Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 89 of 204
Found at i:27285121 original size:22 final size:24
Alignment explanation
Indices: 27285095--27285138 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
27285085 GAAAAATATT
27285095 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
27285117 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
27285139 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:27285247 original size:9 final size:9
Alignment explanation
Indices: 27285235--27285262 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
27285225 TTTTATTATA
27285235 ACAATTAAT
1 ACAATTAAT
27285244 ACAATTAAT
1 ACAATTAAT
27285253 ACAATTAAT
1 ACAATTAAT
27285262 A
1 A
27285263 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:27285284 original size:68 final size:68
Alignment explanation
Indices: 27285205--27285414 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
27285195 TCAAGTTTGT
*
27285205 TTTACTAATCAAATGTTAGATTTTATTATAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
27285270 AAA
66 AAA
27285273 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
27285338 AAA
66 AAA
27285341 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
27285404 AAT
66 AAA
27285407 TTTACTAA
1 TTTACTAA
27285415 CAATTAATTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:27285315 original size:9 final size:9
Alignment explanation
Indices: 27285303--27285330 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
27285293 TTTTATTACA
27285303 ACAATTAAT
1 ACAATTAAT
27285312 ACAATTAAT
1 ACAATTAAT
27285321 ACAATTAAT
1 ACAATTAAT
27285330 A
1 A
27285331 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:27285424 original size:16 final size:16
Alignment explanation
Indices: 27285403--27285444 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
27285393 AATAATTTGA
*
27285403 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
27285419 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
27285435 TAGTTTTAAT
1 TAATTTTAAT
27285445 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:27286363 original size:15 final size:15
Alignment explanation
Indices: 27286343--27286392 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
27286333 AATACCAAAA
27286343 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
27286358 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
27286373 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
27286391 TA
1 TA
27286393 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:27286397 original size:18 final size:18
Alignment explanation
Indices: 27286361--27286398 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27286351 ATTAAATTAG
*
27286361 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
27286379 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
27286397 AG
1 AG
27286399 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:27286734 original size:28 final size:28
Alignment explanation
Indices: 27286701--27286766 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
27286691 TTTTTTTGGT
**
27286701 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
27286729 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
27286757 ATATTTTGGT
1 ATATTTTGGT
27286767 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:27290153 original size:48 final size:48
Alignment explanation
Indices: 27290082--27290176 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
27290072 TTCTTTGCTT
27290082 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
* *
27290130 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAG
27290177 AATTCCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
Found at i:27290429 original size:36 final size:36
Alignment explanation
Indices: 27290381--27290451 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
27290371 ATCAAAGGCT
27290381 ACAATTAAAAGTTGTATACAATTAAAACTCTAAGAC
1 ACAATTAAAAGTTGTATACAATTAAAACTCTAAGAC
* *
27290417 ACAATTAGAAGTTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGTTGTATACAATTAAAACTCTAAGA
27290452 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ACAATTAAAAGTTGTATACAATTAAAACTCTAAGAC
Found at i:27290443 original size:17 final size:17
Alignment explanation
Indices: 27290380--27290440 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
27290370 CATCAAAGGC
27290380 TACAATTAAAAGTTGTA
1 TACAATTAAAAGTTGTA
*
27290397 TACAATTAAAACTCTAAG-A
1 TACAATTAAAAGT-T--GTA
* *
27290416 CACAATTAGAAGTTGTA
1 TACAATTAAAAGTTGTA
27290433 TACAATTA
1 TACAATTA
27290441 GAACTCTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 20 0.57
18 2 0.06
19 11 0.31
20 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (17 bp):
TACAATTAAAAGTTGTA
Found at i:27292944 original size:5 final size:5
Alignment explanation
Indices: 27292936--27292993 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
27292926 GTAGTTCGTG
* * * *
27292936 TTTTA TTTTA TTTTA TCTTA TTTTA -TATA TATGTA -TTTA TTAT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA
27292984 TTTTA TTTTA
1 TTTTA TTTTA
27292994 AATTATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
4 9 0.21
5 30 0.71
6 3 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:27293258 original size:30 final size:30
Alignment explanation
Indices: 27293194--27293329 Score: 93
Period size: 29 Copynumber: 4.6 Consensus size: 30
27293184 CAAAAAATAT
* * **
27293194 AAATTACATTTTGGCCCTTAAAC-TTTTCC
1 AAATTACATTTTGACCCCTAAACTTTTTTG
27293223 AAATTTACATTTTGACCCCTAAACTTTTTTG
1 AAA-TTACATTTTGACCCCTAAACTTTTTTG
* * ** *
27293254 AATTTGCATCGTGACCCC-AAA-TATTTTTT
1 AAATTACATTTTGACCCCTAAACT-TTTTTG
* * *
27293283 AAATTACATTTGGGA--CCTAAACTTTCTAG
1 AAATTACATTT-TGACCCCTAAACTTTTTTG
*
27293312 AAATTACATTTTGGCCCC
1 AAATTACATTTTGACCCC
27293330 ATGTTTTCCT
Statistics
Matches: 80, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
28 4 0.05
29 35 0.44
30 35 0.44
31 6 0.08
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTAAACTTTTTTG
Found at i:27293576 original size:21 final size:21
Alignment explanation
Indices: 27293527--27293568 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
27293517 CTTAAAAAGA
27293527 AAAAAATTGAAGAGAAATGAG
1 AAAAAATTGAAGAGAAATGAG
27293548 AAAAAATTGAAGAGAAATGAG
1 AAAAAATTGAAGAGAAATGAG
27293569 GGGGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (21 bp):
AAAAAATTGAAGAGAAATGAG
Found at i:27294121 original size:17 final size:17
Alignment explanation
Indices: 27294078--27294125 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
27294068 TTTTTTAAAA
27294078 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAAGTTT
*
27294095 TCATGTTTTCAAAA-TTT
1 TCGTG-TTTCAAAAGTTT
27294112 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
27294126 AATAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (17 bp):
TCGTGTTTCAAAAGTTT
Found at i:27294170 original size:20 final size:20
Alignment explanation
Indices: 27294143--27294196 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
27294133 ATAAAATTTC
27294143 TCGTGTTTCAAAAAATATATT
1 TCGTGTTTCAAAAAATA-ATT
*
27294164 T-GTGTTTTTAAAAAATAATT
1 TCGTG-TTTCAAAAAATAATT
27294184 TCCGTGTTTCAAA
1 T-CGTGTTTCAAA
27294197 TTTTCTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (20 bp):
TCGTGTTTCAAAAAATAATT
Found at i:27294269 original size:62 final size:62
Alignment explanation
Indices: 27294194--27294416 Score: 344
Period size: 62 Copynumber: 3.6 Consensus size: 62
27294184 TCCGTGTTTC
* * *
27294194 AAATTTTCTTGTTTTCAAAAATTTCTCATGTTTCAAAAAATTTTCGACTTTT-GCGTTTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTT-TAAAAATTTTCGACTTTTCGCGTTTTCAA
* *
27294256 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTTAAAAATTTTTGACTTTTCACGTTTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTTAAAAATTTTCGACTTTTCGCGTTTTCAA
*
27294318 AAATTTTCATGTTTTCAAAAATTTCTCGTGTTTTAAAAATTTTCGACTTTTCGCGTTTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTTAAAAATTTTCGACTTTTCGCGTTTTCAA
*
27294380 AAATTTTCGTGTTTT-AGAAATTT-TCGTGTTTCTAAAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTT-TAAAA
27294417 TTCTCGTATT
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
60 8 0.05
61 28 0.19
62 113 0.76
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (62 bp):
AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTTAAAAATTTTCGACTTTTCGCGTTTTCAA
Found at i:27294272 original size:44 final size:44
Alignment explanation
Indices: 27294204--27294405 Score: 144
Period size: 44 Copynumber: 4.8 Consensus size: 44
27294194 AAATTTTCTT
*
27294204 GTTTTCAAAAATTTCTCATG-TTTCAAAAAATTTTCGACTTTT-GC
1 GTTTTCAAAAATTT-TCGTGTTTTC-AAAAATTTTCGACTTTTAGC
** **
27294248 GTTTTCAAAAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTTAAAA
1 GTTTTCAAAAATTTTCGTGTTTTCAAAAATTT-TCGACTTTT-AGC
* ** * **
27294294 ATTTT--TGACTTTTCACGTTTTCAAAAATTTTC-A----T---
1 GTTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCGACTTTTAGC
*
27294328 GTTTTCAAAAATTTCTCGTGTTTT-AAAAATTTTCGACTTTTCGC
1 GTTTTCAAAAATTT-TCGTGTTTTCAAAAATTTTCGACTTTTAGC
*
27294372 GTTTTCAAAAATTTTCGTGTTTT-AGAAATTTTCG
1 GTTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCG
27294406 TGTTTCTAAA
Statistics
Matches: 124, Mismatches: 19, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
34 4 0.03
36 14 0.11
37 8 0.06
38 1 0.01
41 1 0.01
43 33 0.27
44 59 0.48
46 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (44 bp):
GTTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCGACTTTTAGC
Found at i:27294275 original size:17 final size:18
Alignment explanation
Indices: 27294194--27294451 Score: 141
Period size: 18 Copynumber: 13.2 Consensus size: 18
27294184 TCCGTGTTTC
*
27294194 AAATTTTCTTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
*
27294212 AAATTTCTCATG-TTTCAAA
1 AAATTT-TCGTGTTTTC-AA
27294231 AAATTTTCGACTTTTGCGTTTTCAA
1 AAATTTTCG-----T--GTTTTCAA
27294256 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
27294274 AAATTTCTCGTGTTTT-AA
1 AAATTT-TCGTGTTTTCAA
*
27294292 AAATTTTTGACTTTTCACGTTTTCAA
1 AAA-TTTT--C--GT---GTTTTCAA
*
27294318 AAATTTTCATGTTTTCAA
1 AAATTTTCGTGTTTTCAA
27294336 AAATTTCTCGTGTTTT-AA
1 AAATTT-TCGTGTTTTCAA
27294354 AAATTTTCGACTTTTCGCGTTTTCAA
1 AAATTTTCG-----T---GTTTTCAA
*
27294380 AAATTTTCGTGTTTT-AG
1 AAATTTTCGTGTTTTCAA
*
27294397 AAATTTTCGTG-TTTCTA
1 AAATTTTCGTGTTTTCAA
* *
27294414 AAATTCTCGT-ATTTCAA
1 AAATTTTCGTGTTTTCAA
* *
27294431 AAATTTCCGTGTTCTCAA
1 AAATTTTCGTGTTTTCAA
27294449 AAA
1 AAA
27294452 AAATTATTAT
Statistics
Matches: 193, Mismatches: 14, Indels: 66
0.71 0.05 0.24
Matches are distributed among these distances:
16 3 0.02
17 37 0.19
18 67 0.35
19 32 0.17
20 2 0.01
21 2 0.01
22 2 0.01
23 2 0.01
25 26 0.13
26 20 0.10
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (18 bp):
AAATTTTCGTGTTTTCAA
Found at i:27294418 original size:34 final size:34
Alignment explanation
Indices: 27294365--27294451 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
27294355 AATTTTCGAC
* * * * *
27294365 TTTTCGCGTTTTCAAAAATTTTCGTGTTTTAGAAA
1 TTTTCGTG-TTTCAAAAATTCTCGTATTTCAAAAA
*
27294400 TTTTCGTGTTTCTAAAATTCTCGTATTTCAAAAA
1 TTTTCGTGTTTCAAAAATTCTCGTATTTCAAAAA
*
27294434 TTTCCGTGTTCTCAAAAA
1 TTTTCGTGTT-TCAAAAA
27294452 AAATTATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 30 0.70
35 13 0.30
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (34 bp):
TTTTCGTGTTTCAAAAATTCTCGTATTTCAAAAA
Found at i:27306150 original size:6 final size:6
Alignment explanation
Indices: 27306139--27306181 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
27306129 TATGCCTAAA
27306139 AAAAAC AAAAAC AAAAAC AAAGAAAC AAAAA- AGAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC -AA-AAAC AAAAAC A-AAAAC AAAAA
27306182 AAAGAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 1 0.03
6 23 0.70
7 5 0.15
8 4 0.12
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:27306166 original size:20 final size:20
Alignment explanation
Indices: 27306141--27306193 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
27306131 TGCCTAAAAA
27306141 AAACAAAAACA-AAAACAAAG
1 AAACAAAAA-AGAAAACAAAG
27306161 AAACAAAAAAGAAAACAAA-
1 AAACAAAAAAGAAAACAAAG
*
27306180 AAA-AAGAAAGAAAA
1 AAACAAAAAAGAAAA
27306194 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 10 0.32
19 4 0.13
20 17 0.55
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (20 bp):
AAACAAAAAAGAAAACAAAG
Found at i:27306193 original size:11 final size:10
Alignment explanation
Indices: 27306136--27306205 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 10
27306126 TATTATGCCT
*
27306136 AAAAA-AAAC
1 AAAAAGAAAA
*
27306145 AAAAACAAAA
1 AAAAAGAAAA
*
27306155 ACAAAGAAACA
1 AAAAAGAAA-A
27306166 AAAAAG-AAA
1 AAAAAGAAAA
*
27306175 ACAAA-AAAA
1 AAAAAGAAAA
*
27306184 AGAAAGAAAA
1 AAAAAGAAAA
27306194 GAAAAAGAAAA
1 -AAAAAGAAAA
27306205 A
1 A
27306206 TCAAGATGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 17 0.35
10 17 0.35
11 15 0.31
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:27306198 original size:15 final size:14
Alignment explanation
Indices: 27306146--27306203 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
27306136 AAAAAAAACA
*
27306146 AAAACAAAAACAAAG
1 AAAA-AAAAAGAAAG
27306161 AAACAAAAAAGAAA-
1 AAA-AAAAAAGAAAG
27306175 ACAAAAAAAAGAAAG
1 A-AAAAAAAAGAAAG
27306190 AAAAGAAAAAGAAA
1 AAAA-AAAAAGAAA
27306204 AATCAAGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 14 0.37
15 23 0.61
16 1 0.03
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:27307471 original size:152 final size:152
Alignment explanation
Indices: 27307057--27307619 Score: 461
Period size: 154 Copynumber: 3.7 Consensus size: 152
27307047 TCAAGAATTA
** * * * *
27307057 TATTTTTCAATTTTTGTCTCTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-T
1 TATTTTTCAATTTCCGT-TTTTAAATATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCA
*
27307121 CACGCTGAGGTATTTTCAATTTCTGTT-TTTCAAAAAAAAAATCAACTTATATTGCGAGAGGTGA
65 CACGCTGAGGTATTTTCAATTTCT-TTATTT--AAAAAAAAATCAACTCATATTGCGAGAGGTGA
*** * *
27307185 GTTGAGCCTTGGGTCACATCCTGAGG
127 GTTGAGCCTCAAGCCACATCCCGAGG
* * * * *
27307211 TATTTTTCAATTTCTGTTTTTCAAATATCAACTCATATTGCGAGAGGTGTGTTGAGCGTCAGGTC
1 TATTTTTCAATTTCCGTTTTT-AAATATAAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGC
* * * *** * * *
27307276 ACACACTGAGGTATTTCTTTTAAATT-TTTATTT-TTCAAAAATCAAATCATAATACGAGAGGTG
64 ACACGCTGAGGTA--T-TTTCAATTTCTTTATTTAAAAAAAAATCAACTCATATTGCGAGAGGTG
*
27307339 AGTTGAGCCTCAAGCCGCA-CGCCGAGG
126 AGTTGAGCCTCAAGCCACATC-CCGAGG
** * * *
27307366 TA-TTTTCAATTTCCGTTTTT-TTTTTAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCG
1 TATTTTTCAATTTCCGTTTTTAAATATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CA
* *
27307429 CACGCCGAGGTATTTTCAATTTCCTTTATTTAAAAAAAAATCAACTCATATTGTGAGAGGTGAGT
65 CACGCTGAGGTATTTTCAATTT-CTTTATTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
** *
27307494 TGAGCCTC--GGGACA-CGCCAAGG
129 TGAGCCTCAAGCCACATC-CCGAGG
** * * * *
27307516 TATTTTCTCAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTT-AGCCT--GGA
1 TATTTT-TCAATTTCCGTTTTT-AAATATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC
* *
27307578 ATCATGCTGATGTATTTTCAATTTCTATT-TTTCAAAAAAAAA
64 A-CACGCTGAGGTATTTTCAATTTCT-TTATTT-AAAAAAAAA
27307620 ATTAACAATC
Statistics
Matches: 330, Mismatches: 60, Indels: 41
0.77 0.14 0.10
Matches are distributed among these distances:
149 7 0.02
150 18 0.05
151 44 0.13
152 88 0.27
153 8 0.02
154 94 0.28
155 46 0.14
156 11 0.03
157 2 0.01
158 5 0.02
159 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (152 bp):
TATTTTTCAATTTCCGTTTTTAAATATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
ACGCTGAGGTATTTTCAATTTCTTTATTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTCAAGCCACATCCCGAGG
Found at i:27307618 original size:75 final size:75
Alignment explanation
Indices: 27307079--27307618 Score: 367
Period size: 79 Copynumber: 7.1 Consensus size: 75
27307069 TTTGTCTCTT
* ** *
27307079 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGAACACGCCGAGGTATTTTCAATTTC
27307144 TGTTTTTCAAAAA
66 T-TTTTTC--AAA
* * * ** *
27307157 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATCCTGAGGTATTTTTCAAT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGAACAC-GCC-GAGGTA-TTTTCAAT
27307222 TTCTGTTTTTC---
63 TTCT-TTTTTCAAA
* * * * * * * *
27307233 AAATATCAACTCATATTGCGAGAGGTGTGTTGAGCGTCAGGTCACACACTGAGGTATTTCTTTTA
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GG-AACACGCCGAGGTA----TTTTC
*
27307298 AATTTTTATTTTTC---
60 AATTTCT-TTTTTCAAA
* * ***
27307312 AAAAATCAAATCATAATACGAGAGGTGAGTTGAGCCTCAAGCCGCACGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC--GGAACACGCCGAGGTATTTTCAATT
27307377 TCCGTTTTTT----
64 T-C-TTTTTTCAAA
*** * **
27307387 --TTTTAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCGCACGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GG-AACACGCCGAGGTATTTTCAATT
*
27307450 TCCTTTATTTAAAA
64 T-CTTT-TTTCAAA
* * * *
27307464 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCCAAGGTATTTTCTCAATT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGAACACGCCGAGGTA-TTT-TCAATT
*
27307529 TATGTTTTTC---
64 TCT-TTTTTCAAA
* * *
27307539 AAAAATCAACTCATAATGCGAGAGGTGAGTT-AGCCT-GGAATCATGCTGATGTATTTTCAATTT
1 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGAA-CACGCCGAGGTATTTTCAATTT
27307602 CTATTTTTCAAA
65 CT-TTTTTCAAA
27307614 AAAAA
1 AAAAA
27307619 AATTAACAAT
Statistics
Matches: 379, Mismatches: 57, Indels: 55
0.77 0.12 0.11
Matches are distributed among these distances:
72 18 0.05
73 65 0.17
74 13 0.03
75 43 0.11
76 44 0.12
77 15 0.04
78 55 0.15
79 99 0.26
80 8 0.02
81 19 0.05
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (75 bp):
AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGAACACGCCGAGGTATTTTCAATTTC
TTTTTTCAAA
Found at i:27307743 original size:5 final size:5
Alignment explanation
Indices: 27307735--27307798 Score: 62
Period size: 5 Copynumber: 13.0 Consensus size: 5
27307725 ATAGTTCGTG
* * *
27307735 TTTTA TTTTA TTTTA TCTTA TTTTA TTTTA -TATA TATGTA TTTTA --TTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA
27307783 TTATTA TTTTA TTTTA
1 TT-TTA TTTTA TTTTA
27307799 AATTATGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 34 0.69
6 9 0.18
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:27307757 original size:15 final size:14
Alignment explanation
Indices: 27307736--27307796 Score: 70
Period size: 15 Copynumber: 4.2 Consensus size: 14
27307726 TAGTTCGTGT
27307736 TTTATTTTATTTTA
1 TTTATTTTATTTTA
27307750 TCTTATTTTATTTTA
1 T-TTATTTTATTTTA
* *
27307765 TATATATGTATTTTA
1 TTTAT-TTTATTTTA
27307780 -TTATTATTATTTTA
1 TTTATT-TTATTTTA
27307794 TTT
1 TTT
27307797 TAAATTATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.03
14 14 0.36
15 24 0.62
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:27308657 original size:15 final size:14
Alignment explanation
Indices: 27308637--27308697 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 14
27308627 ACAAACGAGC
27308637 AAAAACAAGAAAATA
1 AAAAACAAGAAAA-A
27308652 AAAAAC-AGCAAACAA
1 AAAAACAAG-AAA-AA
*
27308667 AAAAACAAGCAAAGA
1 AAAAACAAG-AAAAA
*
27308682 AGAAA-AAGAAAAA
1 AAAAACAAGAAAAA
27308695 AAA
1 AAA
27308698 GGAAAAGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 6 0.15
14 5 0.13
15 21 0.54
16 7 0.18
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAACAAGAAAAA
Found at i:27308677 original size:16 final size:16
Alignment explanation
Indices: 27308637--27308679 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
27308627 ACAAACGAGC
27308637 AAAAACAAG-AAAATA
1 AAAAACAAGCAAAATA
27308652 AAAAAC-AGCAAACA-A
1 AAAAACAAGCAAA-ATA
27308667 AAAAACAAGCAAA
1 AAAAACAAGCAAA
27308680 GAAGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 16 0.64
16 7 0.28
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (16 bp):
AAAAACAAGCAAAATA
Found at i:27308842 original size:14 final size:14
Alignment explanation
Indices: 27308810--27308857 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
27308800 CGAAGGAGAA
*
27308810 AAAGAAAGAAGAAGG
1 AAAG-AAGAAAAAGG
27308825 -AAGAAGAAAAAGG
1 AAAGAAGAAAAAGG
27308838 AAAGAAGAAAAAGG
1 AAAGAAGAAAAAGG
27308852 AAAGAA
1 AAAGAA
27308858 AAATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAAAGG
Found at i:27308859 original size:24 final size:23
Alignment explanation
Indices: 27308806--27308860 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
27308796 AGTCCGAAGG
*
27308806 AGAAAAAGAAAGAAGAAGGAAGA
1 AGAAAAAGAAAGAAGAAGAAAGA
27308829 AGAAAAAGGAAAGAAGAA-AAAGGAA
1 AGAAAAA-GAAAGAAGAAGAAA-G-A
27308854 AGAAAAA
1 AGAAAAA
27308861 TAAATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.32
24 11 0.39
25 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (23 bp):
AGAAAAAGAAAGAAGAAGAAAGA
Found at i:27309730 original size:19 final size:18
Alignment explanation
Indices: 27309706--27309814 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
27309696 AAAAATAATA
27309706 AAAAAATTTCTCGTGTTTC
1 AAAAAATTT-TCGTGTTTC
*
27309725 AAAAAATATATTCGTGTTTTTTA
1 AAAAAAT-T-TTCGTG---TTTC
27309748 AAAAAATAATTTCCGTGTTTC
1 AAAAAAT--TTT-CGTGTTTC
27309769 ---AAATTTTCGTGTTTTC
1 AAAAAATTTTCGTG-TTTC
27309785 -AAAAATTTCTCGTGTTTC
1 AAAAAATTT-TCGTGTTTC
27309803 AAAAAATTTTCG
1 AAAAAATTTTCG
27309815 ACTTTTCGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 25
0.74 0.02 0.24
Matches are distributed among these distances:
15 4 0.05
16 7 0.09
18 17 0.22
19 20 0.26
20 6 0.08
21 4 0.05
23 12 0.16
24 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAAAATTTTCGTGTTTC
Found at i:27309790 original size:18 final size:18
Alignment explanation
Indices: 27309769--27310027 Score: 134
Period size: 18 Copynumber: 13.2 Consensus size: 18
27309759 TCCGTGTTTC
27309769 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
27309787 AAATTTCTCGTG-TTTCAAA
1 AAATTT-TCGTGTTTTC-AA
27309806 AAATTTTCGACTTTTCGCGTTTTCAA
1 AAATTTTCG-----T---GTTTTCAA
*
27309832 AAATTTTCGTGTTTTTAA
1 AAATTTTCGTGTTTTCAA
*
27309850 AATTTTCTCGTGTTTT-AA
1 AAATTT-TCGTGTTTTCAA
27309868 AAATTTTCGACTTTTCGCGTTTTCAA
1 AAATTTTCG-----T---GTTTTCAA
27309894 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
27309912 AAATTTCTCGTGTTTT-AA
1 AAATTT-TCGTGTTTTCAA
*
27309930 AAATTTTCAAATTTTTGCGTTTTCAA
1 AAATTTTC--------GTGTTTTCAA
* *
27309956 AAATTTTCATGTTTT-AG
1 AAATTTTCGTGTTTTCAA
*
27309973 AAATTTTCGTG-TTTCTA
1 AAATTTTCGTGTTTTCAA
* *
27309990 AAATTCTCGT-ATTTCAA
1 AAATTTTCGTGTTTTCAA
* *
27310007 AAATTTCCGTGTTCTCAA
1 AAATTTTCGTGTTTTCAA
27310025 AAA
1 AAA
27310028 AAATTATTAT
Statistics
Matches: 191, Mismatches: 16, Indels: 68
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.02
17 38 0.20
18 67 0.35
19 31 0.16
21 2 0.01
22 1 0.01
23 1 0.01
25 11 0.06
26 33 0.17
27 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (18 bp):
AAATTTTCGTGTTTTCAA
Found at i:27309806 original size:17 final size:17
Alignment explanation
Indices: 27309755--27309806 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
27309745 TTAAAAAAAT
27309755 AATTTC-CGTGTTTC-A
1 AATTTCTCGTGTTTCAA
27309770 AATTT-TCGTGTTTTCAAA
1 AATTTCTCGTG-TTTC-AA
27309788 AATTTCTCGTGTTTCAA
1 AATTTCTCGTGTTTCAA
27309805 AA
1 AA
27309807 AATTTTCGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 9 0.28
16 4 0.12
17 4 0.12
18 10 0.31
19 5 0.16
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (17 bp):
AATTTCTCGTGTTTCAA
Found at i:27309874 original size:27 final size:26
Alignment explanation
Indices: 27309844--27309900 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
27309834 ATTTTCGTGT
* *
27309844 TTTTAAAATTTTCTCGTGTTTTAAAAA
1 TTTTAAAATTTTCGCGT-TTTCAAAAA
** *
27309871 TTTTCGACTTTTCGCGTTTTCAAAAA
1 TTTTAAAATTTTCGCGTTTTCAAAAA
27309897 TTTT
1 TTTT
27309901 CGTGTTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTAAAATTTTCGCGTTTTCAAAAA
Found at i:27309883 original size:62 final size:63
Alignment explanation
Indices: 27309769--27309992 Score: 348
Period size: 62 Copynumber: 3.6 Consensus size: 63
27309759 TCCGTGTTTC
*
27309769 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAATTTTCGACTTTTCGCGTTTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAA
* *
27309832 AAATTTTCGTGTTTTTAAAATTTTCTCGTGTTT-TAAAAATTTTCGACTTTTCGCGTTTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAA
* * *
27309894 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTT-TAAAAATTTTCAAATTTTTGCGTTTTCAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAA
* *
27309956 AAATTTTCATGTTTT-AGAAATTT-TCGTGTTTCTAAAA
1 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAA
27309993 TTCTCGTATT
Statistics
Matches: 150, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
60 8 0.05
61 12 0.08
62 99 0.66
63 31 0.21
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (63 bp):
AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAA
Found at i:27309942 original size:44 final size:43
Alignment explanation
Indices: 27309894--27309980 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 43
27309884 GCGTTTTCAA
* *
27309894 AAATTTTCGTGTTTTCAAAAATTTCTCGTGTTTTAAAAATTTTC
1 AAATTTTCGCGTTTTCAAAAATTT-TCATGTTTTAAAAATTTTC
* *
27309938 AAATTTTTGCGTTTTCAAAAATTTTCATGTTTTAGAAATTTTC
1 AAATTTTCGCGTTTTCAAAAATTTTCATGTTTTAAAAATTTTC
27309981 GTGTTTCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 17 0.44
44 22 0.56
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (43 bp):
AAATTTTCGCGTTTTCAAAAATTTTCATGTTTTAAAAATTTTC
Found at i:27309962 original size:17 final size:16
Alignment explanation
Indices: 27309933--27310027 Score: 68
Period size: 17 Copynumber: 5.6 Consensus size: 16
27309923 GTTTTAAAAA
*
27309933 TTTTC-AAATTTTTGCG
1 TTTTCAAAAATTTT-CG
27309949 TTTTCAAAAATTTTCATG
1 TTTTCAAAAATTTTC--G
*
27309967 TTTT-AGAAATTTTCG
1 TTTTCAAAAATTTTCG
* *
27309982 TGTTTCTAAAATTCTCG
1 T-TTTCAAAAATTTTCG
*
27309999 TATTTCAAAAATTTCCG
1 T-TTTCAAAAATTTTCG
27310016 TGTTCTCAAAAA
1 T-TT-TCAAAAA
27310028 AAATTATTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.03
16 9 0.14
17 40 0.63
18 12 0.19
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.47
Consensus pattern (16 bp):
TTTTCAAAAATTTTCG
Found at i:27311273 original size:25 final size:25
Alignment explanation
Indices: 27311188--27311275 Score: 74
Period size: 24 Copynumber: 3.6 Consensus size: 25
27311178 TGTATAACGA
* *
27311188 GAAGTTCATAAGAGCCATA-ATTAG
1 GAAGCTCATAAGAGCCATATATCAG
* * *
27311212 GAAGTTCA-AGCGAGCCA-ATATCGG
1 GAAGCTCATA-AGAGCCATATATCAG
* **
27311236 GAAACTCCGAAGAGCCATATATCAG
1 GAAGCTCATAAGAGCCATATATCAG
27311261 GAAGCTCATAAGAGC
1 GAAGCTCATAAGAGC
27311276 TATGGTGTGT
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
23 2 0.04
24 28 0.57
25 19 0.39
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCATATATCAG
Found at i:27323704 original size:2 final size:2
Alignment explanation
Indices: 27323697--27323721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27323687 TAAATAATAA
27323697 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27323722 ACTTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27325709 original size:20 final size:20
Alignment explanation
Indices: 27325684--27325738 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
27325674 AAAACCTCTG
*
27325684 GTATCGATATTTTTACACTA
1 GTATCGATATTTTTACAATA
*
27325704 GTATCGATATTTTTATAATA
1 GTATCGATATTTTTACAATA
*
27325724 GTATCAATATTTTTA
1 GTATCGATATTTTTA
27325739 AGTTGGTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
GTATCGATATTTTTACAATA
Found at i:27332061 original size:23 final size:23
Alignment explanation
Indices: 27332034--27332084 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
27332024 ATTTTGTCAA
*
27332034 TTTTAACTTA-TATTTAAAAATAC
1 TTTTAACTTATTATATAAAAAT-C
* *
27332057 TTTTAATTTATTATATCAAAATC
1 TTTTAACTTATTATATAAAAATC
27332080 TTTTA
1 TTTTA
27332085 TCAAATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAACTTATTATATAAAAATC
Found at i:27338868 original size:62 final size:59
Alignment explanation
Indices: 27338760--27338877 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 59
27338750 TAATTTGCCT
*
27338760 AGGGTAGCTTAAAGGAGAAGATCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
1 AGGGTAGCTTAAAGGAGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
* *
27338819 AGGGTAGCTTAAAGAAGAAGAAGAGCCTGTTATCATCGTGCCTTGGGGTATTTATAGGG
1 AGGGTAGCTTAAAG--G-AGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGG
27338878 GGAAGGTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 14 0.26
61 1 0.02
62 38 0.72
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (59 bp):
AGGGTAGCTTAAAGGAGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
Found at i:27345064 original size:4 final size:4
Alignment explanation
Indices: 27345055--27345083 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
27345045 ATAGTAACCT
27345055 TAAC TAAC TAAC TAAC TAAC TAAC TAAC T
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC T
27345084 TAACATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAC
Found at i:27347499 original size:22 final size:22
Alignment explanation
Indices: 27347460--27347506 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
27347450 ATAATAGTTC
**
27347460 AAAAATTTTCTTTTCATTTATTA
1 AAAAATTTTCTTGACATTTA-TA
27347483 AAAAATTTTC-TGACATTTATA
1 AAAAATTTTCTTGACATTTATA
27347504 AAA
1 AAA
27347507 TCTATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 7 0.32
23 10 0.45
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAATTTTCTTGACATTTATA
Found at i:27354862 original size:2 final size:2
Alignment explanation
Indices: 27354855--27354884 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27354845 ATGCTACATA
27354855 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27354885 AAGCTGTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27359005 original size:19 final size:21
Alignment explanation
Indices: 27358943--27358999 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
27358933 ATTTTCGAGG
27358943 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
27358964 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
27358985 ATATACAATCTTAGA
1 ATATACAATCTTAGA
27359000 AGATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:27359684 original size:26 final size:26
Alignment explanation
Indices: 27359605--27359687 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
27359595 CATATACGCA
*
27359605 TATTTTTTT-TGTAGTATA-ATATAAT
1 TATTTTTTTATCTA-TATATATATAAT
* * *
27359630 TATTTTTTTATTTATTTATATGTAAT
1 TATTTTTTTATCTATATATATATAAT
* *
27359656 TATTTTTTTATCTATATGTATATATT
1 TATTTTTTTATCTATATATATATAAT
27359682 TATTTT
1 TATTTT
27359688 AGTATACATA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 12 0.25
26 36 0.75
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (26 bp):
TATTTTTTTATCTATATATATATAAT
Found at i:27359693 original size:22 final size:22
Alignment explanation
Indices: 27359635--27359688 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
27359625 ATAATTATTT
*
27359635 TTTTATTTATTTATATGTAATTA
1 TTTT-TTTATCTATATGTAATTA
27359658 TTTTTTTATCTATATGT-ATATA
1 TTTTTTTATCTATATGTAAT-TA
27359680 TTTATTTTA
1 TTT-TTTTA
27359689 GTATACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 17 0.61
23 9 0.32
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTTTATCTATATGTAATTA
Found at i:27369686 original size:19 final size:19
Alignment explanation
Indices: 27369662--27369698 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27369652 ATTCAAGCCC
*
27369662 CAAGATTAAATAATAAAAG
1 CAAGATTAAATAAGAAAAG
27369681 CAAGATTAAATAAGAAAA
1 CAAGATTAAATAAGAAAA
27369699 CAATTCACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.19
Consensus pattern (19 bp):
CAAGATTAAATAAGAAAAG
Found at i:27374192 original size:41 final size:40
Alignment explanation
Indices: 27374135--27374243 Score: 137
Period size: 41 Copynumber: 2.6 Consensus size: 40
27374125 TGATCGAATG
* * *
27374135 TAATTCAGACTTATTGTCTAGCAGGCTTGATGCCGGTGATA
1 TAATTCAGAC-TATTGTCTAGCAGGCTTAATGCCAGTGAAA
27374176 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACT-ATTGTCTAGCAGGCTTAATGCCAGTGAAA
* * *
27374217 TTATTCAAACTATAAGTCTAGCAGGCT
1 TAATTCAGACTAT-TGTCTAGCAGGCT
27374244 AAAAGTCGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
40 3 0.05
41 57 0.95
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (40 bp):
TAATTCAGACTATTGTCTAGCAGGCTTAATGCCAGTGAAA
Found at i:27374389 original size:21 final size:21
Alignment explanation
Indices: 27374340--27374389 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
27374330 ACGTGATATG
27374340 TAAATAA-TATAGATATTTGA
1 TAAATAAGTATAGATATTTGA
* *
27374360 -AGATCAAGTATATATATTTGA
1 TAAAT-AAGTATAGATATTTGA
27374381 TAAATAAGT
1 TAAATAAGT
27374390 TTGATGAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 16 0.67
22 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (21 bp):
TAAATAAGTATAGATATTTGA
Found at i:27375660 original size:41 final size:41
Alignment explanation
Indices: 27375603--27375719 Score: 189
Period size: 41 Copynumber: 2.9 Consensus size: 41
27375593 TAAAATAGAT
27375603 TCACCGGCACTTAGCCTGCTAGGTTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTAAAGCCTGATTCAGA
* * * *
27375644 TCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGTTTAAAGCCTGATTCAGA
*
27375685 TCACCGGCACTTAGCCTGCTAGGTTTTAAGCCTGA
1 TCACCGGCACTTAGCCTGCTAGGTTTAAAGCCTGA
27375720 ATTGATTCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTAAAGCCTGATTCAGA
Found at i:27375729 original size:41 final size:40
Alignment explanation
Indices: 27375600--27375734 Score: 166
Period size: 41 Copynumber: 3.3 Consensus size: 40
27375590 AATTAAAATA
*
27375600 GATTCACCGGCACTTAGCCTGCTAGGTTTAAAGCCTGATT
1 GATTCACCGGCACTTAGCCTGCTAGGTTTTAAGCCTGATT
* *
27375640 CAGA-TCACCGGCACTTAGCCTGCTAGG-CTTATAGTCTGATT
1 --GATTCACCGGCACTTAGCCTGCTAGGTTTTA-AGCCTGATT
*
27375681 CAGTTCACCGGCACTTAGCCTGCTAGGTTTTAAGCCTGAATT
1 GA-TTCACCGGCACTTAGCCTGCTAGGTTTTAAGCCTG-ATT
*
27375723 GATTCACTGGCA
1 GATTCACCGGCA
27375735 ATATACCTGC
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 68 0.85
42 9 0.11
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (40 bp):
GATTCACCGGCACTTAGCCTGCTAGGTTTTAAGCCTGATT
Found at i:27381231 original size:21 final size:21
Alignment explanation
Indices: 27381179--27381220 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
27381169 TGCGATTGGT
**
27381179 TATTGTAGTGGTGAGATTAAA
1 TATTGTAGTAATGAGATTAAA
27381200 TATTGTAGTAATGAGATTAAA
1 TATTGTAGTAATGAGATTAAA
27381221 ATTAGTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (21 bp):
TATTGTAGTAATGAGATTAAA
Found at i:27386859 original size:22 final size:21
Alignment explanation
Indices: 27386816--27386860 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
27386806 TATAGTCAAG
*
27386816 TATCGATACCAAATGTTAAAA
1 TATCGATACCAAATGCTAAAA
27386837 TATCGATACCCAAAT-CTAGAAA
1 TATCGATA-CCAAATGCTA-AAA
27386859 TA
1 TA
27386861 GTAAAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.27
Consensus pattern (21 bp):
TATCGATACCAAATGCTAAAA
Found at i:27403844 original size:6 final size:6
Alignment explanation
Indices: 27403828--27403877 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
27403818 TAATTTTCTC
*
27403828 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AGAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG
27403877 A
1 A
27403878 TTCATTTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 35 0.85
7 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:27407166 original size:2 final size:2
Alignment explanation
Indices: 27407161--27407203 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
27407151 TAAATACATA
27407161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27407202 AT
1 AT
27407204 GATTAGTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27409054 original size:3 final size:3
Alignment explanation
Indices: 27409048--27409074 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27409038 TCTATTATTT
27409048 TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC
27409075 CCATTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:27409832 original size:25 final size:23
Alignment explanation
Indices: 27409761--27409817 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
27409751 CTTCCATAAT
27409761 TTCATTATATAAGTTCTTATCAC
1 TTCATTATATAAGTTCTTATCAC
27409784 TTCATTATATAAGTTCTTATCAC
1 TTCATTATATAAGTTCTTATCAC
27409807 TTCATTATATA
1 TTCATTATATA
27409818 CAATTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.49
Consensus pattern (23 bp):
TTCATTATATAAGTTCTTATCAC
Found at i:27425755 original size:53 final size:53
Alignment explanation
Indices: 27425501--27425757 Score: 300
Period size: 53 Copynumber: 4.8 Consensus size: 53
27425491 AGCACTAAAG
* * * * * *
27425501 GACCATATCATGTAAAATCATAATTAGTGGGTTATGACATCATATGGAATGAA
1 GACCATATCATGTAAGACCGTAACTAGTGGGTTATGGCATCATATGGAAAGAA
* * *
27425554 GACCATATCGTGTAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAGAA
1 GACCATATCATGTAAGACCGTAACTAGTGGGTTATGGCATCATATGGAAAGAA
* * * * *
27425607 AAACATATCATGTAAGACCATAACTGGTGGGTTAAGGCATCATATGGAAAGAA
1 GACCATATCATGTAAGACCGTAACTAGTGGGTTATGGCATCATATGGAAAGAA
* ** * * *
27425660 GATCATATTGTGTAAGACCGTCACT-GATGGGTTATAGCATCATATGAAAAGAA
1 GACCATATCATGTAAGACCGTAACTAG-TGGGTTATGGCATCATATGGAAAGAA
* *
27425713 GACCATATCATGTAAGACCGTAACTAGTGGGTTATCGTATCATAT
1 GACCATATCATGTAAGACCGTAACTAGTGGGTTATGGCATCATAT
27425758 AGAAGAACTT
Statistics
Matches: 172, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
52 1 0.01
53 170 0.99
54 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (53 bp):
GACCATATCATGTAAGACCGTAACTAGTGGGTTATGGCATCATATGGAAAGAA
Found at i:27425755 original size:106 final size:105
Alignment explanation
Indices: 27425501--27425757 Score: 334
Period size: 106 Copynumber: 2.4 Consensus size: 105
27425491 AGCACTAAAG
* * * *
27425501 GACCATATCATGTAAAATCATAATTAGTGGGTTATGACATCATATGGAATGAAGACCATATCGTG
1 GACCATATCATGTAAGACCATAACTAGTGGGTTATG-CATCATATGGAAAGAAGACCATATCGTG
* * *
27425566 TAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAGAA
65 TAAGACCGTAACTGATGAGTTATAGCATCATATGAAAAGAA
* * * * * *
27425607 AAACATATCATGTAAGACCATAACTGGTGGGTTAAGGCATCATATGGAAAGAAGATCATATTGTG
1 GACCATATCATGTAAGACCATAACTAGTGGGTT-ATGCATCATATGGAAAGAAGACCATATCGTG
* *
27425672 TAAGACCGTCACTGATGGGTTATAGCATCATATGAAAAGAA
65 TAAGACCGTAACTGATGAGTTATAGCATCATATGAAAAGAA
* *
27425713 GACCATATCATGTAAGACCGTAACTAGTGGGTTATCGTATCATAT
1 GACCATATCATGTAAGACCATAACTAGTGGGTTAT-GCATCATAT
27425758 AGAAGAACTT
Statistics
Matches: 128, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
105 1 0.01
106 125 0.98
107 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (105 bp):
GACCATATCATGTAAGACCATAACTAGTGGGTTATGCATCATATGGAAAGAAGACCATATCGTGT
AAGACCGTAACTGATGAGTTATAGCATCATATGAAAAGAA
Found at i:27431444 original size:49 final size:51
Alignment explanation
Indices: 27431359--27431468 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 51
27431349 AATATAAAAA
* **
27431359 TATTACAAATTGATTAAAAATATAGAAAAT-TTAAAAAA-GAGT-AAATTT
1 TATTAAAAATTGATTAAAAATATAGAAAATCAAAAAAAATGAGTAAAATTT
*
27431407 TATTATAAAATT-ATTATAAAATAT-GAAAATACAAAAAAAATGATTAAAATTT
1 TATTA-AAAATTGATTA-AAAATATAGAAAAT-CAAAAAAAATGAGTAAAATTT
27431459 TATTAAAAAT
1 TATTAAAAAT
27431469 CATAAAACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
48 15 0.29
49 12 0.23
50 6 0.12
51 8 0.15
52 11 0.21
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (51 bp):
TATTAAAAATTGATTAAAAATATAGAAAATCAAAAAAAATGAGTAAAATTT
Found at i:27431487 original size:21 final size:19
Alignment explanation
Indices: 27431463--27431537 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 19
27431453 AAATTTTATT
27431463 AAAAATCATAAAACTATAAAA
1 AAAAAT-ATAAAA-TATAAAA
*
27431484 AAAAATTTAAAAATTATAAAA
1 AAAAATAT-AAAA-TATAAAA
* *
27431505 AATTAATATAAAAGATAAAA
1 AA-AAATATAAAATATAAAA
* *
27431525 AAATATAGAAAAT
1 AAAAATATAAAAT
27431538 TATTAAAAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 7 0.16
20 9 0.21
21 23 0.53
22 4 0.09
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAATATAAAATATAAAA
Found at i:27431517 original size:11 final size:10
Alignment explanation
Indices: 27431483--27431545 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
27431473 AAACTATAAA
27431483 AAAAAATT-T
1 AAAAAATTAT
27431492 -AAAAATTAT
1 AAAAAATTAT
27431501 AAAAAATTAAT
1 AAAAAATT-AT
* *
27431512 ATAAAA-GAT
1 AAAAAATTAT
*
27431521 AAAAAAATAT
1 AAAAAATTAT
*
27431531 AGAAAATTATT
1 AAAAAATTA-T
27431542 AAAA
1 AAAA
27431546 GTTTATTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
8 7 0.17
9 8 0.19
10 16 0.38
11 11 0.26
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:27433365 original size:17 final size:17
Alignment explanation
Indices: 27433343--27433377 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
27433333 TGTTTTAGAG
27433343 AAAAATTGTCACAATTT
1 AAAAATTGTCACAATTT
27433360 AAAAATTGTCACAATTT
1 AAAAATTGTCACAATTT
27433377 A
1 A
27433378 CATAATGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
AAAAATTGTCACAATTT
Found at i:27435868 original size:27 final size:28
Alignment explanation
Indices: 27435816--27435869 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
27435806 TTTTTTCTAA
*
27435816 TTTTTTATCTTTTATAATAAAATTTTAG
1 TTTTTTATCTTTTATAAGAAAATTTTAG
* *
27435844 TTTTTTATGTTTT-TAAGAAATTTTTA
1 TTTTTTATCTTTTATAAGAAAATTTTA
27435870 AATTTCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.63
Consensus pattern (28 bp):
TTTTTTATCTTTTATAAGAAAATTTTAG
Found at i:27435943 original size:18 final size:18
Alignment explanation
Indices: 27435908--27435984 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
27435898 ATAAATGTTG
27435908 AATATTTTATATATTTTTAAT
1 AATATTTT-TA-A-TTTTAAT
27435929 AATATTTTTAATTTTAAAT
1 AATATTTTTAATTTT-AAT
* *
27435948 GAT-TTTTTCA-TTT-AT
1 AATATTTTTAATTTTAAT
* *
27435963 ATATATCTGTAATTTTAAT
1 A-ATATTTTTAATTTTAAT
27435982 AAT
1 AAT
27435985 TTTATTCATT
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
15 2 0.04
16 2 0.04
17 7 0.16
18 15 0.33
19 9 0.20
20 2 0.04
21 8 0.18
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
AATATTTTTAATTTTAAT
Found at i:27436372 original size:16 final size:16
Alignment explanation
Indices: 27436318--27436383 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
27436308 TATTAAAATA
*
27436318 AAATTATAATATTGAAT
1 AAATTATTATATT-AAT
* * *
27436335 AATTTATTAAAATAAT
1 AAATTATTATATTAAT
27436351 -AA--ATTATATTAAT
1 AAATTATTATATTAAT
*
27436364 AAATTATTATATTATT
1 AAATTATTATATTAAT
27436380 AAAT
1 AAAT
27436384 ATAAATAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 1 0.03
16 17 0.45
17 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTATTATATTAAT
Found at i:27436838 original size:25 final size:24
Alignment explanation
Indices: 27436810--27436857 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
27436800 CAAATCCAAA
27436810 TGATTAGAACCTAAAATAATTCAAT
1 TGATTAGAACCTAAAAT-ATTCAAT
* * *
27436835 TGATTTGAACTTACAATATTCAA
1 TGATTAGAACCTAAAATATTCAA
27436858 ACTAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (24 bp):
TGATTAGAACCTAAAATATTCAAT
Found at i:27439610 original size:2 final size:2
Alignment explanation
Indices: 27439603--27439635 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27439593 GTTATATCGT
27439603 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27439636 AACTGCACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27442727 original size:3 final size:3
Alignment explanation
Indices: 27442721--27442747 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27442711 CAAAAAAAAG
27442721 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
27442748 TTCGGTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27445406 original size:2 final size:2
Alignment explanation
Indices: 27445399--27445429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27445389 AAGATACATC
27445399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27445430 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27457517 original size:65 final size:65
Alignment explanation
Indices: 27457413--27457545 Score: 266
Period size: 65 Copynumber: 2.0 Consensus size: 65
27457403 TTGATGTCAT
27457413 TGTCAGTTCTTCCAGGCAATTGTGCTGCAATTATAGACCATCTGCGCATTCAAAGAAAGCATATA
1 TGTCAGTTCTTCCAGGCAATTGTGCTGCAATTATAGACCATCTGCGCATTCAAAGAAAGCATATA
27457478 TGTCAGTTCTTCCAGGCAATTGTGCTGCAATTATAGACCATCTGCGCATTCAAAGAAAGCATATA
1 TGTCAGTTCTTCCAGGCAATTGTGCTGCAATTATAGACCATCTGCGCATTCAAAGAAAGCATATA
27457543 TGT
1 TGT
27457546 AATTGAAGTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (65 bp):
TGTCAGTTCTTCCAGGCAATTGTGCTGCAATTATAGACCATCTGCGCATTCAAAGAAAGCATATA
Found at i:27466199 original size:5 final size:5
Alignment explanation
Indices: 27466189--27466219 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
27466179 TACAGTATCC
27466189 CTCAA CTCAA CTCAA CTCAA CTCAA CTCAA C
1 CTCAA CTCAA CTCAA CTCAA CTCAA CTCAA C
27466220 AGTCCAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CTCAA
Found at i:27471161 original size:45 final size:45
Alignment explanation
Indices: 27471107--27471199 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
27471097 TAACATGAAC
*
27471107 GTGTTTTCATTCACTCTCATTACCCATAATTTATAACACATAGTT
1 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATAGTT
*
27471152 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
1 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATAGTT
27471197 GTG
1 GTG
27471200 AATTAGCCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.42
Consensus pattern (45 bp):
GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATAGTT
Found at i:27473999 original size:2 final size:2
Alignment explanation
Indices: 27473992--27474022 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27473982 CTTTAGTTTG
*
27473992 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27474023 TTATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:27474027 original size:10 final size:10
Alignment explanation
Indices: 27473992--27474030 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
27473982 CTTTAGTTTG
*
27473992 TATATATATA
1 TATATTTATA
*
27474002 TATATATATA
1 TATATTTATA
27474012 TATATTTATA
1 TATATTTATA
*
27474022 TTTATTTAT
1 TATATTTAT
27474031 TTTGGTATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATTTATA
Found at i:27474062 original size:31 final size:31
Alignment explanation
Indices: 27474024--27474087 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
27474014 TATTTATATT
* *
27474024 TATTTATTTTGGTATCCGAATTTGATAACTA
1 TATTTATTTTGGTATCCAAATTTGATAAATA
* *
27474055 TATTTATTTTGGTCTCTAAATTTGATAAATA
1 TATTTATTTTGGTATCCAAATTTGATAAATA
27474086 TA
1 TA
27474088 AAATTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (31 bp):
TATTTATTTTGGTATCCAAATTTGATAAATA
Found at i:27475292 original size:19 final size:19
Alignment explanation
Indices: 27475270--27475309 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27475260 TCAATTTTTC
* *
27475270 ATTTTGCTTCTTAAATAAA
1 ATTTTGCTTCTAAAAGAAA
*
27475289 ATTTTGTTTCTAAAAGAAA
1 ATTTTGCTTCTAAAAGAAA
27475308 AT
1 AT
27475310 CATTTTCGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (19 bp):
ATTTTGCTTCTAAAAGAAA
Found at i:27480439 original size:15 final size:15
Alignment explanation
Indices: 27480414--27480448 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27480404 TACTTTATTT
*
27480414 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
27480428 TAATTAATATTAAGA
1 TAATTAATATTAAGA
27480443 TAATTA
1 TAATTA
27480449 TTAACGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:27483304 original size:69 final size:69
Alignment explanation
Indices: 27483193--27483333 Score: 219
Period size: 69 Copynumber: 2.0 Consensus size: 69
27483183 CTCGAAACAT
* * *
27483193 TTAGGAATGTCGAGATCAACATTCCGCTGTTGGACGCCATCAAGCAAATACCACAGTATGCTAAA
1 TTAGGAATGTCGAGATCAACATTCCACTGTTGGACGCAATCAAGAAAATACCACAGTATGCTAAA
27483258 TTTC
66 TTTC
* * * *
27483262 TTAGGAATGTCGAGATTAAGATTCCACTGTTGGACGCAATCAAGAAAATACCGCGGTATGCTAAA
1 TTAGGAATGTCGAGATCAACATTCCACTGTTGGACGCAATCAAGAAAATACCACAGTATGCTAAA
27483327 TTTC
66 TTTC
27483331 TTA
1 TTA
27483334 AAGATCTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (69 bp):
TTAGGAATGTCGAGATCAACATTCCACTGTTGGACGCAATCAAGAAAATACCACAGTATGCTAAA
TTTC
Found at i:27484465 original size:5 final size:5
Alignment explanation
Indices: 27484450--27484516 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
27484440 GCAACCCAAT
* * *
27484450 TTTTA TTTT- TTATTT TTTTA -TTT- TTTTA TTTTT TTTTA CTTTA TTTATTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA
*
27484500 CTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
27484517 ATTTATTACT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 8 0.16
5 34 0.69
6 4 0.08
7 3 0.06
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:27484466 original size:8 final size:8
Alignment explanation
Indices: 27484449--27484520 Score: 69
Period size: 8 Copynumber: 9.1 Consensus size: 8
27484439 GGCAACCCAA
27484449 TTTTTA-T
1 TTTTTATT
27484456 TTTTTATT
1 TTTTTATT
27484464 TTTTTATT
1 TTTTTATT
27484472 TTTTTATT
1 TTTTTATT
27484480 TTTTT-TT
1 TTTTTATT
**
27484487 ACTTTA-T
1 TTTTTATT
*
27484494 TTATTACTT
1 TTTTTA-TT
27484503 TATTTTATT
1 T-TTTTATT
*
27484512 TTATTATT
1 TTTTTATT
27484520 T
1 T
27484521 ATTACTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
7 15 0.28
8 29 0.55
9 5 0.09
10 4 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTATT
Found at i:27484474 original size:22 final size:22
Alignment explanation
Indices: 27484449--27484520 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
27484439 GGCAACCCAA
27484449 TTTTTATTTTTTATTTTTTTATT
1 TTTTTATTTTTTATTTTTTTA-T
*
27484472 TTTTTATTTTTT-TTTACTTTAT
1 TTTTTATTTTTTATTT-TTTTAT
* *
27484494 TTATTACTTTATTTTATTTTATTAT
1 TTTTTA--TT-TTTTATTTTTTTAT
27484519 TT
1 TT
27484521 ATTACTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.22
23 16 0.40
24 2 0.05
25 10 0.25
26 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTATTTTTTATTTTTTTAT
Found at i:27484492 original size:23 final size:23
Alignment explanation
Indices: 27484449--27484495 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
27484439 GGCAACCCAA
*
27484449 TTTTTATTTTTTATTTTTTTATT
1 TTTTTATTTTTTATTTCTTTATT
27484472 TTTTTATTTTTT-TTTACTTTATT
1 TTTTTATTTTTTATTT-CTTTATT
27484495 T
1 T
27484496 ATTACTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.85
Consensus pattern (23 bp):
TTTTTATTTTTTATTTCTTTATT
Found at i:27484500 original size:12 final size:12
Alignment explanation
Indices: 27484485--27484531 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
27484475 TTATTTTTTT
27484485 TTACTTTATTTA
1 TTACTTTATTTA
27484497 TTACTTTATTTTA
1 TTACTTTA-TTTA
*
27484510 TT-TTATTATTTA
1 TTACT-TTATTTA
27484522 TTAC-TTATTT
1 TTACTTTATTT
27484532 GGATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 9 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:27485998 original size:25 final size:24
Alignment explanation
Indices: 27485970--27486085 Score: 99
Period size: 25 Copynumber: 4.7 Consensus size: 24
27485960 GTATAACGAA
* *
27485970 AAGCTCTTGCGAGCCAATTATCGGG
1 AAGCTCATGAGAGCC-ATTATCGGG
* *
27485995 AAGCTCAT-ATGAGCCATAAACGGG
1 AAGCTCATGA-GAGCCATTATCGGG
*
27486019 AAGCTCAAGAGAGCCATTAATCGGG
1 AAGCTCATGAGAGCCATT-ATCGGG
* * *
27486044 AAGCTCTTGAGAGCCAAATATCGAG
1 AAGCTCATGAGAGCC-ATTATCGGG
**
27486069 AAGCTTGTGAGAGCCAT
1 AAGCTCATGAGAGCCAT
27486086 AAAACGGAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
24 22 0.30
25 49 0.67
26 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.20
Consensus pattern (24 bp):
AAGCTCATGAGAGCCATTATCGGG
Found at i:27489471 original size:17 final size:17
Alignment explanation
Indices: 27489449--27489484 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
27489439 TGTAACTTTA
27489449 TTAAGAAATG-TGAAAGG
1 TTAAGAAA-GATGAAAGG
27489466 TTAAGAAAGATGAAAGG
1 TTAAGAAAGATGAAAGG
27489483 TT
1 TT
27489485 GAACATCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (17 bp):
TTAAGAAAGATGAAAGG
Found at i:27490216 original size:29 final size:29
Alignment explanation
Indices: 27490174--27490231 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
27490164 ATTGGATACT
27490174 CAATAGCAATTCTTTATAATATCATTGTG
1 CAATAGCAATTCTTTATAATATCATTGTG
*
27490203 CAATAGCTATTCTTTATAATATCATTGTG
1 CAATAGCAATTCTTTATAATATCATTGTG
27490232 TAACAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (29 bp):
CAATAGCAATTCTTTATAATATCATTGTG
Found at i:27498707 original size:25 final size:25
Alignment explanation
Indices: 27498663--27498724 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
27498653 GGAATTTTTT
*
27498663 TTAATATTAATATAATTATTTTTCA
1 TTAATATTAATATAATTATTTTTAA
*
27498688 TTAATATTAATATTGA-TATTTTTAA
1 TTAATATTAATA-TAATTATTTTTAA
*
27498713 TCATATATTAAT
1 TTA-ATATTAAT
27498725 TATTTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAATATTAATATAATTATTTTTAA
Found at i:27501649 original size:12 final size:11
Alignment explanation
Indices: 27501618--27501669 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
27501608 ACTTTTTTAA
27501618 TTTTAAAATAT
1 TTTTAAAATAT
27501629 TTTTAAAATACT
1 TTTTAAAATA-T
*
27501641 TTTTTAAAT-T
1 TTTTAAAATAT
27501651 TTTT-AAAT-T
1 TTTTAAAATAT
27501660 TTTTAAAATA
1 TTTTAAAATA
27501670 AAAATAGGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 9 0.24
10 9 0.24
11 10 0.27
12 9 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:27501661 original size:8 final size:9
Alignment explanation
Indices: 27501640--27501666 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
27501630 TTTAAAATAC
27501640 TTTTTTAAA
1 TTTTTTAAA
27501649 TTTTTTAAA
1 TTTTTTAAA
27501658 TTTTTTAAA
1 TTTTTTAAA
27501667 ATAAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:27501663 original size:31 final size:31
Alignment explanation
Indices: 27501578--27501669 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 31
27501568 AATATATTTA
* *
27501578 TTTTTTAAAATTTTAAAATATTTTTTACATAC
1 TTTTTT-AAATTTTAAAATATTTTTAAAATAC
27501610 TTTTTT-AATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC
*
27501640 TTTTTTAAATTTTTTAAAT-TTTTTAAAATA
1 TTTTTTAAA-TTTTAAAATATTTTTAAAATA
27501670 AAAATAGGCC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
30 28 0.51
31 13 0.24
32 14 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:27522137 original size:12 final size:12
Alignment explanation
Indices: 27522120--27522153 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27522110 GTTTTTGCCA
27522120 AAATTGACTAAC
1 AAATTGACTAAC
27522132 AAATTGACTAAC
1 AAATTGACTAAC
*
27522144 CAATCTGACT
1 AAAT-TGACT
27522154 CATGATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (12 bp):
AAATTGACTAAC
Found at i:27528468 original size:309 final size:309
Alignment explanation
Indices: 27527909--27528526 Score: 1119
Period size: 309 Copynumber: 2.0 Consensus size: 309
27527899 ATATTTAGAA
27527909 GACTGTGATGCACTCAGTAGGTGGATTTGTAGCATCCAAAAAATCGGGTTAGTAGAAATTAAGTT
1 GACTGTGATGCACTCAGTAGGTGGATTTGTAGCATCCAAAAAATCGGGTTAGTAGAAATTAAGTT
* *
27527974 CATGAACTGAGAGCGGTCACACCCTAATTTTTTTAAGGTTATCTTCGCATATTTGGTAATAAATA
66 CATGAACTGAGAACGGTCACACCCTAATTTTTTTAAGGTTATCTTCGCACATTTGGTAATAAATA
*
27528039 GATATCAATTATAATGATTGAGTAGTGGTGGAGCTGTCCTTGATGATTTGTGTTCAAATCCCTTC
131 GATATCAATTATAATGATTGAGTAGTGGTGGAGCTGTCATTGATGATTTGTGTTCAAATCCCTTC
* *
27528104 CCTCTCATTAATTTCTATTTGGTGCAAATTTGTTTCAAACCCTTACGTAGATCATCTCATGTTTT
196 CCTCTCATTAATTTCTATTTGGTGCAAATTTGTTTCAAACCCTTACATAGATCATCCCATGTTTT
27528169 ATTTATTTTCTTATTAAATTAATATCATATGAGTTATAGATTCAAGTCT
261 ATTTATTTTCTTATTAAATTAATATCATATGAGTTATAGATTCAAGTCT
* *
27528218 GACTGTGATGCACTCAGTAGGTGGATTTGTAGCATCCCAAAAATCGGGTTAGTAGAAATTGAGTT
1 GACTGTGATGCACTCAGTAGGTGGATTTGTAGCATCCAAAAAATCGGGTTAGTAGAAATTAAGTT
* * *
27528283 CATGAACTGAGAACGGTCACGCCTTGATTTTTTTAAGGTTATCTTCGCACATTTGGTAATAAATA
66 CATGAACTGAGAACGGTCACACCCTAATTTTTTTAAGGTTATCTTCGCACATTTGGTAATAAATA
*
27528348 GATATCAATTATAATGATTGAGTAGTGGTGGAGCTGTCATTGATGATTTGTGTTCGAATCCCTTC
131 GATATCAATTATAATGATTGAGTAGTGGTGGAGCTGTCATTGATGATTTGTGTTCAAATCCCTTC
* *
27528413 CTTCTCGTTAATTTCTATTTGGTGCAAATTTGTTTCAAACCCTTACATAGATCATCCCATGTTTT
196 CCTCTCATTAATTTCTATTTGGTGCAAATTTGTTTCAAACCCTTACATAGATCATCCCATGTTTT
27528478 ATTTATTTTCTTATTAAATTAATATCATATGAGTTATAGATTCAAGTCT
261 ATTTATTTTCTTATTAAATTAATATCATATGAGTTATAGATTCAAGTCT
27528527 CCTAATCAAC
Statistics
Matches: 296, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
309 296 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (309 bp):
GACTGTGATGCACTCAGTAGGTGGATTTGTAGCATCCAAAAAATCGGGTTAGTAGAAATTAAGTT
CATGAACTGAGAACGGTCACACCCTAATTTTTTTAAGGTTATCTTCGCACATTTGGTAATAAATA
GATATCAATTATAATGATTGAGTAGTGGTGGAGCTGTCATTGATGATTTGTGTTCAAATCCCTTC
CCTCTCATTAATTTCTATTTGGTGCAAATTTGTTTCAAACCCTTACATAGATCATCCCATGTTTT
ATTTATTTTCTTATTAAATTAATATCATATGAGTTATAGATTCAAGTCT
Found at i:27530292 original size:19 final size:20
Alignment explanation
Indices: 27530261--27530301 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
27530251 TGGGTAGGAC
27530261 TGTTTTCACAAAATCTGCAT
1 TGTTTTCACAAAATCTGCAT
*
27530281 TGTTTT-ACAAAATGTGCAT
1 TGTTTTCACAAAATCTGCAT
27530300 TG
1 TG
27530302 ACGTGATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTTTTCACAAAATCTGCAT
Found at i:27532199 original size:26 final size:26
Alignment explanation
Indices: 27532165--27532224 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
27532155 TTTATAACAG
* **
27532165 TAAAATTTTGACAATTTTATTCCTGA
1 TAAAATTTTGACAATTTTACTCCCAA
**
27532191 TAAAATTTTGATGATTTTACTCCCAA
1 TAAAATTTTGACAATTTTACTCCCAA
27532217 TAAAATTT
1 TAAAATTT
27532225 CGAGAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (26 bp):
TAAAATTTTGACAATTTTACTCCCAA
Found at i:27538680 original size:7 final size:7
Alignment explanation
Indices: 27538668--27538693 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27538658 TGTTTAAAAT
27538668 GGAGGAA
1 GGAGGAA
27538675 GGAGGAA
1 GGAGGAA
27538682 GGAGGAA
1 GGAGGAA
27538689 GGAGG
1 GGAGG
27538694 TGATTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (7 bp):
GGAGGAA
Found at i:27540416 original size:12 final size:12
Alignment explanation
Indices: 27540399--27540424 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27540389 AATCAAAAGC
27540399 AACTCTTAGCCA
1 AACTCTTAGCCA
27540411 AACTCTTAGCCA
1 AACTCTTAGCCA
27540423 AA
1 AA
27540425 ATTGGTACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (12 bp):
AACTCTTAGCCA
Found at i:27541165 original size:3 final size:3
Alignment explanation
Indices: 27541148--27541248 Score: 123
Period size: 3 Copynumber: 34.0 Consensus size: 3
27541138 AGGTTAGATC
* * * * *
27541148 AAT AAA AAT -AT AAT AAT AGT AGT AGT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
27541195 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAC AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27541243 AAT AAT
1 AAT AAT
27541249 GAAGCTCAAG
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 85 0.98
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27541344 original size:20 final size:21
Alignment explanation
Indices: 27541305--27541344 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
27541295 AATCACGATG
* *
27541305 AAAAAAACTAAAATAGTAAAT
1 AAAAAAACTAAAAAAATAAAT
27541326 AAAAAAA-TAAAAAAATAAA
1 AAAAAAACTAAAAAAATAAA
27541345 ACACAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (21 bp):
AAAAAAACTAAAAAAATAAAT
Found at i:27542096 original size:4 final size:4
Alignment explanation
Indices: 27542087--27542119 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
27542077 TTTTCCTTCG
27542087 AAAT AAAT AAAT AAAT -AA- AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
27542120 CTGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:27542110 original size:14 final size:14
Alignment explanation
Indices: 27542091--27542119 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27542081 CCTTCGAAAT
27542091 AAATAAATAAATAA
1 AAATAAATAAATAA
27542105 AAATAAATAAATAA
1 AAATAAATAAATAA
27542119 A
1 A
27542120 CTGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:27542870 original size:51 final size:51
Alignment explanation
Indices: 27542792--27542914 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
27542782 GTCAATTTTA
* * * * * **
27542792 AATGCTAGGGAGATGAGATTCGTTGCCTTCAACTTTAATCTGTTCCGTTAG-
1 AATGCCAGGGAAATAAGATTCGCTGCCTTCAACTTTAATCCGTTCCACT-GC
* *
27542843 AATGCCAGGGAAATAAGATTTGCTGCCTTCAGCTTTAATCCGTTCCACTGC
1 AATGCCAGGGAAATAAGATTCGCTGCCTTCAACTTTAATCCGTTCCACTGC
*
27542894 AATGCCAGGGAAATAAAATTC
1 AATGCCAGGGAAATAAGATTC
27542915 ACTATCTTCG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.02
51 59 0.98
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (51 bp):
AATGCCAGGGAAATAAGATTCGCTGCCTTCAACTTTAATCCGTTCCACTGC
Found at i:27543115 original size:44 final size:43
Alignment explanation
Indices: 27543061--27543665 Score: 259
Period size: 44 Copynumber: 13.8 Consensus size: 43
27543051 TTTTTTTTTG
* *
27543061 ATCTACTCCACTACTGCTTAGGGAGACAAGATCTACATTCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TACATTCTTCA
* * * * * * * * *
27543105 ACCTACTCCACTGCTGCTCAGGGAGATGAGATTA-GTAGCCTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTACAT-TCTTCA
* *
27543148 ATCTGCTTCC-CTACTACCTT-GGGAAGATAAGATTCACCA-TCTTCG
1 ATCTGC-TCCACTACT-GCTTAGGG-AGATAAGATT-A-CATTCTTCA
* **
27543193 ATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TACATTCTTCA
* * * * * * * *
27543237 ACCTACTCCACTGCTGCTCAGGGAGATAGGATTA-GTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTACAT-TCTTCA
* *
27543280 ATCTGTTTCCTTACTAC--CTT-GGGAAGATAAGATT-CATCGTCTTCG
1 ATCTG-CTCC--ACTACTGCTTAGGG-AGATAAGATTACAT--TCTTCA
* * **
27543325 ATCTGCTCCGCTGCTGCTTAGGGAGACCAGATCTACATTCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TACATTCTTCA
* * * * * * *
27543369 ACCTACTCTACTGCTGCTTAGGGAGATAAGATTA-GTAGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTACAT-TCTTCA
* ** *
27543412 ATCTGCTTCC-CTACTAGCTTAGGAAGATAAGATTCACCGTCTTCG
1 ATCTGC-TCCACTACT-GCTTAGGGAGATAAGATT-ACATTCTTCA
* * **
27543457 ATCTGCTCCGCTGCTGCTTAGGGAGACCAGATCTACATTCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TACATTCTTCA
* * ** * * * * * *
27543501 ACCTACTCCACTGTTGCTCAAGGAGATAGGATTA-GTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTACAT-TCTTCA
* * *
27543544 ATCTGCTTCC-CTATTAACTT-GGGAAGATAAGATT-CATCGTCTTCG
1 ATCTGC-TCCACTACT-GCTTAGGG-AGATAAGATTACAT--TCTTCA
* *
27543589 ATCTGCTCCACTACTGCTTAGGGAAACAAGATCTACATTCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TACATTCTTCA
* * * * * *
27543633 ACCTACTCCACTTCTACTCAGGGAGATAGGATT
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATT
27543666 GGTGGCTTAA
Statistics
Matches: 408, Mismatches: 113, Indels: 81
0.68 0.19 0.13
Matches are distributed among these distances:
42 7 0.02
43 61 0.15
44 266 0.65
45 64 0.16
46 10 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATTACATTCTTCA
Found at i:27543252 original size:132 final size:132
Alignment explanation
Indices: 27542901--27543795 Score: 1213
Period size: 132 Copynumber: 6.8 Consensus size: 132
27542891 TGCAATGCCA
* ** ** * * * *
27542901 GGGAA-ATAAAATTCACTATCTTCGATCTGCTCTACTACTGCTCAAGGAGA-CATGATCTGCAAT
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCA-GATCTACATT
* *
27542964 CTTCAACCTACTCCACTACTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTAC
65 CTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTAC
27543029 CTT
130 CTT
* * * * * * * *
27543032 GGGAAGACAAGATTCGCCATTTTTTTTTGATCTACTCCACTACTGCTTAGGGAGACAAGATCTAC
1 GGGAAGATAAGATTCACC----GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTAC
* *
27543097 ATTCTTCAACCTACTCCACTGCTGCTCAGGGAGAT-GAGATTAGTAGCCTAAATCTGCTTCCCTA
62 ATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAGTGGCTTAAATCTGCTTCCCTA
27543161 CTACCTT
126 CTACCTT
*
27543168 GGGAAGATAAGATTCACCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
* *
27543233 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGTTTCCTTACTACC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
27543298 TT
131 TT
* *
27543300 GGGAAGATAAGATTCATCGTCTTCGATCTGCTCCGCTGCTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
* * * * *
27543365 TTCAACCTACTCTACTGCTGCTTAGGGAGATAAGATTAGTAGCTTAAATCTGCTTCCCTACTAGC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
27543430 TT
131 TT
* *
27543432 AGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTGCTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
* * * *
27543497 TTCAACCTACTCCACTGTTGCTCAAGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTATTAAC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
27543562 TT
131 TT
* * * *
27543564 GGGAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACTGCTTAGGGAAACAAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
* * * * *
27543629 TTCAACCTACTCCACTTCTACTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTTACTACT
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
27543694 TT
131 TT
* * * * * *
27543696 GGGAAGATAAGACTCAACGTCTTCAATCTGCTCCGCTACTTCTTAGAGAGA-CAGGATCTACAAT
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCA-GATCTACATT
* *
27543760 ATTCAAACTACTCCACTGCTGCTCAGGGAGATAGGA
65 CTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGA
27543796 CTTGTTATCT
Statistics
Matches: 677, Mismatches: 78, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
131 6 0.01
132 556 0.82
133 1 0.00
135 1 0.00
136 112 0.17
137 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
TT
Found at i:27552208 original size:30 final size:30
Alignment explanation
Indices: 27552174--27552236 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
27552164 ACTTAACAAG
*
27552174 CAAATATCTCTAACATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* *
27552204 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
27552234 CAA
1 CAA
27552237 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:27558538 original size:25 final size:26
Alignment explanation
Indices: 27558500--27558564 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
27558490 TATGACCCAC
* *
27558500 AGCTCATGTGAGCAGA-ACACTTTAT
1 AGCTCGTGTAAGCAGACACACTTTAT
* * *
27558525 AGCTTGTGTAAGCAGACCCATTTTAT
1 AGCTCGTGTAAGCAGACACACTTTAT
*
27558551 AGCTCGTGTGAGCA
1 AGCTCGTGTAAGCA
27558565 CTATAGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (26 bp):
AGCTCGTGTAAGCAGACACACTTTAT
Found at i:27560654 original size:16 final size:15
Alignment explanation
Indices: 27560628--27560657 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
27560618 TATGATAAAT
27560628 TTTAAAAAATAATAA
1 TTTAAAAAATAATAA
27560643 TTTAAAATAATAATA
1 TTTAAAA-AATAATA
27560658 TATCACATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAAAATAATAA
Found at i:27560818 original size:3 final size:3
Alignment explanation
Indices: 27560810--27560853 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
27560800 AAAGTACAGA
27560810 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27560854 AATGTTTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27565760 original size:17 final size:17
Alignment explanation
Indices: 27565738--27565771 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27565728 AATAAAGGAA
27565738 GTAATCTTAGAAGATTT
1 GTAATCTTAGAAGATTT
*
27565755 GTAATCTTAGAGGATTT
1 GTAATCTTAGAAGATTT
27565772 TATTCTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
GTAATCTTAGAAGATTT
Found at i:27567718 original size:18 final size:18
Alignment explanation
Indices: 27567695--27567732 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27567685 ACTCGAGTAA
27567695 AACCGAAAAAATTCGGTT
1 AACCGAAAAAATTCGGTT
**
27567713 AACCGACTAAATTCGGTT
1 AACCGAAAAAATTCGGTT
27567731 AA
1 AA
27567733 TCGGTCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (18 bp):
AACCGAAAAAATTCGGTT
Found at i:27567877 original size:12 final size:13
Alignment explanation
Indices: 27567845--27567880 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27567835 AAATTATCTA
27567845 ACCCAACCCAATT
1 ACCCAACCCAATT
*
27567858 ACCCAACCCAGTT
1 ACCCAACCCAATT
27567871 A-CCAACCCAA
1 ACCCAACCCAA
27567881 CCTAATTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.39, C:0.47, G:0.03, T:0.11
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:27567880 original size:17 final size:18
Alignment explanation
Indices: 27567858--27567898 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
27567848 CAACCCAATT
*
27567858 ACCCAACCCAGTTA-CCA
1 ACCCAACCCAATTACCCA
*
27567875 ACCCAACCTAATTACCCA
1 ACCCAACCCAATTACCCA
27567893 ACCCAA
1 ACCCAA
27567899 TAAAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.39, C:0.46, G:0.02, T:0.12
Consensus pattern (18 bp):
ACCCAACCCAATTACCCA
Found at i:27567980 original size:38 final size:39
Alignment explanation
Indices: 27567884--27567996 Score: 201
Period size: 39 Copynumber: 2.9 Consensus size: 39
27567874 AACCCAACCT
27567884 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
*
27567923 AATTACCCAACCCAATAAAACTAAAATTAAAGTCTACCC
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
*
27567962 AATTA-CCAACCCAATAAAAATAAAACTAAAGTCTA
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTA
27567997 ACTCTTAAGT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
38 28 0.39
39 43 0.61
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.19
Consensus pattern (39 bp):
AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
Found at i:27568151 original size:17 final size:17
Alignment explanation
Indices: 27568131--27568193 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
27568121 TAATTTCAAG
27568131 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
27568148 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
27568166 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
27568185 AATTATGTA
1 AATTATGTA
27568194 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:27568174 original size:37 final size:37
Alignment explanation
Indices: 27568128--27568202 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
27568118 TGTTAATTTC
*
27568128 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
27568165 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
27568202 A
1 A
27568203 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:27568215 original size:9 final size:9
Alignment explanation
Indices: 27568201--27568231 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27568191 GTAGTGATTC
*
27568201 AATTCGGGT
1 AATTCGGTT
27568210 AATTCGGTT
1 AATTCGGTT
27568219 AATTCGGTT
1 AATTCGGTT
27568228 AATT
1 AATT
27568232 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Done.