Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 289 of 333
Found at i:95526559 original size:6 final size:6
Alignment explanation
Indices: 95526550--95526580 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
95526540 ATGCAAATTA
95526550 AAATAT AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT AAATAT A
95526581 CCCTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:95535725 original size:31 final size:31
Alignment explanation
Indices: 95535690--95535751 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
95535680 AATGCTTAGT
*
95535690 AAGTTCATAAAACTGGGAATTTAACTTACCA
1 AAGTTCATAAAACTGGAAATTTAACTTACCA
*
95535721 AAGTTCATATAACTGGAAATTTAACTTACCA
1 AAGTTCATAAAACTGGAAATTTAACTTACCA
95535752 TTCATTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (31 bp):
AAGTTCATAAAACTGGAAATTTAACTTACCA
Found at i:95536221 original size:24 final size:25
Alignment explanation
Indices: 95536167--95536221 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
95536157 GCTTATTCGG
95536167 GCTTAATAACATGAAACTCATAAGA
1 GCTTAATAACATGAAACTCATAAGA
* **
95536192 GTTTAA-AACA-GAAAGCTCATGTGA
1 GCTTAATAACATGAAA-CTCATAAGA
95536216 GCTTAA
1 GCTTAA
95536222 CGGGAACACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 4 0.16
24 16 0.64
25 5 0.20
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (25 bp):
GCTTAATAACATGAAACTCATAAGA
Found at i:95536320 original size:25 final size:24
Alignment explanation
Indices: 95536286--95536338 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
95536276 AAGTTCAAGC
95536286 GAGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
*
95536310 GAGCCTATATCAGGATGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
95536335 GAGC
1 GAGC
95536339 TGCAGTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:95536871 original size:12 final size:12
Alignment explanation
Indices: 95536854--95536878 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95536844 ACTCATTCAC
95536854 ATCTTAGGCAAA
1 ATCTTAGGCAAA
95536866 ATCTTAGGCAAA
1 ATCTTAGGCAAA
95536878 A
1 A
95536879 GTACAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
ATCTTAGGCAAA
Found at i:95537892 original size:30 final size:30
Alignment explanation
Indices: 95537858--95537959 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
95537848 AAAAAAATAA
* *
95537858 AAATTTCATTTTGACCCCCAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
95537888 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
95537918 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
95537948 AAATTTCATTTT
1 AAATTTCATTTT
95537960 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.06
30 58 0.94
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:95538522 original size:7 final size:7
Alignment explanation
Indices: 95538510--95538591 Score: 51
Period size: 7 Copynumber: 11.3 Consensus size: 7
95538500 AGAAGAGAAG
95538510 AAGAAAA
1 AAGAAAA
95538517 AAGAAAA
1 AAGAAAA
**
95538524 AA-AGAGG
1 AAGA-AAA
95538531 AAGAAAA
1 AAGAAAA
*
95538538 AGAGAGAA
1 A-AGAAAA
95538546 AA-AAAA
1 AAGAAAA
95538552 AAGAAAAA
1 AAG-AAAA
95538560 AAGAAAAAA
1 AAG--AAAA
*
95538569 AATAAAA
1 AAGAAAA
*
95538576 AATAAAA
1 AAGAAAA
*
95538583 AATAAAA
1 AAGAAAA
95538590 AA
1 AA
95538592 CAGCAGGCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
6 6 0.10
7 35 0.56
8 14 0.23
9 7 0.11
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:95538533 original size:21 final size:19
Alignment explanation
Indices: 95538507--95538570 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 19
95538497 AGAAGAAGAG
95538507 AAGAAGAAAAAAGAAAAAA
1 AAGAAGAAAAAAGAAAAAA
95538526 AGAGGAAGAAAAAGAGAGAAAAA
1 A-A-GAAGAAAAA-AGA-AAAAA
*
95538549 AAAAAGAAAAAAAGAAAAAA
1 AAGAAG-AAAAAAGAAAAAA
95538569 AA
1 AA
95538571 TAAAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.03
20 8 0.21
21 15 0.38
22 9 0.23
23 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAAAAGAAAAAA
Found at i:95538533 original size:29 final size:30
Alignment explanation
Indices: 95538496--95538584 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 30
95538486 GCTTTGAGAC
*
95538496 AAGAAGAAG-AGAAGA-AGAAAAAAGAAAAA
1 AAGAAGAAGAAAAAGAGAGAAAAAA-AAAAA
*
95538525 AAGAGGAAGAAAAAGAGAGAAAAAAAAAAGA
1 AAGAAGAAGAAAAAGAGAGAAAAAAAAAA-A
* * *
95538556 AA-AA-AAGAAAAA-AAATAAAAAATAAAA
1 AAGAAGAAGAAAAAGAGAGAAAAAAAAAAA
95538583 AA
1 AA
95538585 TAAAAAACAG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 3 0.06
28 11 0.22
29 16 0.31
30 10 0.20
31 11 0.22
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (30 bp):
AAGAAGAAGAAAAAGAGAGAAAAAAAAAAA
Found at i:95538536 original size:14 final size:13
Alignment explanation
Indices: 95538517--95538555 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
95538507 AAGAAGAAAA
95538517 AAGAAAAAAAGAGG
1 AAGAAAAAAAGA-G
*
95538531 AAGAAAAAGAGAG
1 AAGAAAAAAAGAG
*
95538544 AAAAAAAAAAGA
1 AAGAAAAAAAGA
95538556 AAAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAG
Found at i:95538548 original size:1 final size:1
Alignment explanation
Indices: 95538544--95538591 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
95538534 AAAAAGAGAG
* * * * *
95538544 AAAAAAAAAAGAAAAAAAGAAAAAAAATAAAAAATAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
95538592 CAGCAGGCTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.00, G:0.04, T:0.06
Consensus pattern (1 bp):
A
Found at i:95538561 original size:14 final size:14
Alignment explanation
Indices: 95538510--95538591 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 14
95538500 AGAAGAGAAG
95538510 AAGAAAAAAGAAAAA
1 AAGAAAAAA-AAAAA
* *
95538525 AAGAGGAAGAAAAAGA
1 AAGA--AAAAAAAAAA
*
95538541 GAGAAAAAAAAAAGA
1 AAGAAAAAAAAAA-A
*
95538556 AA-AAAAGAAAAAA
1 AAGAAAAAAAAAAA
* *
95538569 AATAAAAAATAAAA
1 AAGAAAAAAAAAAA
*
95538583 AATAAAAAA
1 AAGAAAAAA
95538592 CAGCAGGCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
13 3 0.06
14 34 0.63
15 6 0.11
16 7 0.13
17 4 0.07
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:95538583 original size:35 final size:35
Alignment explanation
Indices: 95538513--95538589 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
95538503 AGAGAAGAAG
* * * *
95538513 AAAAAAGAAAAAAAGAGGAAGAAAAAGAGAGAAAA
1 AAAAAAGAAAAAAAGAGAAAAAAAAAAAAAGAAAA
*
95538548 AAAAAAGAAAAAAAGA-AAAAAAATAAAAAATAAAA
1 AAAAAAGAAAAAAAGAGAAAAAAA-AAAAAAGAAAA
95538583 AATAAAA
1 AA-AAAA
95538590 AACAGCAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 5 0.14
35 26 0.74
36 4 0.11
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (35 bp):
AAAAAAGAAAAAAAGAGAAAAAAAAAAAAAGAAAA
Found at i:95538591 original size:8 final size:8
Alignment explanation
Indices: 95538513--95538584 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
95538503 AGAGAAGAAG
95538513 AAAAAAGAA
1 AAAAAAG-A
95538522 AAAAAGAGGA
1 AAAAA-A-GA
95538532 AGAAAAAGA
1 A-AAAAAGA
* *
95538541 GAGAAA-A
1 AAAAAAGA
95538548 AAAAAAGA
1 AAAAAAGA
95538556 AAAAAAGA
1 AAAAAAGA
95538564 AAAAAA-A
1 AAAAAAGA
*
95538571 TAAAAAATA
1 -AAAAAAGA
95538580 AAAAA
1 AAAAA
95538585 TAAAAAACAG
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
7 6 0.11
8 30 0.57
9 8 0.15
10 4 0.08
11 5 0.09
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:95539287 original size:18 final size:18
Alignment explanation
Indices: 95539253--95539287 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
95539243 ACTTTTCGAC
*
95539253 TTTTCGCGTTTTCAAAAG
1 TTTTCGCGTTTTAAAAAG
*
95539271 TTTTCGTGTTTTAAAAA
1 TTTTCGCGTTTTAAAAA
95539288 AAAATTCGCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTCGCGTTTTAAAAAG
Found at i:95539313 original size:24 final size:24
Alignment explanation
Indices: 95539284--95539363 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
95539274 TCGTGTTTTA
*
95539284 AAAAAAAATTCGCGTTTTAAAATG
1 AAAAAAAATTCGTGTTTTAAAATG
** *
95539308 AAAAAATTTTCGTGTTTTCAAATG
1 AAAAAAAATTCGTGTTTTAAAATG
** *
95539332 -AAAAATTTTCGTGTTTTAAAATA
1 AAAAAAAATTCGTGTTTTAAAATG
95539355 AAACAAAAA
1 AAA-AAAAA
95539364 ACAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 21 0.46
24 22 0.48
25 3 0.07
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (24 bp):
AAAAAAAATTCGTGTTTTAAAATG
Found at i:95539335 original size:23 final size:22
Alignment explanation
Indices: 95539266--95539357 Score: 109
Period size: 23 Copynumber: 4.2 Consensus size: 22
95539256 TCGCGTTTTC
*
95539266 AAAAGTTTTCGTGTTTTAAAA-
1 AAAAATTTTCGTGTTTTAAAAT
*
95539287 AAAAA--TTCGCGTTTTAAAAT
1 AAAAATTTTCGTGTTTTAAAAT
*
95539307 GAAAAAATTTTCGTGTTTTCAAAT
1 --AAAAATTTTCGTGTTTTAAAAT
95539331 GAAAAATTTTCGTGTTTTAAAAT
1 -AAAAATTTTCGTGTTTTAAAAT
95539354 AAAA
1 AAAA
95539358 CAAAAAACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
19 13 0.22
21 4 0.07
22 9 0.15
23 21 0.35
24 13 0.22
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
AAAAATTTTCGTGTTTTAAAAT
Found at i:95539409 original size:35 final size:34
Alignment explanation
Indices: 95539370--95539438 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
95539360 AAAAACAAAA
** *
95539370 AAAAACTCCCGTCTTTCAGAAATTTTCGTGTTTTC
1 AAAAACTCCCGTCTTAAAAAAATTTT-GTGTTTTC
* *
95539405 AAAAATTCCCGTGTTAAAAAAATTTTGTGTTTTC
1 AAAAACTCCCGTCTTAAAAAAATTTTGTGTTTTC
95539439 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
AAAAACTCCCGTCTTAAAAAAATTTTGTGTTTTC
Found at i:95539410 original size:18 final size:18
Alignment explanation
Indices: 95539383--95539489 Score: 65
Period size: 18 Copynumber: 5.6 Consensus size: 18
95539373 AACTCCCGTC
*
95539383 TTTCAGAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
**
95539401 TTTCAAAAATTCCCGTG-
1 TTTCAAAAATTTTCGTGT
** *
95539418 TTAAAAAAATTTTGTGTTTTCGT
1 TTTCAAAAATTTT-CG---T-GT
95539441 GTTTTCAAAAAATTTTCGTG-
1 -TTT-CAA-AAATTTTCGTGT
*
95539461 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATTTTCGTGT
95539479 TTTCAAAAATT
1 TTTCAAAAATT
95539490 ATTATTTTGT
Statistics
Matches: 66, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
17 19 0.29
18 28 0.42
19 3 0.05
21 2 0.03
22 2 0.03
24 2 0.03
25 3 0.05
26 7 0.11
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:95539458 original size:19 final size:19
Alignment explanation
Indices: 95539434--95539487 Score: 85
Period size: 17 Copynumber: 2.9 Consensus size: 19
95539424 AAATTTTGTG
95539434 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
95539453 TTTTCGTG-TTTC-AAAAA
1 TTTTCGTGTTTTCAAAAAA
*
95539470 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
95539488 TTATTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 12 0.38
18 8 0.25
19 12 0.38
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTTCGTGTTTTCAAAAAA
Found at i:95539469 original size:43 final size:43
Alignment explanation
Indices: 95539392--95539482 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
95539382 CTTTCAGAAA
*
95539392 TTTTCGTGTTTTCAAAAATTCCCGTGTTAAAAAAAT-TTTGTG
1 TTTTCGTGTTTTCAAAAATTCCCGTGTTAAAAAAATCTTCGTG
** **
95539434 TTTTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATCTTCGTG
1 TTTTCGTGTTTTC-AAAAATTCCCGTGTTAAAAAAATCTTCGTG
95539478 TTTTC
1 TTTTC
95539483 AAAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 13 0.31
43 19 0.45
44 10 0.24
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.48
Consensus pattern (43 bp):
TTTTCGTGTTTTCAAAAATTCCCGTGTTAAAAAAATCTTCGTG
Found at i:95539470 original size:17 final size:18
Alignment explanation
Indices: 95539434--95539489 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
95539424 AAATTTTGTG
95539434 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
95539453 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
95539470 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
95539488 TT
1 TT
95539490 ATTATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 8 0.24
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:95540437 original size:60 final size:59
Alignment explanation
Indices: 95540310--95540448 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 59
95540300 TTTAGTGTTA
*
95540310 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCCTTACAGT-ACAGAGTAT
* * *
95540371 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTGTTACAAGT-C-GAGATAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-CTTAC-AGTACAGAG-TAT
* *
95540431 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
95540449 TGACACAGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
59 3 0.04
60 51 0.74
61 12 0.17
62 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCCTTACAGTACAGAGTAT
Found at i:95544657 original size:22 final size:22
Alignment explanation
Indices: 95544626--95544670 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
95544616 AAGATATAAT
* **
95544626 GCCTTTCTCATTAATGGATTCA
1 GCCTTCCTCATTAAAAGATTCA
95544648 GCCTTCCTCATTAAAAGATTCA
1 GCCTTCCTCATTAAAAGATTCA
95544670 G
1 G
95544671 GTTTGATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (22 bp):
GCCTTCCTCATTAAAAGATTCA
Found at i:95547620 original size:16 final size:16
Alignment explanation
Indices: 95547594--95547635 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
95547584 TTTATAAATG
95547594 AAATAAAATTTATT-TT
1 AAAT-AAATTTATTATT
95547610 CAAATAAATTTATTATT
1 -AAATAAATTTATTATT
95547627 AAATAAATT
1 AAATAAATT
95547636 AAATAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAAATTTATTATT
Found at i:95547668 original size:29 final size:25
Alignment explanation
Indices: 95547611--95547657 Score: 71
Period size: 23 Copynumber: 1.9 Consensus size: 25
95547601 ATTTATTTTC
95547611 AAATAAATTTATTATTAAATAAATT
1 AAATAAATTTATTATTAAATAAATT
95547636 AAATAAA-TT-TTATTAATATAAA
1 AAATAAATTTATTATTAA-ATAAA
95547658 AATATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATAAATTTATTATTAAATAAATT
Found at i:95548392 original size:26 final size:27
Alignment explanation
Indices: 95548310--95548392 Score: 63
Period size: 26 Copynumber: 3.3 Consensus size: 27
95548300 ATATCAAAAA
*
95548310 TATTATTAAATTATATATT--T-TTATT
1 TATTATTAAAATATAT-TTAATATTATT
* * *
95548335 T-TTATTAAATTATATTTAATAATAAT
1 TATTATTAAAATATATTTAATATTATT
95548361 TA-TATTAAAATATGA-TTAA-ATTATT
1 TATTATTAAAATAT-ATTTAATATTATT
95548386 TATTATT
1 TATTATT
95548393 TATTTATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.04
24 14 0.30
25 8 0.17
26 22 0.47
27 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TATTATTAAAATATATTTAATATTATT
Found at i:95548425 original size:58 final size:60
Alignment explanation
Indices: 95548306--95548429 Score: 173
Period size: 58 Copynumber: 2.1 Consensus size: 60
95548296 TATTATATCA
* *
95548306 AAAATATTATTAAATTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATT
1 AAAATATGATTAAATTATATATTTTTA-TTTTATTAAATTATATTTAATAATAATGATATT
* *
95548367 AAAATATGATTAAATTATTTATTATTTA-TTTATTAAATT-T-TTTAATAATAATGCTATT
1 AAAATATGATTAAATTATATATT-TTTATTTTATTAAATTATATTTAATAATAATGATATT
95548425 AAAAT
1 AAAAT
95548430 TTAATAACAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
58 21 0.36
59 1 0.02
60 11 0.19
61 21 0.36
62 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (60 bp):
AAAATATGATTAAATTATATATTTTTATTTTATTAAATTATATTTAATAATAATGATATT
Found at i:95556220 original size:13 final size:13
Alignment explanation
Indices: 95556202--95556227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95556192 GGACATAATG
95556202 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
95556215 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
95556228 GTAGACAGCA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:95569891 original size:6 final size:6
Alignment explanation
Indices: 95569880--95569918 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
95569870 GGACAATGGC
95569880 TCCTAG TCCTAG TCCTAG TCCTAG TCCTAG TCCTAG TCC
1 TCCTAG TCCTAG TCCTAG TCCTAG TCCTAG TCCTAG TCC
95569919 CAGAGCTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.36, G:0.15, T:0.33
Consensus pattern (6 bp):
TCCTAG
Found at i:95571344 original size:19 final size:19
Alignment explanation
Indices: 95571307--95571343 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
95571297 AATATATTCT
95571307 TTAATTTAACATATAAAAA
1 TTAATTTAACATATAAAAA
95571326 TTAATTTAACAT-TAAAAA
1 TTAATTTAACATATAAAAA
95571344 AAAAATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAATTTAACATATAAAAA
Found at i:95573563 original size:150 final size:150
Alignment explanation
Indices: 95573292--95573582 Score: 433
Period size: 150 Copynumber: 1.9 Consensus size: 150
95573282 AGTCATTTTG
*
95573292 TTATGTTAATATACGTGATTAGAGATGGATTTAATTACAATATATGTAACAAAAGTCGCATTAGT
1 TTATGTTAATATACGTGATTAGAGATGGATTTAATTACAATATATGTAACAAAAGTCACATTAGT
*
95573357 TCTATGTTAACATGGTTAATGAACAAGATTATTTGGAATACCTTTTGGATATGATAGAAAGATTT
66 TCTATGTTAACATGGTTAATGAACAAGATTATTCGGAATACCTTTTGGATATGATAGAAAGATTT
95573422 TGAGCTCATGAATCAGTTGA
131 TGAGCTCATGAATCAGTTGA
* * * *
95573442 TTATGTTGATATACGTGATTTTG-GATGGATTTAGTTACAATATATGTAACGAAAGTCACATT-G
1 TTATGTTAATATACGTGA-TTAGAGATGGATTTAATTACAATATATGTAACAAAAGTCACATTAG
* * * * * *
95573505 ATTCTATGTTAACATGGTTATTGGACGAGATTGTTCGGAATACTTTTTGGATATGATAGTAAGAT
65 -TTCTATGTTAACATGGTTAATGAACAAGATTATTCGGAATACCTTTTGGATATGATAGAAAGAT
*
95573570 TTTGAGCTTATGA
129 TTTGAGCTCATGA
95573583 GGTTATATAA
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
149 1 0.01
150 122 0.97
151 3 0.02
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (150 bp):
TTATGTTAATATACGTGATTAGAGATGGATTTAATTACAATATATGTAACAAAAGTCACATTAGT
TCTATGTTAACATGGTTAATGAACAAGATTATTCGGAATACCTTTTGGATATGATAGAAAGATTT
TGAGCTCATGAATCAGTTGA
Found at i:95575757 original size:10 final size:10
Alignment explanation
Indices: 95575742--95575841 Score: 51
Period size: 12 Copynumber: 8.9 Consensus size: 10
95575732 AATAAAGATT
95575742 ATATAATAAA
1 ATATAATAAA
95575752 ATATAATAAAA
1 ATATAAT-AAA
*
95575763 ATAATAGATATA
1 AT-ATA-ATAAA
*
95575775 ATATGAAGTAAC
1 ATAT-AA-TAAA
95575787 ATATAA-AACA
1 ATATAATAA-A
95575797 ATATATATAAGTA
1 ATATA-ATAA--A
95575810 AT-TAATAAA
1 ATATAATAAA
95575819 TATAATATATGAAA
1 -AT-ATA-AT-AAA
95575833 ATATAATAA
1 ATATAATAA
95575842 TATGTAAAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 28
0.68 0.05 0.27
Matches are distributed among these distances:
9 3 0.04
10 16 0.23
11 17 0.24
12 23 0.32
13 9 0.13
14 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATAATAAA
Found at i:95575775 original size:9 final size:9
Alignment explanation
Indices: 95575742--95575898 Score: 50
Period size: 10 Copynumber: 17.8 Consensus size: 9
95575732 AATAAAGATT
95575742 ATATAATAAA
1 ATATAAT-AA
95575752 ATATAATAA
1 ATATAATAA
* *
95575761 AAATAATAG
1 ATATAATAA
95575770 ATATAAT--
1 ATATAATAA
*
95575777 ATGA-AGTAA
1 AT-ATAATAA
*
95575786 CATATAAAACA
1 -ATATAATA-A
95575797 ATATATATAA
1 ATATA-ATAA
*
95575807 GTAATTAATAA
1 AT-A-TAATAA
95575818 ATATAAT--
1 ATATAATAA
*
95575825 ATATGA-AA
1 ATATAATAA
95575833 ATATAAT-A
1 ATATAATAA
*
95575841 ATAT-GTAA
1 ATATAATAA
95575849 A-ATAAT-A
1 ATATAATAA
* *
95575856 ATTTAAGAA
1 ATATAATAA
*
95575865 AAATAAT--
1 ATATAATAA
95575872 ATATAATAA
1 ATATAATAA
*
95575881 GTAATAATAA
1 AT-ATAATAA
95575891 TATATAAT
1 -ATATAAT
95575899 TTAAAATAAT
Statistics
Matches: 106, Mismatches: 21, Indels: 40
0.63 0.13 0.24
Matches are distributed among these distances:
7 20 0.19
8 17 0.16
9 26 0.25
10 31 0.29
11 10 0.09
12 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (9 bp):
ATATAATAA
Found at i:95575836 original size:15 final size:15
Alignment explanation
Indices: 95575816--95575875 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
95575806 AGTAATTAAT
95575816 AAATATAATATATGA
1 AAATATAATATATGA
95575831 AAATATAATAATATGTA
1 AAATATAAT-ATATG-A
* *
95575848 AAATAATAATTTAAGA
1 AAAT-ATAATATATGA
95575864 AAA-ATAATATAT
1 AAATATAATATAT
95575876 AATAAGTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.18
15 9 0.24
16 9 0.24
17 8 0.21
18 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
AAATATAATATATGA
Found at i:95575843 original size:18 final size:16
Alignment explanation
Indices: 95575823--95575876 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
95575813 AATAAATATA
95575823 ATATATGAAAATATAAT
1 ATATATGAAAA-ATAAT
*
95575840 A-ATATGTAAAATAAT
1 ATATATGAAAAATAAT
* *
95575855 AATTTAAGAAAAATAAT
1 -ATATATGAAAAATAAT
95575872 ATATA
1 ATATA
95575877 ATAAGTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 5 0.17
16 13 0.43
17 12 0.40
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
ATATATGAAAAATAAT
Found at i:95575855 original size:20 final size:19
Alignment explanation
Indices: 95575790--95575898 Score: 88
Period size: 20 Copynumber: 5.8 Consensus size: 19
95575780 AAGTAACATA
*
95575790 TAAAACAATATAT-ATAAG
1 TAAAATAATATATAATAAG
95575808 TAATTAATAA-ATATAATATA-
1 TAA--AATAATATATAATA-AG
*
95575828 TGAAAAT-ATA-ATAATATG
1 T-AAAATAATATATAATAAG
*
95575846 TAAAATAATA-AT-TTAAG
1 TAAAATAATATATAATAAG
*
95575863 AAAAATAATATATAATAAG
1 TAAAATAATATATAATAAG
95575882 TAATAATAATATATAAT
1 TAA-AATAATATATAAT
95575899 TTAAAATAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
17 17 0.23
18 18 0.25
19 14 0.19
20 21 0.29
21 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.34
Consensus pattern (19 bp):
TAAAATAATATATAATAAG
Found at i:95575886 original size:17 final size:17
Alignment explanation
Indices: 95575745--95575894 Score: 50
Period size: 17 Copynumber: 8.7 Consensus size: 17
95575735 AAAGATTATA
*
95575745 TAATAAAATATAATAA-
1 TAATAATATATAATAAG
* *
95575761 AAATAATAGATATAATATG
1 TAATAAT--ATATAATAAG
*
95575780 -AAGTAACATATAA-AA-
1 TAA-TAATATATAATAAG
* *
95575795 CAAT-ATATATAAGTAAT
1 TAATAATATATAA-TAAG
95575812 TAATAA-ATATAATATA-
1 TAATAATATATAATA-AG
*
95575828 TGAA-AATATAATAATATG
1 T-AATAATAT-ATAATAAG
95575846 TAA-AATA-ATAATTTAAG
1 TAATAATATATAA--TAAG
*
95575863 AAAAATAATATATAATAAG
1 --TAATAATATATAATAAG
95575882 TAATAATAATATA
1 TAATAAT-ATATA
95575895 TAATTTAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 40
0.67 0.07 0.26
Matches are distributed among these distances:
14 7 0.07
15 5 0.05
16 15 0.15
17 35 0.34
18 23 0.23
19 9 0.09
20 4 0.04
21 4 0.04
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (17 bp):
TAATAATATATAATAAG
Found at i:95575897 original size:10 final size:10
Alignment explanation
Indices: 95575820--95575898 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
95575810 ATTAATAAAT
*
95575820 ATAATATATG
1 ATAATATATA
95575830 A-AA-ATATA
1 ATAATATATA
*
95575838 ATAATATGTA
1 ATAATATATA
95575848 A-AATA-ATA
1 ATAATATATA
* *
95575856 ATTTAAGA-AAA
1 A--TAATATATA
95575867 ATAATATATA
1 ATAATATATA
95575877 ATAAGTA-ATA
1 ATAA-TATATA
95575887 ATAATATATA
1 ATAATATATA
95575897 AT
1 AT
95575899 TTAAAATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
8 8 0.15
9 14 0.26
10 24 0.44
11 8 0.15
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (10 bp):
ATAATATATA
Found at i:95575906 original size:20 final size:21
Alignment explanation
Indices: 95575849--95575909 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
95575839 TAATATGTAA
*
95575849 AATA-ATAATTTAAGAAAAAT
1 AATATATAATTTAAGAATAAT
95575869 AATATATAA--TAAGTAATAAT
1 AATATATAATTTAAG-AATAAT
95575889 AATATATAATTTAA-AATAAT
1 AATATATAATTTAAGAATAAT
95575909 A
1 A
95575910 CTTATAACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.11
20 25 0.69
21 4 0.11
22 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (21 bp):
AATATATAATTTAAGAATAAT
Found at i:95577656 original size:28 final size:28
Alignment explanation
Indices: 95577613--95577696 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
95577603 AGATCGTGTG
95577613 TCCCCTA-TTTTTTAGATTTTACAA-TT
1 TCCCCTATTTTTTTAGATTTTACAATTT
*
95577639 TCCCACTATTTTTTTAGATTTTATAATTT
1 TCCC-CTATTTTTTTAGATTTTACAATTT
* * * *
95577668 TCTCGTATTTTGTTAGATTTTACAGTTT
1 TCCCCTATTTTTTTAGATTTTACAATTT
95577696 T
1 T
95577697 GTCCCATACT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.08
27 3 0.06
28 37 0.76
29 5 0.10
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (28 bp):
TCCCCTATTTTTTTAGATTTTACAATTT
Found at i:95578019 original size:34 final size:34
Alignment explanation
Indices: 95577981--95578054 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
95577971 AGCATGACTT
*
95577981 TTGCTATTG-AGTTAAACTGTTGTAAGCATATTAA
1 TTGCTATTGTA-TTAAACTGTTATAAGCATATTAA
* ** *
95578015 TTGCTATTGTATTGAGTTGTTATAAGTATATTAA
1 TTGCTATTGTATTAAACTGTTATAAGCATATTAA
95578049 TTGCTA
1 TTGCTA
95578055 CCATATTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGCTATTGTATTAAACTGTTATAAGCATATTAA
Found at i:95578069 original size:34 final size:34
Alignment explanation
Indices: 95577998--95578062 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
95577988 TGAGTTAAAC
* ***
95577998 TGTTGTAAGCATATTAATTGCTATTGTATTGAGT
1 TGTTATAAGCATATTAATTGCTACCATATTGAGT
*
95578032 TGTTATAAGTATATTAATTGCTACCATATTG
1 TGTTATAAGCATATTAATTGCTACCATATTG
95578063 TTTTGTTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (34 bp):
TGTTATAAGCATATTAATTGCTACCATATTGAGT
Found at i:95578213 original size:45 final size:45
Alignment explanation
Indices: 95578164--95578251 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
95578154 TAGCATCTTG
* * *
95578164 TTTGCACCGTTTAGTGGTTTATCTACACCGTATTAGCAACTTTTA
1 TTTGCACCGATTAGTGGTTTACCCACACCGTATTAGCAACTTTTA
*
95578209 TTTGCACCGATTAGTGGTTTACCCACACTGTATTAGCAACTTT
1 TTTGCACCGATTAGTGGTTTACCCACACCGTATTAGCAACTTT
95578252 AATATGCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (45 bp):
TTTGCACCGATTAGTGGTTTACCCACACCGTATTAGCAACTTTTA
Found at i:95584000 original size:24 final size:24
Alignment explanation
Indices: 95583927--95584001 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
95583917 CGGTTAGATA
* * *
95583927 ACAGAAGCAATTTTAGTTT-AGAT
1 ACAGAAGCAATTTCAATTTCAAAT
* *
95583950 ACAGAA-CGAA--TCAATTACATAT
1 ACAGAAGC-AATTTCAATTTCAAAT
*
95583972 GCAGAAGCAATTTCAATTTCAAAT
1 ACAGAAGCAATTTCAATTTCAAAT
95583996 ACAGAA
1 ACAGAA
95584002 CAAATCAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 4 0.10
22 11 0.28
23 9 0.23
24 15 0.38
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (24 bp):
ACAGAAGCAATTTCAATTTCAAAT
Found at i:95584566 original size:42 final size:42
Alignment explanation
Indices: 95584519--95584702 Score: 224
Period size: 42 Copynumber: 4.4 Consensus size: 42
95584509 ACACAACCTG
* *
95584519 GACACATGTCCATGTACTTGCCCGTGTGGCTCACATGGCCTA
1 GACACATGCCCATGTCCTTGCCCGTGTGGCTCACATGGCCTA
*
95584561 GACACACGCCCATGTCCTTGCCCGTGTGGCTCACATGGCCTA
1 GACACATGCCCATGTCCTTGCCCGTGTGGCTCACATGGCCTA
* ** * *
95584603 GACACATGCCCATGTCCTTGCCCGTGTGACTCACACAGCTTG
1 GACACATGCCCATGTCCTTGCCCGTGTGGCTCACATGGCCTA
* * ** * *
95584645 GACACACGCCCATGTCCTTACCCGTGTAACTCACACGGCCTG
1 GACACATGCCCATGTCCTTGCCCGTGTGGCTCACATGGCCTA
* *
95584687 GACAAATGCTCATGTC
1 GACACATGCCCATGTC
95584703 TCTGGCTGTG
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 125 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.23
Consensus pattern (42 bp):
GACACATGCCCATGTCCTTGCCCGTGTGGCTCACATGGCCTA
Found at i:95588509 original size:37 final size:37
Alignment explanation
Indices: 95588423--95588543 Score: 145
Period size: 37 Copynumber: 3.2 Consensus size: 37
95588413 TTCCAATCGA
* *
95588423 AACACGCCA-ATCGCTCATAAGAGCTAATCCACATGAAT
1 AACACGCCAGAT-GCTCATAAGAGCTAGTCCACCTG-AT
* * * *
95588461 AACATGCCAGATGCTCATAATAGTTAGTCCACCCGAT
1 AACACGCCAGATGCTCATAAGAGCTAGTCCACCTGAT
* *
95588498 AACACGCCAGATGCTCATAAGAGCTAGTCCAACTGAA
1 AACACGCCAGATGCTCATAAGAGCTAGTCCACCTGAT
95588535 AACACGCCA
1 AACACGCCA
95588544 AAACAAGGAG
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
37 42 0.60
38 26 0.37
39 2 0.03
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (37 bp):
AACACGCCAGATGCTCATAAGAGCTAGTCCACCTGAT
Found at i:95596235 original size:64 final size:66
Alignment explanation
Indices: 95596124--95596253 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 66
95596114 AATAAAATTG
95596124 TTGTTTTGAAAAATATGTTTATAAAATTGAGAATAAATTTTCTCTA-TTTTTGTCAAAATAACAA
1 TTGTTTTGAAAAATATGTTTATAAAATTGAGAATAAATTTTCTCTATTTTTTGTCAAAATAACAA
95596188 T
66 T
95596189 TTGTTTTGAAAAATATGTTTAT-AAATTGAGAATAAATTTTCTCTATTTTTTGTCAAAATAACAA
1 TTGTTTTGAAAAATATGTTTATAAAATTGAGAATAAATTTTCTCTATTTTTTGTCAAAATAACAA
95596253 T
66 T
95596254 CTCTCAAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 23 0.36
65 41 0.64
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (66 bp):
TTGTTTTGAAAAATATGTTTATAAAATTGAGAATAAATTTTCTCTATTTTTTGTCAAAATAACAA
T
Found at i:95596617 original size:25 final size:25
Alignment explanation
Indices: 95596588--95596637 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
95596578 TTTCTCACCC
95596588 AATTTTATCCC-AATAAAATTTTGAT
1 AATTTTA-CCCTAATAAAATTTTGAT
95596613 AATTTTACCCTTAATAAAATTTTGA
1 AATTTTACCC-TAATAAAATTTTGA
95596638 AAAAATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 3 0.13
25 7 0.30
26 13 0.57
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (25 bp):
AATTTTACCCTAATAAAATTTTGAT
Found at i:95597233 original size:23 final size:23
Alignment explanation
Indices: 95597207--95597252 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
95597197 CATCCATCAC
* *
95597207 ACAAACGGATGACTAGTGGCCAT
1 ACAAACGGACGACCAGTGGCCAT
*
95597230 ACAAACGGACGACCCGTGGCCAT
1 ACAAACGGACGACCAGTGGCCAT
95597253 GTTTTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.26, T:0.13
Consensus pattern (23 bp):
ACAAACGGACGACCAGTGGCCAT
Found at i:95601370 original size:19 final size:19
Alignment explanation
Indices: 95601338--95601374 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
95601328 ATTTCATACG
95601338 TTGGCCCAATTTCTTCGTTT
1 TTGGCCCAATTTC-TCGTTT
95601358 TTGGCCC-ATTTCTCGTT
1 TTGGCCCAATTTCTCGTT
95601375 ACTTTTACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.08, C:0.27, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGGCCCAATTTCTCGTTT
Found at i:95604998 original size:40 final size:40
Alignment explanation
Indices: 95604937--95605154 Score: 305
Period size: 40 Copynumber: 5.5 Consensus size: 40
95604927 AAGCCAAGTA
* ** * *
95604937 CCTTCGGGATTTA-CCCGGATATAGTTGCTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
95604976 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
95605016 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
95605056 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
95605096 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
95605136 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
95605155 TTATCATCCA
Statistics
Matches: 164, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 12 0.07
40 152 0.93
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:95613298 original size:40 final size:40
Alignment explanation
Indices: 95613215--95613472 Score: 297
Period size: 40 Copynumber: 6.5 Consensus size: 40
95613205 AAGCCAAGTA
* * * * *
95613215 CCTTCGGGATTTA-CCCGGATATAGCT-GCTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* ** * *
95613254 CCTTCGGGACATAGCCCATAAATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
95613294 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACCAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
95613334 CCTTCGAGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
95613374 CCTTCGGGACTTAGCCCAGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
95613414 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
95613454 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
95613473 TTATCATCCA
Statistics
Matches: 189, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
39 13 0.07
40 176 0.93
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:95624871 original size:6 final size:6
Alignment explanation
Indices: 95624860--95624893 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
95624850 TCCTCTTATC
95624860 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTT
95624894 CAATTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:95630271 original size:29 final size:29
Alignment explanation
Indices: 95630239--95630296 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
95630229 TATTATTCTG
95630239 GAATAATATATTTAATAGATGAGAATAAA
1 GAATAATATATTTAATAGATGAGAATAAA
95630268 GAATAATATATTTAATAGATGAGAATAAA
1 GAATAATATATTTAATAGATGAGAATAAA
95630297 TTCTATCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (29 bp):
GAATAATATATTTAATAGATGAGAATAAA
Found at i:95630908 original size:18 final size:19
Alignment explanation
Indices: 95630881--95630919 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
95630871 TAATGTTTTC
*
95630881 CATTTCTTTC-TTTTTATT
1 CATTTCTTTCATTTTAATT
*
95630899 CATTTTTTTCATTTTAATT
1 CATTTCTTTCATTTTAATT
95630918 CA
1 CA
95630920 AACATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (19 bp):
CATTTCTTTCATTTTAATT
Found at i:95638890 original size:62 final size:59
Alignment explanation
Indices: 95638779--95638895 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
95638769 ATCACTTTAA
* * * *
95638779 TATTAAATTAATATAATATTTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCAAGATAAAGATTAAATTAAAATTAATATTAAATCT
*
95638838 TATTAAAATAATAGAATATTTATCTACAAGATAAAGATTAAATTAAAATTAATTTTAA
1 TATTAAAATAATAGAATATTTA--T-CAAGATAAAGATTAAATTAAAATTAATATTAA
95638896 GATAATCAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATCAAGATAAAGATTAAATTAAAATTAATATTAAATCT
Found at i:95653049 original size:40 final size:40
Alignment explanation
Indices: 95652994--95653208 Score: 242
Period size: 40 Copynumber: 5.4 Consensus size: 40
95652984 ATGATAACCA
* *
95652994 GGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTA-ATTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TCCG
* * *
95653034 GGCTAAGCCCCGAAGGCATTTGTGCTAGTGACTA-ATTCTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TCCG
* *
95653074 GGCTAAGTCTCGAAGGCATTTGAGCGAGT-AGCTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATATCCG
* * * *
95653114 GGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATAACTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCG
*
95653154 GGCTAAGTCCCGAAGGCATTTGAGCGAGT-AGCTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATATCCG
*
95653193 GGCTAAATCCCGAAGG
1 GGCTAAGTCCCGAAGG
95653209 TACTTGGTTT
Statistics
Matches: 155, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
39 17 0.11
40 136 0.88
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCG
Found at i:95653127 original size:80 final size:80
Alignment explanation
Indices: 95652994--95653208 Score: 294
Period size: 80 Copynumber: 2.7 Consensus size: 80
95652984 ATGATAACCA
* * * *
95652994 GGCTAAGTCTCGAAGGCATTTGTGCTAGT-GACTA-ATTCCGGGCTAAGCCCCGAAGGCATTTGT
1 GGCTAAGTCTCGAAGGCATTTGAGCGAGTAG-CTATA-TCCGGGCTAAGTCCCGAAGGCATTTGC
* *
95653057 GCTAGTGACTA-ATTCTG
64 GCGAGTGACTATA-ACTG
95653074 GGCTAAGTCTCGAAGGCATTTGAGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGGCATTTGCGC
1 GGCTAAGTCTCGAAGGCATTTGAGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGGCATTTGCGC
*
95653139 GAGTTACTATAACTG
66 GAGTGACTATAACTG
* *
95653154 GGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC-GGCTAAATCCCGAAGG
1 GGCTAAGTCTCGAAGGCATTTGAGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGG
95653209 TACTTGGTTT
Statistics
Matches: 123, Mismatches: 9, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
79 15 0.12
80 105 0.85
81 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
GGCTAAGTCTCGAAGGCATTTGAGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGGCATTTGCGC
GAGTGACTATAACTG
Found at i:95658754 original size:15 final size:15
Alignment explanation
Indices: 95658731--95658772 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
95658721 GAAGCCCAGA
*
95658731 ATAAGGAAATCTAAG
1 ATAAGGAAATCCAAG
* *
95658746 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
95658761 ATAAGGAAATCC
1 ATAAGGAAATCC
95658773 CATTTACAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:95661780 original size:38 final size:38
Alignment explanation
Indices: 95661737--95662115 Score: 218
Period size: 38 Copynumber: 9.0 Consensus size: 38
95661727 TTTCAAATTA
*
95661737 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
* *
95661775 ACATGTTTAACCGTGGTATATCCACTTAGCACCATGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* * * *
95661816 GAATCAATATATGTAACCGTAGCATATCCACTTAGAACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
95661860 ACATGTTTAACCATGGTATATCCACTTAACACCACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* * *
95661901 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCATGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
95661945 ACATGTTTAACCGTGGTACATCCACTTAACACCACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
95661986 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
** * *
95662030 ACATGTATCAATATGTGTAATTGTGGTATATCCACTTAGCAACACTTT
1 ACATG------TA----TAACCGTGGTATATCCACTTAGCACCACGTT
*
95662078 ACATGTATAACCGTGGTATATTCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
95662116 TATCCATTCC
Statistics
Matches: 262, Mismatches: 44, Indels: 70
0.70 0.12 0.19
Matches are distributed among these distances:
38 108 0.41
39 3 0.01
40 8 0.03
41 6 0.02
42 5 0.02
43 3 0.01
44 6 0.02
45 9 0.03
46 5 0.02
47 76 0.29
48 33 0.13
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (38 bp):
ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
Found at i:95661841 original size:85 final size:85
Alignment explanation
Indices: 95661744--95662035 Score: 521
Period size: 85 Copynumber: 3.4 Consensus size: 85
95661734 TTAACATGTA
*
95661744 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAACACCA
*
95661809 TGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
* * *
95661829 TAACCGTAGCATATCCACTTAGAACCACGTTACATGTTTAACCATGGTATATCCACTTAACACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAACACCA
95661894 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
* *
95661914 TAACCGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTACATCCACTTAACACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAACACCA
95661979 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
95661999 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
95662036 ATCAATATGT
Statistics
Matches: 196, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 196 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAACACCA
CGTTAATGAATCAATATATG
Found at i:95661940 original size:47 final size:47
Alignment explanation
Indices: 95661867--95662115 Score: 228
Period size: 47 Copynumber: 5.7 Consensus size: 47
95661857 GTTACATGTT
* *
95661867 TAACCATGGTATATCCACTTAACACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * *
95661914 TAACCGTGGCATATCCACTTAGCACCATG-T--T--A-C-ATGT-T-
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* *
95661952 TAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * *
95661999 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
** * *
95662047 TAATTGTGGTATATCCACTTAGCAACAC-TT--T--A-C-ATGTA--
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
*
95662085 TAACCGTGGTATATTCACTTAGCACCACGTT
1 TAACCGTGGTATATCCACTTAGCACCACGTT
95662116 TATCCATTCC
Statistics
Matches: 166, Mismatches: 25, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
38 49 0.30
39 4 0.02
40 6 0.04
41 3 0.02
42 2 0.01
43 1 0.01
44 3 0.02
45 3 0.02
46 2 0.01
47 56 0.34
48 37 0.22
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (47 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
Found at i:95662061 original size:48 final size:48
Alignment explanation
Indices: 95661952--95662085 Score: 180
Period size: 48 Copynumber: 2.8 Consensus size: 48
95661942 GTTACATGTT
* * *
95661952 TAACCGTGGTACATCCACTTAACACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
95661999 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
** * *
95662047 TAATTGTGGTATATCCACTTAGCAACACTTTACATGTAT
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
95662086 AACCGTGGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
47 29 0.38
48 47 0.62
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:95662104 original size:133 final size:132
Alignment explanation
Indices: 95661867--95662115 Score: 356
Period size: 133 Copynumber: 1.9 Consensus size: 132
95661857 GTTACATGTT
*
95661867 TAACCATGGTATATCCACTTAACACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCATGGCATATCCACTTAACACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
* *
95661932 TTAGCACCATGTTACATGTTTAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATA
66 TTAGCAACATGTTACATGTATAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATA
95661997 TG
131 TG
* * * * ** *
95661999 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATTGTGGTATATCCA
1 TAACCATGGCATATCCACTTAACACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCA
* * *
95662064 CTTAGCAACACT-TTACATGTATAACCGTGGTATATTCACTTAGCACCACGTT
65 CTTAGCAACA-TGTTACATGTATAACCGTGGTACATCCACTTAACACCACGTT
95662116 TATCCATTCC
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
132 29 0.28
133 72 0.71
134 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (132 bp):
TAACCATGGCATATCCACTTAACACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
TTAGCAACATGTTACATGTATAACCGTGGTACATCCACTTAACACCACGTTAATGAATCAATATA
TG
Found at i:95668540 original size:12 final size:13
Alignment explanation
Indices: 95668523--95668560 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
95668513 ATCCTGGAAT
95668523 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
95668535 ATTAAGAACACATA
1 ATTAAGAACA-AGA
95668549 ATTAAGAACAAG
1 ATTAAGAACAAG
95668561 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:95670958 original size:43 final size:43
Alignment explanation
Indices: 95670813--95670958 Score: 113
Period size: 43 Copynumber: 3.4 Consensus size: 43
95670803 TGTGTTTTCG
* *
95670813 TGTAAGACCACGTCTGGGAC-GTTGGCATCGA-GTTATGTTTTACG
1 TGTAAGACCACGTCTGGGACAG-TGGCATCGATGTT-TG-ATTACA
* * * * * * *
95670857 TCTAAGACCATGTCTAGGACA-TCGGCATC-CTATCTGATTTCA
1 TGTAAGACCACGTCTGGGACAGT-GGCATCGATGTTTGATTACA
* *
95670899 TGTAAGACC-CTATCTGGGACAGTGGCATCGATGTTTGATGACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGATGTTTGATTACA
95670942 TGTAAGACCACGTCTGG
1 TGTAAGACCACGTCTGG
95670959 AACTTTGGCA
Statistics
Matches: 76, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
42 25 0.33
43 26 0.34
44 25 0.33
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGATGTTTGATTACA
Found at i:95678843 original size:19 final size:20
Alignment explanation
Indices: 95678819--95678857 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
95678809 ATAAAATATA
*
95678819 TTTAATATATTTA-ACATTT
1 TTTAATATATATATACATTT
*
95678838 TTTAATTTATATATACATTT
1 TTTAATATATATATACATTT
95678858 CAAATCCGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATATATATACATTT
Found at i:95701626 original size:22 final size:22
Alignment explanation
Indices: 95701600--95701647 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
95701590 CCTGAGTTGT
95701600 ATGTTTCTTTGATAAGTTGATC
1 ATGTTTCTTTGATAAGTTGATC
95701622 ATGTTTCTTTGATAAGTTGATC
1 ATGTTTCTTTGATAAGTTGATC
95701644 -TGTT
1 ATGTT
95701648 GTGGTTCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (22 bp):
ATGTTTCTTTGATAAGTTGATC
Found at i:95704144 original size:15 final size:15
Alignment explanation
Indices: 95704102--95704147 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
95704092 AAAGAAACTT
* *
95704102 GAAAAATGAAAAAAAA
1 GAAAAA-GAAAAGAAG
*
95704118 GAAAAAAAAAAGAAG
1 GAAAAAGAAAAGAAG
95704133 GAAAAAGAAAAGAAG
1 GAAAAAGAAAAGAAG
95704148 AGGAGCAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAGAAG
Found at i:95705975 original size:21 final size:21
Alignment explanation
Indices: 95705947--95706002 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
95705937 AACAGCGGTG
* *
95705947 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATAATGTA
* *
95705968 GTGGTGAGATTGGATAATGTA
1 GCGGTGAGATTAGATAATGTA
*
95705989 GCGGTAAGATTAGA
1 GCGGTGAGATTAGA
95706003 AACAATGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATAATGTA
Found at i:95708062 original size:30 final size:29
Alignment explanation
Indices: 95708025--95708101 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
95708015 TAGCAATTAA
95708025 TTAATTCTTTAAAAATTAAAAATATTTTT
1 TTAATTCTTTAAAAATTAAAAATATTTTT
* **
95708054 TATAATTC-TT-AAATTTTTAAATATTTTT
1 T-TAATTCTTTAAAAATTAAAAATATTTTT
95708082 TTATATT-TTTAAAAATTAAA
1 TTA-ATTCTTTAAAAATTAAA
95708102 TAATTGCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.05
28 21 0.55
29 9 0.24
30 6 0.16
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TTAATTCTTTAAAAATTAAAAATATTTTT
Found at i:95713952 original size:5 final size:5
Alignment explanation
Indices: 95713944--95713972 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
95713934 TCTTAATATA
95713944 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
95713973 AAAGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:95721660 original size:46 final size:46
Alignment explanation
Indices: 95721593--95721839 Score: 404
Period size: 46 Copynumber: 5.4 Consensus size: 46
95721583 CGCGGGAGTG
95721593 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
95721639 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
*
95721685 TGAAAGATACCATGACAACCTGATATGAAATGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
* **
95721731 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
* * * ** *
95721777 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGT
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
95721823 TGAAAGATACCATGGCA
1 TGAAAGATACCATGGCA
95721840 GCATGACAGA
Statistics
Matches: 193, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 193 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
Found at i:95721854 original size:92 final size:92
Alignment explanation
Indices: 95721593--95721889 Score: 398
Period size: 92 Copynumber: 3.2 Consensus size: 92
95721583 CGCGGGAGTG
95721593 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
95721658 CTGATATGAAATGTGTAAGACCATGGT
66 ATGATATGAAATGAATAAGACCATGGT
*
95721685 TGAAAGATACCATGACAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
95721750 GTGATATGAAATGAATAAGACCATGGT
66 ATGATATGAAATGAATAAGACCATGGT
* * * ** * *
95721777 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGGCAGC
1 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
95721842 ATGACA-GAAAATGAATGAGTAAGACCATAGT
66 ATGATATG-AAATG-A--A-TAAGACCATGGT
* *
95721873 TGAAAGACACTATGGCA
1 TGAAAGATACCATGGCA
95721890 TCATGTCAAA
Statistics
Matches: 183, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
91 1 0.01
92 154 0.84
93 1 0.01
95 1 0.01
96 26 0.14
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (92 bp):
TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
ATGATATGAAATGAATAAGACCATGGT
Found at i:95721854 original size:138 final size:140
Alignment explanation
Indices: 95721593--95721889 Score: 402
Period size: 138 Copynumber: 2.1 Consensus size: 140
95721583 CGCGGGAGTG
**
95721593 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * * *
95721658 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACCTGATATGAAATG-T-GTA
66 CTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGACAACATGACATGAAATGATAGTA
*
95721721 AGACCATGGT
131 AGACCATAGT
*
95721731 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
95721796 GTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGGCAGCATGACA-GAAAATGAATGA
66 CTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGACAACATGACATG-AAATG-AT-A
95721860 GTAAGACCATAGT
128 GTAAGACCATAGT
* *
95721873 TGAAAGACACTATGGCA
1 TGAAAGATACCATGGCA
95721890 TCATGTCAAA
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
137 1 0.01
138 109 0.79
140 1 0.01
142 27 0.20
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (140 bp):
TGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
CTGACATGAAAAGAATAAGACCATAGTTGAAAGATACCATGACAACATGACATGAAATGATAGTA
AGACCATAGT
Found at i:95721888 original size:50 final size:49
Alignment explanation
Indices: 95721593--95721894 Score: 276
Period size: 46 Copynumber: 6.4 Consensus size: 49
95721583 CGCGGGAGTG
* * * *
95721593 TGAAAGATACCATGGCAACCTGATATGAAATG--TG-TAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATGATAAGACCATAGT
* * * *
95721639 TGAAAGATACCATGGCAACCTGATATGAAATG--TG-TAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATGATAAGACCATAGT
* * * * *
95721685 TGAAAGATACCATGACAACCTGATATGAAATG--TG-TAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATGATAAGACCATAGT
* * * *
95721731 TGAAAGATACCATGGCAACGTGATATGAAATG-A--ATAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATGATAAGACCATAGT
*
95721777 TGAAAGATACCATGGCAACGTGACATGAAAAG-A--ATAAGACCATAGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATGATAAGACCATAGT
*
95721823 TGAAAGATACCATGGCAGCATGACA-GAAAATGAATGAGTAAGACCATAGT
1 TGAAAGATACCATGGCAACATGACATGAAAA-GAATGA-TAAGACCATAGT
* * *
95721873 TGAAAGACACTATGGCATCATG
1 TGAAAGATACCATGGCAACATG
95721895 TCAAAGATAA
Statistics
Matches: 238, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
45 5 0.02
46 200 0.84
47 1 0.00
49 1 0.00
50 31 0.13
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (49 bp):
TGAAAGATACCATGGCAACATGACATGAAAAGAATGATAAGACCATAGT
Found at i:95724451 original size:196 final size:196
Alignment explanation
Indices: 95724105--95724499 Score: 754
Period size: 196 Copynumber: 2.0 Consensus size: 196
95724095 TAATGTGAGC
95724105 TTTGTAAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
1 TTTGTAAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
95724170 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
*
95724235 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
95724300 T
196 T
*
95724301 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
1 TTTGTAAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
*
95724366 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGTAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
*
95724431 ATAAATGAAATATTTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
95724496 T
196 T
95724497 TTT
1 TTT
95724500 ATGTATTTTG
Statistics
Matches: 195, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
196 195 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (196 bp):
TTTGTAAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
ATAAATGAAATATGTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
T
Found at i:95725000 original size:44 final size:42
Alignment explanation
Indices: 95724934--95725088 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 42
95724924 TGTTATCGTA
*
95724934 TAAGACCATGTTTGGGATGTTGGCATCGACTTATGATTTACGTG
1 TAAGACCATGTTTGGGACGTTGGCATCGA-TT-TGATTTACGTG
*
95724978 TAAGACCATGTTTGAGACGTTGGCATCGTATTTGATTT-CGTG
1 TAAGACCATGTTTGGGACGTTGGCATCG-ATTTGATTTACGTG
* * * * *
95725020 TAAAACCCTGTCTGGGATAG-TGGCATCGATATTTGA-TTACATG
1 TAAGACCATGTTTGGGA-CGTTGGCATCG--ATTTGATTTACGTG
* *
95725063 TAAGACCACGTTCGGGACGTTGGCAT
1 TAAGACCATGTTTGGGACGTTGGCAT
95725089 TGTACGACAT
Statistics
Matches: 92, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
42 28 0.30
43 35 0.38
44 28 0.30
45 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (42 bp):
TAAGACCATGTTTGGGACGTTGGCATCGATTTGATTTACGTG
Found at i:95728450 original size:26 final size:26
Alignment explanation
Indices: 95728414--95728471 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
95728404 TGCCTATGTG
95728414 ATTGATTCGAAAATGTCAGAAAAGAA
1 ATTGATTCGAAAATGTCAGAAAAGAA
95728440 ATTGATTCGAAAATGTCAGAAAAGAA
1 ATTGATTCGAAAATGTCAGAAAAGAA
95728466 AGTTGA
1 A-TTGA
95728472 ATCAGTGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (26 bp):
ATTGATTCGAAAATGTCAGAAAAGAA
Found at i:95730720 original size:39 final size:37
Alignment explanation
Indices: 95730653--95730745 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
95730643 ACCAGAATGG
* *
95730653 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
95730692 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
95730729 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
95730746 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:95731871 original size:17 final size:16
Alignment explanation
Indices: 95731839--95731872 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
95731829 TTGGCTATTC
*
95731839 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
95731855 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
95731872 T
1 T
95731873 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:95731920 original size:14 final size:14
Alignment explanation
Indices: 95731870--95731914 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
95731860 CTTTTATTCT
*
95731870 TTTATTTTAACTTAC
1 TTTATTTT-ATTTAC
*
95731885 TTTACTTTATTTAC
1 TTTATTTTATTTAC
95731899 TTTATTTTATTT-C
1 TTTATTTTATTTAC
95731912 TTT
1 TTT
95731915 TGTTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 4 0.15
14 16 0.59
15 7 0.26
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTTATTTAC
Found at i:95732080 original size:14 final size:17
Alignment explanation
Indices: 95732061--95732097 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
95732051 ATTTATTTCT
95732061 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
95732075 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
95732092 TAATAT
1 TAATAT
95732098 CTTTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:95732092 original size:23 final size:23
Alignment explanation
Indices: 95732060--95732123 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
95732050 AATTTATTTC
*
95732060 TTAATATAATATTTATAATATAA
1 TTAATTTAATATTTATAATATAA
* **
95732083 TTAATTTAATA-ATATCTTTATAA
1 TTAATTTAATATTTAT-AATATAA
95732106 TTAATTTATATATTTATA
1 TTAATTTA-ATATTTATA
95732124 TAAATAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 3 0.09
23 23 0.72
24 3 0.09
25 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAATTTAATATTTATAATATAA
Found at i:95735427 original size:43 final size:42
Alignment explanation
Indices: 95735309--95735430 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 42
95735299 AACTTATGAT
* * *
95735309 TTACGTGTAAGACAACGTTTGGGATGTTGGCATCGTATTTGA
1 TTACGTGTAAGACCACGTTTGGGACGTTGGCATTGTATTTGA
* ** * ** *
95735351 TTTCGTGTAAGACCTTGTCTGGGACAATAGCATTGATATTTGA
1 TTACGTGTAAGACCACGTTTGGGACGTTGGCATTG-TATTTGA
* *
95735394 TTACATGTAAGACCACATTTGGGACGTTGGCATTGTA
1 TTACGTGTAAGACCACGTTTGGGACGTTGGCATTGTA
95735431 CGAGATTTTT
Statistics
Matches: 60, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
42 27 0.45
43 33 0.55
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (42 bp):
TTACGTGTAAGACCACGTTTGGGACGTTGGCATTGTATTTGA
Found at i:95738094 original size:21 final size:21
Alignment explanation
Indices: 95738044--95738096 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
95738034 TAGAAACTCG
95738044 AAAGCTGAACAGAACCTCATA
1 AAAGCTGAACAGAACCTCATA
* *
95738065 AGAGCTGAACAGGAA-CTCGTA
1 AAAGCTGAACA-GAACCTCATA
*
95738086 AAAGTTGAACA
1 AAAGCTGAACA
95738097 AAAGCTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAGCTGAACAGAACCTCATA
Found at i:95738117 original size:21 final size:21
Alignment explanation
Indices: 95738093--95738136 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
95738083 GTAAAAGTTG
95738093 AACAAAAGCTCGAAAGAACTA
1 AACAAAAGCTCGAAAGAACTA
* * *
95738114 AACAGAGGCTCGAAAGAGCTA
1 AACAAAAGCTCGAAAGAACTA
95738135 AA
1 AA
95738137 TAGAAAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.20, T:0.09
Consensus pattern (21 bp):
AACAAAAGCTCGAAAGAACTA
Found at i:95741441 original size:39 final size:40
Alignment explanation
Indices: 95741384--95741471 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
95741374 ATACTTTTAA
* * *
95741384 AATC-AGTGAAAATGATTTTAAC-CAAGCCAAATGA-TTTC
1 AATCAAGTTAAAATCATTTTAACAC-AGCAAAATGATTTTC
*
95741422 AATCAAGTTAAAATCATTTTAACACATCAAAATGATTTTC
1 AATCAAGTTAAAATCATTTTAACACAGCAAAATGATTTTC
*
95741462 AAACAAGTTA
1 AATCAAGTTA
95741472 GAATTGCTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.10
39 24 0.57
40 14 0.33
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (40 bp):
AATCAAGTTAAAATCATTTTAACACAGCAAAATGATTTTC
Found at i:95741459 original size:19 final size:19
Alignment explanation
Indices: 95741392--95741460 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
95741382 AAAATCAGTG
*
95741392 AAAATGATTTTAAC-CAAGC
1 AAAATGATTTTAACAC-ATC
* * *
95741411 CAAATGATTTCAATCA-AGTT
1 AAAATGATTTTAA-CACA-TC
*
95741431 AAAATCATTTTAACACATC
1 AAAATGATTTTAACACATC
95741450 AAAATGATTTT
1 AAAATGATTTT
95741461 CAAACAAGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAATGATTTTAACACATC
Found at i:95749238 original size:23 final size:22
Alignment explanation
Indices: 95749187--95749238 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
95749177 CCTCGTCTTT
*
95749187 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
95749209 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
95749232 TTCTTTT
1 TTCTTTT
95749239 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:95752495 original size:40 final size:38
Alignment explanation
Indices: 95752412--95752495 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
95752402 ATATTTTATA
* *
95752412 TATATATATGGTAAATAGTATTATGATAATTGTTCTTT
1 TATATATACGGTAAATAATATTATGATAATTGTTCTTT
* * *
95752450 AATATATACGGT-AGTAATATTATGGTAATTGCTCTCTCTT
1 TATATATACGGTAAATAATATTATGATAATTG-T-TCT-TT
95752490 TATATA
1 TATATA
95752496 GATTTGACGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
37 16 0.43
38 11 0.30
39 3 0.08
40 7 0.19
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (38 bp):
TATATATACGGTAAATAATATTATGATAATTGTTCTTT
Found at i:95757760 original size:35 final size:36
Alignment explanation
Indices: 95757696--95757763 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
95757686 CATTGTTCGT
**
95757696 GAACATGTTCAATTATATGTTCATGAACATGTTTGA
1 GAACATGTTCAATTATATGTTCACAAACATGTTTGA
**
95757732 GAACATGTTCGTTTA-ATGTTCACAAACATGTT
1 GAACATGTTCAATTATATGTTCACAAACATGTT
95757764 CGTTTAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 15 0.54
36 13 0.46
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (36 bp):
GAACATGTTCAATTATATGTTCACAAACATGTTTGA
Found at i:95757809 original size:300 final size:297
Alignment explanation
Indices: 95757269--95757857 Score: 984
Period size: 300 Copynumber: 2.0 Consensus size: 297
95757259 ATTAATAAAA
*
95757269 ATATTATGGTTTGTATGCTTTTATATTTATAATATAATTTTAATATTTATATTTGACTATTTTAT
1 ATATTATGGTTTGTATGCTTTTATATTTATAATATAATTTTAATATTTATATTTGACTAGTTTAT
*
95757334 ATCTAAAAAATTCTATATATATGTTTATTTATTGTTGGATTGTTTATTATTACATTGTTCGTGAA
66 ATCTAAAAAATTATATATATATGTTTATTTATTGTTGGATTGTTTATTATTACATTGTTCGTGAA
*
95757399 CATGCTCAATTATATGTTAATGAACATGTTTGGGAACATGTTCATTTAATGTTCACAAACATGTT
131 CATGCTCAATTATATGTTAATGAACATGTTTGAGAACATGTTCATTTAATGTTCACAAACATGTT
* **
95757464 TGTTTAACTTAAGCGAACAAACACGCAAAAAAAATTTGAAATTCTTAACGAACATGAACAAACTT
196 CGTTTAACTTAAGCGAACAAACAC-CAAAAAAAATTTGAAATTCTTAACGAACACAAACAAACTT
*
95757529 AAAAATAAACAAACGAACATGAAAAGAGGTCCGTTCTT
260 AAAAATAAACAAACGAACACGAAAAGAGGTCCGTTCTT
95757567 ATATTATGGTTTGTATGCTTTT-TATTTATAATATAATTATTAATATTTATATTTGACTAGTTTA
1 ATATTATGGTTTGTATGCTTTTATATTTATAATATAATT-TTAATATTTATATTTGACTAGTTTA
* *
95757631 TATCTAAAAAATAATATATATATATGTTTATTTATTGTTGGTTTGTTTCTTATTACATTGTTCGT
65 TATCTAAAAAAT--TATATATATATGTTTATTTATTGTTGGATTGTTTATTATTACATTGTTCGT
* * *
95757696 GAACATGTTCAATTATATGTTCATGAACATGTTTGAGAACATGTTCGTTTAATGTTCACAAACAT
128 GAACATGCTCAATTATATGTTAATGAACATGTTTGAGAACATGTTCATTTAATGTTCACAAACAT
*
95757761 GTTCGTTTAACTTAAGCGAACGAACA-CAAACAAAAATTTTGAAATTCTTAACGAACACAAACAA
193 GTTCGTTTAACTTAAGCGAACAAACACCAAA-AAAAA-TTTGAAATTCTTAACGAACACAAACAA
*
95757825 ACTTAAAAATAAACAAATGAACACGAAAAGAGG
256 ACTTAAAAATAAACAAACGAACACGAAAAGAGG
95757858 CCCATTTGTT
Statistics
Matches: 272, Mismatches: 14, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
297 16 0.06
298 62 0.23
299 5 0.02
300 189 0.69
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (297 bp):
ATATTATGGTTTGTATGCTTTTATATTTATAATATAATTTTAATATTTATATTTGACTAGTTTAT
ATCTAAAAAATTATATATATATGTTTATTTATTGTTGGATTGTTTATTATTACATTGTTCGTGAA
CATGCTCAATTATATGTTAATGAACATGTTTGAGAACATGTTCATTTAATGTTCACAAACATGTT
CGTTTAACTTAAGCGAACAAACACCAAAAAAAATTTGAAATTCTTAACGAACACAAACAAACTTA
AAAATAAACAAACGAACACGAAAAGAGGTCCGTTCTT
Found at i:95765017 original size:15 final size:13
Alignment explanation
Indices: 95765008--95765063 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 13
95764998 AATATTATTA
95765008 AATTATATATTTT
1 AATTATATATTTT
95765021 AATTATAATATATTT
1 AATTAT-ATAT-TTT
* *
95765036 AATAATAATTATGTT
1 AATTAT-A-TATTTT
95765051 AATT-TATATTTT
1 AATTATATATTTT
95765063 A
1 A
95765064 TAGTATCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 6 0.17
13 7 0.19
14 5 0.14
15 15 0.42
16 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
AATTATATATTTT
Found at i:95765033 original size:16 final size:16
Alignment explanation
Indices: 95765012--95765054 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
95765002 TTATTAAATT
95765012 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
95765028 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
95765043 AT-TATGTTAATT
1 ATATATTTTAATT
95765055 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:95765094 original size:120 final size:120
Alignment explanation
Indices: 95764949--95765170 Score: 426
Period size: 120 Copynumber: 1.9 Consensus size: 120
95764939 GCAATAACAG
*
95764949 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAATATTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATATTATTAAATTAT
95765014 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
66 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
*
95765069 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATATTATTAAATTAT
95765134 ATATTTTAATTATAATATATTTAATAATAATTATGTT
66 ATATTTTAATTATAATATATTTAATAATAATTATGTT
95765171 TAAATATGAT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATATTATTAAATTAT
ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
Found at i:95765136 original size:61 final size:60
Alignment explanation
Indices: 95764951--95765138 Score: 188
Period size: 61 Copynumber: 3.1 Consensus size: 60
95764941 AATAACAGTC
*
95764951 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAATATTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAA-AATTTTATTAAATT
* * * * * * * * * *
95765012 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTATATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAAATTTTATTA-AATT
95765071 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAA-AATTTTATTAAATT
95765132 ATATATT
1 ATATATT
95765139 TTAATTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 28 0.29
60 26 0.27
61 36 0.38
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAAATTTTATTAAATT
Found at i:95765153 original size:16 final size:16
Alignment explanation
Indices: 95765132--95765173 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
95765122 TTATTAAATT
*
95765132 ATATATTTTAATTATA
1 ATATATTTTAATAATA
95765148 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
95765163 AT-TATGTTTAA
1 ATATAT-TTTAA
95765174 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:95765158 original size:15 final size:15
Alignment explanation
Indices: 95765123--95765164 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
95765113 TTAAGAATTT
*
95765123 TATTAAATTAT-ATA
1 TATTTAATTATAATA
95765137 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
95765151 TATTTAATAATAAT
1 TATTTAATTATAAT
95765165 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:95765409 original size:16 final size:16
Alignment explanation
Indices: 95765388--95765456 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
95765378 TGATTTGCTC
*
95765388 TTACACCTCTATTCCA
1 TTACACCTCTAATCCA
95765404 TTACACCTCTAATCCA
1 TTACACCTCTAATCCA
95765420 TTACACCTCTAATCCA
1 TTACACCTCTAATCCA
* * *
95765436 ATACAGCTTTAATCCA
1 TTACACCTCTAATCCA
*
95765452 ATACA
1 TTACA
95765457 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.33, C:0.33, G:0.01, T:0.32
Consensus pattern (16 bp):
TTACACCTCTAATCCA
Found at i:95767871 original size:56 final size:56
Alignment explanation
Indices: 95767762--95767872 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
95767752 TTAAAAAATA
******
95767762 TTATAGTGGAGATGCTCAAATTGGGTTAAAATAATTAAATTGGGTTTAATTTTTTT
1 TTATAGTGGAGATGCTCAAATTGGGTTAAAATAATTAAATAAAAACTAATTTTTTT
95767818 TTATAGTGGAGATGCTCAAATTGGGTTAAAATAATTAAATAAAAACT-ATTTTTTT
1 TTATAGTGGAGATGCTCAAATTGGGTTAAAATAATTAAATAAAAACTAATTTTTTT
95767873 CGAATGTGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
55 8 0.16
56 41 0.84
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (56 bp):
TTATAGTGGAGATGCTCAAATTGGGTTAAAATAATTAAATAAAAACTAATTTTTTT
Found at i:95771866 original size:58 final size:57
Alignment explanation
Indices: 95771803--95771967 Score: 181
Period size: 58 Copynumber: 2.9 Consensus size: 57
95771793 TTTTTATACT
* * * *
95771803 ATTATATATTATGATTT-TTTAATT-TATTTAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTAAATTATATTTAATAATAATCATATTAA-AATATGATTAA
* *
95771861 ATTATATATTATTTTATTAAATTATATTTAGTAATAATCATGTTAAAATATGATTAA
1 ATTATATATTATTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAA
* * * * *
95771918 ATTATTTATTATTTTTATTAAAATATTTTTAATATTAATCTTATTAAAAT
1 ATTATATATTA-TTTTATTAAATTATATTTAATAATAATCATATTAAAAT
95771968 TTAATAATAA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
56 3 0.03
57 25 0.27
58 63 0.69
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAA
Found at i:95772106 original size:12 final size:13
Alignment explanation
Indices: 95772089--95772159 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 13
95772079 TGAAATGTTC
95772089 TTAATAATAATT-
1 TTAATAATAATTA
*
95772101 TTAATATAAAATTA
1 TTAATA-ATAATTA
*
95772115 TTATTAA-ATATTA
1 TTAATAATA-ATTA
*
95772128 TTAATAATTA-TA
1 TTAATAATAATTA
*
95772140 TTAATAAT-GTTA
1 TTAATAATAATTA
95772152 TTAA-AATA
1 TTAATAATA
95772160 TATATTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
11 3 0.06
12 23 0.48
13 17 0.35
14 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (13 bp):
TTAATAATAATTA
Found at i:95772394 original size:39 final size:40
Alignment explanation
Indices: 95772338--95772443 Score: 99
Period size: 44 Copynumber: 2.5 Consensus size: 40
95772328 TTTGCTTATG
*
95772338 CTATTACAACATC-ATTCCATTCAACCAAACACAAGAATT-
1 CTATTACAGC-TCTATTCCATTCAACCAAACACAAGAATTA
***
95772377 CTATTACAGCTCTATTCCATTCCATTCAACCAAACAGTTGAATTA
1 CTATTACAGCTC---T--ATTCCATTCAACCAAACACAAGAATTA
95772422 CTGATTACAGCTCTATTCCATT
1 CT-ATTACAGCTCTATTCCATT
95772444 ACACGTCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
38 2 0.04
39 9 0.16
41 8 0.15
43 1 0.02
44 23 0.42
45 2 0.04
46 10 0.18
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (40 bp):
CTATTACAGCTCTATTCCATTCAACCAAACACAAGAATTA
Found at i:95772420 original size:44 final size:46
Alignment explanation
Indices: 95772350--95772443 Score: 147
Period size: 44 Copynumber: 2.1 Consensus size: 46
95772340 ATTACAACAT
95772350 CATTCCATTCAACCAAACACAAGAATT-CT-ATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
***
95772394 CATTCCATTCAACCAAACAGTTGAATTACTGATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
95772440 CATT
1 CATT
95772444 ACACGTCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 24 0.53
45 2 0.04
46 19 0.42
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (46 bp):
CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
Found at i:95772446 original size:16 final size:16
Alignment explanation
Indices: 95772425--95772479 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
95772415 TGAATTACTG
95772425 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
95772441 ATTACA-CGTCTATTCA
1 ATTACAGC-TCTATTCC
* *
95772457 ATTACAGCCCTATTTC
1 ATTACAGCTCTATTCC
95772473 ATTACAG
1 ATTACAG
95772480 TGAACCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:95778037 original size:25 final size:23
Alignment explanation
Indices: 95777985--95778039 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
95777975 TATAAATAGT
95777985 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
95778008 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
95778033 AATAGTG
1 AATAGTG
95778040 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:95778108 original size:23 final size:24
Alignment explanation
Indices: 95778082--95778128 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
95778072 ATATATACAT
95778082 ATGTATAA-AATAGA-TGTAAAAAA
1 ATGTA-AATAATAGAGTGTAAAAAA
*
95778105 ATGTAAATAATATAGTGTAAAAAA
1 ATGTAAATAATAGAGTGTAAAAAA
95778129 TACATACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 10 0.48
24 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (24 bp):
ATGTAAATAATAGAGTGTAAAAAA
Found at i:95778139 original size:25 final size:26
Alignment explanation
Indices: 95778111--95778160 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
95778101 AAAAATGTAA
*
95778111 ATAATATAGTGTAAAA-A-ATACATAC
1 ATAATATAAT-TAAAATATATACATAC
95778136 ATAATATAATTAAAATATATACATA
1 ATAATATAATTAAAATATATACATA
95778161 AGATAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 10 0.45
26 7 0.32
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (26 bp):
ATAATATAATTAAAATATATACATAC
Found at i:95778157 original size:22 final size:22
Alignment explanation
Indices: 95778125--95778166 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
95778115 TATAGTGTAA
*
95778125 AAAATACATACATAATATAATT
1 AAAATACATACATAAGATAATT
*
95778147 AAAATATATACATAAGATAA
1 AAAATACATACATAAGATAA
95778167 CATGTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATACATACATAAGATAATT
Found at i:95778227 original size:25 final size:25
Alignment explanation
Indices: 95778184--95778317 Score: 102
Period size: 25 Copynumber: 5.6 Consensus size: 25
95778174 AAAAAAATTT
* *
95778184 ATATATAAATAATACAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
95778209 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * *
95778234 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
95778258 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
*
95778280 AATATATACATAATATAATATT-AAG
1 -ATATATACATAATATAGTATTAAAG
*
95778305 AAATATA-ATAATA
1 ATATATACATAATA
95778318 ACAAAAAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 20 0.23
24 24 0.28
25 37 0.43
26 2 0.02
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:95778831 original size:30 final size:30
Alignment explanation
Indices: 95778795--95778892 Score: 178
Period size: 30 Copynumber: 3.3 Consensus size: 30
95778785 AGGTACAAGT
*
95778795 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
95778825 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
95778855 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
95778885 GGTGGTGG
1 GGTGGTGG
95778893 CAAAGGTTAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.18, C:0.06, G:0.51, T:0.24
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:95778852 original size:18 final size:18
Alignment explanation
Indices: 95778829--95778882 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
95778819 GGAGTAGGTG
95778829 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
95778847 GTGGAG-TAG-GT-G---
1 GTGGAGCAAGTGTGGCTA
95778859 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
95778877 GTGGAG
1 GTGGAG
95778883 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 2 0.07
15 2 0.07
16 2 0.07
17 2 0.07
18 12 0.43
ACGTcount: A:0.20, C:0.07, G:0.50, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:95779679 original size:87 final size:87
Alignment explanation
Indices: 95779528--95779733 Score: 229
Period size: 87 Copynumber: 2.4 Consensus size: 87
95779518 TCCTGAGCTT
* * *
95779528 AACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAAACATTAAAAACAGAAATTGAAAATA
1 AACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAACTAAACATTAAAAACAGAAATTGAAAATA
*
95779593 GCTCAGCACGTGAGCC-AAGGCTC
65 CCTCAGCACGTGA-CCTAAGGCTC
* **
95779616 AACTCACTTCTCGCAATATGAGTTGATTTTTAAAAC-AAA-ATTTGTAAAACAGATTTTGAAAAT
1 AACTCACTTCTCGCAATATGAGTTGATTTTTAAAACTAAACA-TT-AAAAACAGAAATTGAAAAT
* * * *
95779679 ACCTCGGTATGTGACCTGAGGCTC
64 ACCTCAGCACGTGACCTAAGGCTC
* * *
95779703 AACTCACCTCTCGTAATATAAGTTGATTTTT
1 AACTCACTTCTCGCAATATGAGTTGATTTTT
95779734 GCAAAGCATA
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
85 1 0.01
86 7 0.07
87 69 0.68
88 24 0.24
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (87 bp):
AACTCACTTCTCGCAATATGAGTTGATTTTTAAAACTAAACATTAAAAACAGAAATTGAAAATAC
CTCAGCACGTGACCTAAGGCTC
Found at i:95779789 original size:106 final size:107
Alignment explanation
Indices: 95779671--95779864 Score: 293
Period size: 106 Copynumber: 1.8 Consensus size: 107
95779661 AAAACAGATT
* *
95779671 TTGAAAATACCTCGGTATGTGACCTGAGGCTCAACTCACCTCTCGTAATATAAGTTGA-TTTTTG
1 TTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTG
*
95779735 -CAAAGCATAAATTGAAATAAAATAAAATAAAATAAAAATCAA
66 ACAAA-CATAAATTGAAAAAAAATAAAATAAAATAAAAATCAA
* * * *
95779777 TTGAACATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTT
95779842 GACAAACATAAATTGAAAAAAAA
65 GACAAACATAAATTGAAAAAAAA
95779865 GAAATTGAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 52 0.67
108 22 0.28
109 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (107 bp):
TTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTG
ACAAACATAAATTGAAAAAAAATAAAATAAAATAAAAATCAA
Found at i:95779921 original size:90 final size:89
Alignment explanation
Indices: 95779800--95780130 Score: 357
Period size: 88 Copynumber: 3.7 Consensus size: 89
95779790 GGCGTGTGAT
* *
95779800 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGACAA-ACATAAATTGAAAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGA-AACACAGAAATTG-AAAAA
* *
95779863 AAGAAATTGAAAATATCTCAACGTGTC
64 CAGAAATTGAAAATACCTCAA-GTGTC
* * * * *
95779890 CTGAGGCTGAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGGAAAAATA-AAATTTGAAAAAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGAAACACAGAAA-TTGAAAAAC
* * *
95779953 AGAATTTGAAAATACCTCAGTGTGTGA
65 AGAAATTGAAAATACCTCA-AGTGT-C
* * * *
95779980 GTCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTTGAAACACAGAAATTGAAGAAC
1 CT-GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGAAACACAGAAATTGAAAAAC
* * *
95780045 AGAAATGGAAAACACCTC-AGCGTC
65 AGAAATTGAAAATACCTCAAGTGTC
* * * *
95780069 TTGAGGTTCAACTCACCCCTCGCAATATGAGCTGATTTTTTTTGAAAGACAGAAATTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGAAACACAGAAATTGAAAA
95780131 TACCTCAATG
Statistics
Matches: 205, Mismatches: 29, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
88 55 0.27
89 32 0.16
90 51 0.25
91 29 0.14
92 35 0.17
93 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (89 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGAAACACAGAAATTGAAAAACA
GAAATTGAAAATACCTCAAGTGTC
Found at i:95780112 original size:181 final size:181
Alignment explanation
Indices: 95779777--95780109 Score: 442
Period size: 181 Copynumber: 1.9 Consensus size: 181
95779767 TAAAAATCAA
* * * * *
95779777 TTGAACATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTT
* * * * * *
95779842 GACAAACATAAATTGAAAAAAAAGAAATTGAAAATATCTCAACGTGTCCTGAGGCTGAACTCACC
66 GACAAACAGAAATTGAAAAAAAAGAAATGGAAAACACCTCAACGCGTCCTGAGGCTCAACTCACC
* *
95779907 TCTCGCAATATGAGTTGATTTTTTGGAAAAATAAAATTTGAAAAACAGAAT
131 CCTCGCAATATGAGCTGATTTTTTGGAAAAATAAAATTTGAAAAACAGAAT
*
95779958 TTGAAAATACCTCAGTGTGTGAGTC-AAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTT
1 TTGAAAATACCTCAGCGTGTGA-TCTAAGGCTCAACTCACCACTCGCAATATGAGCTGA-TTTTT
* * * *
95780022 TTGA-AACACAGAAATTG-AAGAACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTC
64 TTGACAA-ACAGAAATTGAAAAAAAAGAAATGGAAAACACCTCAACGCGTCCTGAGGCTCAACTC
95780083 ACCCCTCGCAATATGAGCTGATTTTTT
128 ACCCCTCGCAATATGAGCTGATTTTTT
95780110 TTGAAAGACA
Statistics
Matches: 131, Mismatches: 18, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
179 40 0.31
180 1 0.01
181 70 0.53
182 20 0.15
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (181 bp):
TTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTT
GACAAACAGAAATTGAAAAAAAAGAAATGGAAAACACCTCAACGCGTCCTGAGGCTCAACTCACC
CCTCGCAATATGAGCTGATTTTTTGGAAAAATAAAATTTGAAAAACAGAAT
Found at i:95780257 original size:73 final size:75
Alignment explanation
Indices: 95780066--95780549 Score: 601
Period size: 73 Copynumber: 6.5 Consensus size: 75
95780056 ACACCTCAGC
* * *
95780066 GTCTTGAGGTTCAACTCACCCCTCGCAATATGAGCTGATTTTTTTTGA-AAGACAGAAATTGAAA
1 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGACAA-ACAAAAATTGAAA
*
95780130 ATACCTCAATGT
64 ATACCTCAACGT
* * *
95780142 GTTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGACAAACAAAAATTGAAATT
1 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAAATTGAAAAT
*
95780205 ACCTC-A-GC
66 ACCTCAACGT
* * * *
95780213 GTCTTGAGGTTCAACTCACCTATCACAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAT
1 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAAATTGAAAAT
95780278 ACCTCAACGT
66 ACCTCAACGT
* *
95780288 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGA--TTTTTGACAAACAAAAATTGAAATT
1 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAAATTGAAAAT
95780351 ACCTCAACGT
66 ACCTCAACGT
* * * * * * *
95780361 GTCCTGAGGCTCAACTCACTTATCGTAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAT
1 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAAATTGAAAAT
*
95780426 ACTTCAACGT
66 ACCTCAACGT
* * * * *
95780436 GTCTTGAGGCTT-AACTCATCTCTTGCAATCTGAGTTGA--GTTTTGACAAACAAAAATTGAAAT
1 GTCTTGAGG-TTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAAATTGAAAA
*
95780498 TACCTCAGCGT
65 TACCTCAACGT
* *
95780509 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTT
95780550 GAAAAGTAGA
Statistics
Matches: 346, Mismatches: 51, Indels: 23
0.82 0.12 0.05
Matches are distributed among these distances:
71 35 0.10
72 2 0.01
73 176 0.51
74 3 0.01
75 95 0.27
76 35 0.10
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (75 bp):
GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAAATTGAAAAT
ACCTCAACGT
Found at i:95780327 original size:146 final size:146
Alignment explanation
Indices: 95780058--95780549 Score: 725
Period size: 148 Copynumber: 3.3 Consensus size: 146
95780048 AATGGAAAAC
* * ** * *
95780058 ACCTCAGCGTCTTGAGGTTCAACTCACCCCTCGCAATATGAGCTGATTTTTTTTGAAAGACAGAA
1 ACCTCAGCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAA
* * *
95780123 ATTGAAAATACCTCAATGTGTTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
65 ATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
95780188 AAACAAAAATTGAAATT
130 AAACAAAAATTGAAATT
* * *
95780205 ACCTCAGCGTCTTGAGGTTCAACTCACCTATCACAATATGAGTTGATTTTTTTGAAAAACAGAAA
1 ACCTCAGCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA
*
95780270 TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTGACA
66 TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
95780335 AACAAAAATTGAAATT
131 AACAAAAATTGAAATT
* * *
95780351 ACCTCAACGTGTCCTGAGGCTCAACTCACTTATCGTAATATGAGTTGATTTTTTTGAAAAACAGA
1 ACCTC-A-GCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGA
* * * * *
95780416 AATTGAAAATACTTCAACGTGTCTTGAGGCTT-AACTCATCTCTTGCAATCTGAGTTGAGTTTTG
64 AATTGAAAATACCTCAACGTGTCTTGAGG-TTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
95780480 ACAAACAAAAATTGAAATT
128 ACAAACAAAAATTGAAATT
*
95780499 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 ACCTCAGC--GTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTT
95780550 GAAAAGTAGA
Statistics
Matches: 315, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
146 101 0.32
147 44 0.14
148 168 0.53
149 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (146 bp):
ACCTCAGCGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA
TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
AACAAAAATTGAAATT
Done.