Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 13 of 144
Found at i:3212314 original size:24 final size:25
Alignment explanation
Indices: 3212287--3212341 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
3212277 TTATTTTTAT
3212287 TTTTTTAAAATATTAATA-T-AATTA
1 TTTTTT-AAATATTAATATTAAATTA
*
3212311 TTTTATTCAATATTAATATTAAATTA
1 TTTT-TTAAATATTAATATTAAATTA
3212337 TTTTT
1 TTTTT
3212342 AATTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 14 0.52
25 4 0.15
26 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTTTAAATATTAATATTAAATTA
Found at i:3222667 original size:25 final size:24
Alignment explanation
Indices: 3222639--3222739 Score: 118
Period size: 23 Copynumber: 4.3 Consensus size: 24
3222629 ACACTAGCAC
*
3222639 GCTCTCTGTTGTTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
*
3222664 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
** *
3222687 GCTCTCTG-ATTAATACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
*
3222710 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
3222733 GCTCTCT
1 GCTCTCT
3222740 ATTGCCTAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 58 0.88
25 8 0.12
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:3222728 original size:69 final size:67
Alignment explanation
Indices: 3222640--3222789 Score: 196
Period size: 69 Copynumber: 2.1 Consensus size: 67
3222630 CACTAGCACG
*
3222640 CTCTCTGTTGTTAGCACTGTGTGTGCTCTCTGA-T-TAGCACTTTGTGTGCTCTCTGATTAATAC
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCT-ATTCTAGCAC-TTATGTGCTCTCTG-TTAATAC
3222703 TTTGTGTA
61 TTTG-GTA
*
3222711 CTCTCTGTTTAGCACTGTGTGTGCTCTCTATTGCCTAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTATT--CTAGCACTTATGTGCTCTCTGTTAATACTTT
3222776 GGTA
64 GGTA
3222780 CTCTCTGTTT
1 CTCTCTGTTT
3222790 GTTCCGTATA
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
68 1 0.01
69 35 0.48
70 11 0.15
71 20 0.27
72 6 0.08
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (67 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTATTCTAGCACTTATGTGCTCTCTGTTAATACTTTGG
TA
Found at i:3222788 original size:21 final size:23
Alignment explanation
Indices: 3222650--3222786 Score: 129
Period size: 23 Copynumber: 6.0 Consensus size: 23
3222640 CTCTCTGTTG
*
3222650 TTAGCACTGTGTGTGCTCTCTGA
1 TTAGCACTTTGTGTGCTCTCTGA
3222673 TTAGCACTTTGTGTGCTCTCTGA
1 TTAGCACTTTGTGTGCTCTCTGA
** * *
3222696 TTAATACTTTGTGTACTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGA
*
3222719 TTAGCACTGTGTGTGCTCTCT-A
1 TTAGCACTTTGTGTGCTCTCTGA
*
3222741 TTGCCTAGCAC-TTATGTGCTCTCTG-
1 -T---TAGCACTTTGTGTGCTCTCTGA
* *
3222766 TTAGTACTTTG-GTACTCTCTG
1 TTAGCACTTTGTGTGCTCTCTG
3222787 TTTGTTCCGT
Statistics
Matches: 93, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
21 14 0.15
22 2 0.02
23 59 0.63
24 1 0.01
25 11 0.12
26 6 0.06
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (23 bp):
TTAGCACTTTGTGTGCTCTCTGA
Found at i:3227200 original size:20 final size:19
Alignment explanation
Indices: 3227168--3227205 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3227158 TGGTGTTTAG
3227168 AGTTTAAAGTTTGAGGTTTT
1 AGTTTAAAGTTTG-GGTTTT
3227188 AGTTT-AAGATTTGGGTTT
1 AGTTTAAAG-TTTGGGTTT
3227206 GGGGTTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (19 bp):
AGTTTAAAGTTTGGGTTTT
Found at i:3227244 original size:34 final size:33
Alignment explanation
Indices: 3227197--3227299 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 33
3227187 TAGTTTAAGA
* * * *
3227197 TTTGGGTTTGGGGTTTAAGTTTAAGGTTCGAAG
1 TTTGGGTTTGGGGTTCAAGATCAAGCTTCGAAG
3227230 TTTGAGGTTTGGGGTTCAAGATCAAGCTTCG-A-
1 TTTG-GGTTTGGGGTTCAAGATCAAGCTTCGAAG
*
3227262 --T--GTTTGGGGTTCAAGATCAAGCTTCGATG
1 TTTGGGTTTGGGGTTCAAGATCAAGCTTCGAAG
3227291 TTTGAGGTT
1 TTTG-GGTT
3227300 CAAAGTTTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
27 25 0.44
30 1 0.02
31 1 0.02
33 5 0.09
34 25 0.44
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (33 bp):
TTTGGGTTTGGGGTTCAAGATCAAGCTTCGAAG
Found at i:3227274 original size:27 final size:27
Alignment explanation
Indices: 3227236--3227302 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
3227226 GAAGTTTGAG
3227236 GTTTGGGGTTCAAGATCAAGCTTCGAT
1 GTTTGGGGTTCAAGATCAAGCTTCGAT
3227263 GTTTGGGGTTCAAGATCAAGCTTCGAT
1 GTTTGGGGTTCAAGATCAAGCTTCGAT
*
3227290 GTTTGAGGTTCAA
1 GTTTGGGGTTCAA
3227303 AGTTTGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.34
Consensus pattern (27 bp):
GTTTGGGGTTCAAGATCAAGCTTCGAT
Found at i:3227373 original size:34 final size:33
Alignment explanation
Indices: 3227325--3227409 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
3227315 TAAATTAGGG
* * *
3227325 TTTGGAGTTTAAGTTTATGGTTTGAGATTTGAGA
1 TTTGGGGTTCAAGTTTATGGTTTG-GATTCGAGA
* *
3227359 TTTGGGGTTCAAGTTCATGGTTTGGGTTCGAGA
1 TTTGGGGTTCAAGTTTATGGTTTGGATTCGAGA
* *
3227392 TTTGAGATTCAAAGTTTA
1 TTTGGGGTTC-AAGTTTA
3227410 GAATTCATGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 15 0.36
34 27 0.64
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (33 bp):
TTTGGGGTTCAAGTTTATGGTTTGGATTCGAGA
Found at i:3227403 original size:33 final size:34
Alignment explanation
Indices: 3227335--3227403 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
3227325 TTTGGAGTTT
* * * *
3227335 AAGTTTATGGTTTGAGATTTGAGATTTGGGGTTC
1 AAGTTCATGGTTTGAGATTCGAGATTTGAGATTC
*
3227369 AAGTTCATGGTTTG-GGTTCGAGATTTGAGATTC
1 AAGTTCATGGTTTGAGATTCGAGATTTGAGATTC
3227402 AA
1 AA
3227404 AGTTTAGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.23, C:0.06, G:0.30, T:0.41
Consensus pattern (34 bp):
AAGTTCATGGTTTGAGATTCGAGATTTGAGATTC
Found at i:3228787 original size:2 final size:2
Alignment explanation
Indices: 3228782--3228808 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3228772 AAATTAAAAA
3228782 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 A
3228809 AAAACTTTAG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3229011 original size:13 final size:12
Alignment explanation
Indices: 3228983--3229026 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3228973 ACAAATCCAA
*
3228983 TATTATTATATT
1 TATTTTTATATT
3228995 TATTTTTATATTT
1 TATTTTTATA-TT
* *
3229008 TATTTTAAAATT
1 TATTTTTATATT
3229020 TATTTTT
1 TATTTTT
3229027 CTTATACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTTTATATT
Found at i:3250184 original size:35 final size:34
Alignment explanation
Indices: 3250144--3250213 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 34
3250134 AAATCACCAA
3250144 AAAAAAATACATCAACTTAAATCACCAAAAAAAAT
1 AAAAAAATACATCAA-TTAAATCACCAAAAAAAAT
3250179 AAAAAAATACATCAATTAAATCACCAAAAAAAAT
1 AAAAAAATACATCAATTAAATCACCAAAAAAAAT
3250213 A
1 A
3250214 CATCAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 20 0.57
35 15 0.43
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.17
Consensus pattern (34 bp):
AAAAAAATACATCAATTAAATCACCAAAAAAAAT
Found at i:3253582 original size:2 final size:2
Alignment explanation
Indices: 3253575--3253602 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3253565 TTATCTTTGC
3253575 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3253603 TTTATACTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3260011 original size:6 final size:6
Alignment explanation
Indices: 3259996--3260033 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
3259986 ATTCAAACTC
*
3259996 CCCTCG CCCTCA CCCTCG CCCTCG CCCTCG CCCTCG CC
1 CCCTCG CCCTCG CCCTCG CCCTCG CCCTCG CCCTCG CC
3260034 TGTTTGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.68, G:0.13, T:0.16
Consensus pattern (6 bp):
CCCTCG
Found at i:3260424 original size:8 final size:8
Alignment explanation
Indices: 3260411--3260445 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
3260401 ACATGAATTT
3260411 AAATTTTA
1 AAATTTTA
3260419 AAATTTTA
1 AAATTTTA
3260427 AAATTTTA
1 AAATTTTA
3260435 AAATTTTA
1 AAATTTTA
3260443 AAA
1 AAA
3260446 ATAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:3267401 original size:51 final size:52
Alignment explanation
Indices: 3267341--3267444 Score: 201
Period size: 51 Copynumber: 2.0 Consensus size: 52
3267331 TAACATAATT
3267341 AACATATATAAATTATTTGATTATCAAAAAA-AATGCCAATAAAAAATTATA
1 AACATATATAAATTATTTGATTATCAAAAAATAATGCCAATAAAAAATTATA
3267392 AACATATATAAATTATTTGATTATCAAAAAATAATGCCAATAAAAAATTATA
1 AACATATATAAATTATTTGATTATCAAAAAATAATGCCAATAAAAAATTATA
3267444 A
1 A
3267445 TCATTATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 31 0.60
52 21 0.40
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.32
Consensus pattern (52 bp):
AACATATATAAATTATTTGATTATCAAAAAATAATGCCAATAAAAAATTATA
Found at i:3280822 original size:72 final size:72
Alignment explanation
Indices: 3280746--3280891 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 72
3280736 AAAGTAAGTG
*
3280746 GTATATAATGATGAATAGGTGAGAAAAATATATGTGTGAAATATTATGTGGTTAATTATAAAGAT
1 GTATATAATGATGAATAAGTGAGAAAAATATATGTGTGAAATATTATGTGGTTAATTATAAAGAT
3280811 TGATTGT
66 TGATTGT
3280818 GTATATAATGATGAATAAGTGAGAAAAATATATGTGTGAAATATTATGTGGTTAATTATAAAGAT
1 GTATATAATGATGAATAAGTGAGAAAAATATATGTGTGAAATATTATGTGGTTAATTATAAAGAT
3280883 TGATTGT
66 TGATTGT
3280890 GT
1 GT
3280892 GATTAATTGG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (72 bp):
GTATATAATGATGAATAAGTGAGAAAAATATATGTGTGAAATATTATGTGGTTAATTATAAAGAT
TGATTGT
Found at i:3281002 original size:6 final size:6
Alignment explanation
Indices: 3280991--3281029 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3280981 TGATCAAAAT
* * *
3280991 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
3281030 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:3284469 original size:20 final size:20
Alignment explanation
Indices: 3284440--3284526 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
3284430 TATCCTGCAC
3284440 AAAGCCTGATATACCGGCAT
1 AAAGCCTGATATACCGGCAT
* * *
3284460 AAAGCTTGATACACCGGCAC
1 AAAGCCTGATATACCGGCAT
3284480 AAAGCCTGA-AT-CTCTGGCAT
1 AAAGCCTGATATAC-C-GGCAT
* *
3284500 AAAGCTTGATTTACCGGCAT
1 AAAGCCTGATATACCGGCAT
3284520 AAAGCCT
1 AAAGCCT
3284527 AAATACTTAG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 48 0.89
21 2 0.04
22 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAGCCTGATATACCGGCAT
Found at i:3284499 original size:40 final size:40
Alignment explanation
Indices: 3284436--3284526 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
3284426 TGTATATCCT
3284436 GCACAAAGCCTGATATACCGGCATAAAGCTTGATACACCG
1 GCACAAAGCCTGATATACCGGCATAAAGCTTGATACACCG
**
3284476 GCACAAAGCCTGA-AT-CTCTGGCATAAAGCTTGATTTACCG
1 GCACAAAGCCTGATATAC-C-GGCATAAAGCTTGATACACCG
*
3284516 GCATAAAGCCT
1 GCACAAAGCCT
3284527 AAATACTTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 3 0.07
40 42 0.91
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (40 bp):
GCACAAAGCCTGATATACCGGCATAAAGCTTGATACACCG
Found at i:3288559 original size:13 final size:13
Alignment explanation
Indices: 3288540--3288573 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3288530 AAATGTGGTA
3288540 GAAAAGTTCTTTT
1 GAAAAGTTCTTTT
* *
3288553 GATAAGTACTTTT
1 GAAAAGTTCTTTT
3288566 GAAAAGTT
1 GAAAAGTT
3288574 TGGTTAAATA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (13 bp):
GAAAAGTTCTTTT
Found at i:3291249 original size:3 final size:3
Alignment explanation
Indices: 3291241--3291277 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
3291231 AATGTATTAG
3291241 TTC TTC TTC TTC TTC TTC TTC TCTC TTC TTTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC T-TC TTC -TTC TTC TT
3291278 TATCGCAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3291436 original size:12 final size:11
Alignment explanation
Indices: 3291414--3291441 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3291404 GAATTCGTTC
3291414 TTTTTTATTTT
1 TTTTTTATTTT
3291425 TTTTTTATTTT
1 TTTTTTATTTT
3291436 TTTTTT
1 TTTTTT
3291442 GGGATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:3295426 original size:8 final size:8
Alignment explanation
Indices: 3295413--3295445 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
3295403 TTCTAAATTA
3295413 TTTATAAT
1 TTTATAAT
3295421 TTTATAAT
1 TTTATAAT
3295429 TTTATAAT
1 TTTATAAT
3295437 TTTA-AAT
1 TTTATAAT
3295444 TT
1 TT
3295446 GTGGTTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATAAT
Found at i:3297674 original size:19 final size:20
Alignment explanation
Indices: 3297626--3297674 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
3297616 TACATAATAT
3297626 ATATTGAAAAAAAATACATA
1 ATATTGAAAAAAAATACATA
* *
3297646 ATA-T-ATAAAAAATATTATA
1 ATATTGAAAAAAAATA-CATA
3297665 ATATTGAAAA
1 ATATTGAAAA
3297675 TAAGTTGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 9 0.39
19 7 0.30
20 4 0.17
21 3 0.13
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
ATATTGAAAAAAAATACATA
Found at i:3298032 original size:19 final size:18
Alignment explanation
Indices: 3297999--3298048 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3297989 TTACTTTAAA
*
3297999 AAAATATTTAA-AAATTTAT
1 AAAATA-TTAATAAA-TTAG
3298018 AAAATATTAATAAATTAG
1 AAAATATTAATAAATTAG
3298036 AAAA-ATTAATAAA
1 AAAATATTAATAAA
3298049 AAATATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 9 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATATTAATAAATTAG
Found at i:3299391 original size:2 final size:2
Alignment explanation
Indices: 3299384--3299421 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3299374 CGCTTAATCC
3299384 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3299422 ATCAAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3303038 original size:14 final size:11
Alignment explanation
Indices: 3303006--3303037 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3302996 TGACATAGAA
3303006 TATGATGATGG
1 TATGATGATGG
3303017 TATGATGATGG
1 TATGATGATGG
3303028 TATGATGATG
1 TATGATGATG
3303038 AAATGGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (11 bp):
TATGATGATGG
Found at i:3307895 original size:23 final size:23
Alignment explanation
Indices: 3307869--3307948 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 23
3307859 TAAAGATCAT
*
3307869 TTTATTTCTAGACCTAAATTAAG
1 TTTATTTCAAGACCTAAATTAAG
* * *
3307892 TTTATCTT-AAGA--TAAAGATCAC
1 TTTAT-TTCAAGACCTAAA-TTAAG
**
3307914 TTTATTTTTAGACCTAAATTAAG
1 TTTATTTCAAGACCTAAATTAAG
3307937 TTT-TTTCAAGAC
1 TTTATTTCAAGAC
3307949 TAGCTTTATA
Statistics
Matches: 42, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
21 6 0.14
22 17 0.40
23 13 0.31
24 6 0.14
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (23 bp):
TTTATTTCAAGACCTAAATTAAG
Found at i:3307920 original size:45 final size:45
Alignment explanation
Indices: 3307851--3307939 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
3307841 TGTGCCATTG
* *
3307851 TCTTGAGATAAAGATCATTTTATTTCTAGACCTAAATTAAGTTTA
1 TCTTAAGATAAAGATCACTTTATTTCTAGACCTAAATTAAGTTTA
*
3307896 TCTTAAGATAAAGATCACTTTATTTTTAGACCTAAATTAAGTTT
1 TCTTAAGATAAAGATCACTTTATTTCTAGACCTAAATTAAGTTT
3307940 TTTCAAGACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (45 bp):
TCTTAAGATAAAGATCACTTTATTTCTAGACCTAAATTAAGTTTA
Found at i:3310263 original size:39 final size:39
Alignment explanation
Indices: 3310220--3310417 Score: 198
Period size: 39 Copynumber: 5.1 Consensus size: 39
3310210 GGTCACAATA
** * *
3310220 TCACTGCCAGTTCAGGGTAGTATCGCAGTGTTTACAGTG
1 TCACTGCCAGTTCAGTATGGTATCACAGTGTTTACAGTG
* * * * *
3310259 TCACTGCTAATTCAGTTTGGTATCGCAGTGTTTATAGTG
1 TCACTGCCAGTTCAGTATGGTATCACAGTGTTTACAGTG
* * *
3310298 TCACTACCAGTTCAGTATGGTAGCACAGTGTTTACAATG
1 TCACTGCCAGTTCAGTATGGTATCACAGTGTTTACAGTG
* * *
3310337 TCACTGCTAGTTTAGTATGGTATCACAATGTTTACAGTG
1 TCACTGCCAGTTCAGTATGGTATCACAGTGTTTACAGTG
* * ** ** *
3310376 TCACTGCTAATTCAGTATAATATCACAACGTTTACGGTG
1 TCACTGCCAGTTCAGTATGGTATCACAGTGTTTACAGTG
3310415 TCA
1 TCA
3310418 TTGGTCATGG
Statistics
Matches: 133, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 133 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (39 bp):
TCACTGCCAGTTCAGTATGGTATCACAGTGTTTACAGTG
Found at i:3311253 original size:14 final size:15
Alignment explanation
Indices: 3311234--3311264 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3311224 AACTAAACAT
3311234 AATAAATAAA-AATA
1 AATAAATAAATAATA
3311248 AATAAATAAATAATA
1 AATAAATAAATAATA
3311263 AA
1 AA
3311265 AGAAAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAATAAATAATA
Found at i:3317177 original size:13 final size:13
Alignment explanation
Indices: 3317161--3317186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3317151 TTTCACTTTT
3317161 CTAATATAATGGC
1 CTAATATAATGGC
3317174 CTAATATAATGGC
1 CTAATATAATGGC
3317187 ACATGAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CTAATATAATGGC
Found at i:3324259 original size:6 final size:6
Alignment explanation
Indices: 3324248--3324273 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3324238 TTTAATATCT
3324248 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
3324274 TTATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:3333076 original size:23 final size:23
Alignment explanation
Indices: 3333046--3333102 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
3333036 TGACGTGGCG
3333046 TCCAGTCAGCAGCTTCTAGAAGA
1 TCCAGTCAGCAGCTTCTAGAAGA
*
3333069 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGA
*
3333092 TCTAGTCAGCA
1 TCCAGTCAGCA
3333103 AGGATGGACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAGAAGA
Found at i:3339652 original size:24 final size:23
Alignment explanation
Indices: 3339610--3339659 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3339600 ATTTTTCGTC
3339610 ATTAATTTATTTTGATTATTTAT
1 ATTAATTTATTTTGATTATTTAT
* * *
3339633 ATTATTTTATTTTTACTTATTTTT
1 ATTAATTTATTTTGA-TTATTTAT
3339657 ATT
1 ATT
3339660 TTTGGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTAATTTATTTTGATTATTTAT
Found at i:3343641 original size:21 final size:21
Alignment explanation
Indices: 3343608--3343647 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3343598 TTCCTCCTTC
* *
3343608 GCTTGCTCATCTACTTGATTG
1 GCTTCCTCATCTACATGATTG
*
3343629 GCTTCCTCTTCTACATGAT
1 GCTTCCTCATCTACATGAT
3343648 GTTCATCCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (21 bp):
GCTTCCTCATCTACATGATTG
Found at i:3346376 original size:125 final size:125
Alignment explanation
Indices: 3346154--3346403 Score: 473
Period size: 125 Copynumber: 2.0 Consensus size: 125
3346144 GATGCTTCAT
3346154 ACCATATCGTTTCAATGCAGTCGCCACTTGATTGTTATAGAAATGAGTGTCTTGGTCGCTTATCA
1 ACCATATCGTTTCAATGCAGTCGCCACTTGATTGTTATAGAAATGAGTGTCTTGGTCGCTTATCA
*
3346219 ACGCGCTTGGGGTTCCAAACCTTGTGAGGATGTATGTATGAAAGAATTTCAAGATTGTCC
66 ACGCGCTTGGGGTTCCAAACCTTGTGAGGATGTATGTATGAAAGAATTTCAAGACTGTCC
*
3346279 ACCATATCGTTTCAATGTAGTCGCCACTTGATTGTTATAGAAATGAGTGTCTTGGTCGCTTATCA
1 ACCATATCGTTTCAATGCAGTCGCCACTTGATTGTTATAGAAATGAGTGTCTTGGTCGCTTATCA
*
3346344 ACGCTCTTGGGGTTCCAAACCTTGTGAGGATGTATGTATGAAAGAATTTCAAGACTGTCC
66 ACGCGCTTGGGGTTCCAAACCTTGTGAGGATGTATGTATGAAAGAATTTCAAGACTGTCC
3346404 GAGCGTCATC
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 122 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (125 bp):
ACCATATCGTTTCAATGCAGTCGCCACTTGATTGTTATAGAAATGAGTGTCTTGGTCGCTTATCA
ACGCGCTTGGGGTTCCAAACCTTGTGAGGATGTATGTATGAAAGAATTTCAAGACTGTCC
Found at i:3353048 original size:9 final size:9
Alignment explanation
Indices: 3353040--3353083 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
3353030 GAATAAAGAA
3353040 AAAAAAGAAG
1 AAAAAA-AAG
3353050 AAAAAAAAG
1 AAAAAAAAG
*
3353059 AGAAAAAAG
1 AAAAAAAAG
* *
3353068 GAGAAAAAG
1 AAAAAAAAG
3353077 AAAAAAA
1 AAAAAAA
3353084 CATGGTTGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
9 22 0.79
10 6 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3353052 original size:12 final size:12
Alignment explanation
Indices: 3353035--3353066 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3353025 AGTTTGAATA
3353035 AAGAAAAAAAAG
1 AAGAAAAAAAAG
3353047 AAGAAAAAAAAG
1 AAGAAAAAAAAG
3353059 -AGAAAAAA
1 AAGAAAAAA
3353067 GGAGAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:3353064 original size:21 final size:21
Alignment explanation
Indices: 3353034--3353083 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3353024 GAGTTTGAAT
3353034 AAAGAAAAAAAAGAAGAAAAA
1 AAAGAAAAAAAAGAAGAAAAA
* *
3353055 AAAGAGAAAAAAGGAGAAAAA
1 AAAGAAAAAAAAGAAGAAAAA
*
3353076 GAA-AAAAA
1 AAAGAAAAA
3353084 CATGGTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAGAAAAA
Found at i:3353806 original size:23 final size:23
Alignment explanation
Indices: 3353775--3353831 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
3353765 CGACGTGGCG
* *
3353775 TCCATTCAGTAGCTTCTAAAAGA
1 TCCAGTCAGCAGCTTCTAAAAGA
* *
3353798 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAAAAGA
*
3353821 TCTAGTCAGCA
1 TCCAGTCAGCA
3353832 AGGATGGACG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAAAAGA
Found at i:3363363 original size:22 final size:22
Alignment explanation
Indices: 3363344--3363401 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
3363334 TGACGAAGGT
3363344 GATATCATGATATCGAGAAGAA
1 GATATCATGATATCGAGAAGAA
3363366 GATATCATGATATCGAGAAGAA
1 GATATCATGATATCGAGAAGAA
3363388 GATATCATGATATC
1 GATATCATGATATC
3363402 TTGGGCAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (22 bp):
GATATCATGATATCGAGAAGAA
Found at i:3368174 original size:21 final size:21
Alignment explanation
Indices: 3368137--3368178 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3368127 AAAAAACATG
*
3368137 TTTATCTAATCACTAACTTCA
1 TTTATCTAATCAATAACTTCA
3368158 TTTATCTAA-CAAATAACTTCA
1 TTTATCTAATC-AATAACTTCA
3368179 CAAACACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTATCTAATCAATAACTTCA
Found at i:3386722 original size:8 final size:7
Alignment explanation
Indices: 3386691--3386721 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
3386681 AAAAAACTAT
3386691 AATATTA
1 AATATTA
3386698 AATATTA
1 AATATTA
3386705 AATATTAA
1 AATATT-A
3386713 AATATTA
1 AATATTA
3386720 AA
1 AA
3386722 AAAACCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AATATTA
Found at i:3388150 original size:31 final size:31
Alignment explanation
Indices: 3388108--3388242 Score: 146
Period size: 31 Copynumber: 4.4 Consensus size: 31
3388098 GAGTTTAAAG
* *
3388108 TTTAAGGTTTAAGGTTTAGCGTGATATATGA
1 TTTAAGGTTTAAGGTTTAGAGTGATATAAGA
* * *
3388139 TTTAAGATTTAAAGTTTATAGTGATATAAGA
1 TTTAAGGTTTAAGGTTTAGAGTGATATAAGA
* * * *
3388170 TTTAAGGTTTAAGGTTCAAAGTAATATAAAA
1 TTTAAGGTTTAAGGTTTAGAGTGATATAAGA
* * *
3388201 TTTAGGGTTTAAGGTTTAAAGTAATA-AAGGA
1 TTTAAGGTTTAAGGTTTAGAGTGATATAA-GA
3388232 TTTAAGGTTTA
1 TTTAAGGTTTA
3388243 GCCATTTTGT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
30 2 0.02
31 86 0.98
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (31 bp):
TTTAAGGTTTAAGGTTTAGAGTGATATAAGA
Found at i:3388163 original size:24 final size:23
Alignment explanation
Indices: 3388132--3388180 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
3388122 TTTAGCGTGA
*
3388132 TATATGATTTAAGATTTAAAGTT
1 TATATGATATAAGATTTAAAGTT
*
3388155 TATAGTGATATAAGATTTAAGGTT
1 TATA-TGATATAAGATTTAAAGTT
3388179 TA
1 TA
3388181 AGGTTCAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (23 bp):
TATATGATATAAGATTTAAAGTT
Found at i:3394227 original size:12 final size:12
Alignment explanation
Indices: 3394207--3394240 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3394197 ATTTTCACAT
3394207 ATTTTCATTTCC
1 ATTTTCATTTCC
* *
3394219 ATTTCCATTTCT
1 ATTTTCATTTCC
3394231 ATTTTCATTT
1 ATTTTCATTT
3394241 TCTAAAAATC
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:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTCATTTCC
Found at i:3396217 original size:23 final size:22
Alignment explanation
Indices: 3396190--3396274 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 22
3396180 TCATTGGTCC
*
3396190 ATTTACACATAAGTCACATTAAT
1 ATTTA-ACATAAATCACATTAAT
3396213 ATTTAAGCATAAATCACATTAAT
1 ATTTAA-CATAAATCACATTAAT
* *
3396236 ATTTAAATATAAATTACATTAAT
1 ATTT-AACATAAATCACATTAAT
3396259 ATTTAAGCATAAATCA
1 ATTTAA-CATAAATCA
3396275 TATTTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 3 0.06
23 49 0.91
24 2 0.04
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (22 bp):
ATTTAACATAAATCACATTAAT
Found at i:3398636 original size:15 final size:15
Alignment explanation
Indices: 3398616--3398649 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3398606 TACCAAAGAG
3398616 GTATTTACAACAATC
1 GTATTTACAACAATC
* *
3398631 GTATTTACATCAATT
1 GTATTTACAACAATC
3398646 GTAT
1 GTAT
3398650 ACTCAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (15 bp):
GTATTTACAACAATC
Found at i:3402777 original size:6 final size:6
Alignment explanation
Indices: 3402766--3402827 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
3402756 ACCCAAACAG
* *
3402766 AATTTA AATTTA AATTT- ATTTTA AGTTTA AATTT- -ATTTGA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA
3402812 AATTT- -ATTTA AATTTA
1 AATTTA AATTTA AATTTA
3402828 CTAATGTCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 8 0.17
5 4 0.09
6 31 0.66
7 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:3402794 original size:17 final size:17
Alignment explanation
Indices: 3402768--3402827 Score: 95
Period size: 17 Copynumber: 3.6 Consensus size: 17
3402758 CCAAACAGAA
3402768 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
3402785 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
3402802 TTGAAATTTAAATTTA-
1 TTTAAATTTAAATTTAT
3402818 TTTAAATTTA
1 TTTAAATTTA
3402828 CTAATGTCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 9 0.23
17 30 0.77
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:3404593 original size:30 final size:28
Alignment explanation
Indices: 3404551--3404758 Score: 202
Period size: 29 Copynumber: 7.1 Consensus size: 28
3404541 AAGGTTCCTA
3404551 AACTTCTCAAAAATTACATTTTTACTCCCG
1 AACTTC-CAAAAATTACATTTTTAC-CCCG
** * *
3404581 AACTTATTAAAAATTATATTTTTACCCCTA
1 AACTT-CCAAAAATTACATTTTTACCCC-G
3404611 AACTTCCAAAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTACATTTTTACCC-CG
* * *
3404640 AACTTCCAAAAATCATATTTTTGCCCTCG
1 AACTTCCAAAAATTACATTTTTACCC-CG
* *
3404669 AACTTCCAAAAATCACATTTTTACCTCG
1 AACTTCCAAAAATTACATTTTTACCCCG
* * *
3404697 AATTTCCCAAAATTACATTTTTACCCCTAA
1 AACTTCCAAAAATTACATTTTTACCCC--G
* *
3404727 AACTTTCC-AAAATTACATTTTAACCCCA
1 AAC-TTCCAAAAATTACATTTTTACCCCG
3404755 AACT
1 AACT
3404759 CTTCGAAACT
Statistics
Matches: 151, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 29 0.19
29 70 0.46
30 47 0.31
31 4 0.03
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (28 bp):
AACTTCCAAAAATTACATTTTTACCCCG
Found at i:3404679 original size:58 final size:58
Alignment explanation
Indices: 3404550--3404752 Score: 225
Period size: 58 Copynumber: 3.5 Consensus size: 58
3404540 AAAGGTTCCT
**
3404550 AAACTTCTCAAAAATTACATTTTTACTCC-CGAACTTATTAAAAATTATATTTTTACCC-C
1 AAACTTC-CAAAAATTACATTTTTAC-CCTCGAACTT-CCAAAAATTATATTTTTACCCTC
* *
3404609 TAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATCATATTTTTGCCCTC
1 -AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTATATTTTTACCCTC
* * * * * *
3404668 GAACTTCCAAAAATCACATTTTTA-CCTCGAATTTCCCAAAATTACATTTTTACCCCTA
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTATATTTTTA-CCCTC
*
3404726 AAACTTTCC-AAAATTACATTTTAACCC
1 AAAC-TTCCAAAAATTACATTTTTACCC
3404753 CAAACTCTTC
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
57 23 0.19
58 61 0.50
59 32 0.26
60 7 0.06
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTATATTTTTACCCTC
Found at i:3405220 original size:97 final size:97
Alignment explanation
Indices: 3405030--3405212 Score: 296
Period size: 97 Copynumber: 1.9 Consensus size: 97
3405020 AAAATATTTA
*
3405030 AAATCGAGGCAATATTCCTTTATTCCAAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
1 AAATCGAGGCAATATTCCTTTATTCCAAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
3405095 TTTTCTTCAAACCAGGATAATCAAATACCCTT
66 TTTTCTTCAAACCAGGATAATCAAATACCCTT
* **
3405127 AAATCGAGGTAATATTCCTTTA-TCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGA
1 AAATCGAGGCAATATTCCTTTATTC-CAAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGA
**
3405191 CTTTTCTTCAAACTGGGATAAT
65 CTTTTCTTCAAACCAGGATAAT
3405213 TGAATACCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 2 0.03
97 77 0.97
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATTCCAAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
TTTTCTTCAAACCAGGATAATCAAATACCCTT
Found at i:3416846 original size:39 final size:39
Alignment explanation
Indices: 3416803--3417103 Score: 227
Period size: 39 Copynumber: 7.7 Consensus size: 39
3416793 ATCATCATTC
* * *
3416803 AATCTTTTACCTCGAGCTTGGGGTAAATTGCAGCCATCT
1 AATCTTTTACCTCGAGCTTGGGGCAGATTACAGCCATCT
* * *
3416842 AATCTTTTACCTCGAGCTTGGGGCAGATTACCA-TCAGCC
1 AATCTTTTACCTCGAGCTTGGGGCAGATTA-CAGCCATCT
*
3416881 AATCTCTTACC-CTGAGCTTGGGGCAGATTACAGCCAT-T
1 AATCTTTTACCTC-GAGCTTGGGGCAGATTACAGCCATCT
* * * * *
3416919 CGATCTTTTACC-CTGAGCTTGGGGCAGATCACTA-TCAACC
1 -AATCTTTTACCTC-GAGCTTGGGGCAGATTAC-AGCCATCT
* *
3416959 AATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATCT
1 AATCTTTTACCTCGAGCTTGGGGCAGATTACAGCCATCT
* * * * ** * *
3416998 GATCTTTTACCCCGAGCTTGGGACAGATCACAATCAGCC
1 AATCTTTTACCTCGAGCTTGGGGCAGATTACAGCCATCT
* * * *
3417037 AATCTCTTACCCCGAGCTTGAGGG-AGATTACAACCATCC
1 AATCTTTTACCTCGAGCTTG-GGGCAGATTACAGCCATCT
* * * * *
3417076 GATATTTTACCTTGAGCCTGGGGTAGAT
1 AATCTTTTACCTCGAGCTTGGGGCAGAT
3417104 CATCATTAGC
Statistics
Matches: 207, Mismatches: 45, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
38 7 0.03
39 194 0.94
40 6 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (39 bp):
AATCTTTTACCTCGAGCTTGGGGCAGATTACAGCCATCT
Found at i:3416885 original size:78 final size:78
Alignment explanation
Indices: 3416802--3417767 Score: 474
Period size: 78 Copynumber: 12.2 Consensus size: 78
3416792 CATCATCATT
* * * *
3416802 CAATCTTTTACCTCGAGCTTGGGGTAAATTGCAGCCATCTAATCTTTTACCTCGAGCTTGGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCTGATCTTTTACCTCGAGCTTGGGGCA
*
3416867 GATTACCATCAGC
66 GATCACCATCAGC
* * *
3416880 CAATCTCTTACCCTGAGCTTGGGGCAGATTACAGCCAT-TCGATCTTTTACC-CTGAGCTTGGGG
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCT-GATCTTTTACCTC-GAGCTTGGGG
* *
3416943 CAGATCACTATCAAC
64 CAGATCACCATCAGC
* * * *
3416958 CAATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGACA
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCTGATCTTTTACCTCGAGCTTGGGGCA
*
3417023 GATCACAATCAGC
66 GATCACCATCAGC
* * * * * * *
3417036 CAATCTCTTACCCCGAGCTTGAGGG-AGATTACAACCATCCGATATTTTACCTTGAGCCTGGGGT
1 CAATCTCTTACCCCGAGCTTG-GGGTAGATTGCAGCCATCTGATCTTTTACCTCGAGCTTGGGGC
* *
3417100 AGATCATCATTAGC
65 AGATCACCATCAGC
* * * * * ** * *
3417114 AAATCTCTTACCCCGATCATGGGATAGATTGCAACCATCCAATCTCTTCCCTCGAGCTTGGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCTGATCTTTTACCTCGAGCTTGGGGCA
* *
3417179 GATCATCATCAGT
66 GATCACCATCAGC
* * * * * * *
3417192 TAATTTCTTACCCCGAGCCTAGGGTAGATTGCAGCCAT-TCGATATTTTACC-CTGAGCCTGGAG
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCT-GATCTTTTACCTC-GAGCTTGGGG
* **
3417255 TAGATCACCATCATT
64 CAGATCACCATCAGC
** * * * * * * *
3417270 TGATATCTTACCTCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTTCATCAGTAAATCTCTT
1 CAATCTCTTACCCCGAGCTTGGGGTAG---AT--T--GC--A--GC---CATC--T-GATCTTTT
* * * * *** **
3417335 ACCTTGAACCTAGGGCAGATCTTTATCAAT
49 ACCTCGAGCTTGGGGCAGATCACCATCAGC
* * * * * * * * * *
3417365 AAATCTCTTACCCCGATCATGGGGCAAATTGTAGCCAT-TCGATCTCTTACC-CTAAGTTTGAGG
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCT-GATCTTTTACCTC-GAGCTTGGGG
*
3417428 CAGATCACTATCAGC
64 CAGATCACCATCAGC
* *** * ** * * * *
3417443 AAATCTCTTACCCCGAGCCAAGGGCAGA-T-CA-CCATTAACAAATCTCTTACCTCGATCATGAG
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCA-T--CTGATCTTTTACCTCGAGCTTGGG
3417505 GCAGATTGCAGCCAT---C
63 GCAGA-T-CA-CCATCAGC
* * * * * * * * *
3417521 CGATCTTTTACCCCGAGCTTGAGGCAGA-T-CA-CCATTATTTGATATCTTACCCCGAGCCTGGG
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCC---ATCTGATCTTTTACCTCGAGCTTGGG
* *
3417583 GCAAATCATCATCAGC
63 GCAGATCACCATCAGC
* * * * * * *
3417599 AAATCTCTTACCCCGATCATGGGGCAGATTGTAACTAT-TCGATCTTTTACCTCGAGCTTGGGGC
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCT-GATCTTTTACCTCGAGCTTGGGGC
3417663 AGATCACCATCAGC
65 AGATCACCATCAGC
* * * * * * *
3417677 CAGTCTCTTACCCCGATCATGGGGCAAATTGCAGCCAT-TCGATCTTTTACCCCGAGCTTGAGGC
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCT-GATCTTTTACCTCGAGCTTGGGGC
* * *
3417741 AGATCATCATTAAC
65 AGATCACCATCAGC
3417755 CAATCTCTTACCC
1 CAATCTCTTACCC
3417768 TGATCATGGA
Statistics
Matches: 686, Mismatches: 157, Indels: 90
0.74 0.17 0.10
Matches are distributed among these distances:
75 6 0.01
76 4 0.01
77 8 0.01
78 586 0.85
79 8 0.01
80 4 0.01
81 10 0.01
83 1 0.00
84 1 0.00
85 2 0.00
86 1 0.00
87 1 0.00
88 1 0.00
89 1 0.00
90 1 0.00
92 5 0.01
95 46 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (78 bp):
CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCTGATCTTTTACCTCGAGCTTGGGGCA
GATCACCATCAGC
Found at i:3417047 original size:117 final size:115
Alignment explanation
Indices: 3416842--3417183 Score: 278
Period size: 117 Copynumber: 2.9 Consensus size: 115
3416832 GCAGCCATCT
* * *
3416842 AATCTTTTACCTCGAGCTTGGGGCAGATTACCATCAGCCAATCTCTTACCCTGAGCTTGGGGCAG
1 AATCTCTTACCTCGAGCTTGGGGCAGATTACCATCAG-C-ATCTCTTACCCCGAGCTTGGGACAG
* * ** * * *
3416907 ATTACAGCCATTCGATCTTTTACCCTGAGCTTG-GGGCAGATCACTATCAACC
64 ATCACAACCAGCCAATCTCTTACCCCGAGCTTGAGGG-AGATCACTATCAACC
* *
3416959 AATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCATCTG-ATCTTTTACCCCGAGCTTGGGACA
1 AATCTCTTACCTCGAGCTTGGGGCAGATT--A-CCATCAGCATCTCTTACCCCGAGCTTGGGACA
* * * * *
3417023 GATCACAATCAGCCAATCTCTTACCCCGAGCTTGAGGGAGATTACAACCATCC
63 GATCACAACCAGCCAATCTCTTACCCCGAGCTTGAGGGAGATCACTATCAACC
* * * * * * * * * * * *
3417076 GATATTTTACCTTGAGCCTGGGGTAGATCATCATTAGCAAATCTCTTACCCCGATCATGGGATAG
1 AATCTCTTACCTCGAGCTTGGGGCAGATTACCATCAGC--ATCTCTTACCCCGAGCTTGGGACAG
** *
3417141 ATTGCAACCATCCAATCTCTT-CCCTCGAGCTTG-GGGCAGATCA
64 ATCACAACCAGCCAATCTCTTACCC-CGAGCTTGAGGG-AGATCA
3417184 TCATCAGTTA
Statistics
Matches: 180, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
114 4 0.02
115 1 0.01
116 6 0.03
117 159 0.88
118 3 0.02
119 1 0.01
120 6 0.03
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (115 bp):
AATCTCTTACCTCGAGCTTGGGGCAGATTACCATCAGCATCTCTTACCCCGAGCTTGGGACAGAT
CACAACCAGCCAATCTCTTACCCCGAGCTTGAGGGAGATCACTATCAACC
Found at i:3417275 original size:39 final size:39
Alignment explanation
Indices: 3417227--3417306 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
3417217 AGATTGCAGC
* *
3417227 CATTCGATATTTTACC-CTGAGCCTGGAGTAGATCACCAT
1 CATTCGATATCTTACCTC-GAGCCTGGAGCAGATCACCAT
* * *
3417266 CATTTGATATCTTACCTCGAGCCTGGGGCAGATCATCAT
1 CATTCGATATCTTACCTCGAGCCTGGAGCAGATCACCAT
3417305 CA
1 CA
3417307 GCAAATCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (39 bp):
CATTCGATATCTTACCTCGAGCCTGGAGCAGATCACCAT
Found at i:3417323 original size:17 final size:17
Alignment explanation
Indices: 3417301--3417334 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3417291 GGGCAGATCA
3417301 TCATCAGCAAATCTCTT
1 TCATCAGCAAATCTCTT
*
3417318 TCATCAGTAAATCTCTT
1 TCATCAGCAAATCTCTT
3417335 ACCTTGAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (17 bp):
TCATCAGCAAATCTCTT
Found at i:3417390 original size:39 final size:40
Alignment explanation
Indices: 3417314--3417390 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 40
3417304 TCAGCAAATC
* ** *
3417314 TCTTTCATCAGTAAATCTCTTACCTTGAACCTAGGGCAGA
1 TCTTTCATCAATAAATCTCTTACCCCGAACATAGGGCAGA
* *
3417354 TCTTT-ATCAATAAATCTCTTACCCCGATCATGGGGCA
1 TCTTTCATCAATAAATCTCTTACCCCGAACATAGGGCA
3417391 AATTGTAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
39 26 0.84
40 5 0.16
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (40 bp):
TCTTTCATCAATAAATCTCTTACCCCGAACATAGGGCAGA
Found at i:3417526 original size:117 final size:117
Alignment explanation
Indices: 3417319--3417692 Score: 426
Period size: 117 Copynumber: 3.2 Consensus size: 117
3417309 AAATCTCTTT
* ** * * * *
3417319 CATCAGTAAATCTCTTACCTTGAACCTAGGGCAGATCTTTATCAATAAATCTCTTACCCCGATCA
1 CATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAACAAATCTCTTACCCCGATCA
* * * *
3417384 TGGGGCAAATTGTAGCCATTCGATCTCTTACCCTAAGTTTGAGGCAGATCAC
66 TGGGGCAGATTGTAGCCATTCGATCTTTTACCCTGAGCTTGAGGCAGATCAC
* * * * *
3417436 TATCAGCAAATCTCTTACCCCGAGCCAAGGGCAGATCACCATTAACAAATCTCTTACCTCGATCA
1 CATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAACAAATCTCTTACCCCGATCA
* * * *
3417501 TGAGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCAC
66 TGGGGCAGATTGTAGCCATTCGATCTTTTACCCTGAGCTTGAGGCAGATCAC
* **** * * * *
3417553 CATTATTTGATATCTTACCCCGAGCCTGGGGCAAATCATCATCAGCAAATCTCTTACCCCGATCA
1 CATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAACAAATCTCTTACCCCGATCA
* * *
3417618 TGGGGCAGATTGTAACTATTCGATCTTTTA-CCTCGAGCTTGGGGCAGATCAC
66 TGGGGCAGATTGTAGCCATTCGATCTTTTACCCT-GAGCTTGAGGCAGATCAC
* *
3417670 CATCAGCCAGTCTCTTACCCCGA
1 CATCAGCAAATCTCTTACCCCGA
3417693 TCATGGGGCA
Statistics
Matches: 208, Mismatches: 48, Indels: 2
0.81 0.19 0.01
Matches are distributed among these distances:
116 2 0.01
117 206 0.99
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (117 bp):
CATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAACAAATCTCTTACCCCGATCA
TGGGGCAGATTGTAGCCATTCGATCTTTTACCCTGAGCTTGAGGCAGATCAC
Found at i:3417727 original size:117 final size:114
Alignment explanation
Indices: 3417367--3417731 Score: 344
Period size: 117 Copynumber: 3.1 Consensus size: 114
3417357 TTATCAATAA
* * * *
3417367 ATCTCTTACCCCGATCATGGGGCAAATTGTAGCCATTCGATCTCTTACCCTAAGTTTGAGGCAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGTAGCCATTCGATCTTTTACCC-GAGCTTGAGGCAGA
* * * * *
3417432 TCACTATCAGCAAATCTCTTACCCCGAGCCA-AGGGCAGATCACCATTAACAA
65 TCACCATCAGCAAGTCTCTTACCCCGA-CCATGGGGCAAATCACCATT--CAG
* * * *
3417484 ATCTCTTACCTCGATCATGAGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGAGGCAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGTAGCCATTCGATCTTTTA-CCCGAGCTTGAGGCAGA
* *** * *
3417549 TCACCATTA-TTTGATATCTTACCCCGAGCC-TGGGGCAAATCATCA-TCAG
65 TCACCATCAGCAAG-TCTCTTACCCCGA-CCATGGGGCAAATCACCATTCAG
* * *
3417598 CAAATCTCTTACCCCGATCATGGGGCAGATTGTAACTATTCGATCTTTTACCTCGAGCTTGGGGC
1 ---ATCTCTTACCCCGATCATGGGGCAGATTGTAGCCATTCGATCTTTTACC-CGAGCTTGAGGC
* *
3417663 AGATCACCATCAGCCAGTCTCTTACCCCGATCATGGGGCAAATTGCAGCCATTC-G
62 AGATCACCATCAGCAAGTCTCTTACCCCGACCATGGGGCAAA-T-CA-CCATTCAG
*
3417718 ATCTTTTACCCCGA
1 ATCTCTTACCCCGA
3417732 GCTTGAGGCA
Statistics
Matches: 201, Mismatches: 34, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
114 2 0.01
116 4 0.02
117 183 0.91
118 5 0.02
119 2 0.01
120 3 0.01
121 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (114 bp):
ATCTCTTACCCCGATCATGGGGCAGATTGTAGCCATTCGATCTTTTACCCGAGCTTGAGGCAGAT
CACCATCAGCAAGTCTCTTACCCCGACCATGGGGCAAATCACCATTCAG
Found at i:3417766 original size:39 final size:39
Alignment explanation
Indices: 3417406--3417767 Score: 162
Period size: 39 Copynumber: 9.3 Consensus size: 39
3417396 TAGCCATTCG
** * * * *
3417406 ATCTCTTACCCTAAGTTTGAGGCAGATCACTATCAGCAA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
** * *
3417445 ATCTCTTACCCCGAGC-CAAGGGCAGATCACCATTAACAA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATTAGCCA
* * * *
3417484 ATCTCTTACCTCGATCATGAGGCAGATTGCAGCCA-T--CCG
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATTAGCCA
* ****
3417523 ATCTTTTACCCCGAGCTTGAGGCAGATCACCATTATTTG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
* * * * * * *
3417562 ATATCTTACCCCGAGCCTGGGGCAAATCATCATCAGCAA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
* * * **** * ** *
3417601 ATCTCTTACCCCGATCATGGGGCAGATTGTAACTATTCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
* * * *
3417640 ATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
* * * * * *
3417679 GTCTCTTACCCCGATCATGGGGCAAATTGCAGCCATT---CG
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATTAGCCA
* * *
3417718 ATCTTTTACCCCGAGCTTGAGGCAGATCATCATTAACCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
3417757 ATCTCTTACCC
1 ATCTCTTACCC
3417768 TGATCATGGA
Statistics
Matches: 235, Mismatches: 74, Indels: 28
0.70 0.22 0.08
Matches are distributed among these distances:
36 7 0.03
37 5 0.02
38 3 0.01
39 205 0.87
40 3 0.01
41 5 0.02
42 7 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
Found at i:3418222 original size:17 final size:17
Alignment explanation
Indices: 3418196--3418238 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3418186 CCAAACAGCA
3418196 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
3418213 TTTAAGTTTAAATTTA-
1 TTTAAATTTAAATTTAT
3418229 TTTAAATTTA
1 TTTAAATTTA
3418239 CTAATGTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:3418881 original size:14 final size:14
Alignment explanation
Indices: 3418862--3418888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3418852 AAAACGTATC
3418862 AAATAAATAATATT
1 AAATAAATAATATT
3418876 AAATAAATAATAT
1 AAATAAATAATAT
3418889 CATTAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAATAATATT
Found at i:3420018 original size:30 final size:30
Alignment explanation
Indices: 3419980--3420267 Score: 251
Period size: 29 Copynumber: 9.9 Consensus size: 30
3419970 CCTAGAAAGT
*
3419980 CCCT-GAACTTCTCAAAAATTACATTTTTG
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
* *
3420009 CTCTCGAACTTTTCAAAAATTACATTTTTA
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
*
3420039 CCC-CTGAACTTC-CAAAAATCACATTTTTA
1 CCCTC-GAACTTCTCAAAAATTACATTTTTA
** *
3420068 ATCTCGAACTTCTAAAAAATTACATTTTTA
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
* * *
3420098 CCC-CTAAAC-T-TCAAAACTTACATTTTTT
1 CCCTC-GAACTTCTCAAAAATTACATTTTTA
* *
3420126 CCCTTGAACTTCT-AAAAATTACATTTTTG
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
*
3420155 CCCTCGAACTTC-CAAAAA-TACATTTTTG
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
* *
3420183 CCCCCGAACTT-TCAAAAATTACGTTTTTA
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
* * * *
3420212 CAC-CGAATTTC-CTAAAATGACATTTTTA
1 CCCTCGAACTTCTCAAAAATTACATTTTTA
** * *
3420240 CGCCTAAAACTT-TCTAAAATTGCATTTT
1 C-CCTCGAACTTCTCAAAAATTACATTTT
3420268 AACTCCAAAA
Statistics
Matches: 209, Mismatches: 35, Indels: 29
0.77 0.13 0.11
Matches are distributed among these distances:
28 68 0.33
29 72 0.34
30 69 0.33
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
CCCTCGAACTTCTCAAAAATTACATTTTTA
Found at i:3420054 original size:29 final size:29
Alignment explanation
Indices: 3419980--3420267 Score: 237
Period size: 28 Copynumber: 9.9 Consensus size: 29
3419970 CCTAGAAAGT
*
3419980 CCCTGAACTTCTCAAAAATTACATTTTT-G
1 CCCTGAACTTC-CAAAAATTACATTTTTAC
* *
3420009 CTCTCGAACTTTTCAAAAATTACATTTTTAC
1 CCCT-GAAC-TTCCAAAAATTACATTTTTAC
*
3420040 CCCTGAACTTCCAAAAATCACATTTTTA-
1 CCCTGAACTTCCAAAAATTACATTTTTAC
** *
3420068 ATCTCGAACTTCTAAAAAATTACATTTTTAC
1 CCCT-GAACTTC-CAAAAATTACATTTTTAC
* * *
3420099 CCCTAAACTT-CAAAACTTACATTTTTTC
1 CCCTGAACTTCCAAAAATTACATTTTTAC
* * *
3420127 CCTTGAACTTCTAAAAATTACATTTTT-G
1 CCCTGAACTTCCAAAAATTACATTTTTAC
*
3420155 CCCTCGAACTTCCAAAAA-TACATTTTTGC
1 CCCT-GAACTTCCAAAAATTACATTTTTAC
* * *
3420184 CCCCGAACTTTCAAAAATTACGTTTTTAC
1 CCCTGAACTTCCAAAAATTACATTTTTAC
* * * *
3420213 ACC-GAATTTCCTAAAATGACATTTTTAC
1 CCCTGAACTTCCAAAAATTACATTTTTAC
* * * * *
3420241 GCCTAAAACTTTCTAAAATTGCATTTT
1 CCCT-GAACTTCCAAAAATTACATTTT
3420268 AACTCCAAAA
Statistics
Matches: 207, Mismatches: 40, Indels: 23
0.77 0.15 0.09
Matches are distributed among these distances:
28 71 0.34
29 68 0.33
30 61 0.29
31 7 0.03
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
CCCTGAACTTCCAAAAATTACATTTTTAC
Found at i:3420177 original size:57 final size:57
Alignment explanation
Indices: 3419984--3420238 Score: 273
Period size: 57 Copynumber: 4.4 Consensus size: 57
3419974 GAAAGTCCCT
* *
3419984 GAACTTCTCAAAAATTACATTTTTGCTCTCGAACTTTTCAAAAATTACATTTTTACCCC
1 GAACTTC-CAAAAA-TACATTTTTGCCCTCGAACTTCTCAAAAATTACATTTTTACCCC
*** *
3420043 TGAACTTCCAAAAATCACATTTTTAATCTCGAACTTCTAAAAAATTACATTTTTACCCC
1 -GAACTTCCAAAAAT-ACATTTTTGCCCTCGAACTTCTCAAAAATTACATTTTTACCCC
* * * * *
3420102 TAAACTT-CAAAACTTACATTTTTTCCCTTGAACTTCT-AAAAATTACATTTTTGCCCTC
1 -GAACTTCCAAAA-ATACATTTTTGCCCTCGAACTTCTCAAAAATTACATTTTTACCC-C
* * *
3420160 GAACTTCCAAAAATACATTTTTGCCCCCGAACTT-TCAAAAATTACGTTTTTACACC
1 GAACTTCCAAAAATACATTTTTGCCCTCGAACTTCTCAAAAATTACATTTTTACCCC
* *
3420216 GAATTTCCTAAAATGACATTTTT
1 GAACTTCCAAAAAT-ACATTTTT
3420239 ACGCCTAAAA
Statistics
Matches: 168, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
56 14 0.08
57 65 0.39
58 30 0.18
59 52 0.31
60 7 0.04
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.38
Consensus pattern (57 bp):
GAACTTCCAAAAATACATTTTTGCCCTCGAACTTCTCAAAAATTACATTTTTACCCC
Found at i:3420279 original size:19 final size:19
Alignment explanation
Indices: 3420255--3420295 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3420245 AAAACTTTCT
* *
3420255 AAAATTGCATTTTAACTCC
1 AAAATTACATTTTAACCCC
3420274 AAAATTACATTTTAACCCC
1 AAAATTACATTTTAACCCC
3420293 AAA
1 AAA
3420296 CTCTCCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTACATTTTAACCCC
Found at i:3420668 original size:97 final size:97
Alignment explanation
Indices: 3420562--3420752 Score: 337
Period size: 97 Copynumber: 2.0 Consensus size: 97
3420552 AAAATATTTA
* * *
3420562 AAATCGAGGCAATATTCCTTTATTTCAGGTTTTGAAATTTTGTGCCTTAACTTACTAGGCGCGAT
1 AAATCGAGGCAATATTCCTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
3420627 TTTTCTTCAAACCGGGATAATCGAATACCTTT
66 TTTTCTTCAAACCGGGATAATCGAATACCTTT
*
3420659 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
1 AAATCGAGGCAATATTCCTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
*
3420724 TTTTCTTCAAACCGGGATAATTGAATACC
66 TTTTCTTCAAACCGGGATAATCGAATACC
3420753 CTTTTTCAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
TTTTCTTCAAACCGGGATAATCGAATACCTTT
Found at i:3422393 original size:24 final size:25
Alignment explanation
Indices: 3422361--3422416 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 25
3422351 TGAACTTAAC
3422361 ACTTTTTT-TTAATTTGGTACCTAA
1 ACTTTTTTATTAATTTGGTACCTAA
*
3422385 ACTTTTTTTGACTTAATTTGGTACCTGA
1 AC-TTTTTT-A-TTAATTTGGTACCTAA
3422413 ACTT
1 ACTT
3422417 GACAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.07
25 6 0.22
27 2 0.07
28 17 0.63
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (25 bp):
ACTTTTTTATTAATTTGGTACCTAA
Found at i:3422451 original size:59 final size:59
Alignment explanation
Indices: 3422341--3422453 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
3422331 TTAATATAAC
* *
3422341 ATTTGGTACCTGAACTTAACACTTTTTTTTAATTTGGTACCTAAACTTTTTTTGACTTA
1 ATTTGGTACCTGAACTTAACAATTTTTTCTAATTTGGTACCTAAACTTTTTTTGACTTA
* *
3422400 ATTTGGTACCTGAACTTGACAATTTTTTCCTAATTTGGTACCTAAGCTTTTTTT
1 ATTTGGTACCTGAACTTAACAATTTTTT-CTAATTTGGTACCTAAACTTTTTTT
3422454 TTAGATTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 26 0.53
60 23 0.47
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTAACAATTTTTTCTAATTTGGTACCTAAACTTTTTTTGACTTA
Found at i:3422660 original size:31 final size:31
Alignment explanation
Indices: 3422625--3422754 Score: 98
Period size: 31 Copynumber: 4.3 Consensus size: 31
3422615 AAAAAAATAT
3422625 GTACCAAATTAGGAAAAA-TAGTCAAGTTTAG
1 GTACCAAATTAGGAAAAAGT-GTCAAGTTTAG
* *
3422656 GTACCAAATT-GGACCCCAAA-----AAGTTTAA
1 GTACCAAATTAGGA---AAAAGTGTCAAGTTTAG
* * *
3422684 GTACTAACTTA-AAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAGGAAAAAGTGTCAAGTTTAG
*
3422714 GTACCAAATTAGGAAAAAGTGTCAA-TTTCG
1 GTACCAAATTAGGAAAAAGTGTCAAGTTTAG
3422744 AGTACCAAATT
1 -GTACCAAATT
3422755 TGACCAAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.04
28 16 0.21
30 23 0.30
31 32 0.42
33 3 0.04
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAGGAAAAAGTGTCAAGTTTAG
Found at i:3422730 original size:89 final size:90
Alignment explanation
Indices: 3422625--3422813 Score: 260
Period size: 89 Copynumber: 2.1 Consensus size: 90
3422615 AAAAAAATAT
**
3422625 GTACCAAATTAGGAAAAA-TAGTCAAGTTTAG-GTACCAAATTGGACCCCAAAAAGTTTA-AGTA
1 GTACCAAATTAGGAAAAAGT-GTCAA-TTTAGAGTACCAAATTGGACCAAAAAAAGTTTAGA-TA
* *
3422687 CTAACTT-AAAAAAAGTGTCAAGTTTAG
63 CTAAATTAAAAAAAAATGTCAAGTTTAG
* *
3422714 GTACCAAATTAGGAAAAAGTGTCAATTTCGAGTACCAAATTTGACCAAAAAAAGTTTAGATACTA
1 GTACCAAATTAGGAAAAAGTGTCAATTTAGAGTACCAAATTGGACCAAAAAAAGTTTAGATACTA
3422779 AATTAAAAAAAAATGTCAAGTTTAG
66 AATTAAAAAAAAATGTCAAGTTTAG
*
3422804 ATACCAAATT
1 GTACCAAATT
3422814 TTATATTAAG
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
88 4 0.04
89 55 0.62
90 30 0.34
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (90 bp):
GTACCAAATTAGGAAAAAGTGTCAATTTAGAGTACCAAATTGGACCAAAAAAAGTTTAGATACTA
AATTAAAAAAAAATGTCAAGTTTAG
Found at i:3424310 original size:40 final size:38
Alignment explanation
Indices: 3424242--3424376 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
3424232 ACCAGAATGG
* *
3424242 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
3424282 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
3424319 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
3424360 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3424377 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:3424374 original size:41 final size:38
Alignment explanation
Indices: 3424274--3424377 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
3424264 TTCGAAGCAA
* *
3424274 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
3424311 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
3424349 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
3424378 CTCAAGGTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:3427515 original size:245 final size:245
Alignment explanation
Indices: 3427064--3427547 Score: 756
Period size: 245 Copynumber: 2.0 Consensus size: 245
3427054 TCACTCACTA
* *
3427064 TATAAAGGCTTCATTGGCCACTCTTTTGAAGCAAACCAGTTCTATCCTTCACCCATTGTTAAAAG
1 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAATTCTATCCTTCACCCATTGTTAAAAG
* * * * *
3427129 GGGTTTACAAAGCAATAACAATAGCAATGGCGGGAGAAAAAGTTAAAGTTGCTTGGATAGCCGAC
66 GGGTTTACAAAGCAATAACAATAGCAATGACAGGAGAAAAACTTAAACTTGCTTGGATAACCGAC
* * * *
3427194 AATGCTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTTAACGATTCCCTTCTACTTCAACAT
131 AACGCTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAACGACTCCCTTCTACTTCAACAC
*
3427259 CTCCTGCTCAAGGAGATGTTAATATTATTGTTGTTGTTATTATTTTTGTT
196 CTCCTGCTCAAGGAGATGTTAATATTATTGTTGTTGTCATTATTTTTGTT
*
3427309 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAATTCTCTCCTTCACCCATTGTT-AAAG
1 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAATTCTATCCTTCACCCATTGTTAAAAG
* *
3427373 GCGGTTTACAAAGCAATAACAATAGCAATGATAGGAGAAAAACTTAAACTTTCTTGGATAACCGA
66 G-GGTTTACAAAGCAATAACAATAGCAATGACAGGAGAAAAACTTAAACTTGCTTGGATAACCGA
* * * * *
3427438 CAACGCTGCTCGACGAGCTGGCCTTAAGAAAAGGAGATGTTCAATGACTCCCTTCTTCTTCACCA
130 CAACGCTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAACGACTCCCTTCTACTTCAACA
3427503 CCT-CTCGCTCAAGGAGATGTTAATATTATTGTTGTTGTCATTATT
195 CCTCCT-GCTCAAGGAGATGTTAATATTATTGTTGTTGTCATTATT
3427548 GTTTTGGTTT
Statistics
Matches: 217, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
244 7 0.03
245 210 0.97
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (245 bp):
TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAATTCTATCCTTCACCCATTGTTAAAAG
GGGTTTACAAAGCAATAACAATAGCAATGACAGGAGAAAAACTTAAACTTGCTTGGATAACCGAC
AACGCTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAACGACTCCCTTCTACTTCAACAC
CTCCTGCTCAAGGAGATGTTAATATTATTGTTGTTGTCATTATTTTTGTT
Found at i:3435598 original size:20 final size:20
Alignment explanation
Indices: 3435573--3435612 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3435563 TTATATAGAT
3435573 AACCCATAGGATTTATGCAC
1 AACCCATAGGATTTATGCAC
3435593 AACCCATAGGATTTATGCAC
1 AACCCATAGGATTTATGCAC
3435613 CATAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
AACCCATAGGATTTATGCAC
Found at i:3439180 original size:18 final size:18
Alignment explanation
Indices: 3439126--3439181 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3439116 GGAGAAGTAA
3439126 ATATTATTGTTGTTG-TC
1 ATATTATTGTTGTTGTTC
* *
3439143 --GTTATTGTT-TTGGTTT
1 ATATTATTGTTGTT-GTTC
3439159 ATATTATTGTTGTTGTTC
1 ATATTATTGTTGTTGTTC
3439177 ATATT
1 ATATT
3439182 GTTTTGCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.07
15 9 0.30
16 1 0.03
18 16 0.53
19 2 0.07
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (18 bp):
ATATTATTGTTGTTGTTC
Found at i:3448138 original size:4 final size:4
Alignment explanation
Indices: 3448129--3448154 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3448119 AAAACCTAAA
3448129 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3448155 CAAATTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3448287 original size:18 final size:17
Alignment explanation
Indices: 3448203--3448287 Score: 66
Period size: 18 Copynumber: 4.9 Consensus size: 17
3448193 TAGATTAGTA
*
3448203 ATTTTATATACATATTT
1 ATTTTATATAAATATTT
* * *
3448220 -TTTTTTACAAATTTTAT
1 ATTTTATATAAATATT-T
*
3448237 ATTTTATACAAATATTT
1 ATTTTATATAAATATTT
3448254 -TTTTATAAATAAATATTGT
1 ATTTTAT--ATAAATATT-T
*
3448273 ATTTTATATATATAT
1 ATTTTATATAAATAT
3448288 ATATACCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
16 17 0.31
17 2 0.04
18 28 0.52
19 1 0.02
20 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (17 bp):
ATTTTATATAAATATTT
Found at i:3448361 original size:16 final size:16
Alignment explanation
Indices: 3448342--3448395 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3448332 TTTTATATGC
* *
3448342 ATATATTTTTTTACAT
1 ATATATTGTTATACAT
*
3448358 ATATATTGTTATATAT
1 ATATATTGTTATACAT
*
3448374 ATATATATG-TATATAT
1 ATATAT-TGTTATACAT
3448390 ATATAT
1 ATATAT
3448396 ACATATCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 32 0.94
17 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (16 bp):
ATATATTGTTATACAT
Found at i:3448372 original size:2 final size:2
Alignment explanation
Indices: 3448367--3448401 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3448357 TATATATTGT
* *
3448367 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3448402 CTATTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3448396 original size:16 final size:17
Alignment explanation
Indices: 3448356--3448396 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
3448346 ATTTTTTTAC
3448356 ATATATAT-TGTTATAT
1 ATATATATATGTTATAT
3448372 ATATATATATG-TATAT
1 ATATATATATGTTATAT
3448388 ATATATATA
1 ATATATATA
3448397 CATATCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATATATATATGTTATAT
Found at i:3453697 original size:19 final size:20
Alignment explanation
Indices: 3453673--3453712 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3453663 GAGGAAATTC
3453673 AGAGGAAAGAGA-AGGAAAG
1 AGAGGAAAGAGATAGGAAAG
**
3453692 AGAGGATGGAGATAGGAAAG
1 AGAGGAAAGAGATAGGAAAG
3453712 A
1 A
3453713 AATAGTAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (20 bp):
AGAGGAAAGAGATAGGAAAG
Found at i:3461311 original size:12 final size:12
Alignment explanation
Indices: 3461294--3461330 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
3461284 ATGAGTCATC
3461294 ACCAACACCTAA
1 ACCAACACCTAA
3461306 ACCAACACCTAA
1 ACCAACACCTAA
3461318 ACCAACACC-AA
1 ACCAACACCTAA
3461329 AC
1 AC
3461331 TCAGCAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.51, C:0.43, G:0.00, T:0.05
Consensus pattern (12 bp):
ACCAACACCTAA
Found at i:3461847 original size:17 final size:16
Alignment explanation
Indices: 3461820--3461892 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
3461810 AAATCTTTAT
*
3461820 TTTAAATTTATTTTAAG
1 TTTAAA-TTATTTTAAA
3461837 TTTAGAATTATTTTAAAA
1 TTTA-AATTATTTT-AAA
* *
3461855 TTTAAATT-TATTAAG
1 TTTAAATTATTTTAAA
3461870 TTTAAATTTATTTTAAA
1 TTTAAA-TTATTTTAAA
3461887 TTTAAA
1 TTTAAA
3461893 ATTTGAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
15 8 0.17
16 5 0.11
17 26 0.55
18 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:3463882 original size:29 final size:30
Alignment explanation
Indices: 3463809--3463953 Score: 97
Period size: 29 Copynumber: 4.9 Consensus size: 30
3463799 TGAACTATCC
* *
3463809 AAAAATCATATTTTGACCCCTGAACTTTTT
1 AAAAATTATATTTTGACCCCTAAACTTTTT
* *
3463839 TAAAATTCCAT-TTTTGA-CCTTAAACTTTTT
1 AAAAATT--ATATTTTGACCCCTAAACTTTTT
* * *
3463869 AAAAATTATATTTTTA-CCCTCGAACTTTCT
1 AAAAATTATATTTTGACCCCT-AAACTTTTT
* * *
3463899 -AGAATTTTATTTTGA-CCCTAAA-TTTTCC
1 AAAAATTATATTTTGACCCCTAAACTTTT-T
* *
3463927 AAAAATTACATTTT-CCCCCTAAACTTT
1 AAAAATTATATTTTGACCCCTAAACTTT
3463954 CCAAAATTCC
Statistics
Matches: 88, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.03
28 4 0.05
29 41 0.47
30 32 0.36
31 6 0.07
32 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.43
Consensus pattern (30 bp):
AAAAATTATATTTTGACCCCTAAACTTTTT
Found at i:3463934 original size:58 final size:59
Alignment explanation
Indices: 3463806--3464029 Score: 222
Period size: 58 Copynumber: 3.8 Consensus size: 59
3463796 CCCTGAACTA
* * * * *
3463806 TCCAAAAATCATATTTTGACCC-CTGAACTTTTTTAAAATTCCATTTTTGACCTTAAACTTT
1 TCCAAAAATTACATTTTTACCCTC-GAAC-TTTCTAAAATTCCATTTTTGACCCTAAA-TTT
* * * **
3463867 T-TAAAAATTATATTTTTACCCTCGAACTTTCTAGAATTTTA-TTTTGACCCTAAATTT
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTGACCCTAAATTT
** * * * *
3463924 TCCAAAAATTACATTTTCCCCCT-AAACTTTCCAAAATTCCATTTTTTACCCCAAATTT
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTGACCCTAAATTT
*
3463982 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTT
1 TCCAAAAATTACATTTTTACCCTCGAACTTT-CTAAAATT-CCATTTT
3464030 ACCCTTGGAT
Statistics
Matches: 134, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 17 0.13
58 64 0.48
59 16 0.12
60 28 0.21
61 9 0.07
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (59 bp):
TCCAAAAATTACATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTGACCCTAAATTT
Found at i:3463997 original size:30 final size:29
Alignment explanation
Indices: 3463840--3464033 Score: 144
Period size: 30 Copynumber: 6.6 Consensus size: 29
3463830 GAACTTTTTT
* ** **
3463840 AAAATTCCATTTTTGACCTTAAACTTTTTA
1 AAAATTACATTTTT-ACCCCAAACTTTCCA
* * *
3463870 AAAATTATATTTTTACCCTCGAACTTT-CT
1 AAAATTACATTTTTACCC-CAAACTTTCCA
* ** * * *
3463899 AGAATTTTATTTTGACCCTAAATTTTCCA
1 AAAATTACATTTTTACCCCAAACTTTCCA
*
3463928 AAAATTACA-TTTTCCCCCTAAACTTTCC-
1 AAAATTACATTTTTACCCC-AAACTTTCCA
* *
3463956 AAAATTCCATTTTTTACCCCAAATTTTCCA
1 AAAATTACA-TTTTTACCCCAAACTTTCCA
*
3463986 AAAATTACATTTTTACCCTCGAACTTTCCA
1 AAAATTACATTTTTACCC-CAAACTTTCCA
3464016 AAAATTACCA-TTTTACCC
1 AAAATTA-CATTTTTACCC
3464034 TTGGATGTCT
Statistics
Matches: 129, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
28 19 0.15
29 50 0.39
30 58 0.45
31 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.41
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCAAACTTTCCA
Found at i:3464048 original size:59 final size:58
Alignment explanation
Indices: 3463985--3464152 Score: 169
Period size: 59 Copynumber: 2.9 Consensus size: 58
3463975 CAAATTTTCC
** **
3463985 AAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCTTGGATGTCT
1 AAAAATT-CATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCTCAGACATCT
* * * **
3464044 AAAAACTCTATTTTTAACCC-CAAACTTTCCAAAAATCACCATTACACCCTCAGACATCT
1 AAAAATTC-ATTTTT-ACCCTCGAACTTTCCAAAAATTACCATTTTACCCTCAGACATCT
* * * *
3464103 AAAATTTTATTTTTA-ACTCTGAACTTTCCAAAAATTACCATTTTTCCCTC
1 AAAAATTCATTTTTACCCTC-GAACTTTCCAAAAATTACCATTTTACCCTC
3464153 GAGTGTCCAA
Statistics
Matches: 87, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 32 0.37
59 48 0.55
60 4 0.05
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (58 bp):
AAAAATTCATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCTCAGACATCT
Found at i:3464143 original size:58 final size:59
Alignment explanation
Indices: 3463994--3464144 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 59
3463984 CAAAAATTAC
** ** **
3463994 ATTTTT-ACCCTCGAACTTTCCAAAAATTACCATTTTACCCTTGGATGTCTAAAAACTCT
1 ATTTTTAACCC-CGAACTTTCCAAAAATTACCATTACACCCTCAGACATCTAAAAACTCT
* * * *
3464053 ATTTTTAACCCCAAACTTTCCAAAAATCACCATTACACCCTCAGACATCT-AAAATTTT
1 ATTTTTAACCCCGAACTTTCCAAAAATTACCATTACACCCTCAGACATCTAAAAACTCT
* *
3464111 ATTTTTAACTCTGAACTTTCCAAAAATTACCATT
1 ATTTTTAACCCCGAACTTTCCAAAAATTACCATT
3464145 TTTCCCTCGA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 36 0.47
59 37 0.48
60 4 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
ATTTTTAACCCCGAACTTTCCAAAAATTACCATTACACCCTCAGACATCTAAAAACTCT
Found at i:3464165 original size:58 final size:59
Alignment explanation
Indices: 3463984--3464166 Score: 178
Period size: 58 Copynumber: 3.1 Consensus size: 59
3463974 CCAAATTTTC
*
3463984 CAAAAATTAC-ATTTTT-ACCCTCGAACTTTCCAAAAATTACCATTTTACCCTTG-GATGT
1 CAAAAATT-CTATTTTTAACCC-CGAACTTTCCAAAAATTACCATTTTACCCTCGAGATGT
* * * ** **
3464042 CTAAAAACTCTATTTTTAACCCCAAACTTTCCAAAAATCACCATTACACCCTC-AGACAT
1 C-AAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAGATGT
* * * * *
3464101 CTAAAATTTTATTTTTAACTCTGAACTTTCCAAAAATTACCATTTTTCCCTCGAG-TGT
1 CAAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAGATGT
*
3464159 CCAAAATT
1 CAAAAATT
3464167 ACCGTTTTAC
Statistics
Matches: 99, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
58 51 0.52
59 44 0.44
60 4 0.04
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (59 bp):
CAAAAATTCTATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCTCGAGATGT
Found at i:3468667 original size:5 final size:5
Alignment explanation
Indices: 3468657--3468691 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
3468647 TTAAAAGGAA
3468657 AAAAG AAAAG AAAAG AAAAG AAGAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAA
3468692 AGGAAAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3468683 original size:16 final size:15
Alignment explanation
Indices: 3468657--3468691 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
3468647 TTAAAAGGAA
3468657 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
3468672 AAAAGAAGAAGAAAAG
1 AAAAGAA-AAGAAAAG
3468688 AAAA
1 AAAA
3468692 AGGAAAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:3468698 original size:11 final size:11
Alignment explanation
Indices: 3468656--3468698 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
3468646 TTTAAAAGGA
3468656 AAAAAGAAAAG
1 AAAAAGAAAAG
3468667 -AAAAGAAAAG
1 AAAAAGAAAAG
*
3468677 AAGAAGAAAAG
1 AAAAAGAAAAG
*
3468688 AAAAAGGAAAG
1 AAAAAGAAAAG
3468699 TCATGATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:3469396 original size:6 final size:6
Alignment explanation
Indices: 3469372--3469423 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
3469362 AATAAAAAAG
* *
3469372 AAGAGA AAGAAA AA-AAA AAGGAAAA AAGAAA AGGAAA AAGAAA ATAGAAA
1 AAGAAA AAGAAA AAGAAA AA-G-AAA AAGAAA AAGAAA AAGAAA A-AGAAA
3469422 AA
1 AA
3469424 ATGGAAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.13
6 22 0.56
7 7 0.18
8 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:3469397 original size:12 final size:12
Alignment explanation
Indices: 3469380--3469424 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
3469370 AGAAGAGAAA
3469380 GAAAAAAAAAAG
1 GAAAAAAAAAAG
3469392 GAAAAAAGAAAAG
1 GAAAAAA-AAAAG
3469405 GAAAAAGAAAATA-
1 GAAAAA-AAAA-AG
3469418 GAAAAAA
1 GAAAAAA
3469425 TGGAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.27
13 20 0.67
14 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:3469399 original size:19 final size:18
Alignment explanation
Indices: 3469353--3469424 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
3469343 CAGATGTAAT
* *
3469353 GAAAAAATAAATAAAAAA
1 GAAAAAAGAAAAAAAAAA
3469371 GAAGAGAAAGAAAAAAAAAA
1 GAA-A-AAAGAAAAAAAAAA
*
3469391 GGAAAAAAGAAAAGGAAAAA
1 -GAAAAAAGAAAA-AAAAAA
*
3469411 GAAAATAGAAAAAA
1 GAAAAAAGAAAAAA
3469425 TGGAAAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 4 0.09
19 20 0.44
20 18 0.40
21 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (18 bp):
GAAAAAAGAAAAAAAAAA
Found at i:3469424 original size:28 final size:27
Alignment explanation
Indices: 3469353--3469424 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 27
3469343 CAGATGTAAT
*
3469353 GAAAAAATAAATA-AAAAAGAAGAGAAA
1 GAAAAAA-AAATAGAAAAAAAAGAGAAA
*
3469380 GAAAAAAAAA-AG-GAAAAAAGA-AAA
1 GAAAAAAAAATAGAAAAAAAAGAGAAA
3469404 GGAAAAAGAAAATAGAAAAAA
1 -GAAAAA-AAAATAGAAAAAA
3469425 TGGAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 3 0.08
25 14 0.38
26 7 0.19
27 9 0.24
28 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (27 bp):
GAAAAAAAAATAGAAAAAAAAGAGAAA
Found at i:3470423 original size:49 final size:48
Alignment explanation
Indices: 3470367--3470468 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 48
3470357 GCGAATCTAA
* * *
3470367 TACCATGAAGA-TGAAATGGCAAAGATTGAGGTCATAACGGGGAACCCGG
1 TACCATGAAGATTGAAA-GG-AAAGATTGAGGCCATAACAGCGAACCCGG
* *
3470416 TACCATGAAGATTTGAAAGGAAAGGTTGAGGCCATAGCAGCGAACCCGG
1 TACCATGAAGA-TTGAAAGGAAAGATTGAGGCCATAACAGCGAACCCGG
3470465 TACC
1 TACC
3470469 TTAGCAGATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 39 0.85
50 2 0.04
51 5 0.11
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (48 bp):
TACCATGAAGATTGAAAGGAAAGATTGAGGCCATAACAGCGAACCCGG
Found at i:3470515 original size:50 final size:50
Alignment explanation
Indices: 3470461--3470611 Score: 175
Period size: 50 Copynumber: 3.0 Consensus size: 50
3470451 AGCAGCGAAC
*
3470461 CCGGTACCTTAGCAGATATTATGGGAAGGATTGAGGCCGTAACGGTAAAT
1 CCGGTACCTTAGCAGATATTATGGGAAGGATTGAGGCCGCAACGGTAAAT
* * * * *
3470511 CCGGTTCCGTTAGGAAGA-A--ATGGGAAAGG-TTCAGGCCGCAACGGTGAAC
1 CCGGTACC-TTA-GCAGATATTATGGG-AAGGATTGAGGCCGCAACGGTAAAT
* *
3470560 CCGGTACCTTAGCAGATATTATGGGAAGGATTGAAGCCGCAACGGCAAAT
1 CCGGTACCTTAGCAGATATTATGGGAAGGATTGAGGCCGCAACGGTAAAT
3470610 CC
1 CC
3470612 AATTCCATGA
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
47 4 0.05
48 4 0.05
49 32 0.40
50 33 0.41
51 4 0.05
52 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (50 bp):
CCGGTACCTTAGCAGATATTATGGGAAGGATTGAGGCCGCAACGGTAAAT
Found at i:3470561 original size:99 final size:99
Alignment explanation
Indices: 3470457--3470653 Score: 295
Period size: 99 Copynumber: 2.0 Consensus size: 99
3470447 CCATAGCAGC
* * * ** * *
3470457 GAACCCGGTACCTTAGCAGATATTATGGGAAGGATTGAGGCCGTAACGGTAAATCCGGTTCCGTT
1 GAACCCGGTACCTTAGCAGATATTATGGGAAGGATTGAAGCCGCAACGGCAAATCCAATTCCATG
* * *
3470522 AGGAAGAAATGGGAAAGGTTCAGGCCGCAACGGT
66 AGGAAGAAAAGGGAAAGATTCAAGCCGCAACGGT
3470556 GAACCCGGTACCTTAGCAGATATTATGGGAAGGATTGAAGCCGCAACGGCAAATCCAATTCCATG
1 GAACCCGGTACCTTAGCAGATATTATGGGAAGGATTGAAGCCGCAACGGCAAATCCAATTCCATG
*
3470621 AGGAAGAAAAGGGAAAGATTTAAGCCGCAACGG
66 AGGAAGAAAAGGGAAAGATTCAAGCCGCAACGG
3470654 CAAATCTAGT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (99 bp):
GAACCCGGTACCTTAGCAGATATTATGGGAAGGATTGAAGCCGCAACGGCAAATCCAATTCCATG
AGGAAGAAAAGGGAAAGATTCAAGCCGCAACGGT
Found at i:3470683 original size:49 final size:49
Alignment explanation
Indices: 3470629--3471448 Score: 623
Period size: 49 Copynumber: 16.8 Consensus size: 49
3470619 TGAGGAAGAA
* *
3470629 AAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACGAAGATATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
* * * * * *
3470678 GAGGGAAAGGTTTAAGTCGCAACGACG-ATCCTTGTACCTCAGAAG-CATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAAT-CTAGTACCAC-GAAGACATG
* * * *
3470727 AAGGGAAAGATTTAAGCCGCAAC-GCGAATCCAATACCAC-AAGGAAATA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAA-GACATG
* * * * * * *
3470775 AAAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTAGGAAG-CATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACC-ACGAAGACATG
* * * * * *
3470824 AAGGGAAAGATTTAAACTGCAATGGCGAATCCAATACCACGAAGATATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
* * * * * * *
3470873 GAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAG-CATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGACATG
* * *
3470922 AAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACGAAGATATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
* * * *
3470971 AA-GGAAAG-TTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGACATG
* * * *
3471018 AAGGGAAAGATTTAAGCTGTAACGGCGAATCTAGTACCACAAAGATATGG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACAT-G
* * * * * * * *
3471068 AA-CGAAAGGTTTAAGTCGCAACGGTGGACCTTGTACCTC-AGAGACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGA-AGACATG
* * * * * *
3471116 AAGGGATAGATTTAAGCCGCAACGGTGAATCCAATACCATGAAGACA-C
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
* * * * *
3471164 AGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCTG-AGACATG
1 A-AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGACATG
* *
3471214 AAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGACAT-
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
* * * * *** * * *
3471262 AGATGGAAAGGTTTAAGTCGCAATGATTAACCTTGTACCTC-AGAGACATG
1 A-AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGA-AGACATG
* **
3471312 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
* * * *
3471361 AAGGGAAAGTTTTAAGTCGCAACAGCGAACCTTA-TACC-CTAGAAG-CATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCAC--GAAGACATG
* * *
3471410 AAAGGAAAAATTTAAGCCGCAACGGCGAATTTAGTACCA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCA
3471449 TGCGGATTGA
Statistics
Matches: 583, Mismatches: 156, Indels: 63
0.73 0.19 0.08
Matches are distributed among these distances:
46 2 0.00
47 30 0.05
48 70 0.12
49 456 0.78
50 23 0.04
51 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.18
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACATG
Found at i:3470731 original size:98 final size:98
Alignment explanation
Indices: 3470629--3471448 Score: 1064
Period size: 98 Copynumber: 8.4 Consensus size: 98
3470619 TGAGGAAGAA
* * *
3470629 AAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
* *
3470694 TCGCAACGACGATCCTTGTACCTCAGAAGCATG
66 TCGCAACGGCGAACCTTGTACCTCAGAAGCATG
* * * *
3470727 AAGGGAAAGATTTAAGCCGCAAC-GCGAATCCAATACCAC-AAGGAAATAAAAGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GATATAGAGGGAAAGGTTTAA
*
3470790 GTCGCAATGGCGAACCTTGTACCT-AGGAAGCATG
65 GTCGCAACGGCGAACCTTGTACCTCA-GAAGCATG
* * * * *
3470824 AAGGGAAAGATTTAAACTGCAATGGCGAATCCAATACCACGAAGATATGGAGGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
*
3470889 TCACAACGGCGAACCTTGTACCTCAGAAGCATG
66 TCGCAACGGCGAACCTTGTACCTCAGAAGCATG
* *
3470922 AAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACGAAGATAT-GAAGGAAA-GTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
3470985 TCGCAACGGCGAACCTTGTACCTCAGAAGCATG
66 TCGCAACGGCGAACCTTGTACCTCAGAAGCATG
* * * * * **
3471018 AAGGGAAAGATTTAAGCTGTAACGGCGAATCTAGTACCACAAAGATATGGAACGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
* *
3471083 TCGCAACGGTGGACCTTGTACCTCAG-AGACATG
66 TCGCAACGGCGAACCTTGTACCTCAGAAG-CATG
* * * * * *
3471116 AAGGGATAGATTTAAGCCGCAACGGTGAATCCAATACCATGAAGACACAGAGGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
*
3471181 TCGCAACGGCGAACCTTGTACCTCTG-AGACATG
66 TCGCAACGGCGAACCTTGTACCTCAGAAG-CATG
* * *
3471214 AAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAGACATAGATGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
* ***
3471279 TCGCAATGATTAACCTTGTACCTCAG-AGACATG
66 TCGCAACGGCGAACCTTGTACCTCAGAAG-CATG
* * * *
3471312 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGTTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
* *
3471377 TCGCAACAGCGAACCTTATACC-CTAGAAGCATG
66 TCGCAACGGCGAACCTTGTACCTC-AGAAGCATG
* * **
3471410 AAAGGAAAAATTTAAGCCGCAACGGCGAATTTAGTACCA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
3471449 TGCGGATTGA
Statistics
Matches: 637, Mismatches: 75, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
96 85 0.13
97 96 0.15
98 451 0.71
99 5 0.01
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.18
Consensus pattern (98 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAG
TCGCAACGGCGAACCTTGTACCTCAGAAGCATG
Found at i:3471914 original size:18 final size:16
Alignment explanation
Indices: 3471876--3471933 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
3471866 AAATCTTTAT
*
3471876 TTTAAATTTATTTTAAG
1 TTTAAA-TTATTTTAAA
3471893 TTTAGAATTATTTTAAAA
1 TTTA-AATTATTTT-AAA
3471911 TTTAAATTTATTTTAAA
1 TTTAAA-TTATTTTAAA
3471928 TTTAAA
1 TTTAAA
3471934 ATTTGAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 22 0.59
18 15 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:3471935 original size:18 final size:18
Alignment explanation
Indices: 3471874--3471937 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
3471864 CCAAATCTTT
*
3471874 ATTTTAAATTTATTTTAA
1 ATTTAAAATTTATTTTAA
* *
3471892 GTTTAGAA-TTATTTTAAA
1 ATTTAAAATTTATTTT-AA
3471910 ATTT-AAATTTATTTTAA
1 ATTTAAAATTTATTTTAA
3471927 ATTTAAAATTT
1 ATTTAAAATTT
3471938 GAAATATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 15 0.39
18 23 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTAAAATTTATTTTAA
Found at i:3473950 original size:30 final size:29
Alignment explanation
Indices: 3473916--3474335 Score: 231
Period size: 30 Copynumber: 14.2 Consensus size: 29
3473906 GAGCTTTATT
* *
3473916 AAAATTCCATTTTTGACCTTAAACTTTCTA
1 AAAATTACATTTTT-ACCTCAAACTTTCTA
*
3473946 AAAATTACATTTTTACCCTCGAACTTTCT-
1 AAAATTACATTTTTA-CCTCAAACTTTCTA
* *
3473975 AAAATT-CTATTTTTTACC-CTAAATTTTCCA
1 AAAATTAC-A-TTTTTACCTC-AAACTTTCTA
* *
3474005 AAAATTACATTTTTAGCTCTAAACTTTC-C
1 AAAATTACATTTTTACCTC-AAACTTTCTA
* *
3474034 AAAATTCCATTCTTGACC-CTAAA-TTTACTA
1 AAAATTACATT-TTTACCTC-AAACTTT-CTA
* * *
3474064 AAAGTTACATTTTTACCCCTAAACTTTC-C
1 AAAATTACATTTTTACCTC-AAACTTTCTA
* * *
3474093 AAAATT-CTATTTTTGACCTCGAATTTTCCA
1 AAAATTAC-ATTTTT-ACCTCAAACTTTCTA
* * *
3474123 TAAATTACATTTTTACCCCTCAAACTGTC-C
1 AAAATTACATTTTTA--CCTCAAACTTTCTA
* *
3474153 AAAATTTCATTTTTGACCTCAAATTTTCTA
1 AAAATTACATTTTT-ACCTCAAACTTTCTA
* *
3474183 GAAATTACATTTTTACCCTCGAACTTTCT-
1 AAAATTACATTTTTA-CCTCAAACTTTCTA
* * *
3474212 AATATT-CTATTTTTAACC-CTAAATTTTCCA
1 AAAATTAC-ATTTTT-ACCTC-AAACTTTCTA
* *
3474242 AAAATTACATTTTTACCCCCAAACTTTCCA
1 AAAATTACATTTTTA-CCTCAAACTTTCTA
* *
3474272 AAAATTACCA-TTTTACCCTCAGA-TGTCTA
1 AAAATTA-CATTTTTA-CCTCAAACTTTCTA
* * *
3474301 AAAACTT-TATTTTTAACCCCAAACTTTCCA
1 AAAA-TTACATTTTT-ACCTCAAACTTTCTA
3474331 AAAAT
1 AAAAT
3474336 CACCATTATA
Statistics
Matches: 305, Mismatches: 52, Indels: 67
0.72 0.12 0.16
Matches are distributed among these distances:
28 9 0.03
29 110 0.36
30 167 0.55
31 19 0.06
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTTACCTCAAACTTTCTA
Found at i:3474290 original size:59 final size:59
Alignment explanation
Indices: 3473916--3474333 Score: 434
Period size: 59 Copynumber: 7.1 Consensus size: 59
3473906 GAGCTTTATT
* * * * *
3473916 AAAATTCCATTTTTGACCTTAAACTTTCTAAAAATTACATTTTTACCCTCGAACTTTCT
1 AAAATTCCATTTTTGACCCTAAATTTTCTAAAAATTACATTTTTACCCCCAAACTTTCC
* * * * * *
3473975 AAAATTCTATTTTTTACCCTAAATTTTCCAAAAATTACATTTTTAGCTCTAAACTTTCC
1 AAAATTCCATTTTTGACCCTAAATTTTCTAAAAATTACATTTTTACCCCCAAACTTTCC
* * * *
3474034 AAAATTCCATTCTTGACCCTAAATTTACTAAAAGTTACATTTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTTGACCCTAAATTTTCTAAAAATTACATTTTTACCCCCAAACTTTCC
* * * * *
3474093 AAAATTCTATTTTTGA-CCTCGAATTTTCCATAAATTACATTTTTACCCCTCAAACTGTCC
1 AAAATTCCATTTTTGACCCT-AAATTTTCTAAAAATTACATTTTTACCCC-CAAACTTTCC
* * * * *
3474153 AAAATTTCATTTTTGA-CCTCAAATTTTCTAGAAATTACATTTTTACCCTCGAACTTTCT
1 AAAATTCCATTTTTGACCCT-AAATTTTCTAAAAATTACATTTTTACCCCCAAACTTTCC
* * * *
3474212 AATATTCTATTTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTGACCCTAAATTTTCTAAAAATTACATTTTTACCCCCAAACTTTCC
* * * *
3474271 AAAAATTACCA-TTTT-ACCCTCAGA-TGTCTAAAAACTT-TATTTTTAACCCCAAACTTTCC
1 -AAAATT-CCATTTTTGACCCT-AAATTTTCTAAAAA-TTACATTTTTACCCCCAAACTTTCC
3474330 AAAA
1 AAAA
3474334 ATCACCATTA
Statistics
Matches: 299, Mismatches: 53, Indels: 15
0.81 0.14 0.04
Matches are distributed among these distances:
58 7 0.02
59 223 0.75
60 67 0.22
61 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCCTAAATTTTCTAAAAATTACATTTTTACCCCCAAACTTTCC
Found at i:3474292 original size:119 final size:117
Alignment explanation
Indices: 3473916--3474292 Score: 478
Period size: 119 Copynumber: 3.2 Consensus size: 117
3473906 GAGCTTTATT
* *
3473916 AAAATTCCATTTTTGA-CCTTAAACTTTCTAAAAATTACATTTTTACCCTCGAACTTTCTAAAAT
1 AAAATTCCA-TTTTGACCCTCAAATTTTCT-AAAATTACATTTTTACCCTCGAACTTTCTAAAAT
* * * *
3473980 TCTATTTTTTACCCTAAATTTTCCAAAAATTACATTTTTAGCTCTAAACTTTCC
64 TCTATTTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCCCAAACTTTCC
* * *
3474034 AAAATTCCATTCTTGACCCT-AAATTTACTAAAAGTTACATTTTTACCC-CTAAACTTTCCAAAA
1 AAAATTCCATT-TTGACCCTCAAATTTTCTAAAA-TTACATTTTTACCCTC-GAACTTTCTAAAA
* * * *
3474097 TTCTATTTTTGA-CCTCGAATTTTCCATAAATTACATTTTTACCCCTCAAACTGTCC
63 TTCTATTTTTAACCCT-AAATTTTCCAAAAATTACATTTTTACCCC-CAAACTTTCC
* *
3474153 AAAATTTCATTTTTGA-CCTCAAATTTTCTAGAAATTACATTTTTACCCTCGAACTTTCTAATAT
1 AAAATTCCA-TTTTGACCCTCAAATTTTCTA-AAATTACATTTTTACCCTCGAACTTTCTAAAAT
3474217 TCTATTTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCCCAAACTTTCC
64 TCTATTTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCCCAAACTTTCC
3474271 AAAAATTACCATTTT-ACCCTCA
1 -AAAATT-CCATTTTGACCCTCA
3474293 GATGTCTAAA
Statistics
Matches: 224, Mismatches: 21, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
117 10 0.04
118 94 0.42
119 109 0.49
120 11 0.05
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (117 bp):
AAAATTCCATTTTGACCCTCAAATTTTCTAAAATTACATTTTTACCCTCGAACTTTCTAAAATTC
TATTTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCCCAAACTTTCC
Found at i:3474334 original size:59 final size:58
Alignment explanation
Indices: 3474242--3474396 Score: 195
Period size: 59 Copynumber: 2.7 Consensus size: 58
3474232 AAATTTTCCA
* * * *
3474242 AAAATTACATTTTTACCCCCAAACTTTCCAAAAATTACCATTTTACCCTCAGATGTCT
1 AAAATTTCATTTTTAACCCCAAACTTTCCAAAAATTACCATTATACCCTCAGACGTCT
* * *
3474300 AAAAACTTT-ATTTTTAACCCCAAACTTTCCAAAAATCACCATTATACTCTCGGACGTCT
1 -AAAA-TTTCATTTTTAACCCCAAACTTTCCAAAAATTACCATTATACCCTCAGACGTCT
* * *
3474359 AGAATTTCATTTTTAACTCCGAACTTTCCAAAAATTAC
1 AAAATTTCATTTTTAACCCCAAACTTTCCAAAAATTAC
3474397 AGTTTTGCCC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 3 0.04
58 30 0.36
59 48 0.58
60 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (58 bp):
AAAATTTCATTTTTAACCCCAAACTTTCCAAAAATTACCATTATACCCTCAGACGTCT
Found at i:3478777 original size:33 final size:33
Alignment explanation
Indices: 3478735--3478800 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3478725 TCAAGGAGAT
*
3478735 GTTAATATTATTGTTGTTG-TCGTTATTGTTTTG
1 GTTAATATTATTGTTGTTGTTC-ATATTGTTTTG
3478768 GTTAATATTATTGTTGTTGTTCATATTGTTTTG
1 GTTAATATTATTGTTGTTGTTCATATTGTTTTG
3478801 CCTGTCATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.61
Consensus pattern (33 bp):
GTTAATATTATTGTTGTTGTTCATATTGTTTTG
Found at i:3478793 original size:18 final size:18
Alignment explanation
Indices: 3478734--3478794 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
3478724 CTCAAGGAGA
3478734 TGTTAATATTATTGTTGT
1 TGTTAATATTATTGTTGT
**
3478752 TG-T--CGTTATTGTT-T
1 TGTTAATATTATTGTTGT
3478766 TGGTTAATATTATTGTTGT
1 T-GTTAATATTATTGTTGT
*
3478785 TGTTCATATT
1 TGTTAATATT
3478795 GTTTTGCCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
14 2 0.06
15 9 0.27
16 1 0.03
17 1 0.03
18 18 0.55
19 2 0.06
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (18 bp):
TGTTAATATTATTGTTGT
Found at i:3488701 original size:18 final size:19
Alignment explanation
Indices: 3488680--3488721 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
3488670 TGTCTTTTTC
3488680 TTTTTTTTTTC-TCCAATT
1 TTTTTTTTTTCTTCCAATT
* *
3488698 TTTTCTTTTTCTTTCAATT
1 TTTTTTTTTTCTTCCAATT
3488717 TTTTT
1 TTTTT
3488722 GATTATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTTTTCTTCCAATT
Found at i:3488706 original size:19 final size:18
Alignment explanation
Indices: 3488680--3488721 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
3488670 TGTCTTTTTC
3488680 TTTTTTTTTTC-TCCAAT
1 TTTTTTTTTTCTTCCAAT
*
3488697 TTTTTCTTTTTCTTTCAAT
1 TTTTT-TTTTTCTTCCAAT
3488716 TTTTTT
1 TTTTTT
3488722 GATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTTCTTCCAAT
Found at i:3488719 original size:20 final size:20
Alignment explanation
Indices: 3488680--3488772 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
3488670 TGTCTTTTTC
*
3488680 TTTTT-TTTTTC-TCCAA-T
1 TTTTTCTTTTTCTTTCAATT
3488697 TTTTTCTTTTTCTTTCAATT
1 TTTTTCTTTTTCTTTCAATT
* * *
3488717 TTTTTGATTATT-TTTAAATT
1 TTTTT-CTTTTTCTTTCAATT
*
3488737 TTTTTCGACTTTTGTCTTTC-TTT
1 TTTTT---CTTTT-TCTTTCAATT
3488760 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
3488773 AAATAATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
17 5 0.08
18 6 0.10
19 7 0.12
20 23 0.39
21 4 0.07
22 3 0.05
23 8 0.14
24 3 0.05
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTCAATT
Found at i:3489708 original size:11 final size:12
Alignment explanation
Indices: 3489692--3489720 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3489682 AATAGTGCAT
3489692 AATAAAAAT-AA
1 AATAAAAATGAA
3489703 AATAAAAATGAA
1 AATAAAAATGAA
3489715 AATAAA
1 AATAAA
3489721 TGTATTAATT
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:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
AATAAAAATGAA
Found at i:3494782 original size:33 final size:33
Alignment explanation
Indices: 3494745--3494810 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3494735 ACATGACGGG
*
3494745 CAAAACAAT-ATGAACAACAACAATAATATTAAC
1 CAAAACAATAACG-ACAACAACAATAATATTAAC
3494778 CAAAACAATAACGACAACAACAATAATATTAAC
1 CAAAACAATAACGACAACAACAATAATATTAAC
3494811 GTCTTCTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.61, C:0.20, G:0.03, T:0.17
Consensus pattern (33 bp):
CAAAACAATAACGACAACAACAATAATATTAAC
Found at i:3498831 original size:20 final size:21
Alignment explanation
Indices: 3498808--3498864 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
3498798 ACTTTTGCCA
* *
3498808 TATTT-TATTTTTTATTTTAT
1 TATTTATATTTTTAATTTAAT
**
3498828 TATTTGCATTTTTAATTTAAT
1 TATTTATATTTTTAATTTAAT
3498849 T-TTTATA-TTTTAATTT
1 TATTTATATTTTTAATTT
3498865 TTTCCCTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 9 0.29
20 9 0.29
21 13 0.42
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TATTTATATTTTTAATTTAAT
Done.