Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 105 of 344
Found at i:35310140 original size:26 final size:26
Alignment explanation
Indices: 35310084--35310141 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
35310074 AAAAAAATTC
* *
35310084 AAAAAAAAATTCAAAAAAAATTGATT
1 AAAAAAAAATTCAAAAAAAAGTGATA
*
35310110 GAAAAAAAATTCAAAAAAAAAGTGA-A
1 AAAAAAAAATTC-AAAAAAAAGTGATA
35310136 AAAAAA
1 AAAAAA
35310142 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (26 bp):
AAAAAAAAATTCAAAAAAAAGTGATA
Found at i:35310152 original size:27 final size:26
Alignment explanation
Indices: 35310121--35310183 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
35310111 AAAAAAAATT
**
35310121 CAAAAAAAAAGTGAAAAAAAA-TCGAG
1 CAAAAAAAAAGAAAAAAAAAAGT-GAG
35310147 CAAAAAAAAAGAAAAAAAAAAGGTGAG
1 CAAAAAAAAAGAAAAAAAAAA-GTGAG
35310174 CAAAAAAAAA
1 CAAAAAAAAA
35310184 TCAAGTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 19 0.58
27 13 0.39
28 1 0.03
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.05
Consensus pattern (26 bp):
CAAAAAAAAAGAAAAAAAAAAGTGAG
Found at i:35310153 original size:38 final size:38
Alignment explanation
Indices: 35310074--35310156 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
35310064 TTGGAGTAAC
* * ***
35310074 AAAAAAATTCAAAAAAAAATTCAAAAAAAATTGATTGA
1 AAAAAAATTCAAAAAAAAAGTCAAAAAAAATCGAGCAA
*
35310112 AAAAAAATTCAAAAAAAAAGTGAAAAAAAATCGAGCAA
1 AAAAAAATTCAAAAAAAAAGTCAAAAAAAATCGAGCAA
35310150 AAAAAAA
1 AAAAAAA
35310157 GAAAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.14
Consensus pattern (38 bp):
AAAAAAATTCAAAAAAAAAGTCAAAAAAAATCGAGCAA
Found at i:35311253 original size:6 final size:6
Alignment explanation
Indices: 35311220--35311327 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
35311210 AAAGAAATTG
* * * ** *
35311220 AAAG-A AAACAA AAAGAA AATGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
35311267 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
35311318 AAAGAA AAAG
1 AAAGAA AAAG
35311328 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:35311268 original size:57 final size:55
Alignment explanation
Indices: 35311207--35311327 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 55
35311197 GAAAGAGATT
* *
35311207 GAAAAAGAAATTGAAAGAA-A-ACAAAAAGAAAATGAAGAAGAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAA-AAGAGACAAAAAGAAAATGAAG-A-AAAAA-AAATTGAAAAA
* *
35311264 GAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAAATCGAAAAA--GAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
35311321 GAAAAAG
1 GAAAAAG
35311328 CGAAAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 2 0.04
57 32 0.57
58 4 0.07
59 2 0.04
60 16 0.29
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.08
Consensus pattern (55 bp):
GAAAAAGAAATCGAAAAAGAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
Found at i:35311281 original size:18 final size:17
Alignment explanation
Indices: 35311206--35311282 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
35311196 AGAAAGAGAT
**
35311206 TGAAAAAGAAATTGAAA
1 TGAAAAAGAAAAAGAAA
*
35311223 -G-AAAACAAAAAGAAAA
1 TGAAAAAGAAAAAG-AAA
*
35311239 TGAAGAAGAAAAAGAAA
1 TGAAAAAGAAAAAGAAA
*
35311256 TTGCAAAAGAAAAAGAAA
1 -TGAAAAAGAAAAAGAAA
35311274 TCGAAAAAG
1 T-GAAAAAG
35311283 TGAGAGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 5 0.11
18 30 0.64
ACGTcount: A:0.69, C:0.04, G:0.18, T:0.09
Consensus pattern (17 bp):
TGAAAAAGAAAAAGAAA
Found at i:35311309 original size:14 final size:13
Alignment explanation
Indices: 35311288--35311325 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
35311278 AAAAGTGAGA
35311288 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
35311300 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
35311315 GAAAAAGAAAA
1 GAAAAAGAAAA
35311326 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:35311339 original size:21 final size:21
Alignment explanation
Indices: 35311289--35311339 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
35311279 AAAGTGAGAG
*
35311289 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
35311310 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
35311331 AAAAAGAAA
1 AAAAAGAAA
35311340 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:35311343 original size:27 final size:27
Alignment explanation
Indices: 35311241--35311345 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
35311231 AAAGAAAATG
* *
35311241 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
35311268 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
35311298 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
35311325 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
35311346 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:35311462 original size:48 final size:47
Alignment explanation
Indices: 35311408--35311513 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 47
35311398 GAGTGTCATG
35311408 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGAAAA-AGAAA-AAATC
* *
35311456 GAAAAAGAAATTGAGATTGAACAAAAGTGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAACAAAAGTGTGA-GAAAAAGAAAAAATC
35311504 GAAAAAGAAA
1 GAAAAAGAAA
35311514 GAAAAGACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
48 40 0.75
49 9 0.17
50 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAACAAAAGTGTGAGAAAAAGAAAAAATC
Found at i:35311750 original size:20 final size:20
Alignment explanation
Indices: 35311704--35311750 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35311694 AGCTCGTTTC
*
35311704 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
35311724 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
35311744 CAGCTCA
1 CAGCTCA
35311751 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35313263 original size:13 final size:13
Alignment explanation
Indices: 35313245--35313283 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
35313235 AAAGGAGAAG
35313245 AAATTCAGAAAAA
1 AAATTCAGAAAAA
35313258 AAATTCA-AAAAA
1 AAATTCAGAAAAA
35313270 AAA-TC-GAAAAA
1 AAATTCAGAAAAA
35313281 AAA
1 AAA
35313284 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.40
12 8 0.32
13 7 0.28
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (13 bp):
AAATTCAGAAAAA
Found at i:35313270 original size:12 final size:12
Alignment explanation
Indices: 35313245--35313283 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
35313235 AAAGGAGAAG
35313245 AAATTCAGAAAAA
1 AAATTCA-AAAAA
35313258 AAATTCAAAAAA
1 AAATTCAAAAAA
35313270 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
35313282 AA
1 AA
35313284 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 16 0.64
13 7 0.28
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:35313279 original size:22 final size:22
Alignment explanation
Indices: 35313254--35313319 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
35313244 GAAATTCAGA
**
35313254 AAAAAAATTCAAAAAAAAA-TCG
1 AAAAAAATGAAAAAAAAAAGT-G
*
35313276 AAAAAAAAGAAAAAAAAAAGTG
1 AAAAAAATGAAAAAAAAAAGTG
*
35313298 AAAAAAATCGAGCAAAAAAAAG
1 AAAAAAAT-GA-AAAAAAAAAG
35313320 AAAGAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 24 0.67
23 3 0.08
24 9 0.25
ACGTcount: A:0.76, C:0.06, G:0.11, T:0.08
Consensus pattern (22 bp):
AAAAAAATGAAAAAAAAAAGTG
Found at i:35313315 original size:27 final size:27
Alignment explanation
Indices: 35313285--35313365 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 27
35313275 GAAAAAAAAG
*
35313285 AAAAAAAAAAGTGAAAAAAA-TCGAGCA
1 AAAAAAAAAAGTAAAAAAAAGT-GAGCA
35313312 AAAAAAAGAAAG-AAAAAAAAGTGAGCA
1 AAAAAAA-AAAGTAAAAAAAAGTGAGCA
35313339 AAAAAAAATCAAGTTAAAAAAAAGTGA
1 AAAAAAAA--AAG-TAAAAAAAAGTGA
35313366 AAAGTCTTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
26 1 0.02
27 26 0.55
28 8 0.17
30 12 0.26
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.09
Consensus pattern (27 bp):
AAAAAAAAAAGTAAAAAAAAGTGAGCA
Found at i:35319162 original size:20 final size:20
Alignment explanation
Indices: 35319116--35319162 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35319106 AGCTCGTTTC
*
35319116 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
35319136 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
35319156 CAGCTCA
1 CAGCTCA
35319163 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35323290 original size:21 final size:21
Alignment explanation
Indices: 35323260--35323309 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
35323250 CAATTCGTAC
*
35323260 CCAATACCATACCATTTCATA
1 CCAATTCCATACCATTTCATA
*
35323281 CCAATTCCATACCATTTCGTA
1 CCAATTCCATACCATTTCATA
35323302 CCAATTCC
1 CCAATTCC
35323310 CAAATACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (21 bp):
CCAATTCCATACCATTTCATA
Found at i:35323293 original size:11 final size:11
Alignment explanation
Indices: 35323247--35323309 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
35323237 TTTGAACCGT
*
35323247 TACCAATT-CG
1 TACCAATTCCA
*
35323257 TACCCAATACCA
1 TA-CCAATTCCA
*
35323269 TACC-ATTTCA
1 TACCAATTCCA
35323279 TACCAATTCCA
1 TACCAATTCCA
* *
35323290 TACC-ATTTCG
1 TACCAATTCCA
35323300 TACCAATTCC
1 TACCAATTCC
35323310 CAAATACCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
10 18 0.44
11 20 0.49
12 3 0.07
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.30
Consensus pattern (11 bp):
TACCAATTCCA
Found at i:35324262 original size:4 final size:4
Alignment explanation
Indices: 35324253--35324286 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
35324243 AAGTTTTATT
35324253 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
35324287 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:35324294 original size:22 final size:22
Alignment explanation
Indices: 35324236--35324295 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
35324226 AAGTGGCCCA
*
35324236 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
35324260 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
35324281 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
35324296 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:35325283 original size:33 final size:33
Alignment explanation
Indices: 35325245--35325307 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35325235 GATTACTCAC
35325245 TTCAC-TCATTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTTCATTTCTTTTCA-AG-CTCTCTTTCTTT
*
35325278 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTTCATTTCTTTTCAAGCTCTCTTTC
35325308 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 14 0.52
34 12 0.44
35 1 0.04
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (33 bp):
TTCACTTCATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:35325334 original size:21 final size:21
Alignment explanation
Indices: 35325305--35325360 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
35325295 CAAGCTCTCT
*
35325305 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
35325326 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
35325347 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
35325361 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:35325353 original size:14 final size:14
Alignment explanation
Indices: 35325304--35325360 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
35325294 TCAAGCTCTC
35325304 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
35325317 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
35325331 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
35325345 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
35325359 TT
1 TT
35325361 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:35325420 original size:18 final size:18
Alignment explanation
Indices: 35325322--35325460 Score: 88
Period size: 18 Copynumber: 7.7 Consensus size: 18
35325312 TCTTTTTTCG
35325322 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
35325341 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
35325361 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
35325379 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
35325397 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
35325415 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCATTTT
** * *
35325430 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCATTTT
*
35325448 CTTTTTCCTTTTC
1 CTTTTTCTTTTTC
35325461 TCGCTCAATG
Statistics
Matches: 91, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.08
16 5 0.05
17 6 0.07
18 54 0.59
19 3 0.03
20 8 0.09
21 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:35325442 original size:6 final size:6
Alignment explanation
Indices: 35325322--35325429 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
35325312 TCTTTTTTCG
* * * **
35325322 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
35325373 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
35325421 -GTTTT CTTT
1 CTTTTT CTTT
35325430 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:35328398 original size:14 final size:14
Alignment explanation
Indices: 35328356--35328400 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
35328346 TTAAAGAAGC
35328356 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
35328370 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
35328383 AACTCATTTAATTA
1 AACTCATTAAATTA
35328397 AACT
1 AACT
35328401 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:35329806 original size:13 final size:13
Alignment explanation
Indices: 35329788--35329812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35329778 TGGTCATCAT
35329788 GGTGTGAACACAA
1 GGTGTGAACACAA
35329801 GGTGTGAACACA
1 GGTGTGAACACA
35329813 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:35331647 original size:17 final size:18
Alignment explanation
Indices: 35331625--35331658 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35331615 ACAACACTCC
*
35331625 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
35331642 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
35331659 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:35332732 original size:15 final size:15
Alignment explanation
Indices: 35332699--35332736 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
35332689 TTTAACTTGA
35332699 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-CT
35332715 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
35332730 TTTTTTT
1 TTTTTTT
35332737 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 12 0.57
17 1 0.05
ACGTcount: A:0.05, C:0.16, G:0.08, T:0.71
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:35332786 original size:13 final size:14
Alignment explanation
Indices: 35332740--35332790 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 14
35332730 TTTTTTTCAC
35332740 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
*
35332753 TTTTTTTTTCAATCAAT
1 TTTTTTTTTC---GAAT
35332770 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
35332784 TTTTTTT
1 TTTTTTT
35332791 GATTTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 9 0.28
14 10 0.31
17 13 0.41
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:35333863 original size:13 final size:13
Alignment explanation
Indices: 35333845--35333869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35333835 TGGTCATCAT
35333845 GGTGTGAACACAA
1 GGTGTGAACACAA
35333858 GGTGTGAACACA
1 GGTGTGAACACA
35333870 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:35345302 original size:22 final size:22
Alignment explanation
Indices: 35345274--35345320 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
35345264 TTGGTTGGAC
35345274 TCTGTTTACTACGAACCACATT
1 TCTGTTTACTACGAACCACATT
35345296 TCTGTTTACTACGAACCACATT
1 TCTGTTTACTACGAACCACATT
35345318 TCT
1 TCT
35345321 CTCTGTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.38
Consensus pattern (22 bp):
TCTGTTTACTACGAACCACATT
Found at i:35346411 original size:93 final size:93
Alignment explanation
Indices: 35346304--35346472 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
35346294 CCATAAGCGA
*
35346304 ACTCGGACTCAACTCAACGAGCTCAGG-CGTTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 ACTCGGACTCAACTCAACGAGCTC-GGACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
35346368 GAGTTCGGATGCCTAGTTACATCTCACGG
65 GAGTTCGGATGCCTAGTTACATCTCACGG
* *
35346397 ACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAACG
35346462 AGTTCGGATGC
66 AGTTCGGATGC
35346473 TCAACCATCC
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
ACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCACGG
Found at i:35346467 original size:46 final size:46
Alignment explanation
Indices: 35346294--35346469 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 46
35346284 TGTAACCCGC
* * *
35346294 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCACAT
35346340 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* *
35346390 -C-TCACG-G-ACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCAT-AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
35346433 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
35346470 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 6, Indels: 24
0.79 0.04 0.17
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 4 0.04
45 4 0.04
46 59 0.53
47 27 0.24
48 2 0.02
49 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:35353524 original size:46 final size:46
Alignment explanation
Indices: 35353380--35353598 Score: 246
Period size: 46 Copynumber: 4.7 Consensus size: 46
35353370 ATTGTAGGCT
* * * *
35353380 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGAGAGCC
** * * *
35353426 AGTGTAAGACCATGTCTGGGACATGGCATCAACATCGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGAGAGCC
*
35353474 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AGAGCC
* *
35353520 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGAGAGCC
35353566 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
35353599 ACCTTACCCA
Statistics
Matches: 149, Mismatches: 15, Indels: 15
0.83 0.08 0.08
Matches are distributed among these distances:
45 3 0.02
46 72 0.48
47 43 0.29
48 30 0.20
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAGAGCC
Found at i:35360548 original size:16 final size:18
Alignment explanation
Indices: 35360512--35360549 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35360502 ATCATTATTT
*
35360512 AAATAAAATACAGTGGTA
1 AAATAAAATACAATGGTA
35360530 AAATAAAATA-AAT-GTA
1 AAATAAAATACAATGGTA
35360546 AAAT
1 AAAT
35360550 CCATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.24
Consensus pattern (18 bp):
AAATAAAATACAATGGTA
Found at i:35363748 original size:13 final size:13
Alignment explanation
Indices: 35363732--35363758 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35363722 GTACAAGAGG
35363732 TTTGATTCCTTTA
1 TTTGATTCCTTTA
35363745 TTTGATTCCTTTA
1 TTTGATTCCTTTA
35363758 T
1 T
35363759 GATGTCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTGATTCCTTTA
Found at i:35364952 original size:116 final size:116
Alignment explanation
Indices: 35364748--35364982 Score: 470
Period size: 116 Copynumber: 2.0 Consensus size: 116
35364738 CACCATAACA
35364748 AAGTGGTCCATCATACGGACTGAGTTCTTGTTTGCTTTATATCCTGTTTAAAATCTTTTAGGTGA
1 AAGTGGTCCATCATACGGACTGAGTTCTTGTTTGCTTTATATCCTGTTTAAAATCTTTTAGGTGA
35364813 GATTTTTAAGTTGTTCTTCTGAATCTTCAACTGGCTTATACGTTAGCTGAT
66 GATTTTTAAGTTGTTCTTCTGAATCTTCAACTGGCTTATACGTTAGCTGAT
35364864 AAGTGGTCCATCATACGGACTGAGTTCTTGTTTGCTTTATATCCTGTTTAAAATCTTTTAGGTGA
1 AAGTGGTCCATCATACGGACTGAGTTCTTGTTTGCTTTATATCCTGTTTAAAATCTTTTAGGTGA
35364929 GATTTTTAAGTTGTTCTTCTGAATCTTCAACTGGCTTATACGTTAGCTGAT
66 GATTTTTAAGTTGTTCTTCTGAATCTTCAACTGGCTTATACGTTAGCTGAT
35364980 AAG
1 AAG
35364983 ATTGTTGAAG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 119 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (116 bp):
AAGTGGTCCATCATACGGACTGAGTTCTTGTTTGCTTTATATCCTGTTTAAAATCTTTTAGGTGA
GATTTTTAAGTTGTTCTTCTGAATCTTCAACTGGCTTATACGTTAGCTGAT
Found at i:35368726 original size:19 final size:19
Alignment explanation
Indices: 35368680--35368732 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
35368670 TTGAAATCAA
**
35368680 ATATATTTGTAATATTATAT
1 ATATATTTAAAAT-TTATAT
35368700 ATGATATTATAAAATTTATAT
1 AT-ATATT-TAAAATTTATAT
35368721 AT-TATTTAAAAT
1 ATATATTTAAAAT
35368733 GCCTTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 4 0.14
20 2 0.07
21 13 0.45
22 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
ATATATTTAAAATTTATAT
Found at i:35369380 original size:12 final size:12
Alignment explanation
Indices: 35369363--35369395 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35369353 TTATAAATTG
35369363 ATAATATAT-AGT
1 ATAATATATCA-T
35369375 ATAATATATCAT
1 ATAATATATCAT
35369387 ATAATATAT
1 ATAATATAT
35369396 GGTTTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (12 bp):
ATAATATATCAT
Found at i:35371862 original size:17 final size:18
Alignment explanation
Indices: 35371825--35371873 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
35371815 TAAAAATATT
35371825 TTTTAAAATTTTTATACA
1 TTTTAAAATTTTTATACA
* *
35371843 TTTTAATATTTTT-TATA
1 TTTTAAAATTTTTATACA
35371860 TTTTAAAATTTTTA
1 TTTTAAAATTTTTA
35371874 AATTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAAAATTTTTATACA
Found at i:35379077 original size:17 final size:16
Alignment explanation
Indices: 35379057--35379094 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
35379047 AATATTTTTA
*
35379057 AATAATTTTTATTATT
1 AATAATTTTTACTATT
35379073 CAATAATTTTTACTATT
1 -AATAATTTTTACTATT
35379090 AATAA
1 AATAA
35379095 ATATTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATTTTTACTATT
Found at i:35379618 original size:13 final size:13
Alignment explanation
Indices: 35379600--35379624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35379590 GTTTTTTTTA
35379600 TTATAAAAAAATC
1 TTATAAAAAAATC
35379613 TTATAAAAAAAT
1 TTATAAAAAAAT
35379625 AATGAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TTATAAAAAAATC
Found at i:35380938 original size:23 final size:24
Alignment explanation
Indices: 35380910--35380962 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 24
35380900 CCTCTTAGTG
*
35380910 AAAAAAATAATTTAATATATTATTT
1 AAAAAACTAATTTAATATATT-TTT
35380935 AAAAAACTTAATTTAATATATTTTT
1 AAAAAAC-TAATTTAATATATTTTT
35380960 AAA
1 AAA
35380963 GACATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAACTAATTTAATATATTTTT
Found at i:35381687 original size:16 final size:16
Alignment explanation
Indices: 35381666--35381698 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35381656 AAGTTGCACA
35381666 GGAGGTGCAACAAATG
1 GGAGGTGCAACAAATG
*
35381682 GGAGGTGCAACATATG
1 GGAGGTGCAACAAATG
35381698 G
1 G
35381699 ATTAGGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.39, T:0.15
Consensus pattern (16 bp):
GGAGGTGCAACAAATG
Found at i:35385664 original size:45 final size:45
Alignment explanation
Indices: 35385600--35385761 Score: 263
Period size: 45 Copynumber: 3.6 Consensus size: 45
35385590 TATCACACAG
*
35385600 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCAGGTGAAA
*
35385645 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCAGGTGAAA
* *
35385690 TACTACTCGGGCCTTTGAGCCTAGCAGGCTATAATGCAGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCAGGTGAAA
* *
35385735 TACTATTCAGG-CTTCGAGCCTAGCAGG
1 TACTATTCGGGCCTTTGAGCCTAGCAGG
35385762 AAAAATGCTG
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 15 0.14
45 95 0.86
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCAGGTGAAA
Found at i:35399722 original size:12 final size:10
Alignment explanation
Indices: 35399684--35399733 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
35399674 TGTAATTCTG
*
35399684 TCAAAAATAA
1 TCAAAATTAA
*
35399694 CCAAAATTAA
1 TCAAAATTAA
35399704 TCAAAATTAA
1 TCAAAATTAA
35399714 CTACAAAATTAA
1 -T-CAAAATTAA
*
35399726 TTAAAATT
1 TCAAAATT
35399734 CATAATGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 23 0.68
11 2 0.06
12 9 0.26
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (10 bp):
TCAAAATTAA
Found at i:35400849 original size:8 final size:8
Alignment explanation
Indices: 35400838--35400882 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
35400828 TCAATTTGCA
*
35400838 TAAAATAT
1 TAAAAAAT
*
35400846 TAAAATAT
1 TAAAAAAT
*
35400854 TAATAAATT
1 TAA-AAAAT
35400863 TAAAAAAT
1 TAAAAAAT
35400871 TAAAAAAT
1 TAAAAAAT
35400879 TAAA
1 TAAA
35400883 TAAAAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAAAAT
Found at i:35400866 original size:25 final size:26
Alignment explanation
Indices: 35400838--35400886 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
35400828 TCAATTTGCA
* *
35400838 TAAAATATTAAAATATT-AATAAATT
1 TAAAAAATTAAAAAATTAAATAAATT
35400863 TAAAAAATTAAAAAATTAAATAAA
1 TAAAAAATTAAAAAATTAAATAAA
35400887 AATGAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAAAATTAAAAAATTAAATAAATT
Found at i:35400867 original size:17 final size:17
Alignment explanation
Indices: 35400839--35400879 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
35400829 CAATTTGCAT
*
35400839 AAAATATTAAAATATTAA
1 AAAAT-TTAAAAAATTAA
*
35400857 TAAATTTAAAAAATTAA
1 AAAATTTAAAAAATTAA
35400874 AAAATT
1 AAAATT
35400880 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTTAAAAAATTAA
Found at i:35401680 original size:15 final size:15
Alignment explanation
Indices: 35401662--35401691 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35401652 AAATATAATT
35401662 TTATATTATTTATTA
1 TTATATTATTTATTA
*
35401677 TTATCTTATTTATTA
1 TTATATTATTTATTA
35401692 AAAATTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTATTTATTA
Found at i:35404213 original size:43 final size:43
Alignment explanation
Indices: 35404125--35404227 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
35404115 TACCAAGATG
* * *
35404125 TGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTATTA
1 TGATTACGTATAAGACCATGTCTAGGACATTGGCATCGTATTA
* *
35404168 TGATTACGTCTAAGACCATGTCT-GAGACATTGGCGTCGT-TATA
1 TGATTACGTATAAGACCATGTCTAG-GACATTGGCATCGTAT-TA
*
35404211 TGATTTCGTATAAGACC
1 TGATTACGTATAAGACC
35404228 CTGTTTGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 2 0.04
43 50 0.96
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (43 bp):
TGATTACGTATAAGACCATGTCTAGGACATTGGCATCGTATTA
Found at i:35410736 original size:40 final size:40
Alignment explanation
Indices: 35410638--35410900 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
35410628 TCCTCGTTCA
* * * * *
35410638 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
35410677 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
35410717 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
35410757 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
35410797 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
35410837 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
35410877 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
35410901 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:35416147 original size:19 final size:19
Alignment explanation
Indices: 35416123--35416160 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35416113 GGAACACATC
35416123 ATGAATCCAGTCCAACTCT
1 ATGAATCCAGTCCAACTCT
35416142 ATGAATCCAGTCCAACTCT
1 ATGAATCCAGTCCAACTCT
35416161 GGAGGTAACT
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:0.32, C:0.32, G:0.11, T:0.26
Consensus pattern (19 bp):
ATGAATCCAGTCCAACTCT
Found at i:35433194 original size:27 final size:28
Alignment explanation
Indices: 35433124--35433221 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
35433114 ATAATAAGCC
*
35433124 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATCGAACT
35433152 CGCACACTTAGTGCTATATAATC-AACCT
1 CGCACACTTAGTGCTATATAATCGAA-CT
* * *
35433180 CGC-CACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA-TCGAACT
35433208 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35433222 CAATCTCATG
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
27 18 0.30
28 30 0.49
29 13 0.21
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCGAACT
Found at i:35440565 original size:39 final size:39
Alignment explanation
Indices: 35440522--35440600 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
35440512 TACCATAAAT
35440522 TTCAAATTTTCAGCATATTCATCCATGACCTAATTTCCA
1 TTCAAATTTTCAGCATATTCATCCATGACCTAATTTCCA
*
35440561 TTCAAATTTTTAGCATATTCATCCATGACCTAATTTCCA
1 TTCAAATTTTCAGCATATTCATCCATGACCTAATTTCCA
35440600 T
1 T
35440601 ACTTTGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (39 bp):
TTCAAATTTTCAGCATATTCATCCATGACCTAATTTCCA
Found at i:35443637 original size:27 final size:27
Alignment explanation
Indices: 35443607--35443784 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35443597 ATATTGAGTC
* * * *
35443607 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35443634 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35443661 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35443689 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
35443716 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35443743 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35443770 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35443785 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:35443746 original size:82 final size:81
Alignment explanation
Indices: 35443628--35443783 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35443618 TGCTATATAA
* *
35443628 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
35443693 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
35443710 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
35443774 CACTTAGTGC
65 CACTTAGTGC
35443784 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:35451811 original size:27 final size:27
Alignment explanation
Indices: 35451781--35451957 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
35451771 ATATTGAGTC
* *
35451781 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
35451808 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
35451835 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
35451863 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
35451890 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
35451917 C-CACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
35451943 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35451958 GTACAATTTA
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
26 21 0.17
27 83 0.65
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:35451873 original size:55 final size:54
Alignment explanation
Indices: 35451781--35451957 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 54
35451771 ATATTGAGTC
* * * * *
35451781 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
35451835 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
35451890 CGCACACTTAGTGC-ATCATATTCATTTC-CACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
35451943 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35451958 GTACAATTTA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
53 35 0.34
54 24 0.23
55 45 0.43
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:35459387 original size:47 final size:46
Alignment explanation
Indices: 35459333--35459489 Score: 224
Period size: 47 Copynumber: 3.3 Consensus size: 46
35459323 TTAGGATTTT
** * *
35459333 ATGTGATGAATGTGAATGTGTATTTATGAGATAAGGTCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGG-CGAATGGCCA
*
35459380 ATGTGATGAATGTGAGCATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGG-CGAATGGCCA
*
35459427 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGC-GAATGGCCA
*
35459474 ATGTGATGAACGTGAA
1 ATGTGATGAATGTGAA
35459490 AGTGTATATA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.01
47 99 0.99
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (46 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCGAATGGCCA
Found at i:35461571 original size:40 final size:40
Alignment explanation
Indices: 35461497--35461678 Score: 260
Period size: 40 Copynumber: 4.6 Consensus size: 40
35461487 AACCCAAGTA
* * *
35461497 CCTTCAGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
35461536 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
35461576 CCTTCGGGACTTAGCCCGGATTTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
35461616 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
35461656 CCTTCAGGACTTAGCTCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
35461679 CATTCGAATA
Statistics
Matches: 129, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 11 0.09
40 117 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:35468576 original size:25 final size:26
Alignment explanation
Indices: 35468521--35468577 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
35468511 CAAGGTGCTA
*
35468521 ATATCATGGCCTGAAGCCAACTCATTTG
1 ATATCATGGCCTGAAGCCAA--CATTCG
35468549 ATATGCATGGCCTGAAGCCAA-A-TCG
1 ATAT-CATGGCCTGAAGCCAACATTCG
35468574 ATAT
1 ATAT
35468578 ATCAACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
26 1 0.04
28 4 0.15
29 16 0.59
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (26 bp):
ATATCATGGCCTGAAGCCAACATTCG
Found at i:35470324 original size:17 final size:18
Alignment explanation
Indices: 35470304--35470337 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35470294 AAGTGAATTG
35470304 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
35470321 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
35470338 ATGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:35471080 original size:10 final size:10
Alignment explanation
Indices: 35471053--35471100 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
35471043 TAAAATTTTA
35471053 AAAGATAAAT
1 AAAGATAAAT
35471063 ACAA-ATAAAT
1 A-AAGATAAAT
*
35471073 AAAGATAATT
1 AAAGATAAAT
35471083 AAAGATAAAT
1 AAAGATAAAT
35471093 AAAGATAA
1 AAAGATAA
35471101 TCAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:35471101 original size:20 final size:19
Alignment explanation
Indices: 35471053--35471112 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
35471043 TAAAATTTTA
*
35471053 AAAGATAAATACAAATAAAT
1 AAAGATAATTA-AAATAAAT
35471073 AAAGATAATTAAAGATAAAT
1 AAAGATAATTAAA-ATAAAT
*
35471093 AAAGATAATCAAAAATAAAT
1 AAAGATAAT-TAAAATAAAT
35471113 CCTAGAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 31 0.86
21 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (19 bp):
AAAGATAATTAAAATAAAT
Found at i:35472319 original size:29 final size:29
Alignment explanation
Indices: 35472243--35472311 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
35472233 GTATTTTACC
*
35472243 GATTTGGCTTTAGGCCATGCATATCGGAT
1 GATTTGGCTTTAGGCCATGCAAATCGGAT
*
35472272 GATTTGGCTTCAGGCCATGCAAATCGGAT
1 GATTTGGCTTTAGGCCATGCAAATCGGAT
35472301 GATTTGGCTTT
1 GATTTGGCTTT
35472312 GGGTCATGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (29 bp):
GATTTGGCTTTAGGCCATGCAAATCGGAT
Found at i:35484353 original size:14 final size:14
Alignment explanation
Indices: 35484334--35484362 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35484324 GTATATATGT
35484334 GATAAGGCCTAATA
1 GATAAGGCCTAATA
35484348 GATAAGGCCTAATA
1 GATAAGGCCTAATA
35484362 G
1 G
35484363 CCGATGTGAT
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:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (14 bp):
GATAAGGCCTAATA
Found at i:35484356 original size:61 final size:62
Alignment explanation
Indices: 35484288--35484409 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 62
35484278 TATATATGTA
* *
35484288 ATAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATAG
1 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATAG
35484349 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
1 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAAT
35484410 GGCCGATGTG
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 35 0.61
63 22 0.39
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (62 bp):
ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATAG
Found at i:35484462 original size:47 final size:47
Alignment explanation
Indices: 35484348--35484590 Score: 369
Period size: 47 Copynumber: 5.1 Consensus size: 47
35484338 AGGCCTAATA
*
35484348 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGT
1 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGT
35484397 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
35484444 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
35484491 GATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
* * * * * * * *
35484538 GACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGT
1 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
35484585 GATAAG
1 GATAAG
35484591 TCCCGAAGGG
Statistics
Matches: 179, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 142 0.79
49 37 0.21
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
Found at i:35486867 original size:40 final size:40
Alignment explanation
Indices: 35486813--35487134 Score: 450
Period size: 40 Copynumber: 8.1 Consensus size: 40
35486803 AAGGTCTCGA
35486813 TGATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
*
35486852 TGATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
*
35486892 TGATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
35486932 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
* * *
35486972 TGATGTACCCGGGCTAAGTCCCGAAGAGCATTCGTACTAG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
* *
35487012 TGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
* * * * * * *
35487052 TAATATATCCGTGCTAA-ACCTCAAAGAGCATTCGTGCTGG
1 TGATGTATCCGGGCTAAGTCC-CGAAGAGCATTCATGCTAG
* * * * *
35487092 TGTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGG
1 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
35487132 TGA
1 TGA
35487135 CGTGTATTCG
Statistics
Matches: 256, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 6 0.02
40 248 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAG
Found at i:35487402 original size:58 final size:57
Alignment explanation
Indices: 35487333--35487441 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
35487323 CGAATGATTA
* *
35487333 GAGGCACTGTGTGTGCAAATTCTTTTAACCGAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTC-TTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
* * *
35487391 GAGGCACTGTGTGTGCGAGTTCTTCAACCAAGCACTATGTGTGCGAGATCG
1 GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCG
35487442 ATCAGTGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 26 0.57
58 20 0.43
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (57 bp):
GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:35491333 original size:47 final size:47
Alignment explanation
Indices: 35491281--35491590 Score: 476
Period size: 47 Copynumber: 6.6 Consensus size: 47
35491271 GATAATTGTG
* *
35491281 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
35491328 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
35491375 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
35491424 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
35491471 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
35491518 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
35491565 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
35491591 TCCCGAAGGG
Statistics
Matches: 243, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 197 0.81
49 46 0.19
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:35491388 original size:96 final size:96
Alignment explanation
Indices: 35491281--35491590 Score: 488
Period size: 96 Copynumber: 3.3 Consensus size: 96
35491271 GATAATTGTG
35491281 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
35491344 ATGTGATAAGGCCTAATAGCCGATGTGATGA
66 ATGTGATAAGGCCTAATAGCCGATGTGATGA
35491375 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
35491440 ATGTGATAAGGCCTAATAGCCGATGTGATGA
66 ATGTGATAAGGCCTAATAGCCGATGTGATGA
* *
35491471 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * * * * *
35491534 ATGTGACAGGGCCGAGTGGCCAACGTGATGG
66 ATGTGATAAGGCCTAATAGCCGATGTGATGA
35491565 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
35491591 TCCCGAAGGG
Statistics
Matches: 201, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
94 98 0.49
95 3 0.01
96 100 0.50
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATAGCCGATGTGATGA
Found at i:35491430 original size:143 final size:141
Alignment explanation
Indices: 35491281--35491590 Score: 476
Period size: 143 Copynumber: 2.2 Consensus size: 141
35491271 GATAATTGTG
* * *
35491281 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
* * *
35491346 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
66 GTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTG--TATATATGTGACAAGGCCGAATG
* *
35491411 GCCGATGTGATGA
129 GCCAACGTGATGA
35491424 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * *
35491489 GTGATGAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGC
66 GTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
*
35491554 CAACGTGATGG
131 CAACGTGATGA
*
35491565 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
35491591 TCCCGAAGGG
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
141 54 0.35
143 99 0.65
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (141 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
CAACGTGATGA
Found at i:35494407 original size:23 final size:23
Alignment explanation
Indices: 35494377--35494424 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
35494367 TCATTGAGAT
35494377 TACCTGTGCCCACTTGTACAACA
1 TACCTGTGCCCACTTGTACAACA
*
35494400 TACCTGTGCCCGCTTGTACAACA
1 TACCTGTGCCCACTTGTACAACA
35494423 TA
1 TA
35494425 ACTTATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (23 bp):
TACCTGTGCCCACTTGTACAACA
Found at i:35494574 original size:7 final size:7
Alignment explanation
Indices: 35494562--35494592 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
35494552 AACGCTACCT
35494562 CATATCA
1 CATATCA
35494569 CATATCA
1 CATATCA
35494576 CATATCA
1 CATATCA
35494583 CATATCA
1 CATATCA
35494590 CAT
1 CAT
35494593 GTTGCTCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (7 bp):
CATATCA
Found at i:35499661 original size:26 final size:27
Alignment explanation
Indices: 35499629--35499751 Score: 112
Period size: 26 Copynumber: 4.7 Consensus size: 27
35499619 TTCCTTAGCC
*
35499629 GATAGTCCTTGCAGACTCCCTCA-ATA
1 GATAGTCCTTGCAGACTTCCTCACATA
* **
35499655 GACAGTCCTTGTGGACTTCC-CACATA
1 GATAGTCCTTGCAGACTTCCTCACATA
* *
35499681 GGATAGTCCTTG-TGACTTCCACA-ATA
1 -GATAGTCCTTGCAGACTTCCTCACATA
* *
35499707 GATAGTCCTTACAGACTTCCT-ATATAA
1 GATAGTCCTTGCAGACTTCCTCACAT-A
*
35499734 GATAGTCCTTACAGACTT
1 GATAGTCCTTGCAGACTT
35499752 TCCATAGAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
25 13 0.16
26 38 0.46
27 31 0.38
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (27 bp):
GATAGTCCTTGCAGACTTCCTCACATA
Found at i:35499724 original size:52 final size:53
Alignment explanation
Indices: 35499629--35499750 Score: 138
Period size: 52 Copynumber: 2.3 Consensus size: 53
35499619 TTCCTTAGCC
* *** *
35499629 GATAGTCCTTGCAGACTCCCTCAATAGACAGTCCTTGTGGACTTCCCACATAG
1 GATAGTCCTTGCAGACTCCCACAATAGACAGTCCTTACAGACTTCCCACATAA
* * * * *
35499682 GATAGTCCTTG-TGACTTCCACAATAGATAGTCCTTACAGACTTCCTATATAA
1 GATAGTCCTTGCAGACTCCCACAATAGACAGTCCTTACAGACTTCCCACATAA
*
35499734 GATAGTCCTTACAGACT
1 GATAGTCCTTGCAGACT
35499751 TTCCATAGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
52 41 0.73
53 15 0.27
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (53 bp):
GATAGTCCTTGCAGACTCCCACAATAGACAGTCCTTACAGACTTCCCACATAA
Found at i:35504186 original size:43 final size:44
Alignment explanation
Indices: 35504130--35504263 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 44
35504120 GATATATGTG
* *
35504130 GCATTCGAGCTCGTTAAGAGGTCCGAGTTCATTATGGATGCGA-
1 GCATTTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAT
* * *
35504173 GCATTTGAGCTCGTTGAGTGGTCCGAGTTCATAATGTATGCGAT
1 GCATTTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAT
*
35504217 ACATGTAACATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
1 GCAT-T----T--GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
35504264 TGTTGCATGC
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 38 0.51
44 3 0.04
45 1 0.01
49 1 0.01
51 31 0.42
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (44 bp):
GCATTTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAT
Found at i:35506625 original size:40 final size:40
Alignment explanation
Indices: 35506570--35506827 Score: 353
Period size: 40 Copynumber: 6.5 Consensus size: 40
35506560 TGGATGATAA
* * *
35506570 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
35506610 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
35506650 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35506690 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35506730 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35506770 CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
35506810 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
35506828 TACGTGGCTT
Statistics
Matches: 206, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.07
40 190 0.92
41 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35514784 original size:40 final size:40
Alignment explanation
Indices: 35514729--35514946 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
35514719 TGGATGATAA
* * *
35514729 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
35514769 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35514809 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35514849 CCGGGCTAAGTCCTGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35514889 CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
35514929 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
35514947 TACGTGGCTT
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 16 0.10
40 148 0.90
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35519140 original size:19 final size:18
Alignment explanation
Indices: 35519111--35519162 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
35519101 TAATTTTAAA
35519111 AAAAATCAAAAAATAATTTT
1 AAAAAT-AAAAAATAA-TTT
*
35519131 AAAAATAAAAAATTATTT
1 AAAAATAAAAAATAATTT
35519149 AAAAAGTAAAAAAT
1 AAAAA-TAAAAAAT
35519163 GATAGAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.27
19 16 0.53
20 6 0.20
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATAAAAAATAATTT
Found at i:35525244 original size:18 final size:18
Alignment explanation
Indices: 35525223--35525261 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35525213 GATTGAGAGT
* *
35525223 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
35525241 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
35525259 GAA
1 GAA
35525262 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:35529056 original size:18 final size:18
Alignment explanation
Indices: 35529035--35529073 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35529025 GATTGAGAGT
* *
35529035 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
35529053 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
35529071 GAA
1 GAA
35529074 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:35536160 original size:17 final size:17
Alignment explanation
Indices: 35536138--35536172 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35536128 CTCATGTCTA
35536138 TGTATACTAGTTTATTC
1 TGTATACTAGTTTATTC
* *
35536155 TGTATATTGGTTTATTC
1 TGTATACTAGTTTATTC
35536172 T
1 T
35536173 AAATACTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (17 bp):
TGTATACTAGTTTATTC
Found at i:35541344 original size:21 final size:20
Alignment explanation
Indices: 35541305--35541351 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
35541295 TATTTTAGAA
**
35541305 TTTTTTTAATTTTTCAATTT
1 TTTTTTTAATTTTAAAATTT
35541325 TTTTTTTGAATTTTAAAATTT
1 TTTTTTT-AATTTTAAAATTT
35541346 TATTTT
1 T-TTTT
35541352 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTTTAATTTTAAAATTT
Found at i:35541346 original size:20 final size:20
Alignment explanation
Indices: 35541305--35541360 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
35541295 TATTTTAGAA
* *
35541305 TTTTTTTAATTTTTCAATTT
1 TTTTTTTAATTTTTAAAATT
35541325 TTTTTTTGAA-TTTTAAAATT
1 TTTTTTT-AATTTTTAAAATT
* *
35541345 TTATTTTATTTTTTAA
1 TTTTTTTAATTTTTAA
35541361 TTTGTTGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTTAATTTTTAAAATT
Found at i:35555026 original size:20 final size:20
Alignment explanation
Indices: 35555001--35555044 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
35554991 CGGGTAGGGG
35555001 ACACGAGCGTGTCCCAAAGC
1 ACACGAGCGTGTCCCAAAGC
35555021 ACACGAGCGTGTCCCAAAGC
1 ACACGAGCGTGTCCCAAAGC
35555041 ACAC
1 ACAC
35555045 AGGAGTGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.36, G:0.23, T:0.09
Consensus pattern (20 bp):
ACACGAGCGTGTCCCAAAGC
Found at i:35556388 original size:37 final size:37
Alignment explanation
Indices: 35556326--35556397 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 37
35556316 TACAAGCCAC
*
35556326 AATCATTATAAGCCACATCTCATGGAT-ATATACAATG
1 AATCAATATAAGCCACATCTCATGGATCATA-ACAATG
35556363 AATCAATATAAGCCA-ATACAT-ATGGATCATAACAA
1 AATCAATATAAGCCACAT-C-TCATGGATCATAACAA
35556398 CATCTATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
36 2 0.06
37 25 0.81
38 4 0.13
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (37 bp):
AATCAATATAAGCCACATCTCATGGATCATAACAATG
Found at i:35567915 original size:15 final size:16
Alignment explanation
Indices: 35567897--35567926 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35567887 AATTGTTTTA
35567897 TTACA-AATTTCACTC
1 TTACATAATTTCACTC
35567912 TTACATAATTTCACT
1 TTACATAATTTCACT
35567927 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (16 bp):
TTACATAATTTCACTC
Found at i:35568261 original size:50 final size:49
Alignment explanation
Indices: 35568138--35568267 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 49
35568128 CTGGTACGCA
* *
35568138 TAGTATCCTGCACTTAGTACTACACATGTGACCAACAATCCAGTACACG
1 TAGTAACCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACACG
** * * *
35568187 TAGTAACAAGCACTTAGTACTACACACGTGACCTAACCAT-CTGATACATG
1 TAGTAACCTGCACTTAGTACTACACACGTGACC-AACAATCCAG-TACACG
* *
35568237 TAGTAGCCTGCACTTAATACTACACACGTGA
1 TAGTAACCTGCACTTAGTACTACACACGTGA
35568268 TTGAAATTGT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 31 0.46
50 37 0.54
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (49 bp):
TAGTAACCTGCACTTAGTACTACACACGTGACCAACAATCCAGTACACG
Found at i:35574677 original size:20 final size:20
Alignment explanation
Indices: 35574652--35574691 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35574642 GCTTGTACAA
35574652 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
* *
35574672 GTTTGCACTTTGTTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
35574692 ATAGCACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.28, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:35577264 original size:50 final size:50
Alignment explanation
Indices: 35577054--35577425 Score: 318
Period size: 50 Copynumber: 7.7 Consensus size: 50
35577044 GGGTTATTGT
*
35577054 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-C-ATTAT--GA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGG-CATCGA-TATGCGA
* * *
35577100 GAGCTAGTGTAAGACCATTTCTGGGACATGGCATTGGCATTGAGA--CGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGCGA
* * * *
35577148 GAGCTAGTGTAAGA-AATGTCTGGGACAT-GCATTGGCCTCG-TAAAG-TA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGAT-ATGCGA
* * *
35577195 -AACCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATAGATATGCGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGCGA
* * *
35577244 GAGCTCA-TGTAAGACCATGTCTGGGACATGACATCGGCA-CGAATATGTGA
1 GAGCT-AGTGTAAGACCATGTCTGGGACATGGCATTGGCATCG-ATATGCGA
*** *
35577294 GAGCTAGTGTAAGGTAATGTCTGGGACATGGCATCGGCA-CGAATATGC-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCG-ATATGCGA
* * *
35577343 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCT-ACCTC-A-ATGACGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCAT-TGGCATCGATATG-CGA
*
35577392 TAG-TCAGTGTAAGACCATGTCTGGGACATGGCAT
1 GAGCT-AGTGTAAGACCATGTCTGGGACATGGCAT
35577426 CGCATCGGCA
Statistics
Matches: 268, Mismatches: 37, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
46 36 0.13
47 44 0.16
48 38 0.14
49 68 0.25
50 81 0.30
51 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (50 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGCGA
Found at i:35577316 original size:100 final size:97
Alignment explanation
Indices: 35577054--35577425 Score: 356
Period size: 94 Copynumber: 3.8 Consensus size: 97
35577044 GGGTTATTGT
*
35577054 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-ACAT-TATGAGAGCTAGTGTAAGACCA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCGA-ATATGTGAGAGCTAGTGTAAGACCA
* * *
35577117 TTTCTGGGACATGGCATTGGCATTGAGA--CGA
65 TGTCTGGGACATGGCATTGGCATAGATATGCGA
* * * *
35577148 GAGCTAGTGTAAGAAATGTCTGGGACATGCATTGGCCTCGTAA-A-GT-A-AACCAGTGTAAGAC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CG-AATATGTGAGAGCTAGTGTAAGAC
35577209 CATGTCTGGGACATGGCATTGGCATAGATATGCGA
63 CATGTCTGGGACATGGCATTGGCATAGATATGCGA
*
35577244 GAGCTCA-TGTAAGACCATGTCTGGGACATGACATCGGCACGAATATGTGAGAGCTAGTGTAAGG
1 GAGCT-AGTGTAAGA-CATGTCTGGGACATG-CATCGGC-CGAATATGTGAGAGCTAGTGTAAGA
** * *
35577308 TAATGTCTGGGACATGGCATCGGCA-CGAATATGC-A
62 CCATGTCTGGGACATGGCATTGGCATAG-ATATGCGA
* ** ** * *
35577343 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCTACCTCA-ATGACGATAG-TCAGTGTAAGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCGAATATG-TGAGAGCT-AGTGTAAGA
35577406 CCATGTCTGGGACATGGCAT
62 CCATGTCTGGGACATGGCAT
35577426 CGCATCGGCA
Statistics
Matches: 231, Mismatches: 28, Indels: 34
0.79 0.10 0.12
Matches are distributed among these distances:
94 72 0.31
95 2 0.01
96 19 0.08
97 24 0.10
98 41 0.18
99 34 0.15
100 39 0.17
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (97 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCGAATATGTGAGAGCTAGTGTAAGACCAT
GTCTGGGACATGGCATTGGCATAGATATGCGA
Found at i:35581007 original size:22 final size:22
Alignment explanation
Indices: 35580979--35581024 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
35580969 CGAAACCGTT
*
35580979 ACTCGGTAGCAATTCATGTTTA
1 ACTCGGTAGCAATTCATATTTA
35581001 ACTCGGTAGCAATTCATATTTA
1 ACTCGGTAGCAATTCATATTTA
35581023 AC
1 AC
35581025 AAGTAGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (22 bp):
ACTCGGTAGCAATTCATATTTA
Found at i:35588192 original size:22 final size:22
Alignment explanation
Indices: 35588164--35588209 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
35588154 TGAAACCGTT
*
35588164 ACTCGGTAGCAATTCATGTTTA
1 ACTCGGTAGCAATTCATATTTA
35588186 ACTCGGTAGCAATTCATATTTA
1 ACTCGGTAGCAATTCATATTTA
35588208 AC
1 AC
35588210 AAGTAGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (22 bp):
ACTCGGTAGCAATTCATATTTA
Found at i:35591638 original size:48 final size:48
Alignment explanation
Indices: 35591566--35591660 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
35591556 ATAGCACAAC
* * *
35591566 TATGGTCTTATACATTATAGTCTCATGTTTACAGTCCTGGCAGACTTT
1 TATGGTCTTACACATTATAATCTCATGTTTACAGTCCTGACAGACTTT
*
35591614 TATGGTCTTACACATTATAATCTCATGTTTACTGTCCTGACAGACTT
1 TATGGTCTTACACATTATAATCTCATGTTTACAGTCCTGACAGACTT
35591661 CATATGCTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (48 bp):
TATGGTCTTACACATTATAATCTCATGTTTACAGTCCTGACAGACTTT
Found at i:35602492 original size:17 final size:17
Alignment explanation
Indices: 35602472--35602504 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35602462 ACTAATCATT
*
35602472 AAAATGCGATGACAATA
1 AAAATGCAATGACAATA
35602489 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
35602505 GTGCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:35605851 original size:62 final size:62
Alignment explanation
Indices: 35605750--35605873 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
35605740 TCATTGCATA
* *
35605750 CCTTGAATAAATATAGCTCGTTCCAATGATACTTCACTACTTCACGAAGAAATATTTCTTTT
1 CCTTGAATAAATACAGCTCATTCCAATGATACTTCACTACTTCACGAAGAAATATTTCTTTT
* * *
35605812 CCTTGAATAAATACAGCTCATTCCAATGATACTTTACTACTTCATGAAGAAATCTTTCTTTT
1 CCTTGAATAAATACAGCTCATTCCAATGATACTTCACTACTTCACGAAGAAATATTTCTTTT
35605874 TTATGGTCTG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (62 bp):
CCTTGAATAAATACAGCTCATTCCAATGATACTTCACTACTTCACGAAGAAATATTTCTTTT
Found at i:35610005 original size:37 final size:37
Alignment explanation
Indices: 35609943--35610021 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
35609933 TTATTACGAA
* * *
35609943 GTCTTACCCGGACATAATCTGCACACGAAGTTATCAG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
* *
35609980 GTCTTACCCGGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCT-CCACACGAAGTCATCAG
35610017 GTCTT
1 GTCTT
35610022 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 1 0.03
37 35 0.97
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
Found at i:35610218 original size:47 final size:47
Alignment explanation
Indices: 35610140--35610583 Score: 710
Period size: 47 Copynumber: 9.4 Consensus size: 47
35610130 CCCTTCGGGA
* * * * * *
35610140 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
35610187 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35610234 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35610281 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35610328 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35610375 CTTATCACACATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35610422 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35610471 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35610518 CTTATCACATATATACACTTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35610565 CTTATCACATATATACACT
1 CTTATCACATATATACACT
35610584 GTCTTGGCTG
Statistics
Matches: 374, Mismatches: 20, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
46 2 0.01
47 327 0.87
49 45 0.12
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35634661 original size:39 final size:40
Alignment explanation
Indices: 35634601--35634708 Score: 148
Period size: 39 Copynumber: 2.7 Consensus size: 40
35634591 TATTCGGATG
* *
35634601 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
* * *
35634641 A-ATTCCGGGTTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
35634680 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
35634709 AACAAGTAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 33 0.57
40 25 0.43
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
Found at i:35634722 original size:40 final size:40
Alignment explanation
Indices: 35634601--35634741 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 40
35634591 TATTCGGATG
* *
35634601 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCTAGT-GACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAG-CT
* * *
35634641 A-ATTCCGGGTTAAG-CCCGAAGGCATTTGTGCGAGTTA-CT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCT
**
35634680 ATAACCGGGCTAAGTCCCGAAGGCATTTGAACAAGTAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCT
* * *
35634720 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
35634742 TACTTGGTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
39 47 0.57
40 36 0.43
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCT
Found at i:35656759 original size:19 final size:19
Alignment explanation
Indices: 35656735--35656803 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
35656725 TATGGCGGAG
35656735 ACATGGGGTTGAAGAGGCC
1 ACATGGGGTTGAAGAGGCC
* *
35656754 ACAT-GGG-AGCAGA-G--
1 ACATGGGGTTGAAGAGGCC
35656768 ACATGGGGTTGAAGAGGCC
1 ACATGGGGTTGAAGAGGCC
35656787 ACATGGGAGCTTGAAGA
1 ACATGGG-G-TTGAAGA
35656804 AATCATGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.10
15 3 0.08
16 5 0.13
17 5 0.13
18 3 0.08
19 11 0.28
20 1 0.03
21 7 0.18
ACGTcount: A:0.30, C:0.14, G:0.41, T:0.14
Consensus pattern (19 bp):
ACATGGGGTTGAAGAGGCC
Found at i:35656774 original size:33 final size:33
Alignment explanation
Indices: 35656732--35656796 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
35656722 TGTTATGGCG
35656732 GAGACATGGGGTTGAAGAGGCCACATGGGAGCA
1 GAGACATGGGGTTGAAGAGGCCACATGGGAGCA
35656765 GAGACATGGGGTTGAAGAGGCCACATGGGAGC
1 GAGACATGGGGTTGAAGAGGCCACATGGGAGC
35656797 TTGAAGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.43, T:0.12
Consensus pattern (33 bp):
GAGACATGGGGTTGAAGAGGCCACATGGGAGCA
Found at i:35670355 original size:46 final size:46
Alignment explanation
Indices: 35670279--35670587 Score: 442
Period size: 46 Copynumber: 6.7 Consensus size: 46
35670269 TGATGTCATA
* * * * *
35670279 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACAC-ATTTCATATCATGTTGCCATG
** *
35670325 GTATCTTTCAACCATGGTCTTATTCATTTTC-TCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACA-TTTCAT-ATCATGTTGCCATG
** * *
35670372 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
35670418 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
*
35670464 GTATCTTTCAACTATGGTCTTACACATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
* *
35670510 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
35670556 GTATCTTTCAACCATGGTCTTACACATTTCAT
1 GTATCTTTCAACCATGGTCTTACACATTTCAT
35670588 TTCAGAGAGC
Statistics
Matches: 247, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
46 206 0.83
47 41 0.17
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
Found at i:35672695 original size:21 final size:21
Alignment explanation
Indices: 35672645--35672700 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
35672635 TATATATACA
35672645 CATATGTATTTATATTTAAAT
1 CATATGTATTTATATTTAAAT
* * * *
35672666 AATAAGTATTATTTATTT-ATT
1 CATATGTATT-TATATTTAAAT
35672687 CATATGTATATTAT
1 CATATGTAT-TTAT
35672701 TAGTACATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (21 bp):
CATATGTATTTATATTTAAAT
Found at i:35675006 original size:99 final size:92
Alignment explanation
Indices: 35674811--35675070 Score: 262
Period size: 99 Copynumber: 2.8 Consensus size: 92
35674801 GACGAGTGCT
* * *
35674811 AGTGTAAGA-CATGTCTGGTACAT-GCATC-GCCTCGAGATGTAAGCCAGTGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGTAAGCCAGTGTAAGACATATCTG
* *
35674873 GGACATGCATCGGCTACGAGATGTGTC
66 GGACATGCATAGCCTACGAGATGTGTC
* * *
35674900 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATGGATATGTGAGAGCTAGTGTAAGACCATAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGT-A-AGCCAGTGTAAGA-CATAT
*
35674965 CTGGGACATGACGTTAGCCT-CGATGATGATAGTC
63 CTGGGACATG-C-ATAGCCTACGA-GATG-T-GTC
* * * *
35674999 AGTGTAAGACCATGTCTGGGACATGGCATC-G-AGTTGAGATATGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-TCGAGATGTAAGCCAGTGTAAGA-CATATC
*
35675062 TAGGACATG
64 TGGGACATG
35675071 GCATCGACAA
Statistics
Matches: 143, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
89 9 0.06
90 13 0.09
91 5 0.03
92 9 0.06
93 1 0.01
94 12 0.08
95 14 0.10
96 30 0.21
97 9 0.06
98 8 0.06
99 33 0.23
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (92 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGTAAGCCAGTGTAAGACATATCTG
GGACATGCATAGCCTACGAGATGTGTC
Found at i:35675077 original size:47 final size:47
Alignment explanation
Indices: 35674719--35675076 Score: 269
Period size: 47 Copynumber: 7.6 Consensus size: 47
35674709 TTTAAGCTAC
* *
35674719 TGTAAGA-CATGTCTGGGACAT-GCATCGGC--CACATCATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGAT-AT--GAGCCAG
* * *
35674765 TGTAAGACCATG-CTTGGGACATGGCATCGGCATTGAGACGA-GTGCTAG
1 TGTAAGACCATGTC-TGGGACATGGCATCGGC-TTGAGA-TATGAGCCAG
* * * * *
35674813 TGTAAGA-CATGTCTGGTACAT-GCATCGCCTCGAGATGTAAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATATGAGCCAG
* * *
35674858 TGTAAGA-CATGTCTGGGACAT-GCATCGGC-T-ACGAGATGTGTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-GATATGAGCCAG
* *
35674902 TGTAAGACCATGTCTGGGACATGGCATCGGCATG-GATATGTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATA--T--GAGCCAG
* * * * * * *
35674952 TGTAAGACCATATCTGGGACATGACGTTAGCCTCGATGATGAT-AGTCAG
1 TGTAAGACCATGTCTGGGACATGGC-ATCGGCTTGA-GAT-ATGAGCCAG
35675001 TGTAAGACCATGTCTGGGACATGGCATCGAG-TTGAGATATGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCG-GCTTGAGATATGAGCCAG
*
35675048 TGTAAGACCATGTCTAGGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
35675077 ACAACTTATC
Statistics
Matches: 246, Mismatches: 42, Indels: 47
0.73 0.13 0.14
Matches are distributed among these distances:
43 1 0.00
44 14 0.06
45 50 0.20
46 28 0.11
47 60 0.24
48 27 0.11
49 27 0.11
50 27 0.11
51 7 0.03
52 1 0.00
53 3 0.01
54 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (47 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATATGAGCCAG
Found at i:35677743 original size:2 final size:2
Alignment explanation
Indices: 35677736--35677773 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35677726 GTCCTGAAAT
35677736 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35677774 AAGTAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35682624 original size:45 final size:47
Alignment explanation
Indices: 35682479--35682835 Score: 238
Period size: 47 Copynumber: 7.6 Consensus size: 47
35682469 TATGATCTAC
* * * *
35682479 TGTAAGA-CATGTCTGGGACATGCATCAGCCAC-ATCATG-AGAGCCAG
1 TGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GATGTAGAG-TAG
* * * * * *
35682525 TGTAAGACCATGACTGGGACATGGCATTGGCATTGAGACG-AGTGCTAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAG-TAG
* *
35682573 TGTAAGA-CATGTCTAGGACATGCATCGGCCTTGAGATGTA-AGTAG
1 TGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGTAG
*
35682618 TGTAAGA-CATGTCTGGGACATGCATCGG-ATACGAGATGT---GTCAG
1 TGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGT-AG
* *
35682662 TGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGATATGTGAGAGGTAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGC-CTCGAGATGT-AGA-GTAG
* * *
35682712 TGTAAGACCATGTCTGGGACATGGCGTCGACCTCGATGATG-ATAGTCAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGA-GATGTAGAGT-AG
* * * * * * **
35682761 TGTAAGACCATGTCTAGGACATGGCAT-TGACTTGAGATATAAACCAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGTAG
*
35682808 TGTAAGACCATATCTGGGACATGGCATC
1 TGTAAGACCATGTCTGGGACAT-GCATC
35682836 AACACCATAC
Statistics
Matches: 252, Mismatches: 39, Indels: 38
0.77 0.12 0.12
Matches are distributed among these distances:
43 2 0.01
44 10 0.04
45 51 0.20
46 35 0.14
47 56 0.22
48 29 0.12
49 31 0.12
50 33 0.13
51 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (47 bp):
TGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGTAG
Found at i:35682713 original size:139 final size:141
Alignment explanation
Indices: 35682479--35682835 Score: 345
Period size: 137 Copynumber: 2.5 Consensus size: 141
35682469 TATGATCTAC
* * * *
35682479 TGTAAGACATGTCTGGGACATGCATCAGCCACATC-ATGA-GAGCCAGTGTAAGACCATGACTGG
1 TGTAAGACATGTCTGGGACATGCATC-G-GATA-CGA-GATGTGCCAGTGTAAGACCATGTCTGG
* ** * * *
35682542 GACATGGCATTGGCATTGAGACGAGTGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTT
62 GACATGGCATCGGCACGGAGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTC
35682605 GA-GATG-TAAGT-AG
127 GATGATGAT-AGTCAG
*
35682618 TGTAAGACATGTCTGGGACATGCATCGGATACGAGATGTGTCAGTGTAAGACCATGTCTGGGACA
1 TGTAAGACATGTCTGGGACATGCATCGGATACGAGATGTGCCAGTGTAAGACCATGTCTGGGACA
* * * * *
35682683 TGGCATCGGCACGGATATGTGAGAGGTAGTGTAAGACCATGTCTGGGACATGGCGTCGACCTCGA
66 TGGCATCGGCACGGAGA--CGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGA
35682748 TGATGATAGTCAG
129 TGATGATAGTCAG
* * * * * *
35682761 TGTAAGACCATGTCTAGGACATGGCAT-TGACT-TGAGATATAAACCAGTGTAAGACCATATCTG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGA-TACGAGATGT--GCCAGTGTAAGACCATGTCTG
35682824 GGACATGGCATC
61 GGACATGGCATC
35682836 AACACCATAC
Statistics
Matches: 181, Mismatches: 23, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
136 3 0.02
137 41 0.23
138 1 0.01
139 40 0.22
140 13 0.07
141 10 0.06
142 7 0.04
143 10 0.06
144 21 0.12
145 5 0.03
146 30 0.17
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (141 bp):
TGTAAGACATGTCTGGGACATGCATCGGATACGAGATGTGCCAGTGTAAGACCATGTCTGGGACA
TGGCATCGGCACGGAGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGATG
ATGATAGTCAG
Found at i:35682770 original size:99 final size:91
Alignment explanation
Indices: 35682571--35682787 Score: 264
Period size: 99 Copynumber: 2.3 Consensus size: 91
35682561 GACGAGTGCT
*
35682571 AGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTTGAGATGTAAGTAGTGTAAGACATGTCTGG
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTGGAGATGTAAGTAGTGTAAGACATGTCTGG
35682634 GACATGCATCGGATACGAGATGTGTC
66 GACATGCATCGGATACGAGATGTGTC
* *
35682660 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGATATGTGAGAGGTAGTGTAAGACCATG
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGC-CTGGAGATGT-A-A-GTAGTGTAAGA-CATG
*
35682724 TCTGGGACATGGCGTC-GACCT-CGATGATGATAGTC
61 TCTGGGACAT-GCATCGGA--TACGA-GATG-T-GTC
35682759 AGTGTAAGACCATGTCTAGGACATGGCAT
1 AGTGTAAGACCATGTCTAGGACATGGCAT
35682788 TGACTTGAGA
Statistics
Matches: 110, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
89 9 0.08
90 13 0.12
91 14 0.13
92 2 0.02
93 1 0.01
94 11 0.10
95 16 0.15
96 7 0.06
97 5 0.05
98 1 0.01
99 31 0.28
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.24
Consensus pattern (91 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTGGAGATGTAAGTAGTGTAAGACATGTCTGG
GACATGCATCGGATACGAGATGTGTC
Found at i:35683942 original size:31 final size:31
Alignment explanation
Indices: 35683883--35683946 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
35683873 TGTAGGTTTG
*
35683883 CATTTAGAATTATTTCCACACGACTGGAGGA
1 CATTTAGAATTATTTCCACACAACTGGAGGA
* *
35683914 CATTTAGAATTATTTCCACATAAGTGGAGGA
1 CATTTAGAATTATTTCCACACAACTGGAGGA
35683945 CA
1 CA
35683947 CGGGCGTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (31 bp):
CATTTAGAATTATTTCCACACAACTGGAGGA
Found at i:35684055 original size:20 final size:21
Alignment explanation
Indices: 35684017--35684055 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35684007 TCGAATTGGT
*
35684017 CACACGTGCGTGTTGCCCTTC
1 CACACGAGCGTGTTGCCCTTC
35684038 CACACGAGCGTG-TGCCCT
1 CACACGAGCGTGTTGCCCT
35684056 ATTTCAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.38, G:0.26, T:0.23
Consensus pattern (21 bp):
CACACGAGCGTGTTGCCCTTC
Found at i:35695642 original size:66 final size:66
Alignment explanation
Indices: 35695558--35695688 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
35695548 AGGTACACAA
*
35695558 CCGTGTCCCAGCCCGTGTCCTTACTCGTGTAACTCTCTAACTTGGGTCACACAGCCAACCACACG
1 CCGTGTCCCAGCCCGTGTCCTTACCCGTGTAACTCTCTAACTTGGGTCACACAGCCAACCACACG
35695623 G
66 G
* *
35695624 CCGTGTCCCAGCCTGTGTCCTTACCCGTGTAACTCTCTAACTTGGGTCACACGGCCAACCACACG
1 CCGTGTCCCAGCCCGTGTCCTTACCCGTGTAACTCTCTAACTTGGGTCACACAGCCAACCACACG
35695689 TCTGTGTGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.19, C:0.38, G:0.20, T:0.23
Consensus pattern (66 bp):
CCGTGTCCCAGCCCGTGTCCTTACCCGTGTAACTCTCTAACTTGGGTCACACAGCCAACCACACG
G
Found at i:35696976 original size:45 final size:46
Alignment explanation
Indices: 35696898--35696985 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
35696888 TGAGCCATGT
* *
35696898 ATCAGGAAGCTTATTTAGGCTAAACAGGAAACTCAT-AAGAGTTTTA
1 ATCAGGAAGCTCATTGAGGCTAAACAGGAAACTC-TGAAGAGTTTTA
* *
35696944 ATCAGGAAGCTCATTGA-GCTTAACAGGTAACTCTGAAGAGTT
1 ATCAGGAAGCTCATTGAGGCTAAACAGGAAACTCTGAAGAGTT
35696986 ATTATTAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 1 0.03
45 21 0.57
46 15 0.41
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (46 bp):
ATCAGGAAGCTCATTGAGGCTAAACAGGAAACTCTGAAGAGTTTTA
Found at i:35702446 original size:28 final size:28
Alignment explanation
Indices: 35702390--35702453 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
35702380 ATTCTCGAGA
**
35702390 CATTTTCTCAGAACCCATCTTGTCAAAAT
1 CATTTT-TCAGAACCCATCTCATCAAAAT
* *
35702419 TATTTTTCAGAACCCATCTCATCTAAAT
1 CATTTTTCAGAACCCATCTCATCAAAAT
35702447 CATTTTT
1 CATTTTT
35702454 TCAAAACTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (28 bp):
CATTTTTCAGAACCCATCTCATCAAAAT
Found at i:35702584 original size:18 final size:18
Alignment explanation
Indices: 35702561--35702598 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35702551 CCAAAACTCT
*
35702561 AATT-AATAAACACTTAAA
1 AATTAAATAAA-ACATAAA
35702579 AATTAAATAAAACATAAA
1 AATTAAATAAAACATAAA
35702597 AA
1 AA
35702599 CCATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
AATTAAATAAAACATAAA
Done.