Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold354
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: 1591162
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 188200 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:1243481 original size:25 final size:24
Alignment explanation
Indices: 1243450--1243510 Score: 104
Period size: 25 Copynumber: 2.5 Consensus size: 24
1243440 TGTAATTGTT
1243450 CCACTGCTCAACTATTGAAGAACCA
1 CCACTGC-CAACTATTGAAGAACCA
1243475 CCACTGCCCAACTATTGAAGAACCA
1 CCACTG-CCAACTATTGAAGAACCA
1243500 CCACTGCCAAC
1 CCACTGCCAAC
1243511 CATTTTTCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.14
25 29 0.83
26 1 0.03
ACGTcount: A:0.34, C:0.38, G:0.11, T:0.16
Consensus pattern (24 bp):
CCACTGCCAACTATTGAAGAACCA
Found at i:1247866 original size:19 final size:19
Alignment explanation
Indices: 1247842--1247879 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1247832 AATCTTCAGG
1247842 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1247861 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1247880 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:1262539 original size:7 final size:7
Alignment explanation
Indices: 1262527--1262551 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1262517 CCCTATTGCT
1262527 TTCTTTA
1 TTCTTTA
1262534 TTCTTTA
1 TTCTTTA
1262541 TTCTTTA
1 TTCTTTA
1262548 TTCT
1 TTCT
1262552 CTCCATCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
TTCTTTA
Found at i:1268230 original size:38 final size:36
Alignment explanation
Indices: 1268170--1268263 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
1268160 CTTTTTCTTT
1268170 TTTTGAAACAC--AATTTTTTTAAAAAAATA-AAAGAA
1 TTTTGAAACACGAAATTTTTTTAAAAAAA-ACAAA-AA
*
1268205 TTTTAGAAACACGAAATTTTTTTAAAAAAAACGAAAA
1 TTTT-GAAACACGAAATTTTTTTAAAAAAAACAAAAA
*
1268242 TTTTGAAACACGAGATTTTTTT
1 TTTTGAAACACGAAATTTTTTT
1268264 TGAAAACACG
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
35 4 0.08
36 24 0.45
37 7 0.13
38 18 0.34
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (36 bp):
TTTTGAAACACGAAATTTTTTTAAAAAAAACAAAAA
Found at i:1268271 original size:56 final size:58
Alignment explanation
Indices: 1268211--1268329 Score: 145
Period size: 56 Copynumber: 2.1 Consensus size: 58
1268201 AGAATTTTAG
* * *
1268211 AAACACGAAATTTT-TTTAAAAAAAACGAAAA-TTTTGAAACACGAGATTT-TTTTTGA
1 AAACACG-AATTTTCTTTAAAAAAAACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
*** *
1268267 AAACACGAATTTTCTTTTTGAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
1 AAACACGAATTTTCTTTAAAAAAAACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
1268325 AAACA
1 AAACA
1268330 TAAAAATTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
55 6 0.11
56 20 0.38
57 15 0.28
58 12 0.23
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (58 bp):
AAACACGAATTTTCTTTAAAAAAAACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
Found at i:1268272 original size:20 final size:20
Alignment explanation
Indices: 1268242--1268329 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
1268232 AAAACGAAAA
1268242 TTTTG-AAACACGAGATTT-T
1 TTTTGAAAACACGA-ATTTCT
1268261 TTTTGAAAACACGAATTTTCT
1 TTTTGAAAACACGAA-TTTCT
**
1268282 TTTTG-AAACACGAA--AAT
1 TTTTGAAAACACGAATTTCT
* *
1268299 TTTT-AAAACACAAAATTTGT
1 TTTTGAAAACAC-GAATTTCT
1268319 TTTTGAAAACA
1 TTTTGAAAACA
1268330 TAAAAATTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
17 11 0.20
18 2 0.04
19 6 0.11
20 25 0.45
21 12 0.21
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTTGAAAACACGAATTTCT
Found at i:1268313 original size:16 final size:17
Alignment explanation
Indices: 1268281--1268316 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1268271 ACGAATTTTC
*
1268281 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
1268298 TTTTTAAAACAC-AAAA
1 TTTTTAAAACACGAAAA
1268314 TTT
1 TTT
1268317 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:1268322 original size:37 final size:40
Alignment explanation
Indices: 1268242--1268326 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 40
1268232 AAAACGAAAA
** * *
1268242 TTTTGAAACACGAGATTTTTTTTGAAAACACGAATTTTCT
1 TTTTGAAACACGAGATAATTTTTGAAAACACAAAATTTCT
*
1268282 TTTTGAAACACGA-A-AATTTTT-AAAACACAAAATTTGT
1 TTTTGAAACACGAGATAATTTTTGAAAACACAAAATTTCT
1268319 TTTTGAAA
1 TTTTGAAA
1268327 ACATAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 21 0.52
38 5 0.12
39 1 0.03
40 13 0.32
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (40 bp):
TTTTGAAACACGAGATAATTTTTGAAAACACAAAATTTCT
Found at i:1268329 original size:38 final size:38
Alignment explanation
Indices: 1268260--1268338 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
1268250 CACGAGATTT
* * *
1268260 TTTTTGAAAACACGAATTTTCTTTTTGAAACACGAAAA
1 TTTTTGAAAACACAAAATTTCTTTTTGAAACACAAAAA
* *
1268298 TTTTT-AAAACACAAAATTTGTTTTTGAAAACATAAAAA
1 TTTTTGAAAACACAAAATTTCTTTTTG-AAACACAAAAA
1268336 TTT
1 TTT
1268339 GGATAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 18 0.51
38 17 0.49
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (38 bp):
TTTTTGAAAACACAAAATTTCTTTTTGAAACACAAAAA
Found at i:1268338 original size:22 final size:20
Alignment explanation
Indices: 1268298--1268339 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1268288 AACACGAAAA
*
1268298 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
1268318 TTTTTGAAAACATAAAAATTTG
1 TTTTT-AAAACA-AAAAATTTG
1268340 GATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:1268392 original size:37 final size:39
Alignment explanation
Indices: 1268362--1268498 Score: 113
Period size: 37 Copynumber: 3.6 Consensus size: 39
1268352 AAACACGAGG
*
1268362 ATTTTTTTT-CAAACATGAAAATTTAGGAAACACGATCA
1 ATTTTTTTTGAAAACATGAAAATTTAGGAAACACGATCA
** * **
1268400 ATTTTTTTTGAAAACATGAAAATTTTTGAAAGACG-GGA
1 ATTTTTTTTGAAAACATGAAAATTTAGGAAACACGATCA
* * * * * *
1268438 A-ATTTTTTGAAAACACGGAAATTTATGAAATACAAT--
1 ATTTTTTTTGAAAACATGAAAATTTAGGAAACACGATCA
* *
1268474 TTTTTTTTTGAAAACAAGAAAATTT
1 ATTTTTTTTGAAAACATGAAAATTT
1268499 TCAAAATACG
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
37 47 0.59
38 11 0.14
39 21 0.27
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (39 bp):
ATTTTTTTTGAAAACATGAAAATTTAGGAAACACGATCA
Found at i:1268427 original size:18 final size:18
Alignment explanation
Indices: 1268404--1268700 Score: 202
Period size: 18 Copynumber: 16.7 Consensus size: 18
1268394 CGATCAATTT
*
1268404 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
** *
1268422 TTTTTGAAAGACGGGAAAT
1 TTTTTGAAA-ACACGAAAA
*
1268441 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
* ******
1268459 TTTATGAAATACAATTTTT
1 TTTTTGAAA-ACACGAAAA
*
1268478 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * **
1268496 -TTTTCAAAATACGGGAA
1 TTTTTGAAAACACGAAAA
* *
1268513 TTTTTGAAAACAAGGGAAAT
1 TTTTTGAAAAC-A-CGAAAA
1268533 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
1268551 TTTTTG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
*
1268568 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
1268585 TTTTT-AAAACATGAGAA
1 TTTTTGAAAACACGAAAA
1268602 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
1268620 TTTTTAAAAACCCGGAAA
1 TTTTTGAAAACACGAAAA
* *
1268638 TTTTTGAAACACAAGAAAT
1 TTTTTGAAA-ACACGAAAA
1268657 TTTTCTGAAAACAC--AAA
1 TTTT-TGAAAACACGAAAA
1268674 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
1268688 TTTTTGAAAACAC
1 TTTTTGAAAACAC
1268701 CGTATTCAAC
Statistics
Matches: 214, Mismatches: 51, Indels: 31
0.72 0.17 0.10
Matches are distributed among these distances:
14 7 0.03
15 12 0.06
16 9 0.04
17 45 0.21
18 83 0.39
19 40 0.19
20 18 0.08
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:1268517 original size:37 final size:36
Alignment explanation
Indices: 1268402--1268535 Score: 110
Period size: 37 Copynumber: 3.7 Consensus size: 36
1268392 CACGATCAAT
* *
1268402 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGGGAA
1 TTTTTTTGAAAACAAGAAAA-TTTTGAAATACGGGAA
* * * *****
1268439 ATTTTTTGAAAACACGGAAATTTATGAAATACAATTT
1 TTTTTTTGAAAACAAGAAAATTT-TGAAATACGGGAA
*
1268476 TTTTTTTGAAAACAAGAAAATTTTCAAAATACGGGAA
1 TTTTTTTGAAAACAAGAAAATTTT-GAAATACGGGAA
*
1268513 --TTTTTGAAAACAAGGGAAATTTT
1 TTTTTTTGAAAACAA-GAAAATTTT
1268536 TTGAAAACAC
Statistics
Matches: 75, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
35 13 0.17
36 12 0.16
37 50 0.67
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.36
Consensus pattern (36 bp):
TTTTTTTGAAAACAAGAAAATTTTGAAATACGGGAA
Found at i:1268824 original size:20 final size:20
Alignment explanation
Indices: 1268799--1268837 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1268789 CGGGATTCTA
1268799 ATAAAACACGAGAATTTTTT
1 ATAAAACACGAGAATTTTTT
* *
1268819 ATAAAATACGAGGATTTTT
1 ATAAAACACGAGAATTTTT
1268838 GAATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (20 bp):
ATAAAACACGAGAATTTTTT
Found at i:1269395 original size:11 final size:11
Alignment explanation
Indices: 1269396--1269455 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
1269386 TTTTTTTCTT
1269396 TTTTCTTTTTC
1 TTTTCTTTTTC
1269407 TTTTCTTTTTC
1 TTTTCTTTTTC
*
1269418 TTCCCTCTTTTTC
1 TT--TTCTTTTTC
*
1269431 TTTTCTTTTTT
1 TTTTCTTTTTC
*
1269442 TCTTTCTTTCTC
1 T-TTTCTTTTTC
1269454 TT
1 TT
1269456 CCTCTTCTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
11 22 0.54
12 9 0.22
13 10 0.24
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1269402 original size:18 final size:18
Alignment explanation
Indices: 1269379--1269450 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 18
1269369 GCCTGCTGTC
1269379 TTTCTTATTT-TTTTCTTT
1 TTTCTT-TTTCTTTTCTTT
1269397 TTTCTTTTTCTTTTC-TT
1 TTTCTTTTTCTTTTCTTT
**
1269414 TTTCTTCCCTCTTTTTCTTT
1 TTTCTT-TTTC-TTTTCTTT
1269434 TCTT-TTTTTC-TTTCTTT
1 T-TTCTTTTTCTTTTCTTT
1269451 CTCTTCCTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
17 18 0.40
18 13 0.29
19 7 0.16
20 5 0.11
21 2 0.04
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTCTTTTCTTT
Found at i:1269406 original size:13 final size:13
Alignment explanation
Indices: 1269388--1269452 Score: 64
Period size: 13 Copynumber: 5.1 Consensus size: 13
1269378 CTTTCTTATT
1269388 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
1269401 TTTTTC--TTTTC
1 TTTTTCTTTTTTC
***
1269412 TTTTTCTTCCCTC
1 TTTTTCTTTTTTC
1269425 TTTTTCTTTTCTT-
1 TTTTTCTTTT-TTC
1269438 TTTTTCTTTCTTTC
1 TTTTTCTTT-TTTC
1269452 T
1 T
1269453 CTTCCTCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
11 11 0.27
13 27 0.66
14 3 0.07
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:1269407 original size:24 final size:24
Alignment explanation
Indices: 1269379--1269455 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
1269369 GCCTGCTGTC
*
1269379 TTTCTTATT-TTTTTCTTTTTTCTT
1 TTTCTT-TTCTTTTTCTTCTTTCTT
**
1269403 TTTCTTTTCTTTTTCTTCCCTCTT
1 TTTCTTTTCTTTTTCTTCTTTCTT
1269427 TTTCTTTTCTTTTT-TTCTTTCTT
1 TTTCTTTTCTTTTTCTTCTTTCTT
*
1269450 TCTCTT
1 TTTCTT
1269456 CCTCTTCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 14 0.30
24 32 0.70
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTCTTTTCTTTTTCTTCTTTCTT
Found at i:1269462 original size:42 final size:42
Alignment explanation
Indices: 1269381--1269462 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1269371 CTGCTGTCTT
* **
1269381 TCTTATTTTTTTCTTTTTTCTTTTTCTTTTCTTTTTCTTCCC
1 TCTTATTTTTTTCTTTTTTCTCTTTCTTTTCTTCCTCTTCCC
1269423 TCTT-TTTCTTTTCTTTTTT-TCTTTCTTTCTCTTCCTCTTC
1 TCTTATTT-TTTTCTTTTTTCTCTTTCTTT-TCTTCCTCTTC
1269463 TTCGGGCCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 11 0.31
42 24 0.69
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.74
Consensus pattern (42 bp):
TCTTATTTTTTTCTTTTTTCTCTTTCTTTTCTTCCTCTTCCC
Found at i:1270053 original size:29 final size:28
Alignment explanation
Indices: 1270011--1270171 Score: 135
Period size: 30 Copynumber: 5.5 Consensus size: 28
1270001 TTTTGGGGTA
* * *
1270011 AAAATGCAATTTTAGGAAAATATGGGGGCT
1 AAAATGTAA-TTTA-GAAAATTTAGGGGCT
* *
1270041 AAAATGTAATTTATAGAAATTTTAGGGGCC
1 AAAATGTAA-TT-TAGAAAATTTAGGGGCT
* *
1270071 CAAATGCAATTTAGAAAAGTTTAGGGG-T
1 AAAATGTAATTTAGAAAA-TTTAGGGGCT
* *
1270099 AGAAATGTAATTTTGAGAAAGTTTAGGGGTT
1 A-AAATGTAA-TTT-AGAAAATTTAGGGGCT
* *
1270130 AAAATGTAATTTAGAAAAGTTCAGGGGCG
1 AAAATGTAATTTAGAAAA-TTTAGGGGCT
1270159 AAAATGTAATTTA
1 AAAATGTAATTTA
1270172 TATTTTTTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
28 11 0.10
29 40 0.37
30 48 0.44
31 9 0.08
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.30
Consensus pattern (28 bp):
AAAATGTAATTTAGAAAATTTAGGGGCT
Found at i:1270069 original size:30 final size:29
Alignment explanation
Indices: 1270035--1270173 Score: 147
Period size: 29 Copynumber: 4.7 Consensus size: 29
1270025 GGAAAATATG
*
1270035 GGGGCTAAAATGTAATTTATAGAAATTTTA
1 GGGGCTAAAATGTAATTTATA-AAAGTTTA
** * *
1270065 GGGGCCCAAATGCAATTTAGAAAAGTTTA
1 GGGGCTAAAATGTAATTTATAAAAGTTTA
1270094 GGGG-TAGAAATGTAATTT-TGAGAAAGTTTA
1 GGGGCTA-AAATGTAATTTAT-A-AAAGTTTA
* * *
1270124 GGGGTTAAAATGTAATTTAGAAAAGTTCA
1 GGGGCTAAAATGTAATTTATAAAAGTTTA
*
1270153 GGGGCGAAAATGTAATTTATA
1 GGGGCTAAAATGTAATTTATA
1270174 TTTTTTTTAT
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
29 47 0.52
30 41 0.46
31 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
GGGGCTAAAATGTAATTTATAAAAGTTTA
Found at i:1270106 original size:59 final size:59
Alignment explanation
Indices: 1270011--1270173 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 59
1270001 TTTTGGGGTA
* * *
1270011 AAAATGCAATTTTAGGAAAA-TATGGGGGCTA-AAATGTAATTTATAGAAATTTTAGGGGCC
1 AAAATGCAA-TTTA-GAAAAGTTTAGGGG-TAGAAATGTAATTTATAGAAAGTTTAGGGGCC
* **
1270071 CAAATGCAATTTAGAAAAGTTTAGGGGTAGAAATGTAATTT-TGAGAAAGTTTAGGGGTT
1 AAAATGCAATTTAGAAAAGTTTAGGGGTAGAAATGTAATTTAT-AGAAAGTTTAGGGGCC
* * *
1270130 AAAATGTAATTTAGAAAAGTTCAGGGG-CGAAAATGTAATTTATA
1 AAAATGCAATTTAGAAAAGTTTAGGGGTAG-AAATGTAATTTATA
1270174 TTTTTTTTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
58 9 0.10
59 70 0.80
60 9 0.10
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (59 bp):
AAAATGCAATTTAGAAAAGTTTAGGGGTAGAAATGTAATTTATAGAAAGTTTAGGGGCC
Found at i:1270621 original size:78 final size:76
Alignment explanation
Indices: 1270516--1270805 Score: 309
Period size: 78 Copynumber: 3.6 Consensus size: 76
1270506 TGAGTTGACC
* * * *
1270516 TTTGAAAAATAGATATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCACTTCTAGCATTATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGCATTATG
1270581 AGTTGATTTTTT
66 AGTTGA-TTTTT
1270593 TTTGAAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAAAC-CA-TCTCTCGCATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTC-AACTCACT-TCTCGCATT
*
1270656 ATGAATTGATTTTT
63 ATGAGTTGATTTTT
* *
1270670 TTTGAAAAA-AGAAATTTAAAAGAAATACCTTAGCGTGCGACCCGAGGCTCAACTCACTTCTCGC
1 TTTGAAAAACAGAAA-TT--GA-AAATACCTCAGCGT--GACCCGAGGCTCAACTCACTTCTCGC
*
1270734 AATATGAGTTGA-TTTT
60 ATTATGAGTTGATTTTT
1270750 TTTGAAAAAACAGAGAAACATAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAA
1 TTTG-AAAAAC--AG------AAATTGAAAATACCTCAGCGTGACCCGAGGCTCAA
1270806 NNNNNNNNNN
Statistics
Matches: 181, Mismatches: 11, Indels: 35
0.80 0.05 0.15
Matches are distributed among these distances:
75 5 0.03
76 7 0.04
77 14 0.08
78 57 0.31
79 16 0.09
80 11 0.06
81 35 0.19
82 1 0.01
84 16 0.09
86 13 0.07
87 1 0.01
89 2 0.01
90 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (76 bp):
TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGCATTATG
AGTTGATTTTT
Found at i:1271932 original size:15 final size:15
Alignment explanation
Indices: 1271908--1271948 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1271898 TTCATCTTGA
1271908 TTTTTC-TTTTTCTT
1 TTTTTCTTTTTTCTT
*
1271922 TTTTTCTTTTTTGTT
1 TTTTTCTTTTTTCTT
*
1271937 TTTTTGTTTTTT
1 TTTTTCTTTTTT
1271949 TTATTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:1271948 original size:17 final size:16
Alignment explanation
Indices: 1271908--1271982 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 16
1271898 TTCATCTTGA
1271908 TTTTTCTTTTTCTTTTT-
1 TTTTT-TTTTT-TTTTTG
1271925 TTCTTTTTTGTTTTTTTG
1 TT-TTTTTT-TTTTTTTG
*
1271943 TTTTTTTTATTTGTTTG
1 TTTTTTTT-TTTTTTTG
* *
1271960 TTTGTTTTTTGTTGTTG
1 TTT-TTTTTTTTTTTTG
1271977 TTTTTT
1 TTTTTT
1271983 CTAGGCATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.06
17 34 0.69
18 12 0.24
ACGTcount: A:0.01, C:0.04, G:0.11, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTG
Found at i:1271955 original size:21 final size:23
Alignment explanation
Indices: 1271921--1271969 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
1271911 TTCTTTTTCT
*
1271921 TTTTTTCTTTTTTGTTT-TTT-TG
1 TTTTTT-TTATTTGTTTGTTTGTG
1271943 TTTTTTTTATTTGTTTGTTTGT-
1 TTTTTTTTATTTGTTTGTTTGTG
1271965 TTTTT
1 TTTTT
1271970 GTTGTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (23 bp):
TTTTTTTTATTTGTTTGTTTGTG
Found at i:1271977 original size:13 final size:13
Alignment explanation
Indices: 1271936--1271982 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1271926 TCTTTTTTGT
*
1271936 TTTTTTGTT-TTT
1 TTTTTTGTTGTTG
1271948 TTTATTTGTTTGTTTG
1 TTT-TTTG-TTG-TTG
1271964 TTTTTTGTTGTTG
1 TTTTTTGTTGTTG
1271977 TTTTTT
1 TTTTTT
1271983 CTAGGCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.10
13 13 0.43
14 5 0.17
15 4 0.13
16 5 0.17
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (13 bp):
TTTTTTGTTGTTG
Found at i:1271977 original size:21 final size:21
Alignment explanation
Indices: 1271932--1271979 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1271922 TTTTTCTTTT
* *
1271932 TTGTTTTTTTGTTTTTTTTAT
1 TTGTTTGTTTGTTTTTTTTAG
1271953 TTGTTTGTTTGTTTTTTGTT-G
1 TTGTTTGTTTGTTTTTT-TTAG
1271974 TTGTTT
1 TTGTTT
1271980 TTTCTAGGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.02, C:0.00, G:0.17, T:0.81
Consensus pattern (21 bp):
TTGTTTGTTTGTTTTTTTTAG
Found at i:1282827 original size:38 final size:37
Alignment explanation
Indices: 1282770--1282866 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 37
1282760 CTTTTTCTTT
*
1282770 TTTTGAAACAC-AAATTTTTTTTAAAAAAATA-AAAGAA
1 TTTTGAAACACGAAA-TTTTTTTAAAAAAACACAAA-AA
*
1282807 TTTTAGAAACACGAAATTTTTTTAAAAAAACACGAAAA
1 TTTT-GAAACACGAAATTTTTTTAAAAAAACACAAAAA
* *
1282845 GTTTGAAACACGAGATTTTTTT
1 TTTTGAAACACGAAATTTTTTT
1282867 TTAAAACACG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
37 21 0.40
38 27 0.51
39 5 0.09
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (37 bp):
TTTTGAAACACGAAATTTTTTTAAAAAAACACAAAAA
Found at i:1282875 original size:20 final size:20
Alignment explanation
Indices: 1282850--1282898 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1282840 GAAAAGTTTG
1282850 AAACACGAGATTTT-TTTTTA
1 AAACACGA-ATTTTCTTTTTA
*
1282870 AAACACGAATTTTCTTTTTG
1 AAACACGAATTTTCTTTTTA
1282890 AAACACGAA
1 AAACACGAA
1282899 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
AAACACGAATTTTCTTTTTA
Found at i:1282916 original size:16 final size:17
Alignment explanation
Indices: 1282884--1282919 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1282874 ACGAATTTTC
*
1282884 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
1282901 TTTTTAAAACAC-AAAA
1 TTTTTAAAACACGAAAA
1282917 TTT
1 TTT
1282920 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:1282930 original size:21 final size:21
Alignment explanation
Indices: 1282901--1282942 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1282891 AACACGAAAA
*
1282901 TTTTTAAAACA-CAAAATTTG
1 TTTTTAAAACATAAAAATTTG
1282921 TTTTTGAAAACATAAAAATTTG
1 TTTTT-AAAACATAAAAATTTG
1282943 GATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTTAAAACATAAAAATTTG
Found at i:1282932 original size:38 final size:37
Alignment explanation
Indices: 1282864--1283107 Score: 118
Period size: 37 Copynumber: 6.2 Consensus size: 37
1282854 ACGAGATTTT
* *
1282864 TTTTTAAAACACGAATTTTCTTTTTG-AAACACGAAAA
1 TTTTTAAAACACAAAATTT-TTTTTGAAAACACGAAAA
**
1282901 TTTTTAAAACACAAAATTTGTTTTTGAAAACATAAAAA
1 TTTTTAAAACACAAAATTT-TTTTTGAAAACACGAAAA
* *
1282939 TTTGGATAAAAATACGAAACATGAGGATTTTTTTTG-AAACACGAAAA
1 TTT---T-TAAA-AC---ACA--A-AATTTTTTTTGAAAACACGAAAA
** * *
1282986 TTTAGAAAACACGATCAATTTTTTTTGAAAACATGAAAA
1 TTTTTAAAACAC-A-AAATTTTTTTTGAAAACACGAAAA
*** *
1283025 TTTTTGAAAGACGGGAAA--TTTTTTGAAAACACGGAAA
1 TTTTT-AAA-ACACAAAATTTTTTTTGAAAACACGAAAA
** * * * *
1283062 TTAATGAAATACAAATTTTTTTTTGAAAACAAGAAAA
1 TTTTTAAAACACAAAATTTTTTTTGAAAACACGAAAA
*
1283099 TTTTCAAAA
1 TTTTTAAAA
1283108 TATGGGAATT
Statistics
Matches: 152, Mismatches: 37, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
35 3 0.02
36 2 0.01
37 65 0.43
38 22 0.14
39 17 0.11
40 4 0.03
41 3 0.02
42 5 0.03
43 5 0.03
46 3 0.02
47 12 0.08
48 7 0.05
49 4 0.03
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (37 bp):
TTTTTAAAACACAAAATTTTTTTTGAAAACACGAAAA
Found at i:1283030 original size:18 final size:18
Alignment explanation
Indices: 1282969--1283288 Score: 180
Period size: 18 Copynumber: 17.7 Consensus size: 18
1282959 ATGAGGATTT
1282969 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
1282986 -TTTAGAAAACACGATCAATTT
1 TTTTTGAAAACACGA--AA--A
*
1283007 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
** *
1283025 TTTTTGAAAGACGGGAAAT
1 TTTTTGAAA-ACACGAAAA
*
1283044 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
** **
1283062 TTAATGAAATACA--AATTTT
1 TTTTTGAAA-ACACGAA--AA
*
1283081 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * * **
1283099 -TTTTCAAAATATGGGAA
1 TTTTTGAAAACACGAAAA
* *
1283116 TTTTTGAAAACAAGGGAAAT
1 TTTTTGAAAAC-A-CGAAAA
*
1283136 TTTTTGAAAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
*
1283154 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
1283171 TTTTT-AAAACATGAGAA
1 TTTTTGAAAACACGAAAA
1283188 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
1283206 TTTTTAAAAACCCTG-AAA
1 TTTTTGAAAACAC-GAAAA
* *
1283224 TTTTTGAAACACAAGAAAT
1 TTTTTGAAA-ACACGAAAA
1283243 TTTTCTGAAAACACGAAAA
1 TTTT-TGAAAACACGAAAA
1283262 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
1283276 TTTTTGAAAACAC
1 TTTTTGAAAACAC
1283289 CGTATTTAAC
Statistics
Matches: 229, Mismatches: 51, Indels: 48
0.70 0.16 0.15
Matches are distributed among these distances:
14 7 0.03
15 6 0.03
16 6 0.03
17 54 0.24
18 72 0.31
19 50 0.22
20 22 0.10
22 12 0.05
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:1283063 original size:37 final size:36
Alignment explanation
Indices: 1283007--1283275 Score: 137
Period size: 37 Copynumber: 7.4 Consensus size: 36
1282997 CGATCAATTT
* *
1283007 TTTTTGAAAACATGAAAATTTTTGAAAGACGGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAATACGGGAAA
* **
1283043 TTTTTTGAAAACACGGAAATTAATGAAATAC---AAA
1 -TTTTTGAAAACACGAAAATTTTTGAAATACGGGAAA
* ** *
1283077 TTTTTTTTTGAAAACAAGAAAATTTTCAAAATATGGG-AA
1 ----TTTTTGAAAACACGAAAATTTTTGAAATACGGGAAA
* * * *
1283116 TTTTTGAAAACAAGGGAAATTTTTTGAAAACACCGG-AA
1 TTTTTGAAAAC-A-CGAAAATTTTTG-AAATACGGGAAA
* **
1283154 -TTTTGAAAACACGAAGATTTTT-AAA-ACATGAGAA
1 TTTTTGAAAACACGAAAATTTTTGAAATACGGGA-AA
* **
1283188 TTTTTGAAAACACGAAAATTTTT-AAAAACCCTGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAATA-CGGGAAA
* * * *
1283224 TTTTTGAAACACAAGAAATTTTTCTGAAA-ACACGAAAA
1 TTTTTGAAA-ACACGAAAATTTT-TGAAATAC-GGGAAA
1283262 TTTTTG-AAACACGA
1 TTTTTGAAAACACGA
1283276 TTTTTGAAAA
Statistics
Matches: 183, Mismatches: 31, Indels: 37
0.73 0.12 0.15
Matches are distributed among these distances:
32 3 0.02
33 3 0.02
34 5 0.03
35 43 0.23
36 19 0.10
37 85 0.46
38 20 0.11
39 5 0.03
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTTTGAAATACGGGAAA
Found at i:1283127 original size:35 final size:35
Alignment explanation
Indices: 1283081--1283270 Score: 159
Period size: 35 Copynumber: 5.3 Consensus size: 35
1283071 TACAAATTTT
* *
1283081 TTTTTGAAAACAAGAAAATTTTCAAAATATGGGAA
1 TTTTTGAAAACAAGAAAATTTTTAAAACATGGGAA
* **
1283116 TTTTTGAAAACAAGGGAAATTTTTTGAAAACACCGGAA
1 TTTTTGAAAACAA--GAAAATTTTT-AAAACATGGGAA
* * *
1283154 -TTTTGAAAACACGAAGATTTTTAAAACATGAGAA
1 TTTTTGAAAACAAGAAAATTTTTAAAACATGGGAA
* * *
1283188 TTTTTGAAAACACGAAAATTTTTAAAAACCCT-GAAA
1 TTTTTGAAAACAAGAAAATTTTT-AAAA-CATGGGAA
* * **
1283224 TTTTTGAAACACAAGAAATTTTTCTGAAAACACGAAAA
1 TTTTTGAAA-ACAAGAAAATTTT-T-AAAACATGGGAA
1283262 TTTTTGAAA
1 TTTTTGAAA
1283271 CACGATTTTT
Statistics
Matches: 125, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
34 9 0.07
35 42 0.34
36 15 0.12
37 33 0.26
38 26 0.21
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACAAGAAAATTTTTAAAACATGGGAA
Found at i:1283159 original size:17 final size:16
Alignment explanation
Indices: 1283137--1283201 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 16
1283127 AAGGGAAATT
1283137 TTTTGAAAACACCGGAA
1 TTTTGAAAACA-CGGAA
*
1283154 TTTTGAAAACACGAAGA
1 TTTTGAAAACACGGA-A
* *
1283171 TTTTTAAAACATGAGAA
1 TTTTGAAAACACG-GAA
1283188 TTTTTGAAAACACG
1 -TTTTGAAAACACG
1283202 AAAATTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 3 0.08
17 24 0.62
18 12 0.31
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (16 bp):
TTTTGAAAACACGGAA
Found at i:1283417 original size:20 final size:20
Alignment explanation
Indices: 1283388--1283425 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1283378 GGGATTCTAA
1283388 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
1283408 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
1283426 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:1283984 original size:11 final size:11
Alignment explanation
Indices: 1283968--1284024 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
1283958 GCCTGCTGTC
1283968 TTTCTTATTT-T
1 TTTCTT-TTTCT
1283979 TTTCTTTTTCT
1 TTTCTTTTTCT
1283990 TTTCTTTTTCT
1 TTTCTTTTTCT
*
1284001 TCTCCTTTTT-T
1 T-TTCTTTTTCT
*
1284012 CTTTCTTTCTCT
1 -TTTCTTTTTCT
1284024 T
1 T
1284025 CCTCTTCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.08
11 27 0.69
12 9 0.23
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:1283990 original size:17 final size:16
Alignment explanation
Indices: 1283968--1284024 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
1283958 GCCTGCTGTC
1283968 TTTCTTATTTTTTTCTT
1 TTTCTT-TTTTTTTCTT
1283985 TTTCTTTTCTTTTTCTT
1 TTTCTTTT-TTTTTCTT
* *
1284002 CTCCTTTTTTCTTTCTT
1 TTTCTTTTTT-TTTCTT
*
1284019 TCTCTT
1 TTTCTT
1284025 CCTCTTCTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 4 0.12
17 29 0.88
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTTTTCTT
Found at i:1284625 original size:29 final size:29
Alignment explanation
Indices: 1284578--1284736 Score: 137
Period size: 29 Copynumber: 5.4 Consensus size: 29
1284568 TTTTGGGGTA
* *
1284578 AAAACGTAATTTTAGGAAAATAT-GGGGCT
1 AAAATGTAATTTTA-GAAAATTTAGGGGCT
* *
1284607 AAAATGTAATTTATAGAAAGTTTAGGGGCC
1 AAAATGTAATTT-TAGAAAATTTAGGGGCT
* * *
1284637 CAAATGCAA-TTTAAAAAAGTTTAGGGG-T
1 AAAATGTAATTTTAGAAAA-TTTAGGGGCT
* *
1284665 AGAAATGTAATTTTGAGAAAGTTTAGGGGTT
1 A-AAATGTAATTTT-AGAAAATTTAGGGGCT
* *
1284696 GAAATGTAA-TTTAGAAAAGTTTAGGGGCC
1 AAAATGTAATTTTAGAAAA-TTTAGGGGCT
1284725 AAAATGTAATTT
1 AAAATGTAATTT
1284737 ATATTTTTTT
Statistics
Matches: 103, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
28 10 0.10
29 53 0.51
30 35 0.34
31 5 0.05
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAATTTAGGGGCT
Found at i:1284673 original size:59 final size:59
Alignment explanation
Indices: 1284601--1284739 Score: 183
Period size: 59 Copynumber: 2.4 Consensus size: 59
1284591 AGGAAAATAT
*
1284601 GGGGCTAAAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGCAATTTAAAAAAGTTTA
1 GGGGCCAAAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGCAATTTAAAAAAGTTTA
* *** * *
1284660 GGGG-TAGAAATGTAATTT-TGAGAAAGTTTAGGGGTTGAAATGTAATTTAGAAAAGTTTA
1 GGGGCCA-AAATGTAATTTAT-AGAAAGTTTAGGGGCCCAAATGCAATTTAAAAAAGTTTA
1284719 GGGGCCAAAATGTAATTTATA
1 GGGGCCAAAATGTAATTTATA
1284740 TTTTTTTGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
58 3 0.04
59 65 0.93
60 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (59 bp):
GGGGCCAAAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGCAATTTAAAAAAGTTTA
Found at i:1284737 original size:29 final size:30
Alignment explanation
Indices: 1284601--1284737 Score: 163
Period size: 29 Copynumber: 4.6 Consensus size: 30
1284591 AGGAAAATAT
*
1284601 GGGGCTAAAATGTAATTTATAGAAAGTTTA
1 GGGGCTAAAATGTAATTTAGAGAAAGTTTA
** * *
1284631 GGGGCCCAAATGCAATTTA-AAAAAGTTTA
1 GGGGCTAAAATGTAATTTAGAGAAAGTTTA
*
1284660 GGGG-TAGAAATGTAATTTTGAGAAAGTTTA
1 GGGGCTA-AAATGTAATTTAGAGAAAGTTTA
* *
1284690 GGGGTTGAAATGTAATTTAGA-AAAGTTTA
1 GGGGCTAAAATGTAATTTAGAGAAAGTTTA
*
1284719 GGGGCCAAAATGTAATTTA
1 GGGGCTAAAATGTAATTTA
1284738 TATTTTTTTG
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
29 47 0.52
30 42 0.47
31 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.31
Consensus pattern (30 bp):
GGGGCTAAAATGTAATTTAGAGAAAGTTTA
Found at i:1285357 original size:14 final size:14
Alignment explanation
Indices: 1285338--1285368 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1285328 TTAGATTTTA
1285338 TTTTTTTCTAGAAT
1 TTTTTTTCTAGAAT
1285352 TTTTTTTCTAGAAT
1 TTTTTTTCTAGAAT
1285366 TTT
1 TTT
1285369 CTATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTTTTCTAGAAT
Found at i:1286434 original size:6 final size:6
Alignment explanation
Indices: 1286423--1286450 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1286413 CACTGATCTT
1286423 CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1286451 ATCCTTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTTC
Found at i:1286722 original size:6 final size:6
Alignment explanation
Indices: 1286711--1286738 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1286701 CTACCAGGTC
1286711 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1286739 TCCCGCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:1289080 original size:34 final size:35
Alignment explanation
Indices: 1289022--1289088 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
1289012 CAAACACCAG
1289022 AAAATATTTTCCAGCAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGCAAATCATTTTACAGAAAAGT
*
1289057 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGCAAATCATTTTACAGAAAA
1289089 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAATATTTTCCAGCAAATCATTTTACAGAAAAGT
Found at i:1293133 original size:11 final size:11
Alignment explanation
Indices: 1293113--1293209 Score: 50
Period size: 12 Copynumber: 9.4 Consensus size: 11
1293103 CAAAAATTAA
1293113 AAAAAGTATTTT
1 AAAAA-TATTTT
1293125 AAAAATATTTT
1 AAAAATATTTT
1293136 --AAA-A--TT
1 AAAAATATTTT
**
1293142 AAAAA-AACTT
1 AAAAATATTTT
1293152 AAAAAGTATTTT
1 AAAAA-TATTTT
*
1293164 AAAAA-A-ATT
1 AAAAATATTTT
**
1293173 AAAAAT-TTAA
1 AAAAATATTTT
1293183 AAAAAGTATTTT
1 AAAAA-TATTTT
*
1293195 AAAAGTATTTT
1 AAAAATATTTT
1293206 AAAA
1 AAAA
1293210 TAAAAAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
6 2 0.03
8 5 0.08
9 10 0.15
10 13 0.20
11 17 0.26
12 19 0.29
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1293156 original size:39 final size:40
Alignment explanation
Indices: 1293086--1293209 Score: 126
Period size: 39 Copynumber: 3.0 Consensus size: 40
1293076 ACCAAAAATT
1293086 TATTTTGAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATT-AAAAAAGTATTTTAAAAA
*
1293130 TATTTTAAAATTAAAAAAACTT-AAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* * **
1293169 -AATTAAAAATTTAAAAAAAGTATTTTAAAAGTATTTTAAAA
1 TATTTTAAAA-TTAAAAAAA--ATTAAAAAAGTATTTTAAAA
1293210 TAAAAAAATA
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
38 7 0.10
39 26 0.37
41 8 0.11
42 18 0.25
43 6 0.08
44 6 0.08
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:1293161 original size:28 final size:28
Alignment explanation
Indices: 1293123--1293198 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 28
1293113 AAAAAGTATT
*
1293123 TTAAAAA-TATTTTAAAATTAA-AAAAAC
1 TTAAAAAGTATTTTAAAA-AAATAAAAAC
*
1293150 TTAAAAAGTATTTTAAAAAAATTAAAAAT
1 TTAAAAAGTATTTTAAAAAAA-TAAAAAC
1293179 TTAAAAAAAGTATTTTAAAA
1 TT--AAAAAGTATTTTAAAA
1293199 GTATTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 9 0.21
28 10 0.24
29 7 0.17
31 16 0.38
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (28 bp):
TTAAAAAGTATTTTAAAAAAATAAAAAC
Found at i:1293514 original size:21 final size:21
Alignment explanation
Indices: 1293478--1293520 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1293468 TTCGGGTGGA
* *
1293478 TTAGCTCTTATGAGCTTCTGT
1 TTAGCTCTTATAAGCTTATGT
*
1293499 TTAGCTCTTTTAAGCTTATGT
1 TTAGCTCTTATAAGCTTATGT
1293520 T
1 T
1293521 GGCATGTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (21 bp):
TTAGCTCTTATAAGCTTATGT
Found at i:1299751 original size:16 final size:16
Alignment explanation
Indices: 1299726--1299759 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1299716 GAGCTCTGTA
*
1299726 CCTAGCAGGCTTTATG
1 CCTAGCAGGCTTCATG
*
1299742 CCTAGTAGGCTTCATG
1 CCTAGCAGGCTTCATG
1299758 CC
1 CC
1299760 GGTGTACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (16 bp):
CCTAGCAGGCTTCATG
Found at i:1299848 original size:41 final size:41
Alignment explanation
Indices: 1299731--1299848 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 41
1299721 CTGTACCTAG
* *
1299731 CAGGCTTTATGCCTAGTAGGCTTCATGCCGGTGTACCATAT
1 CAGGCTTTATGCCTAGAAGGCTTCATGCCGGTGTATCATAT
* *
1299772 CAGGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTATCATAT
1 CAGGCTTTATGCCTAGAAGGCTTCATGCCGGTGTATCATAT
* * * * *
1299813 CTGGCTTTGTGCCTAGAAGGTTTTATACCGGTGTAT
1 CAGGCTTTATGCCTAGAAGGCTTCATGCCGGTGTAT
1299849 TTTAATAAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (41 bp):
CAGGCTTTATGCCTAGAAGGCTTCATGCCGGTGTATCATAT
Found at i:1303352 original size:16 final size:16
Alignment explanation
Indices: 1303312--1303352 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1303302 AGATCTCTAA
* *
1303312 CAAGCTTCCAATCGAT
1 CAAGCTTCTAATCAAT
1303328 CAAGCTTCTAATCAAT
1 CAAGCTTCTAATCAAT
1303344 CAAGCTTCT
1 CAAGCTTCT
1303353 GATAATCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (16 bp):
CAAGCTTCTAATCAAT
Found at i:1309106 original size:19 final size:18
Alignment explanation
Indices: 1309070--1309124 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1309060 AGGTCTTGGA
*
1309070 AAAATAATAAAACAAAAAT
1 AAAATAATAAAA-TAAAAT
*
1309089 GAAATAATAATAATAAAAT
1 AAAATAATAA-AATAAAAT
1309108 AAAATAA-AAGAATAAAA
1 AAAATAATAA-AATAAAA
1309125 GGTGGAGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 9 0.29
19 20 0.65
20 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAATAATAAAATAAAAT
Found at i:1309121 original size:13 final size:13
Alignment explanation
Indices: 1309070--1309124 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
1309060 AGGTCTTGGA
1309070 AAAATAATAAAA-
1 AAAATAATAAAAT
* *
1309082 CAAA-AATGAAAT
1 AAAATAATAAAAT
1309094 AATAATAATAAAAT
1 AA-AATAATAAAAT
1309108 AAAATAA-AAGAAT
1 AAAATAATAA-AAT
1309121 AAAA
1 AAAA
1309125 GGTGGAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 6 0.17
12 6 0.17
13 14 0.40
14 9 0.26
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:1311338 original size:18 final size:18
Alignment explanation
Indices: 1311311--1311350 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1311301 CAGGTGCATT
* *
1311311 TCCTAGCCCTTATGTGTA
1 TCCTAACCCTTATATGTA
1311329 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
1311347 TCCT
1 TCCT
1311351 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:1314614 original size:19 final size:19
Alignment explanation
Indices: 1314590--1314627 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1314580 ACTAAAGATC
*
1314590 GAGCATTAGCGGCGTTTTT
1 GAGCATTAGCGGCATTTTT
*
1314609 GAGCATTCGCGGCATTTTT
1 GAGCATTAGCGGCATTTTT
1314628 CAGAAAAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (19 bp):
GAGCATTAGCGGCATTTTT
Found at i:1314757 original size:41 final size:41
Alignment explanation
Indices: 1314681--1314960 Score: 282
Period size: 41 Copynumber: 6.9 Consensus size: 41
1314671 CTTACCTTTT
* ** **
1314681 GGGGCTTTAGCGGCGTTTTCAAAAAAGCGTTGCTAATGCTC
1 GGGGTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
*
1314722 GGGGATTTAGCGGCGTTTTTTCAAAAA-CGCCGCTAATGCTC
1 GGGGTTTTAGCGGCGTTTTTT-AAAAAGCGCCGCTAATGCTC
* * * * *
1314763 -GGGCTTTAGCGGCATTTTTGAAAAAGCGCAGCTAATACTC
1 GGGGTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
* * * *
1314803 GGTGTTTTAGTGTCGTTTTTTAAAAGGCGCCGCTAATGCTC
1 GGGGTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
* * * ***
1314844 GGTGTTTTAGTGGTGTTTTTT-AAAAGTCGCTTTTAACT-CTC
1 GGGGTTTTAGCGGCGTTTTTTAAAAAG-CGCCGCTAA-TGCTC
* *
1314885 GGGGTTTTAGCGAC-TTTTTTAAAAAGCGCCGCTAATACTC
1 GGGGTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
*
1314925 GGGGTTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAA
1 GGGGTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAA
1314961 AAACATTTTA
Statistics
Matches: 197, Mismatches: 34, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
39 6 0.03
40 61 0.31
41 124 0.63
42 6 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
GGGGTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
Found at i:1314820 original size:81 final size:79
Alignment explanation
Indices: 1314682--1314960 Score: 283
Period size: 81 Copynumber: 3.4 Consensus size: 79
1314672 TTACCTTTTG
* * * *
1314682 GGGCTTTAGCGGCGTTTTCAAAAAAGCGTTGCTAATGCTCGGGGATTTAGCGGCGTTTTTTCAAA
1 GGGCTTTAGCGGCGTTTTTAAAAAAGCGCTGCTAAT-CTCGGGGTTTTAGCGACGTTTTTT-AAA
1314747 AACGCCGCTAATGCTC
64 AACGCCGCTAATGCTC
* * * * * *
1314763 GGGCTTTAGCGGCATTTTTGAAAAAGCGCAGCTAATACTCGGTGTTTTAGTGTCGTTTTTTAAAA
1 GGGCTTTAGCGGCGTTTTTAAAAAAGCGCTGCTAAT-CTCGGGGTTTTAGCGACGTTTTTTAAAA
*
1314828 GGCGCCGCTAATGCTC
65 -ACGCCGCTAATGCTC
* * * * **
1314844 GGTGTTTTAGTGGTGTTTTT-TAAAAGTCGCTTTTAACTCTCGGGGTTTTAGCGAC-TTTTTTAA
1 GG-GCTTTAGCGGCGTTTTTAAAAAAG-CGCTGCTAA-TCTCGGGGTTTTAGCGACGTTTTTTAA
*
1314907 AAAGCGCCGCTAATACTC
63 AAA-CGCCGCTAATGCTC
* *
1314925 GGGGTTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAA
1 -GGGCTTTAGCGGCGTTTTTAAAAAAGCGCTGCTAA
1314961 AAACATTTTA
Statistics
Matches: 161, Mismatches: 30, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
80 4 0.02
81 116 0.72
82 40 0.25
83 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (79 bp):
GGGCTTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATCTCGGGGTTTTAGCGACGTTTTTTAAAAA
CGCCGCTAATGCTC
Found at i:1315371 original size:21 final size:21
Alignment explanation
Indices: 1315345--1315398 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1315335 TAGGAATTAT
*
1315345 GGTTTAAGGGTT-GAGATTTAA
1 GGTTTAAGGGTTAGAG-GTTAA
*
1315366 GGTTTAGGGGTTAGAGGTTAA
1 GGTTTAAGGGTTAGAGGTTAA
1315387 GAG-TTAAGGGTT
1 G-GTTTAAGGGTT
1315399 TAGGGTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.39, T:0.35
Consensus pattern (21 bp):
GGTTTAAGGGTTAGAGGTTAA
Found at i:1315384 original size:28 final size:29
Alignment explanation
Indices: 1315353--1315410 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1315343 ATGGTTTAAG
* *
1315353 GGTTGAGATTTAA-GGTTTAGGGGTTAGA
1 GGTTAAGAGTTAAGGGTTTAGGGGTTAGA
*
1315381 GGTTAAGAGTTAAGGGTTTAGGGTTTAGA
1 GGTTAAGAGTTAAGGGTTTAGGGGTTAGA
1315410 G
1 G
1315411 ATTTAGGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.26, C:0.00, G:0.40, T:0.34
Consensus pattern (29 bp):
GGTTAAGAGTTAAGGGTTTAGGGGTTAGA
Found at i:1315405 original size:21 final size:21
Alignment explanation
Indices: 1315348--1315410 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1315338 GAATTATGGT
* **
1315348 TTAAGGGTTGAGATTTAAG-G
1 TTAAGGGTTTAGGGTTAAGAG
* *
1315368 TTTAGGGGTTAGAGGTTAAGAG
1 TTAAGGGTTTAG-GGTTAAGAG
*
1315390 TTAAGGGTTTAGGGTTTAGAG
1 TTAAGGGTTTAGGGTTAAGAG
1315411 ATTTAGGAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 9 0.27
21 13 0.39
22 11 0.33
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (21 bp):
TTAAGGGTTTAGGGTTAAGAG
Found at i:1319245 original size:16 final size:17
Alignment explanation
Indices: 1319208--1319254 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
1319198 TTTGGTTCGC
1319208 TGTAATGGAATAGA-TA
1 TGTAATGGAATAGAGTA
* *
1319224 TATAATGAAATAGAGT-
1 TGTAATGGAATAGAGTA
1319240 TGTAATGGAATAGAG
1 TGTAATGGAATAGAG
1319255 GCGTAATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.30
Consensus pattern (17 bp):
TGTAATGGAATAGAGTA
Found at i:1319293 original size:45 final size:45
Alignment explanation
Indices: 1319243--1319336 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
1319233 ATAGAGTTGT
*
1319243 AATGGAATAGAGGC-GT-AATAGACATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAAATAG-CATTC-ATGTGTTTGGTTGAATGG
* *
1319288 AATGGAATAGAACTGTAAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAATAGCATTCATGTGTTTGGTTGAATGG
1319333 AATG
1 AATG
1319337 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
44 2 0.05
45 36 0.84
46 5 0.12
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (45 bp):
AATGGAATAGAACTGTAAATAGCATTCATGTGTTTGGTTGAATGG
Found at i:1321161 original size:49 final size:49
Alignment explanation
Indices: 1321089--1321192 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
1321079 GAAAAAAAAC
* * *
1321089 AAATTAAAATTAAGTTTAATATCATTAATCAAAATG-TGAACACTTCATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAA-GCTCAACACTTCATA
* *
1321138 AAATTAAAATTAAGTTCAATATCATGAATTAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTCATA
1321187 AAATTA
1 AAATTA
1321193 TAACACATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
48 1 0.02
49 48 0.98
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.34
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTCATA
Found at i:1324940 original size:12 final size:12
Alignment explanation
Indices: 1324920--1324949 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1324910 GCGATAAAGG
*
1324920 AAACGCTATATT
1 AAACTCTATATT
1324932 AAACTCTATATT
1 AAACTCTATATT
1324944 AAACTC
1 AAACTC
1324950 AGCAAGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (12 bp):
AAACTCTATATT
Found at i:1326635 original size:43 final size:43
Alignment explanation
Indices: 1326583--1326789 Score: 274
Period size: 43 Copynumber: 4.8 Consensus size: 43
1326573 GTTTGTGAAA
* * * *
1326583 AAGCGCCGCTAAAAGTCAT-TTTTTGTAGTGGCATTTGTGGTAG
1 AAGCGCCGCTAAAGGTCATGGTCTT-TAGTGGCGTTTGTGGTAG
*
1326626 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAG
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGTAG
*
1326669 AAGTGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGTAG
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGTAG
* ** *
1326712 AAGCGCCG-TTAAGGTCATGGTCTTTAGCAGTGTTTGTGGTAG
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGTAG
** *
1326754 AAGCGCCGCTAAAGGTCATAATCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTT
1326790 TTTCAAATAA
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
42 38 0.26
43 104 0.72
44 3 0.02
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGTAG
Found at i:1326737 original size:85 final size:85
Alignment explanation
Indices: 1326551--1326789 Score: 295
Period size: 85 Copynumber: 2.8 Consensus size: 85
1326541 AATATTTTTT
* * * * * * * *
1326551 TAAAAGTCAT-GTTTTTAGCCGCGTTTGT-GAAAAAGCGCCGCTAAAAGTCATTTTTTGTAGTGG
1 TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATATCTT-TAGTGG
*
1326614 CATTTGTGGTAGAAGCGCCGC
65 CGTTTGTGGTAGAAGCGCCGC
* * *
1326635 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAGAAGTGCCGCTAAAGGTCATGGTCTTTAGTGG
1 TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCAT-ATCTTTAGTGG
1326700 CGTTTGTGGTAGAAGCGCCG-
65 CGTTTGTGGTAGAAGCGCCGC
* * *
1326720 TTAAGGTCATGGTCTTTAGCAGTGTTTGTGGTAGAAGCGCCGCTAAAGGTCATAATCTTTAGCGG
1 TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCAT-ATCTTTAGTGG
1326785 CGTTT
65 CGTTT
1326790 TTTCAAATAA
Statistics
Matches: 135, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
84 9 0.07
85 79 0.59
86 44 0.33
87 3 0.02
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (85 bp):
TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATATCTTTAGTGGC
GTTTGTGGTAGAAGCGCCGC
Found at i:1327088 original size:4 final size:4
Alignment explanation
Indices: 1327079--1327106 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1327069 GAGGAAAATG
1327079 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1327107 TGAGCTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1329532 original size:871 final size:860
Alignment explanation
Indices: 1327781--1329610 Score: 2331
Period size: 871 Copynumber: 2.1 Consensus size: 860
1327771 TTAAGGCCGG
* * * *
1327781 TTTAGATTCCCTTGGTTTTCTGAAAATGTAGATGAT--ATTCATTGTATGTATATACATTCTAGA
1 TTTAGATTCTCTTGGTTTTCT-AAAATGTAGATGATGGATTCAGTATATGTATATACATTCTAGC
* *
1327844 TAAGCTTGGGGCAACACAGAA-GAAATAAAAGGCTTTCAGGCTTGCTAAGTTAATATCAAAGTCA
65 TAAGCTTGGGACAACACA-AAGGAAATAAAAGGCTTTCAGGCTTGCTAAGTTAATAGCAAAGTCA
* * *
1327908 TTACTAACCTCTTAATGTACTTAGTCAATTTATTTGAGCACATACCCTTCAAGGGTATTGCTCAC
129 TTACTAACCTCTTAAGGTACCTAGTCAATTTATTTGAGCACACACCCTTCAAGGGTATTGCTCAC
** * *
1327973 TAAGTCAAAAGAAGAGTCGCTTTTAGCCTCTTAAGGCACTTAGCAACTTATTTAAAGCAAACACC
194 TAAGTCAAAAGAAGAACCGCTTCTAACCTCTTAAGGCACTTAGCAACTTATTTAAAGCAAACACC
*
1328038 TATTGCAAATATCCTCACTAAGTCAATAGCAAAAAATAAGGCTAACCTCTGAAGGCATTTAGCCA
259 TATTGCAAATATCCTCACTAAGTCAATAGCAAAAAATAAGGCTAACCTCTGAAGGCACTTAGCCA
* *
1328103 AATTTACAAGTTATAAAACAGACACCCATCATAGATAATGCTTACTAAGTTAATAATAGAAACCA
324 AATTTACAAGTTATAAAACAAACACCCATCACAGATAATGCTTACTAAGTTAATAATAGAAACCA
* *
1328168 TTTCTAGCCTATTAAAGAATGTGCATAGTTTTTTTATTATTATAAAAAGACCTAACATACAACAC
389 TTTCTAGCCTATTAAAGAATGTGCATA--TATCTTATTATTATAAAAAGACCTAACATACAACAC
* **
1328233 AAAGGCTTCACCTCTACTTTTATCTCAGATAAGGCCACGTTATAAACTATTCCTCAACTGAGAGC
452 AAAGGCTTCACCCCTACTTTTATCTCAGATAAAACCACGTTATAAACTATTCCTCAACTGAGAGC
* * *
1328298 AATTATTATGCATATACAAATATTATCTAAACTCATCAAAGGCCTACGTATTTCATCCCCACGCT
517 AATTATTATGCATATACAAATATTATCCAAACTCATCAAAGGCCTACCTATTACATCCCCACGCT
1328363 ATTAGGCTATTATTACAAAGGGCCTACACAAGAGGGCAAATCACCTATTTTATTTTCTAAAAGGA
582 ATTAGGCTATTATTACAAAGGGCCTACACAAGAGGGCAAATCACCTATTTTATTTTCTAAAAGGA
* * * *
1328428 GGGGCTTGAGACAAAAAGGGGAGATTCTTCATTTTAAAAAGATCCACTTCCATGGTCACCATGCA
647 GGGGCTTGAGACAAAAAGGAGAGATTCTTCACTTTAAAAAGACCCACTTCCATGGTCACCACGCA
* *
1328493 CTTTCCGCATTGAACTAAATAGGGTGAATCGCCCTAAATTCCAAACTCTAAATCCTAAATCATCA
712 CTTTCCGCATTGAACTAAATAGGGTGAACCACCCTAAATTCCAAACTCTAAATCCTAAATCATCA
* * * *
1328558 ACTGTCATTTTGTACTTTAACACATCCACATTATAGATATGTCATAGTCTAATATGGATTACAAA
777 ACTATCACTTTGTACATTAACACATCCACATTATAAATATGTCATAGTCTAATATGGATTACAAA
* **
1328623 ATGATTTAATTAAATTTGA
842 ATGAATTAATTAAATGCGA
1328642 TTTAGATTCTCTTGGTTTTCTAAAATTGTAGATGATGGAATTC-GATATATGTATATACATTCTA
1 TTTAGATTCTCTTGGTTTTCTAAAA-TGTAGATGATGG-ATTCAG-TATATGTATATACATTCTA
* * *
1328706 GCTAAGCTTGGGACAACACAAAGGAAATAAAAGGCTTTCAGGCTTTCTAAGTTAATAGCATAGTT
63 GCTAAGCTTGGGACAACACAAAGGAAATAAAAGGCTTTCAGGCTTGCTAAGTTAATAGCAAAGTC
* * * * * * * *
1328771 GTTGCTAGCCTCTTTAAGGTACCTGGTCAATTTATTTGAGCACACACCTTTTAATGGTATTGCTT
128 ATTACTAACCTC-TTAAGGTACCTAGTCAATTTATTTGAGCACACACCCTTCAAGGGTATTGCTC
1328836 ACTAAGTCAATAA-AAGAACCGCTTCTAACCTCTTAAGGCACTTAGCAACTTATTTAAAGCAAAC
192 ACTAAGTCAA-AAGAAGAACCGCTTCTAACCTCTTAAGGCACTTAGCAACTTATTTAAAGCAAAC
* * ** * * ** * * *
1328900 ACCTCTTGCAAATATGCTTGCTAAGTCAATAG-TAGAAATACTGTTAACCTCTTAAGGCACTTAT
256 ACCTATTGCAAATATCCTCACTAAGTCAATAGCAAAAAATAAGGCTAACCTCTGAAGGCACTTAG
* * *
1328964 CCAAAATTTACAAGTTATAAAACAAACACCCCTCACAGATAATGCTTACTAAGTTAATAGTATAA
321 CC-AAATTTACAAGTTATAAAACAAACACCCATCACAGATAATGCTTACTAAGTTAATAATAGAA
* * * * * * *
1329029 ATCATTTCTAGCCTCTTAAGGAATGTGCATA-ATCTT-TT-TTATAAAAAGGCTTAGCGTACAAC
385 ACCATTTCTAGCCTATTAAAGAATGTGCATATATCTTATTATTATAAAAAGACCTAACATACAAC
* * * * * *
1329091 ACAAAGGTTTCTCCCCTACTTTTATCTCGGATAAAACCACTTTATAACCTATATTCCTCAAGTGA
450 ACAAAGGCTTCACCCCTACTTTTATCTCAGATAAAACCACGTTATAAAC--TATTCCTCAACTGA
* * ** *
1329156 GAGCAATTGTTATGCATATACAAATATTA-CCAAATCTCATTAGGGGGTCTACCTATTACATCCC
513 GAGCAATTATTATGCATATACAAATATTATCCAAA-CTCATCA-AAGGCCTACCTATTACATCCC
* * * *
1329220 CATGCTATTAGGCTATTATTACAAAGGGCCTACATAAGAGGGCAAATCTCCTCCTCTCTTTTTTT
576 CACGCTATTAGGCTATTATTACAAAGGGCCTACACAAGAGGGCAAA-----T-CAC-C-TATTTT
* * * *
1329285 TTTTTCTAAAAGGAGGGGCTTGAGATATAAAA-GAGAGATTTTTCGCTTTAAAAAGACCCACTTC
633 ATTTTCTAAAAGGAGGGGCTTGAGACA-AAAAGGAGAGATTCTTCACTTTAAAAAGACCCACTTC
* * * * * * * * **
1329349 CATGGTCATCACGCACTTTTCGCCTTGTATTAAATGGGGTGAACCATCTTAAATTTTAAACTCTA
697 CATGGTCACCACGCACTTTCCGCATTGAACTAAATAGGGTGAACCACCCTAAATTCCAAACTCTA
* *
1329414 AATTCTAAATCATCAATTATCACTTTGTACATTAACACATCCACATTATAAATATGTCATAGTCT
762 AATCCTAAATCATCAACTATCACTTTGTACATTAACACATCCACATTATAAATATGTCATAGTCT
1329479 AATA-GGAATTACAAAAT-AATTAAGTTAAA-GCGAA
827 AATATGG-ATTACAAAATGAATTAA-TTAAATGCG-A
* * * *
1329513 TTTAGATTCTTTTGGTTTTCTGAAACTGTAGATGATGGCATTCAGTACATGTGTATAGCATTCTA
1 TTTAGATTCTCTTGGTTTTCT-AAAATGTAGATGATGG-ATTCAGTATATGTATATA-CATTCTA
* *
1329578 GCTAAGCTTGGGACAAAAC-AGGAGAAATAAAAG
63 GCTAAGCTTGGGACAACACAAAG-GAAATAAAAG
1329611 AAAGAAAATG
Statistics
Matches: 833, Mismatches: 107, Indels: 47
0.84 0.11 0.05
Matches are distributed among these distances:
860 65 0.08
861 36 0.04
862 50 0.06
863 62 0.07
864 113 0.14
865 214 0.26
866 2 0.00
868 1 0.00
869 2 0.00
870 9 0.01
871 236 0.28
872 43 0.05
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (860 bp):
TTTAGATTCTCTTGGTTTTCTAAAATGTAGATGATGGATTCAGTATATGTATATACATTCTAGCT
AAGCTTGGGACAACACAAAGGAAATAAAAGGCTTTCAGGCTTGCTAAGTTAATAGCAAAGTCATT
ACTAACCTCTTAAGGTACCTAGTCAATTTATTTGAGCACACACCCTTCAAGGGTATTGCTCACTA
AGTCAAAAGAAGAACCGCTTCTAACCTCTTAAGGCACTTAGCAACTTATTTAAAGCAAACACCTA
TTGCAAATATCCTCACTAAGTCAATAGCAAAAAATAAGGCTAACCTCTGAAGGCACTTAGCCAAA
TTTACAAGTTATAAAACAAACACCCATCACAGATAATGCTTACTAAGTTAATAATAGAAACCATT
TCTAGCCTATTAAAGAATGTGCATATATCTTATTATTATAAAAAGACCTAACATACAACACAAAG
GCTTCACCCCTACTTTTATCTCAGATAAAACCACGTTATAAACTATTCCTCAACTGAGAGCAATT
ATTATGCATATACAAATATTATCCAAACTCATCAAAGGCCTACCTATTACATCCCCACGCTATTA
GGCTATTATTACAAAGGGCCTACACAAGAGGGCAAATCACCTATTTTATTTTCTAAAAGGAGGGG
CTTGAGACAAAAAGGAGAGATTCTTCACTTTAAAAAGACCCACTTCCATGGTCACCACGCACTTT
CCGCATTGAACTAAATAGGGTGAACCACCCTAAATTCCAAACTCTAAATCCTAAATCATCAACTA
TCACTTTGTACATTAACACATCCACATTATAAATATGTCATAGTCTAATATGGATTACAAAATGA
ATTAATTAAATGCGA
Found at i:1331061 original size:13 final size:13
Alignment explanation
Indices: 1331043--1331089 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1331033 GTTGTCGAAC
*
1331043 ATAATATACTAAA
1 ATAATATACAAAA
1331056 ATAATATA-AAATA
1 ATAATATACAAA-A
* *
1331069 ATAAAATACGAAA
1 ATAATATACAAAA
1331082 ATAATATA
1 ATAATATA
1331090 TTTTTATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 24 0.86
14 2 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (13 bp):
ATAATATACAAAA
Found at i:1331247 original size:8 final size:8
Alignment explanation
Indices: 1331216--1331247 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1331206 ACTAAAATAA
*
1331216 TATAAAAA
1 TATAAAAT
1331224 TATAAAAT
1 TATAAAAT
1331232 TATAAAAT
1 TATAAAAT
1331240 TATAAAAT
1 TATAAAAT
1331248 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TATAAAAT
Found at i:1331268 original size:164 final size:157
Alignment explanation
Indices: 1331040--1331472 Score: 663
Period size: 164 Copynumber: 2.7 Consensus size: 157
1331030 AAAGTTGTCG
* * *
1331040 AACATAATATACTAAAATAATATAAAATAATAAAA-TACGAAAATAATATATTTTTATTGAAAGT
1 AACATAATGTACTAAAATAATATAAAATTATAAAATTA-TAAAATAATATATTTTTATTGAAAGT
* * * *
1331104 AATAAAATGCGGGAAAAAGATACGAACAAAGGGTCGAAATAAGGGTTAATTTTTGAAATTTATTT
65 AATAAAATTCGGGAAAAAAATACAAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTT
*
1331169 -AAAAACACACTAAATTAATACATTTCA
130 AAAAAACACACTAAATGAATACATTTCA
1331196 AACATAATGTACTAAAATAATATAAAAATATAAAATTATAAAATTATAAAATAATATATTTTTAT
1 AACATAATGTACT---A-AA-AT---AATATAAAATTATAAAATTATAAAATAATATATTTTTAT
*
1331261 TGAAAGTAATAGAATTCGGGAAAAAAATACAAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAA
58 TGAAAGTAATAAAATTCGGGAAAAAAATACAAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAA
*
1331326 TTTATTTAAAAAACACACTAAATGAGTACATTTCA
123 TTTATTTAAAAAACACACTAAATGAATACATTTCA
1331361 AACATAATGTACTAAAATAATATAAAATTATAAAATTATAAAATAATATATTTTTATTGAAAGTA
1 AACATAATGTACTAAAATAATATAAAATTATAAAATTATAAAATAATATATTTTTATTGAAAGTA
*
1331426 ATAAAATTCGGGAAGAAAAATACAAACAAATGGCCGAAATAAGGGTT
66 ATAAAATTCGGGAA-AAAAATACAAACAAAGGGCCGAAATAAGGGTT
1331473 TTTTACTAAA
Statistics
Matches: 254, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
156 12 0.05
157 60 0.24
158 31 0.12
159 1 0.00
160 4 0.02
161 4 0.02
162 1 0.00
164 101 0.40
165 40 0.16
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (157 bp):
AACATAATGTACTAAAATAATATAAAATTATAAAATTATAAAATAATATATTTTTATTGAAAGTA
ATAAAATTCGGGAAAAAAATACAAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTA
AAAAACACACTAAATGAATACATTTCA
Found at i:1336689 original size:40 final size:42
Alignment explanation
Indices: 1336645--1336742 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 42
1336635 CACTAATCCT
* *
1336645 AATAACTAAC-ACAATAACAATAATAA-TA-GTTTTTACTCAA
1 AATAA-TAACTACAATAACAATAATAATTAGGGTTTTACTAAA
*
1336685 AATAAT-ACTA-ACTAACAATAATAATTAGGGTTTTACTAAA
1 AATAATAACTACAATAACAATAATAATTAGGGTTTTACTAAA
1336725 AATAATAACTAACAATAA
1 AATAATAACT-ACAATAA
1336743 TATAATGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
38 15 0.31
39 4 0.08
40 21 0.44
41 3 0.06
42 1 0.02
43 4 0.08
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (42 bp):
AATAATAACTACAATAACAATAATAATTAGGGTTTTACTAAA
Found at i:1348314 original size:16 final size:16
Alignment explanation
Indices: 1348293--1348333 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1348283 ATAAAAAAAT
1348293 ATAATTTTAA-TATTTA
1 ATAATTTTAAGT-TTTA
*
1348309 ATAA-TTTAAGTTTTT
1 ATAATTTTAAGTTTTA
1348324 ATAATTTTAA
1 ATAATTTTAA
1348334 AAATTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATAATTTTAAGTTTTA
Found at i:1348366 original size:29 final size:29
Alignment explanation
Indices: 1348292--1348393 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 29
1348282 AATAAAAAAA
* * *
1348292 TATAATTTTAATATTTAATAATTTAAGTTTT
1 TATAATTTTAAAAATTAA-AA-TTAAATTTT
1348323 TATAATTTTAAAAATT-AAATTAAATTTT
1 TATAATTTTAAAAATTAAAATTAAATTTT
1348351 TATAATTTTAAGAAATTAAAATATAAATTTAT
1 TATAATTTTAA-AAATTAAAAT-TAAATTT-T
1348383 TATATATTTTA
1 TATA-ATTTTA
1348394 TAGATTATAG
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
28 19 0.30
29 7 0.11
30 5 0.08
31 21 0.33
32 5 0.08
33 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TATAATTTTAAAAATTAAAATTAAATTTT
Found at i:1348393 original size:41 final size:41
Alignment explanation
Indices: 1348348--1348476 Score: 111
Period size: 41 Copynumber: 3.2 Consensus size: 41
1348338 TAAATTAAAT
1348348 TTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATA
1 TTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATA
* * ****** ** * *
1348389 TTTTATAGATTAT-AGACA-TGCGCGCTGGATTAAATTAAAT-
1 TTTTATA-ATTTTAAGAAATTAAAATATAAATT-TATTATATA
1348429 TTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATA
1 TTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATA
1348470 TTTTATA
1 TTTTATA
1348477 GATTATAGCC
Statistics
Matches: 59, Mismatches: 24, Indels: 10
0.63 0.26 0.11
Matches are distributed among these distances:
39 4 0.07
40 22 0.37
41 29 0.49
42 4 0.07
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (41 bp):
TTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATA
Found at i:1348421 original size:81 final size:81
Alignment explanation
Indices: 1348336--1348484 Score: 298
Period size: 81 Copynumber: 1.8 Consensus size: 81
1348326 AATTTTAAAA
1348336 ATTAAATTAAATTTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATATTTTATAGATTA
1 ATTAAATTAAATTTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATATTTTATAGATTA
1348401 TAGACATGCGCGCTGG
66 TAGACATGCGCGCTGG
1348417 ATTAAATTAAATTTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATATTTTATAGATTA
1 ATTAAATTAAATTTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATATTTTATAGATTA
1348482 TAG
66 TAG
1348485 CCCTGCGAGC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (81 bp):
ATTAAATTAAATTTTTATAATTTTAAGAAATTAAAATATAAATTTATTATATATTTTATAGATTA
TAGACATGCGCGCTGG
Found at i:1348892 original size:5 final size:5
Alignment explanation
Indices: 1348882--1348908 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1348872 TATTATTACT
1348882 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1348909 CATTACACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1349533 original size:23 final size:24
Alignment explanation
Indices: 1349493--1349548 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
1349483 CTCTTCAGGA
* **
1349493 TTAGGGTTTTTTTATTTTTTAGGG
1 TTAGGGTTTTTATATTTTTTAAAG
1349517 TTAGGGTTTTTAT-TTTTTTAAAG
1 TTAGGGTTTTTATATTTTTTAAAG
1349540 TTAGGGTTT
1 TTAGGGTTT
1349549 AGGGTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.16, C:0.00, G:0.23, T:0.61
Consensus pattern (24 bp):
TTAGGGTTTTTATATTTTTTAAAG
Found at i:1352650 original size:937 final size:938
Alignment explanation
Indices: 1350824--1352700 Score: 3713
Period size: 937 Copynumber: 2.0 Consensus size: 938
1350814 TTGCAACCCT
1350824 TAAGAAGCTACAGGGGACACACGGCCGTGTCACTTGGCCGTGTGTCACACACGCCTGAGACACAC
1 TAAGAAGCTACAGGGGACACACGGCCGTGTCACTTGGCCGTGTGTCACACACGCCTGAGACACAC
1350889 GCCCATGTCTCTGCCCGTGTGAACGAATATAGGCCATTTTACAAGCCATATTTCTCACCCAATTT
66 GCCCATGTCTCTGCCCGTGTGAACGAATATAGGCCATTTTACAAGCCATATTTCTCACCCAATTT
1350954 TGGCATCAACCTATACCTAAAATGCACATATATACAAGCTATAATAAGGCACCAAAACTATGCAT
131 TGGCATCAACCTATACCTAAAATGCACATATATACAAGCTATAATAAGGCACCAAAACTATGCAT
1351019 TTTCAAGTCTTATTCAAATGGTACAATCACATACAACCAATATGCCCTTAGGCACCTCAAATGAC
196 TTTCAAGTCTTATTCAAATGGTACAATCACATACAACCAATATGCCCTTAGGCACCTCAAATGAC
1351084 AAATATAAAGATGTGTAACCATATGCTCGATATAACCAAATGATTAACTAACTTATATGTATAAT
261 AAATATAAAGATGTGTAACCATATGCTCGATATAACCAAATGATTAACTAACTTATATGTATAAT
1351149 TGCATCAACACACAACATATAAATCACTTACCAAAACATACCATTTGGTACCAATTGTACTACAT
326 TGCATCAACACACAACATATAAATCACTTACCAAAACATACCATTTGGTACCAATTGTACTACAT
1351214 AATCATTAGCATTAAAATACATATATTCTTACCATAGCAAAACACCAATTCACAACAAGTTATAT
391 AATCATTAGCATTAAAATACATATATTCTTACCATAGCAAAACACCAATTCACAACAAGTTATAT
1351279 GTCATATCTAATATGCACATTCAACTACTTTTCTATCTACCATCATTCAACTATAACAAGTCATA
456 GTCATATCTAATATGCACATTCAACTACTTTTCTATCTACCATCATTCAACTATAACAAGTCATA
*
1351344 TATCAACCATTACAAGGCTACTTATATACACCTTATAATATATACCATTTTACCAACACAAGGCC
521 TATCAACCATTACAAGGCTACTTATATACACCTAATAATATATACCATTTTACCAACACAAGGCC
1351409 AAAATGCAAACTAACTAAATGGTCATTTCCACAACCAAAACACATAGGCTAATATTAGCCAAAAT
586 AAAATGCAAACTAACTAAATGGTCATTTCCACAACCAAAACACATAGGCTAATATTAGCCAAAAT
1351474 AACCTATACATGCCATTATAACCTTAACCAAGACATTAAAATCTACCAATATAATCTCTGGATAG
651 AACCTATACATGCCATTATAACCTTAACCAAGACATTAAAATCTACCAATATAATCTCTGGATAG
1351539 TGTGATAGGTCTCCGACAAGCTTTCAACCCGACTGAGCTTCTAATAATCTGAAAAGTAAGGAAAA
716 TGTGATAGGTCTCCGACAAGCTTTCAACCCGACTGAGCTTCTAATAATCTGAAAAGTAAGGAAAA
1351604 ACAACTCCGTAAGCAATGAATGCTTAGTAAGCTTGTATAAACTTTAATCATATCAATCCATTTCA
781 ACAACTCCGTAAGCAATGAATGCTTAGTAAGCTTGTATAAACTTTAATCATATCAATCCATTTCA
1351669 AATATGAAATTTACATATATGAAGAATAATCCCTATACTGACACTGCAAGATTTATGAATACATA
846 AATATGAAATTTACATATATGAAGAATAATCCCTATACTGACACTGCAAGATTTATGAATACATA
1351734 TTCAACAACTCACAACATCACATATACC
911 TTCAACAACTCACAACATCACATATACC
1351762 TAAGAAGCTACA-GGGACACACGGCCGTGTCACTTGGCCGTGTGTCACACACGCCTGAGACACAC
1 TAAGAAGCTACAGGGGACACACGGCCGTGTCACTTGGCCGTGTGTCACACACGCCTGAGACACAC
1351826 GCCCATGTCTCTGCCCGTGTGAACGAATATAGGCCATTTTACAAGCCATATTTCTCACCCAATTT
66 GCCCATGTCTCTGCCCGTGTGAACGAATATAGGCCATTTTACAAGCCATATTTCTCACCCAATTT
1351891 TGGCATCAACCTATACCTAAAATGCACATATATACAAGCTATAATAAGGCACCAAAACTATGCAT
131 TGGCATCAACCTATACCTAAAATGCACATATATACAAGCTATAATAAGGCACCAAAACTATGCAT
1351956 TTTCAAGTCTTATTCAAATGGTACAATCACATACAACCAATATGCCCTTAGGCACCTCAAATGAC
196 TTTCAAGTCTTATTCAAATGGTACAATCACATACAACCAATATGCCCTTAGGCACCTCAAATGAC
1352021 AAATATAAAGATGTGTAACCATATGCTCGATATAACCAAATGATTAACTAACTTATATGTATAAT
261 AAATATAAAGATGTGTAACCATATGCTCGATATAACCAAATGATTAACTAACTTATATGTATAAT
1352086 TGCATCAACACACAACATATAAATCACTTACCAAAACATACCATTTGGTACCAATTGTACTACAT
326 TGCATCAACACACAACATATAAATCACTTACCAAAACATACCATTTGGTACCAATTGTACTACAT
1352151 AATCATTAGCATTAAAATACATATATTCTTACCATAGCAAAACACCAATTCACAACAAGTTATAT
391 AATCATTAGCATTAAAATACATATATTCTTACCATAGCAAAACACCAATTCACAACAAGTTATAT
1352216 GTCATATCTAATATGCACATTCAACTACTTTTCTATCTACCATCATTCAACTATAACAAGTCATA
456 GTCATATCTAATATGCACATTCAACTACTTTTCTATCTACCATCATTCAACTATAACAAGTCATA
*
1352281 TATCAACCATTACAAGGCTACTTATATACACCTCAAT-ATATATATCATTTTACCAACACAAGGC
521 TATCAACCATTACAAGGCTACTTATATACACCT-AATAATATATACCATTTTACCAACACAAGGC
1352345 CAAAATGCAAACTAACTAAATGGTCATTTCCACAACCAAAACACATAGGCTAATATTAGCCAAAA
585 CAAAATGCAAACTAACTAAATGGTCATTTCCACAACCAAAACACATAGGCTAATATTAGCCAAAA
1352410 TAACCTATACATGCCATTATAACCTTAACCAAGACATTAAAATCTACCAATATAATCTCTGGATA
650 TAACCTATACATGCCATTATAACCTTAACCAAGACATTAAAATCTACCAATATAATCTCTGGATA
1352475 GTGTGATAGGTCTCCGACAAGCTTTCAACCCGACTGAGCTTCTAATAATCTGAAAAGTAAGGAAA
715 GTGTGATAGGTCTCCGACAAGCTTTCAACCCGACTGAGCTTCTAATAATCTGAAAAGTAAGGAAA
1352540 AACAACTCCGTAAGCAATGAATGCTTAGTAAGCTTGTATAAACTTTAATCATATCAATCCATTTC
780 AACAACTCCGTAAGCAATGAATGCTTAGTAAGCTTGTATAAACTTTAATCATATCAATCCATTTC
1352605 AAATATGAAATTTACATATATGAAGAATAATCCCTATACTGACACTGCAAGATTTATGAATACAT
845 AAATATGAAATTTACATATATGAAGAATAATCCCTATACTGACACTGCAAGATTTATGAATACAT
1352670 ATTCAACAACTCACAACATCACATATACC
910 ATTCAACAACTCACAACATCACATATACC
1352699 TA
1 TA
1352701 TTATCCCCAA
Statistics
Matches: 936, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
937 922 0.99
938 14 0.01
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (938 bp):
TAAGAAGCTACAGGGGACACACGGCCGTGTCACTTGGCCGTGTGTCACACACGCCTGAGACACAC
GCCCATGTCTCTGCCCGTGTGAACGAATATAGGCCATTTTACAAGCCATATTTCTCACCCAATTT
TGGCATCAACCTATACCTAAAATGCACATATATACAAGCTATAATAAGGCACCAAAACTATGCAT
TTTCAAGTCTTATTCAAATGGTACAATCACATACAACCAATATGCCCTTAGGCACCTCAAATGAC
AAATATAAAGATGTGTAACCATATGCTCGATATAACCAAATGATTAACTAACTTATATGTATAAT
TGCATCAACACACAACATATAAATCACTTACCAAAACATACCATTTGGTACCAATTGTACTACAT
AATCATTAGCATTAAAATACATATATTCTTACCATAGCAAAACACCAATTCACAACAAGTTATAT
GTCATATCTAATATGCACATTCAACTACTTTTCTATCTACCATCATTCAACTATAACAAGTCATA
TATCAACCATTACAAGGCTACTTATATACACCTAATAATATATACCATTTTACCAACACAAGGCC
AAAATGCAAACTAACTAAATGGTCATTTCCACAACCAAAACACATAGGCTAATATTAGCCAAAAT
AACCTATACATGCCATTATAACCTTAACCAAGACATTAAAATCTACCAATATAATCTCTGGATAG
TGTGATAGGTCTCCGACAAGCTTTCAACCCGACTGAGCTTCTAATAATCTGAAAAGTAAGGAAAA
ACAACTCCGTAAGCAATGAATGCTTAGTAAGCTTGTATAAACTTTAATCATATCAATCCATTTCA
AATATGAAATTTACATATATGAAGAATAATCCCTATACTGACACTGCAAGATTTATGAATACATA
TTCAACAACTCACAACATCACATATACC
Found at i:1359096 original size:42 final size:43
Alignment explanation
Indices: 1359031--1359295 Score: 304
Period size: 43 Copynumber: 6.2 Consensus size: 43
1359021 TAGAAATAAG
* *
1359031 CGCCGCTATAGAT-ATGACTTTTAGCGGCGC-TTTTCGACAAA
1 CGCCGCTATAGATCGTGACTTTTAGCGGCGCTTTTTCCACAAA
* * *
1359072 CGCCGCTATAGGTCATGACTTTTAGCGGAGCTTTTTCCACAAA
1 CGCCGCTATAGATCGTGACTTTTAGCGGCGCTTTTTCCACAAA
*
1359115 CGCTGCTATAGATCGTGACTTTTAGCGGCGCTTTTTCCACAAA
1 CGCCGCTATAGATCGTGACTTTTAGCGGCGCTTTTTCCACAAA
* *
1359158 CGCCGCTATAGATCGCGACTTTTAGCGGCGCTTTTTCTACAAA
1 CGCCGCTATAGATCGTGACTTTTAGCGGCGCTTTTTCCACAAA
* * * *
1359201 CGCCGTTATAGATCGTTAC-TTTAGCGGCGC-ATCTCACACAAA
1 CGCCGCTATAGATCGTGACTTTTAGCGGCGCTTTTTC-CACAAA
* * * * * * *
1359243 TGCCGCTATTGTTTGTTGACTTTTAGTGGCGCTTTTTTCTATAAA
1 CGCCGCTATAGATCG-TGACTTTTAGCGGCGC-TTTTTCCACAAA
1359288 CGCCGCTA
1 CGCCGCTA
1359296 AAGAACAAAA
Statistics
Matches: 189, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
41 15 0.08
42 42 0.22
43 108 0.57
44 10 0.05
45 11 0.06
46 3 0.02
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (43 bp):
CGCCGCTATAGATCGTGACTTTTAGCGGCGCTTTTTCCACAAA
Found at i:1359684 original size:21 final size:21
Alignment explanation
Indices: 1359660--1359711 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1359650 CTTCGTCACA
*
1359660 GCCTCTGCTTCTCTTGCTGCT
1 GCCTCTGCTTCTCTCGCTGCT
1359681 GCCTCTGCTTCTCTCGCTGCT
1 GCCTCTGCTTCTCTCGCTGCT
*
1359702 GCATCTGCTT
1 GCCTCTGCTT
1359712 TAAGTTGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.38, G:0.19, T:0.40
Consensus pattern (21 bp):
GCCTCTGCTTCTCTCGCTGCT
Found at i:1362559 original size:13 final size:12
Alignment explanation
Indices: 1362535--1362579 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
1362525 TCTCGCAAAA
*
1362535 CAGAACTTCATT
1 CAGAAATTCATT
1362547 CAGAAAATTCATT
1 CAG-AAATTCATT
1362560 CAGAAATTCATT
1 CAGAAATTCATT
*
1362572 CAGCAATT
1 CAGAAATT
1362580 TGTATGTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (12 bp):
CAGAAATTCATT
Found at i:1362566 original size:12 final size:13
Alignment explanation
Indices: 1362485--1362574 Score: 85
Period size: 13 Copynumber: 6.8 Consensus size: 13
1362475 CAATTAGTAT
*
1362485 ATTCATTAAGAAA
1 ATTCATTCAGAAA
*
1362498 ATTCATTTAGAAA
1 ATTCATTCAGAAA
1362511 ATTCATTCAGAAA
1 ATTCATTCAGAAA
**
1362524 ATCTCGCAAAACAG-AA
1 AT-T--C-ATTCAGAAA
*
1362540 CTTCATTCAGAAA
1 ATTCATTCAGAAA
1362553 ATTCATTCAG-AA
1 ATTCATTCAGAAA
1362565 ATTCATTCAG
1 ATTCATTCAG
1362575 CAATTTGTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
12 16 0.25
13 38 0.59
14 1 0.02
15 1 0.02
16 4 0.06
17 4 0.06
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (13 bp):
ATTCATTCAGAAA
Found at i:1362832 original size:18 final size:18
Alignment explanation
Indices: 1362809--1362843 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1362799 TTTGCCCTTA
* *
1362809 GTAATCGGCAGAGGCAAC
1 GTAATCGACAAAGGCAAC
1362827 GTAATCGACAAAGGCAA
1 GTAATCGACAAAGGCAA
1362844 ACCCTAGAAA
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:0.40, C:0.20, G:0.29, T:0.11
Consensus pattern (18 bp):
GTAATCGACAAAGGCAAC
Found at i:1363154 original size:14 final size:13
Alignment explanation
Indices: 1363123--1363156 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1363113 TCTCCTCTCC
1363123 CTTTTTTTCTTTG
1 CTTTTTTTCTTTG
*
1363136 ATTTTTTTCTTTGG
1 CTTTTTTTCTTT-G
1363150 CTTTTTT
1 CTTTTTT
1363157 CCCTTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.76
Consensus pattern (13 bp):
CTTTTTTTCTTTG
Found at i:1366171 original size:41 final size:41
Alignment explanation
Indices: 1366127--1366478 Score: 254
Period size: 41 Copynumber: 8.6 Consensus size: 41
1366117 ATGTTTTTGT
* ** *
1366127 GGCGCTTTATAAAAAACGCCACTAAAAACCACAGCATTAGT
1 GGCGCTTTATCAAAAACGCCACTAAAAACCTGAGCATTAGC
** * *
1366168 GGCGC-AAACTCAAAAACACCACTAAAACCCCT-AGCATTAG-
1 GGCGCTTTA-TCAAAAACGCCACTAAAA-ACCTGAGCATTAGC
* * * * **
1366208 GGCGGTTTCTCAAAAACGCCGCTAAAAATCTGAATATTAGC
1 GGCGCTTTATCAAAAACGCCACTAAAAACCTGAGCATTAGC
* * * *
1366249 GGCGCTTTTTTAAAAACACCACTAAAACCCTGAGCATTAGC
1 GGCGCTTTATCAAAAACGCCACTAAAAACCTGAGCATTAGC
* *
1366290 GGCGCTTCA-CAAAAAGCGCCGCT-AAAACCTGAGCATTAGC
1 GGCGCTTTATCAAAAA-CGCCACTAAAAACCTGAGCATTAGC
* * *
1366330 GGTGCTTTATCAAAAACGCCGCTAAAAACCTGAGCATTAGT
1 GGCGCTTTATCAAAAACGCCACTAAAAACCTGAGCATTAGC
* * * * *
1366371 GACG--TTACGTCAAAAACGACACTAAAACCCTGAACATTAGA
1 GGCGCTTTA--TCAAAAACGCCACTAAAAACCTGAGCATTAGC
* * * * * * *
1366412 AGCGCTTTTTTAAAAACGCCGCTGAAAACCCGAGCACTAGC
1 GGCGCTTTATCAAAAACGCCACTAAAAACCTGAGCATTAGC
*
1366453 AGCGC--TACTCCAAAAACGCCACTAAA
1 GGCGCTTTA-T-CAAAAACGCCACTAAA
1366479 TCCCCCGAAA
Statistics
Matches: 240, Mismatches: 57, Indels: 28
0.74 0.18 0.09
Matches are distributed among these distances:
39 6 0.03
40 63 0.26
41 167 0.70
42 2 0.01
43 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (41 bp):
GGCGCTTTATCAAAAACGCCACTAAAAACCTGAGCATTAGC
Found at i:1366273 original size:81 final size:81
Alignment explanation
Indices: 1366179--1366478 Score: 284
Period size: 81 Copynumber: 3.7 Consensus size: 81
1366169 GCGCAAACTC
*
1366179 AAAAACACCACTAAAACCCCT-AGCATTAG-GGCGGTTTCTCAAAAACGCCGCTAAAAATCTGAA
1 AAAAACACCACTAAAA-CCCTGAGCATTAGCGGC-GTTTCTCAAAAACGCCGCTAAAAACCTGAA
*
1366242 TATTAGCGGCGCTTTTTT
64 CATTAGCGGCGCTTTTTT
* * *
1366260 AAAAACACCACTAAAACCCTGAGCATTAGCGGCGCTTCACAAAAAGCGCCGCT-AAAACCTGAGC
1 AAAAACACCACTAAAACCCTGAGCATTAGCGGCGTTTCTCAAAAA-CGCCGCTAAAAACCTGAAC
* * *
1366324 ATTAGCGGTGCTTTATC
65 ATTAGCGGCGCTTTTTT
* * * * * * * * *
1366341 AAAAACGCCGCTAAAAACCTGAGCATTAGTGACGTTACGTCAAAAACGACACTAAAACCCTGAAC
1 AAAAACACCACTAAAACCCTGAGCATTAGCGGCGTTTC-TCAAAAACGCCGCTAAAAACCTGAAC
**
1366406 ATTAGAAGCGCTTTTTT
65 ATTAGCGGCGCTTTTTT
* * * * * * *
1366423 AAAAACGCCGCTGAAAACCC-GAGCACTAGCAGCGCTACTCCAAAAACGCCACTAAA
1 AAAAACACCACT-AAAACCCTGAGCATTAGCGGCGTTTCT-CAAAAACGCCGCTAAA
1366479 TCCCCCGAAA
Statistics
Matches: 180, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
80 4 0.02
81 93 0.52
82 77 0.43
83 6 0.03
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (81 bp):
AAAAACACCACTAAAACCCTGAGCATTAGCGGCGTTTCTCAAAAACGCCGCTAAAAACCTGAACA
TTAGCGGCGCTTTTTT
Found at i:1367207 original size:88 final size:88
Alignment explanation
Indices: 1367102--1367300 Score: 258
Period size: 88 Copynumber: 2.2 Consensus size: 88
1367092 TTCTCAAATT
* * * * *
1367102 TTTTCAAAAAAGTAATTAAGCTACTGC-ATTTTTTTTGCAGTCATTTAGGTACTTGAACTTTCAA
1 TTTTCAAAAAAGCAATTAAGCCACTACTATTTTTTTTGCACTCAATTAGGTACTTGAA-TTTCAA
* *
1367166 AATGCATCAAAAAGGCCCTCAAACC
65 AATGCATCAAAAAGACCCTCAAA-A
* * *
1367191 TTTTC-AAAAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTCAATTCGGTACTTGAATTTCAAA
1 TTTTCAAAAAAGCAATTAAGCCACTACTATTTTTTTTGCACTCAATTAGGTACTTGAATTTCAAA
1367255 ATGCATCAAAAAGACCCTCAAAA
66 ATGCATCAAAAAGACCCTCAAAA
1367278 TTCTTCAAAAAAAGCAATTAAGC
1 TT-TTC-AAAAAAGCAATTAAGC
1367301 ACATCTTTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
87 2 0.02
88 48 0.50
89 31 0.32
90 15 0.16
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (88 bp):
TTTTCAAAAAAGCAATTAAGCCACTACTATTTTTTTTGCACTCAATTAGGTACTTGAATTTCAAA
ATGCATCAAAAAGACCCTCAAAA
Found at i:1367397 original size:28 final size:29
Alignment explanation
Indices: 1367346--1367412 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1367336 CGTAAATCGT
1367346 AAAAAA-TATAAAATATATAGAAATAG-A
1 AAAAAATTATAAAATATATAGAAATAGTA
* *
1367373 AAAAAATTATAAAATTTTATA-AAATCGTA
1 AAAAAATTATAAAA-TATATAGAAATAGTA
*
1367402 AGAAAATTATA
1 AAAAAATTATA
1367413 CAAAATGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.18
28 12 0.35
29 16 0.47
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAAAATTATAAAATATATAGAAATAGTA
Found at i:1367407 original size:21 final size:21
Alignment explanation
Indices: 1367383--1367427 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1367373 AAAAAATTAT
* *
1367383 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
1367404 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
1367425 AAA
1 AAA
1367428 TATAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:1367408 original size:29 final size:28
Alignment explanation
Indices: 1367339--1367412 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1367329 TAAAAATCGT
1367339 AAATCGTAAAAAA-TATAAAATATATAG
1 AAATCGTAAAAAATTATAAAATATATAG
* * *
1367366 AAATAGAAAAAAATTATAAAATTTTATA-
1 AAATCGTAAAAAATTATAAAA-TATATAG
1367394 AAATCGTAAGAAAATTATA
1 AAATCGTAA-AAAATTATA
1367413 CAAAATGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 11 0.28
28 14 0.36
29 14 0.36
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (28 bp):
AAATCGTAAAAAATTATAAAATATATAG
Found at i:1367665 original size:37 final size:37
Alignment explanation
Indices: 1367606--1367679 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
1367596 TTTTTTTATT
*
1367606 TTTTTATAAAAATAATTATAATTTTTAATAATTTTTA
1 TTTTTATAAAAATAATTATAATTTTTAATAACTTTTA
*
1367643 TTTTTATAAAAA-AATTTCTAATTTTTAATAACTTTTA
1 TTTTTATAAAAATAA-TTATAATTTTTAATAACTTTTA
1367680 AATTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 32 0.94
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (37 bp):
TTTTTATAAAAATAATTATAATTTTTAATAACTTTTA
Found at i:1368285 original size:21 final size:20
Alignment explanation
Indices: 1368261--1368299 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1368251 AGAACTTAGG
*
1368261 TTTAAGTCTTATAAATTTTAT
1 TTTAACTCTT-TAAATTTTAT
*
1368282 TTTATCTCTTTAAATTTT
1 TTTAACTCTTTAAATTTT
1368300 TCTGCACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTAACTCTTTAAATTTTAT
Found at i:1384170 original size:19 final size:19
Alignment explanation
Indices: 1384146--1384183 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1384136 AAAATTAATT
1384146 TTTTCTCAAAATATT-TTTA
1 TTTTCT-AAAATATTATTTA
*
1384165 TTTTCTGAAATATTATTTA
1 TTTTCTAAAATATTATTTA
1384184 CCAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTCTAAAATATTATTTA
Found at i:1386507 original size:41 final size:41
Alignment explanation
Indices: 1386450--1386609 Score: 178
Period size: 41 Copynumber: 3.9 Consensus size: 41
1386440 ATATTGGAGA
* *
1386450 TATTGACTCATGCCTTGAGCCTAGTAGGCTTCATGCTAGTG
1 TATTGAATCATGCCTTGAGCCTAGTAGGCTTCGTGCTAGTG
* * *
1386491 TATTGAATCAGGCCTTGAGCCTAGTAGGTTTTGTG-TCAGTG
1 TATTGAATCATGCCTTGAGCCTAGTAGGCTTCGTGCT-AGTG
* * * *
1386532 TATTGAATCATGCTTTTAGCCTAGTAGGCTTCGTGCCAGTT
1 TATTGAATCATGCCTTGAGCCTAGTAGGCTTCGTGCTAGTG
* * * * *
1386573 TATCGAATCAAGCCTTTAACCTAGCAGGCTTCGTGCT
1 TATTGAATCATGCCTTGAGCCTAGTAGGCTTCGTGCT
1386610 GGTCTAGTGT
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.01
41 98 0.99
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (41 bp):
TATTGAATCATGCCTTGAGCCTAGTAGGCTTCGTGCTAGTG
Found at i:1391293 original size:21 final size:21
Alignment explanation
Indices: 1391266--1391313 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1391256 TCAATTGTCT
** *
1391266 CCACAACAAGGTCAGATACAA
1 CCACAACAAACTCAAATACAA
*
1391287 TCACAACAAACTCAAATACAA
1 CCACAACAAACTCAAATACAA
1391308 CCACAA
1 CCACAA
1391314 ATGATGAATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.31, G:0.06, T:0.10
Consensus pattern (21 bp):
CCACAACAAACTCAAATACAA
Found at i:1415169 original size:49 final size:49
Alignment explanation
Indices: 1415107--1415489 Score: 337
Period size: 51 Copynumber: 7.6 Consensus size: 49
1415097 TCATTCGATA
1415107 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
1415156 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
*
1415205 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAGCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAGTT
* * * *
1415255 CACGTAGTAGCCTTCACATAGTACTACATACATGACCAAAGCTTTT-CGGTAT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AG-TTTTACAGT-T
* * * * * * * * *
1415307 C-CATAGTAGCCTTCACTTAGTACCACACATGTAACCA-TAGCTTACCGATA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGT--TTTACAG-TT
* * * * * * *
1415357 CACGTAGTAGCTTTCACACAGTACTACACACGTGCTCAAAACTTCT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC---AGTTTTACAGTT
** * * * *
1415408 CAAATAGTAGCCTTCACTTAGTACTACACATC-TGACCATTATTTATC-GATA
1 CACGTAGTAGCCTTCACATAGTACTACACA-CGTGATCAGT-TTTA-CAG-TT
*
1415459 CACGTAGTAGCCTTCACACAGTACTACACAC
1 CACGTAGTAGCCTTCACATAGTACTACACAC
1415490 TGTTCATCGA
Statistics
Matches: 275, Mismatches: 41, Indels: 35
0.78 0.12 0.10
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 91 0.33
50 50 0.18
51 119 0.43
52 9 0.03
53 1 0.00
54 1 0.00
55 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (49 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
Found at i:1436897 original size:51 final size:51
Alignment explanation
Indices: 1436728--1437060 Score: 265
Period size: 51 Copynumber: 6.6 Consensus size: 51
1436718 TCGATACACG
* *
1436728 TAGTAGCCTTCACATAGTACTACACACGTGATC--AGTTTTACAGT-TCACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGGTATCACA
* * * * *
1436777 TAGTAGCCTTAACATAGTACTACACACGTGATC-AAGTTTTATGG-CTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGGTATCACA
*
1436827 TAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTATC-CA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TTTTCGGTATCACA
* * * * * * * *
1436878 TAGTAGCCTTCACTTAGTACCACACATGTAACCATAGTTTACCG-ATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCGGTAT-CACA
* * * *
1436929 TAGTAGCTTTCACACAGTACTACACACGTG-CTCAAAACTTCTCGGTA-CACA
1 TAGTAGCCTTCACATAGTACTACACACGTGAC-C-AAAGTTTTCGGTATCACA
* * * * * *
1436980 TAGTAGCCTTCACTTAGTACTATACATGTGACCATTA-TTTATCGATA-CACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCGGTATCACA
* *
1437031 GAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
1437061 TTCATCGATA
Statistics
Matches: 226, Mismatches: 45, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
49 34 0.15
50 52 0.23
51 126 0.56
52 13 0.06
53 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCGGTATCACA
Found at i:1436949 original size:102 final size:103
Alignment explanation
Indices: 1436718--1437060 Score: 409
Period size: 102 Copynumber: 3.4 Consensus size: 103
1436708 TTTTTATCAT
* * *
1436718 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AG-TTTTACAGT-TCACATA
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTATCACATA
* * * *
1436779 GTAGCCTTAACATAGTACTACACACGTGATCA-AGTTTTA
65 GTAGCCTTCACTTAGTACTACACATGTGACCATAG-TTTA
* * * *
1436818 TGGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTATC-CATAG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTATCACATAG
* *
1436881 TAGCCTTCACTTAGTACCACACATGTAACCATAGTTTA
66 TAGCCTTCACTTAGTACTACACATGTGACCATAGTTTA
* * * *
1436919 CCGATACACGTAGTAGCTTTCACACAGTACTACACACGTG-CTCAAAACTTCTCGGTA-CACATA
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAGCTTTTCGGTATCACATA
*
1436982 GTAGCCTTCACTTAGTACTATACATGTGACCATTA-TTTA
65 GTAGCCTTCACTTAGTACTACACATGTGACCA-TAGTTTA
*
1437021 TCGATACACGGAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1437061 TTCATCGATA
Statistics
Matches: 209, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
99 35 0.17
100 3 0.01
101 43 0.21
102 126 0.60
103 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (103 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTATCACATAG
TAGCCTTCACTTAGTACTACACATGTGACCATAGTTTA
Found at i:1438834 original size:16 final size:16
Alignment explanation
Indices: 1438813--1438843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1438803 CTATGCATGC
*
1438813 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
1438829 AAAATACAAAAGACA
1 AAAATACAAAAGACA
1438844 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:1442173 original size:18 final size:18
Alignment explanation
Indices: 1442142--1442176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1442132 ACTTAGTTGG
* *
1442142 TTTCTTCTTTCCTTTAGC
1 TTTCTACTTCCCTTTAGC
1442160 TTTCTACTTCCCTTTAG
1 TTTCTACTTCCCTTTAG
1442177 AGAATGAGGG
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:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTCTACTTCCCTTTAGC
Found at i:1444727 original size:68 final size:69
Alignment explanation
Indices: 1444601--1444729 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 69
1444591 AACTTAATCA
* * * *
1444601 CTTTAATATTAAATTAATATACTATTTATCAAGATAAATATTAGATTAAATTTAATATTAAGATA
1 CTTTAATATTAAATTAATAAAATATCTATCAAGAAAAATATTAGATTAAATTTAATATTAAGATA
1444666 ATTT
66 ATTT
*
1444670 CTTTAATATTAAATTAATAAAATA-CTATTAA-AAAAAGTATTA-AGTTAAATTTAATATTAA
1 CTTTAATATTAAATTAATAAAATATCTATCAAGAAAAA-TATTAGA-TTAAATTTAATATTAA
1444730 ACTATTAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
67 5 0.09
68 26 0.49
69 22 0.42
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (69 bp):
CTTTAATATTAAATTAATAAAATATCTATCAAGAAAAATATTAGATTAAATTTAATATTAAGATA
ATTT
Found at i:1451625 original size:19 final size:19
Alignment explanation
Indices: 1451597--1451633 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1451587 GTGTGAGTCT
1451597 AAACAATCAAACATTTTAC
1 AAACAATCAAACATTTTAC
* *
1451616 AAACATTCAAGCATTTTA
1 AAACAATCAAACATTTTA
1451634 TCATGGAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.30
Consensus pattern (19 bp):
AAACAATCAAACATTTTAC
Found at i:1460050 original size:18 final size:19
Alignment explanation
Indices: 1460008--1460052 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1459998 TATAAAAAGG
*
1460008 TTATTAAATATTATGATAAA
1 TTATTAAA-ACTATGATAAA
1460028 -T-TTAAAACTAT-ATAAA
1 TTATTAAAACTATGATAAA
1460044 TTATTAAAA
1 TTATTAAAA
1460053 ATCATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.23
17 5 0.23
18 11 0.50
19 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TTATTAAAACTATGATAAA
Found at i:1464133 original size:35 final size:35
Alignment explanation
Indices: 1464094--1464163 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1464084 AAAAATAGGT
1464094 TTGATTAATTCAAAATGAGAATCGACACAGGGAAA
1 TTGATTAATTCAAAATGAGAATCGACACAGGGAAA
1464129 TTGATTAATTCAAAATGAGAATCGACACAGGGAAA
1 TTGATTAATTCAAAATGAGAATCGACACAGGGAAA
1464164 GGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (35 bp):
TTGATTAATTCAAAATGAGAATCGACACAGGGAAA
Found at i:1471789 original size:20 final size:20
Alignment explanation
Indices: 1471764--1471802 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1471754 TACTTTCTTC
1471764 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
1471784 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
1471803 AAATAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:1472147 original size:50 final size:50
Alignment explanation
Indices: 1472075--1472240 Score: 154
Period size: 50 Copynumber: 3.2 Consensus size: 50
1472065 TATCCCAGAT
** * * * * *
1472075 ATGGTCTTAC-ACGGGAGTTCTCATATCGGTGCCCATGCCATGTCCTAGGC
1 ATGGTCTTACGA-GGGACCTCTCATATCAGTACCAACGCCATGTCCTAGAC
*
1472125 ATGGTCTTACGAGGGACCTCTCATCTCAGTACCAACGCCATGTCCTAGAC
1 ATGGTCTTACGAGGGACCTCTCATATCAGTACCAACGCCATGTCCTAGAC
* * * *
1472175 ATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACGAGGGACCTCTCAT-A--TCAGT-A--CCAACGCCATGTCCTAGAC
1472231 ATGGTCTTAC
1 ATGGTCTTAC
1472241 ATGGGGTCTC
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
50 63 0.66
51 1 0.01
53 4 0.04
54 1 0.01
56 27 0.28
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACGAGGGACCTCTCATATCAGTACCAACGCCATGTCCTAGAC
Found at i:1472231 original size:56 final size:52
Alignment explanation
Indices: 1472104--1472245 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 52
1472094 CTCATATCGG
* * * *
1472104 TGCCCATGCCATGTCCTAGGCATGGTCTTACGAGGGACCTCTCATCTCAGTA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
*
1472156 --CCAACGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCAT---CTCAAT-A
* *
1472210 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGG
1472246 GTCTCATCCC
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
50 39 0.51
53 5 0.07
54 1 0.01
56 31 0.41
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
Found at i:1477467 original size:36 final size:36
Alignment explanation
Indices: 1477426--1477501 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1477416 TGTACCATTG
** *
1477426 TAACATAGATACGGGAAACATGTTATGATTCTTTTC
1 TAACATAGATACGGGAAACACATTATGAATCTTTTC
*
1477462 TAACATAGATACGTGAAACACATTATGAATCTTTTC
1 TAACATAGATACGGGAAACACATTATGAATCTTTTC
1477498 TAAC
1 TAAC
1477502 TCTAATGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (36 bp):
TAACATAGATACGGGAAACACATTATGAATCTTTTC
Found at i:1484821 original size:22 final size:22
Alignment explanation
Indices: 1484796--1484840 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1484786 CCACCACCGG
*
1484796 TTTGAAGATAAACTGCCACTGA
1 TTTGAAGATAAACTACCACTGA
*
1484818 TTTGTAGATAAACTACCACTGA
1 TTTGAAGATAAACTACCACTGA
1484840 T
1 T
1484841 AACACTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (22 bp):
TTTGAAGATAAACTACCACTGA
Found at i:1491601 original size:24 final size:24
Alignment explanation
Indices: 1491563--1491619 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1491553 TTATTTAAAC
* *
1491563 TATCATACATTATAGCTTGAAATT
1 TATCATATACTATAGCTTGAAATT
* * *
1491587 TATTATATACTATAGTTTTAAATT
1 TATCATATACTATAGCTTGAAATT
1491611 TATCATATA
1 TATCATATA
1491620 TTATTATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (24 bp):
TATCATATACTATAGCTTGAAATT
Found at i:1491629 original size:24 final size:25
Alignment explanation
Indices: 1491582--1491698 Score: 78
Period size: 24 Copynumber: 4.8 Consensus size: 25
1491572 TTATAGCTTG
*
1491582 AAATTTATTATATACTA-TAGTTTT
1 AAATTTATTATATATTATTAGTTTT
*
1491606 AAATTTATCATATATTATTA-TTTT
1 AAATTTATTATATATTATTAGTTTT
* ** * ** *
1491630 AGATGCATTATGTATTCGTATTTTT
1 AAATTTATTATATATTATTAGTTTT
* * * *
1491655 AAAGTTATCATATGTTATTA-TTTC
1 AAATTTATTATATATTATTAGTTTT
* *
1491679 AAAATTATTATGTATTATTA
1 AAATTTATTATATATTATTA
1491699 CTTAAAGATA
Statistics
Matches: 68, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
24 51 0.75
25 17 0.25
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (25 bp):
AAATTTATTATATATTATTAGTTTT
Found at i:1496657 original size:18 final size:16
Alignment explanation
Indices: 1496628--1496671 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1496618 GATCCAATTT
**
1496628 TCAAAAAAAAAATCAA
1 TCAAAAAAAAAAAAAA
1496644 TCAAAAAATCAAAAAAAA
1 TCAAAAAA--AAAAAAAA
1496662 TCAAAAAAAA
1 TCAAAAAAAA
1496672 GGGAAGGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (16 bp):
TCAAAAAAAAAAAAAA
Found at i:1496659 original size:10 final size:10
Alignment explanation
Indices: 1496632--1496671 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
1496622 CAATTTTCAA
1496632 AAAAAAAATC
1 AAAAAAAATC
1496642 AATCAAAAAATC
1 AA--AAAAAATC
1496654 AAAAAAAATC
1 AAAAAAAATC
1496664 AAAAAAAA
1 AAAAAAAA
1496672 GGGAAGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 18 0.64
12 10 0.36
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:1497595 original size:14 final size:15
Alignment explanation
Indices: 1497559--1497595 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1497549 GGGCACTTCG
1497559 AGTAAAAAATGAAAA
1 AGTAAAAAATGAAAA
*
1497574 AGT-GAAAATGAAAA
1 AGTAAAAAATGAAAA
1497588 A-TAAAAAA
1 AGTAAAAAA
1497596 ATGATGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.79
15 3 0.16
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AGTAAAAAATGAAAA
Found at i:1498930 original size:44 final size:43
Alignment explanation
Indices: 1498867--1499461 Score: 596
Period size: 44 Copynumber: 13.6 Consensus size: 43
1498857 AAATTACAAG
* * *
1498867 TCCTAACTCCCTGACCAGTAGTGGAATAGGAGGAAGACTGAAA
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTGAAA
* * *
1498910 CTCCTAGCTCCCTGAACAGTAGTGGAATAGGCA-G-AGATTGCAGA
1 -TCCTAGCTCCCTGACCAGCAGTGGAATAGG-AGGAAGATTG-AAA
** *
1498954 TCCTAGCTCCCTGACCAATAGTGGAATAGGTGGAAGATTGAAA
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTGAAA
* * * *
1498997 GTCCTAGCTCCCTGAACAACAGTAGAATAGGTA-G-AGATTGCAGA
1 -TCCTAGCTCCCTGACCAGCAGTGGAATAGG-AGGAAGATTG-AAA
* * * *
1499041 TCCTAGCTCCCTGAGCAACAGTGGAATAGGTGGAAGACTGAAA
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTGAAA
* * *
1499084 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGCAGA
1 -TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTG-AAA
* *
1499129 TCCTAGCTCCCTGACCAGCAGTAGAATAGGAGGAAGACTGAAA
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTGAAA
* * *
1499172 GTCCTAGCTCCCTGAACAACAGTGGAATAAGCA-GAAGATT-ACAGA
1 -TCCTAGCTCCCTGACCAGCAGTGGAAT-AGGAGGAAGATTGA-A-A
* * *
1499217 TCCTAGCTCCCTGACCAACAG-GAGAATAGGTGGAAGACTGAAA
1 TCCTAGCTCCCTGACCAGCAGTG-GAATAGGAGGAAGATTGAAA
* * *
1499260 GTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGCAGA
1 -TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTG-AAA
* * * *
1499305 TCCTAACTCCATGACCAGCAGTGGAATAGGTGGAAGACTGAAA
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTGAAA
*
1499348 GTCCTAGCTCCCTGACCAGCAGTGGAATAGGCA-AAAGATTGTAAA
1 -TCCTAGCTCCCTGACCAGCAGTGGAATAGG-AGGAAGATTG-AAA
* *
1499393 TCCTAGCTCCCTGACCAGCGGTGGAATAGGTA-GAAGATTGTAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGG-AGGAAGATTG-AAA
*
1499437 TCCTAGCTCCCTGAGCAGCAGTGGA
1 TCCTAGCTCCCTGACCAGCAGTGGA
1499462 GTGGGTCAAA
Statistics
Matches: 468, Mismatches: 59, Indels: 48
0.81 0.10 0.08
Matches are distributed among these distances:
43 82 0.18
44 372 0.79
45 14 0.03
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (43 bp):
TCCTAGCTCCCTGACCAGCAGTGGAATAGGAGGAAGATTGAAA
Found at i:1499164 original size:88 final size:88
Alignment explanation
Indices: 1498867--1499461 Score: 872
Period size: 88 Copynumber: 6.8 Consensus size: 88
1498857 AAATTACAAG
* * * * *
1498867 TCCTAACTCCCTGACCAGTAGTGGAATAGGAGGAAGACTGAAACTCCTAGCTCCCTGAACAGTAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
1498932 TGGAATAGGCAG-AGATTGCAGA
66 TGGAATAGGCAGAAGATTGCAGA
** * *
1498954 TCCTAGCTCCCTGACCAATAGTGGAATAGGTGGAAGATTGAAAGTCCTAGCTCCCTGAACAACAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
* *
1499019 TAGAATAGGTAG-AGATTGCAGA
66 TGGAATAGGCAGAAGATTGCAGA
* *
1499041 TCCTAGCTCCCTGAGCAACAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
*
1499106 TGGAATAGGCGGAAGATTGCAGA
66 TGGAATAGGCAGAAGATTGCAGA
* * *
1499129 TCCTAGCTCCCTGACCAGCAGTAGAATAGGAGGAAGACTGAAAGTCCTAGCTCCCTGAACAACAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
* *
1499194 TGGAATAAGCAGAAGATTACAGA
66 TGGAATAGGCAGAAGATTGCAGA
*
1499217 TCCTAGCTCCCTGACCAACAG-GAGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCA
1 TCCTAGCTCCCTGACCAGCAGTG-GAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCA
*
1499281 GTGGAATAGGCGGAAGATTGCAGA
65 GTGGAATAGGCAGAAGATTGCAGA
* * *
1499305 TCCTAACTCCATGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGACCAGCAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
* * *
1499370 TGGAATAGGCAAAAGATTGTAAA
66 TGGAATAGGCAGAAGATTGCAGA
* * * * *
1499393 TCCTAGCTCCCTGACCAGCGGTGGAATAGGTAGAAGATTGTAAGTCCTAGCTCCCTGAGCAGCAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
1499458 TGGA
66 TGGA
1499462 GTGGGTCAAA
Statistics
Matches: 459, Mismatches: 46, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
87 148 0.32
88 310 0.68
89 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (88 bp):
TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
TGGAATAGGCAGAAGATTGCAGA
Done.