-ACTCTGGT-
1 -TTCCAAAATTCCA-TTTTACCCCCAAATC
40621176 TTCACCAAAAATTACCATTTTACCCCCAAA-C
1 TT--CC-AAAATT-CCATTTTACCCCCAAATC
* * *
40621207 TTTCCAAAAATTCCAATTTAACCCCAAAAC
1 -TTCC-AAAATTCCATTTTACCCCCAAATC
40621237 TTCCAAAAATTACCATTTTA-CCCCAGAATC
1 TTCC-AAAATT-CCATTTTACCCCCA-AATC
*
40621267 TTCCAAAATCCCATTTT
1 TTCCAAAATTCCATTTT
40621284 TAAACTCGGT
Statistics
Matches: 258, Mismatches: 52, Indels: 58
0.70 0.14 0.16
Matches are distributed among these distances:
26 4 0.02
27 9 0.03
28 39 0.15
29 112 0.43
30 77 0.30
31 15 0.06
32 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.33
Consensus pattern (28 bp):
TTCCAAAATTCCATTTTACCCCCAAATC
Found at i:40622140 original size:153 final size:152
Alignment explanation
Indices: 40621952--40622282 Score: 481
Period size: 153 Copynumber: 2.2 Consensus size: 152
40621942 TTCTCAAAAC
* *
40621952 ATATATCTATATTACAAATAATTTTAAAGCGAGGCAATGTCCTATCGTGTGAAAACTCCGAAAAA
1 ATATATCTATA-TACAAATAATTTTAAAACGAGGCAATGTCCTATCGTATGAAAACTCCGAAAAA
*
40622017 TCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCGAATCGAATAT-CCTCTTCAAAAG
65 TCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCCTCTTCAAAAG
* *
40622081 TTTCCGAAACA-TCCTTCAATTTTT
130 TTTCCAAAACACT-CTTCAA-TCTT
* * *
40622105 ATATATCTATATCACAAATAATTTTAAAACGAGGCAATGTCCTTTCGTATGAAAACTTCGAGAAA
1 ATATATCTATAT-ACAAATAATTTTAAAACGAGGCAATGTCCTATCGTATGAAAACTCCGAAAAA
* *
40622170 TCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGGATATCCCTTTTCAAAAG
65 TCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCCTCTTCAAAAG
*
40622235 TTTTCAAAACACTCTTCAATCTT
130 TTTCCAAAACACTCTTCAATCTT
*
40622258 ATA-AT-TATATACAAAGTGATTTTAA
1 ATATATCTATATACAAA-TAATTTTAA
40622283 GACCAAAAGA
Statistics
Matches: 162, Mismatches: 12, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
150 5 0.03
151 13 0.08
152 3 0.02
153 114 0.70
154 26 0.16
155 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (152 bp):
ATATATCTATATACAAATAATTTTAAAACGAGGCAATGTCCTATCGTATGAAAACTCCGAAAAAT
CGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCCTCTTCAAAAGT
TTCCAAAACACTCTTCAATCTT
Found at i:40658774 original size:28 final size:29
Alignment explanation
Indices: 40658721--40658790 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
40658711 AGAAATTTAA
* *
40658721 TATAA-ATATATAATTATTGATTTATTAT
1 TATAACATATATAATTAATGATGTATTAT
*
40658749 T-TAACATATATAATTAAT-ATAGTATTTT
1 TATAACATATATAATTAATGAT-GTATTAT
40658777 TATAACATAATATA
1 TATAACAT-ATATA
40658791 TTTGGGCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 5 0.14
28 19 0.54
29 6 0.17
30 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
TATAACATATATAATTAATGATGTATTAT
Found at i:40663934 original size:12 final size:11
Alignment explanation
Indices: 40663911--40663940 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
40663901 TAATAATAAA
40663911 TTAATATTTAT
1 TTAATATTTAT
40663922 TTAATAGTTTAT
1 TTAATA-TTTAT
40663934 TTAATAT
1 TTAATAT
40663941 AGTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (11 bp):
TTAATATTTAT
Found at i:40667325 original size:21 final size:20
Alignment explanation
Indices: 40667297--40667339 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
40667287 TGCACCTCGA
40667297 TTTATTTACAATTGA-ATAAT
1 TTTATTTA-AATTGATATAAT
*
40667317 TTTACTTTAATTTGATATAAT
1 TTTA-TTTAAATTGATATAAT
40667338 TT
1 TT
40667340 AATTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTATTTAAATTGATATAAT
Found at i:40669928 original size:136 final size:137
Alignment explanation
Indices: 40669699--40669950 Score: 337
Period size: 136 Copynumber: 1.8 Consensus size: 137
40669689 CCCCAACACT
* * * ***
40669699 AAAACTATCAAAGCCCAACGGACACCTCCAAAACACGTTATGGGAATATCATGGTCTTCAAGTTC
1 AAAACTACCAAAGCCCAACGGACACCTCCAAAACAAGTTACGGGAATATCACAATCTTCAAGTTC
* **
40669764 GAGCTGATAAGATAACCGTAGCCAAATTCTGCCTTTTTTCCGATGAACTCGGTGACTTGAAACCT
66 GAGCAGATAAGATAACCGTAGCCAAATTCTGCC-TCGTTCCGATGAACTCGGTGACTTGAAACCT
40669829 CAAACTTG
130 CAAACTTG
* * *
40669837 AAAACTACCAAAGCCCAAC-GACACCT-CAAAACAAGTTCCGGGAATGTCACAATCTTCAAGTTT
1 AAAACTACCAAAGCCCAACGGACACCTCCAAAACAAGTTACGGGAATATCACAATCTTCAAGTTC
* ** *
40669900 GGGCAGATAAGATAACCGTAGCTGAATTCTGCCTCGTTCCGATGAGCTCGG
66 GAGCAGATAAGATAACCGTAGCCAAATTCTGCCTCGTTCCGATGAACTCGG
40669951 AACACTACCA
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
135 15 0.15
136 58 0.59
137 7 0.07
138 18 0.18
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (137 bp):
AAAACTACCAAAGCCCAACGGACACCTCCAAAACAAGTTACGGGAATATCACAATCTTCAAGTTC
GAGCAGATAAGATAACCGTAGCCAAATTCTGCCTCGTTCCGATGAACTCGGTGACTTGAAACCTC
AAACTTG
Found at i:40670043 original size:114 final size:114
Alignment explanation
Indices: 40669840--40670046 Score: 326
Period size: 114 Copynumber: 1.8 Consensus size: 114
40669830 AAACTTGAAA
* * * *
40669840 ACTACCAAAGCCCAACGACACCTCAAAACAAGTTCCGGGAATGTCACAATCTTCAAGTTTGGGCA
1 ACTACCAAAGCCCAACAACACCCCAAAACAAGTTCCGGGAATGTCACAAGCTTCAAGTTCGGGCA
*
40669905 GATAAGATAACCGTAGCTGAATTCTGCCTCGTTCCGATGAGCTCGGAAC
66 GATAAGATAACCGTAGCAGAATTCTGCCTCGTTCCGATGAGCTCGGAAC
* *
40669954 ACTACCAAAGCCCAACAACACCCCATAACAAGTTCCGGGAATGTCACAGGCTTCAAGTTCGGGCA
1 ACTACCAAAGCCCAACAACACCCCAAAACAAGTTCCGGGAATGTCACAAGCTTCAAGTTCGGGCA
*
40670019 GATAAGATAACCGTGGACAG-ATTCTGCC
66 GATAAGATAACCGTAG-CAGAATTCTGCC
40670047 CCGCGTCCTA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 82 0.98
115 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.19
Consensus pattern (114 bp):
ACTACCAAAGCCCAACAACACCCCAAAACAAGTTCCGGGAATGTCACAAGCTTCAAGTTCGGGCA
GATAAGATAACCGTAGCAGAATTCTGCCTCGTTCCGATGAGCTCGGAAC
Found at i:40683393 original size:2 final size:2
Alignment explanation
Indices: 40683386--40683414 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40683376 TCAATCTTTC
40683386 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
40683415 TTTTAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40693913 original size:145 final size:144
Alignment explanation
Indices: 40693643--40693917 Score: 412
Period size: 144 Copynumber: 1.9 Consensus size: 144
40693633 AATGCACTTC
*
40693643 ACCTGAAGCAAAAATAACTTAAACCCAAAATAATCAAATAAGTAACTCGAAATATTTGAATTTGA
1 ACCTGAAGCAAAAATAACTTAAACCCAAAATAATCAAATAAGTAACTCGAAATATTTGAATTCGA
* * *
40693708 GTGGCAAACACAAATGATTCAAAATCGAAATGACCCAAATTGAAAAAACCAAACCCAAAATGATT
66 GTGGCAAACACAAATGATCCAAAATCAAAATGACCCAAATTAAAAAAACCAAACCCAAAATGATT
40693773 GACCAAGTAACCTA
131 GACCAAGTAACCTA
* * * *
40693787 ACCTGAAGCAAAAATAACTTAAACCCAAAATGATCAGATAAGTAATTTGAAATGATTTGAATTCG
1 ACCTGAAGCAAAAATAACTTAAACCCAAAATAATCAAATAAGTAACTCGAAAT-ATTTGAATTCG
*
40693852 AG-GGTCAAACACAAATGATCC-AAACCTAAAATGACCCAAA-TAAAAAAACCTAAACCCAAAAT
65 AGTGG-CAAACACAAATGATCCAAAATC-AAAATGACCCAAATTAAAAAAACC-AAACCCAAAAT
40693914 GATT
127 GATT
40693918 AAATAAGTAA
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
144 64 0.54
145 54 0.46
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.20
Consensus pattern (144 bp):
ACCTGAAGCAAAAATAACTTAAACCCAAAATAATCAAATAAGTAACTCGAAATATTTGAATTCGA
GTGGCAAACACAAATGATCCAAAATCAAAATGACCCAAATTAAAAAAACCAAACCCAAAATGATT
GACCAAGTAACCTA
Found at i:40693980 original size:96 final size:97
Alignment explanation
Indices: 40693796--40693982 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 97
40693786 AACCTGAAGC
* * * * *
40693796 AAAAATAACTTAAACCCAAAATGATCAGATAAGTAATTTGAAATGATTTGAATTCGAGGGTCAAA
1 AAAAATAACCTAAACCCAAAATGATCAAATAAGTAATTCGAAATGATTTGAAATCGAAGGTCAAA
*
40693861 CACAAATGATCCAAACCTAAAATGACCCAAAT
66 CACAAACGATCCAAACCTAAAATGACCCAAAT
* **
40693893 AAAAA-AACCTAAACCCAAAATGATTAAATAAGTAA-TCGAAAATGATTTGAAATCGAATTTCAA
1 AAAAATAACCTAAACCCAAAATGATCAAATAAGTAATTCG-AAATGATTTGAAATCGAAGGTCAA
* * * * *
40693956 ATACAAGCGATCTAAACTTGAAATGAC
65 ACACAAACGATCCAAACCTAAAATGAC
40693983 TCAACTCGAA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
95 2 0.03
96 68 0.91
97 5 0.07
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.23
Consensus pattern (97 bp):
AAAAATAACCTAAACCCAAAATGATCAAATAAGTAATTCGAAATGATTTGAAATCGAAGGTCAAA
CACAAACGATCCAAACCTAAAATGACCCAAAT
Found at i:40699770 original size:20 final size:20
Alignment explanation
Indices: 40699745--40699786 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40699735 CCCATTTCTC
40699745 CACCTTAATTTTATATCTAT
1 CACCTTAATTTTATATCTAT
40699765 CACCTTAATTTTATATCTAT
1 CACCTTAATTTTATATCTAT
40699785 CA
1 CA
40699787 GTAATAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (20 bp):
CACCTTAATTTTATATCTAT
Found at i:40701273 original size:19 final size:19
Alignment explanation
Indices: 40701249--40701294 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
40701239 GATTAACATG
40701249 TGCATACTCGAAGTGGATT
1 TGCATACTCGAAGTGGATT
40701268 TGCATACTCGAAGTGGATT
1 TGCATACTCGAAGTGGATT
40701287 TGCATACT
1 TGCATACT
40701295 ATGAGTTCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (19 bp):
TGCATACTCGAAGTGGATT
Found at i:40705301 original size:12 final size:12
Alignment explanation
Indices: 40705280--40705313 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40705270 AGCAGGTCAT
40705280 TTCAAGTTGGCA
1 TTCAAGTTGGCA
*
40705292 TTCAATTTGGCA
1 TTCAAGTTGGCA
*
40705304 CTCAAGTTGG
1 TTCAAGTTGG
40705314 GGTCAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (12 bp):
TTCAAGTTGGCA
Found at i:40705532 original size:32 final size:32
Alignment explanation
Indices: 40705482--40705555 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
40705472 TTTGGGTTAC
* * *
40705482 TTCAAGTTATTTCAAGTTTGGATCATTTTGAA
1 TTCAAGTCATTTCAAGTTTAGACCATTTTGAA
* *
40705514 TTCATGTCATTTCGAGTTTAGACCATTTTGAA
1 TTCAAGTCATTTCAAGTTTAGACCATTTTGAA
40705546 TTCAAGTCAT
1 TTCAAGTCAT
40705556 CTAGTGCCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (32 bp):
TTCAAGTCATTTCAAGTTTAGACCATTTTGAA
Found at i:40709087 original size:23 final size:22
Alignment explanation
Indices: 40709052--40709095 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
40709042 ATTTTGAATC
*
40709052 AACTCAATTCGAATTTGAAAAT
1 AACTCAATTCGAAATTGAAAAT
40709074 AACTCAAATTCGAAATTGAAAA
1 AACTC-AATTCGAAATTGAAAA
40709096 ATATGAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (22 bp):
AACTCAATTCGAAATTGAAAAT
Found at i:40710888 original size:25 final size:24
Alignment explanation
Indices: 40710850--40710916 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
40710840 TAAAATATTA
* *
40710850 TTTTTTTAGTTTTTAAAGAACCTAAT
1 TTTTTTTA-ATTTTAAAG-ACCAAAT
*
40710876 TTTTTTTAATTTTAAAGGCCAAAT
1 TTTTTTTAATTTTAAAGACCAAAT
*
40710900 TTTTTATTAACTTTAAA
1 TTTTT-TTAATTTTAAA
40710917 CGGCCCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 10 0.28
25 18 0.50
26 8 0.22
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTTTTTAATTTTAAAGACCAAAT
Found at i:40710921 original size:26 final size:24
Alignment explanation
Indices: 40710873--40710921 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
40710863 TAAAGAACCT
*
40710873 AATTTTTTTTAATTTTAAAGGCCA
1 AATTTTTTTTAACTTTAAAGGCCA
40710897 AATTTTTTATTAACTTTAAACGGCC
1 AATTTTTT-TTAACTTTAAA-GGCC
40710922 CAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (24 bp):
AATTTTTTTTAACTTTAAAGGCCA
Found at i:40710987 original size:30 final size:29
Alignment explanation
Indices: 40710934--40710990 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40710924 AAAAAAATTT
* *
40710934 TAACTTTTAAGGATCTAAAATTTTTTTAC
1 TAACTTTTAAGAAACTAAAATTTTTTTAC
*
40710963 TAACTTTTAAGAAACTTGAAATTTTTTT
1 TAACTTTTAAGAAAC-TAAAATTTTTTT
40710991 CTTAAAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (29 bp):
TAACTTTTAAGAAACTAAAATTTTTTTAC
Found at i:40731325 original size:20 final size:22
Alignment explanation
Indices: 40731286--40731330 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40731276 AGAATTGAAT
40731286 AATAAAATTTTGAGAAATTA-A
1 AATAAAATTTTGAGAAATTATA
* *
40731307 AATATAATTTT-ATAAATTATA
1 AATAAAATTTTGAGAAATTATA
40731328 AAT
1 AAT
40731331 TTATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AATAAAATTTTGAGAAATTATA
Found at i:40731336 original size:20 final size:19
Alignment explanation
Indices: 40731300--40731341 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40731290 AAATTTTGAG
40731300 AAATTAAAATATAATTTTAT
1 AAATTAAAATATAATTTT-T
*
40731320 AAATTATAAAT-TTATTTTT
1 AAATTA-AAATATAATTTTT
40731339 AAA
1 AAA
40731342 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTAAAATATAATTTTT
Found at i:40734013 original size:3 final size:3
Alignment explanation
Indices: 40734007--40734039 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40733997 TCTCTCTCTC
40734007 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40734040 GAATTATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.