Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 130 of 230
Found at i:37985606 original size:15 final size:15
Alignment explanation
Indices: 37985586--37985625 Score: 73
Period size: 14 Copynumber: 2.7 Consensus size: 15
37985576 TAGCTTCTTC
37985586 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
37985601 -TTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
37985615 TTTTTTTTTCA
1 TTTTTTTTTCA
37985626 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:38003143 original size:20 final size:20
Alignment explanation
Indices: 38003120--38003165 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38003110 CCAGCTCGAA
*
38003120 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
38003140 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
38003160 TTAGCT
1 TTAGCT
38003166 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:38003147 original size:30 final size:30
Alignment explanation
Indices: 38003112--38003185 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
38003102 AGTTTTTCCC
38003112 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
38003142 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
38003172 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
38003186 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:38005256 original size:10 final size:10
Alignment explanation
Indices: 38005241--38005278 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
38005231 TTAGGTTAAG
38005241 ATTGAGCTGA
1 ATTGAGCTGA
38005251 ATTGAGCTCGA
1 ATTGAGCT-GA
38005262 A-TGAGCTGA
1 ATTGAGCTGA
*
38005271 CTTGAGCT
1 ATTGAGCT
38005279 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:38005266 original size:20 final size:20
Alignment explanation
Indices: 38005243--38005289 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
38005233 AGGTTAAGAT
38005243 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
38005263 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
38005283 TGAGCTG
1 TGAGCTG
38005290 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:38006626 original size:20 final size:20
Alignment explanation
Indices: 38006603--38006648 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
38006593 CCAGCTCGAA
*
38006603 TTAGCTC-ACATGAGCTTAAT
1 TTAGCTCGA-ATGAGCTCAAT
*
38006623 TTAGCTCGATTGAGCTCAAT
1 TTAGCTCGAATGAGCTCAAT
38006643 TTAGCT
1 TTAGCT
38006649 TACTTTAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
TTAGCTCGAATGAGCTCAAT
Found at i:38006630 original size:30 final size:30
Alignment explanation
Indices: 38006595--38006668 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
38006585 AGTTTTTCCC
38006595 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* *
38006625 AGCTCGATTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
38006655 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
38006669 TGGCTGATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:38009458 original size:17 final size:18
Alignment explanation
Indices: 38009436--38009469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38009426 ACAACACTCC
*
38009436 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
38009453 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
38009470 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:38010513 original size:22 final size:21
Alignment explanation
Indices: 38010483--38010546 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
38010473 CTCACAAGAC
*
38010483 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTTTTTTCTT-TTT
*
38010505 TTTTTACTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTCTTTTT
*
38010526 TTGCTCACTTTTTTTT-TTTTT
1 TT-TTCACTTTTTTTTCTTTTT
38010547 GAATTTCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 10 0.27
22 27 0.73
ACGTcount: A:0.05, C:0.12, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTCACTTTTTTTTCTTTTT
Found at i:38010546 original size:9 final size:9
Alignment explanation
Indices: 38010492--38010527 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
38010482 CTTTTCACTT
38010492 TTTTTTGTTC
1 TTTTTT-TTC
38010502 TTTTTTTTAC
1 TTTTTTTT-C
38010512 TTTTTTTTC
1 TTTTTTTTC
38010521 TTTTTTT
1 TTTTTTT
38010528 GCTCACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:38012204 original size:20 final size:19
Alignment explanation
Indices: 38012181--38012245 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38012171 AAGCTCAAAC
38012181 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
38012201 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
38012221 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
38012241 GAGCT
1 GAGCT
38012246 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:38013147 original size:10 final size:10
Alignment explanation
Indices: 38013131--38013188 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
38013121 CAACTCCGAC
38013131 CAGCTCAATT
1 CAGCTCAATT
* *
38013141 GAGCTCATTT
1 CAGCTCAATT
38013151 CAGCTCAA-T
1 CAGCTCAATT
38013160 CGAGCTCAATT
1 C-AGCTCAATT
*
38013171 TAGCTACAATT
1 CAGCT-CAATT
38013182 CAGCTCA
1 CAGCTCA
38013189 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:38013154 original size:20 final size:20
Alignment explanation
Indices: 38013131--38013191 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
38013121 CAACTCCGAC
38013131 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
38013151 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
38013172 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
38013192 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:38014621 original size:7 final size:8
Alignment explanation
Indices: 38014605--38014632 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
38014595 AAATCGAGTT
38014605 AAAAGAAA
1 AAAAGAAA
38014613 AAAAGAAA
1 AAAAGAAA
38014621 AAAAGAAA
1 AAAAGAAA
38014629 AAAA
1 AAAA
38014633 AAGTGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:38014641 original size:17 final size:18
Alignment explanation
Indices: 38014569--38014642 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 18
38014559 AAATTTAAAA
38014569 AAAAGAAAAAAAAGAAGTG
1 AAAAG-AAAAAAAGAAGTG
** *
38014588 ACAAA-AAAAATCG-AGTT
1 A-AAAGAAAAAAAGAAGTG
*
38014605 AAAAGAAAAAAAGAA--A
1 AAAAGAAAAAAAGAAGTG
38014621 AAAAGAAAAAAA-AAGTG
1 AAAAGAAAAAAAGAAGTG
38014638 AAAAG
1 AAAAG
38014643 TCTTTCGAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
15 2 0.05
16 15 0.35
17 15 0.35
18 7 0.16
19 1 0.02
20 3 0.07
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAAAGAAGTG
Found at i:38017257 original size:21 final size:21
Alignment explanation
Indices: 38017222--38017262 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38017212 AAAGAGATTG
** *
38017222 AAAAAGAAATTGAAAGAGAAC
1 AAAAAGAAAACGAAAAAGAAC
38017243 AAAAAGAAAACGAAAAAGAA
1 AAAAAGAAAACGAAAAAGAA
38017263 AAAGAAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAACGAAAAAGAAC
Found at i:38017276 original size:18 final size:18
Alignment explanation
Indices: 38017243--38017277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38017233 GAAAGAGAAC
*
38017243 AAAAAGAAAACGAAAAAG
1 AAAAAGAAAACAAAAAAG
*
38017261 AAAAAGAAATCAAAAAA
1 AAAAAGAAAACAAAAAA
38017278 AGTGAGAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAACAAAAAAG
Found at i:38017322 original size:14 final size:13
Alignment explanation
Indices: 38017285--38017341 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
38017275 AAAAGTGAGA
*
38017285 GAAAAAGAAAA-T
1 GAAAAAAAAAATT
38017297 GAAGAAAAAAAATT
1 GAA-AAAAAAAATT
**
38017311 GAAAAAGAAAAAGC
1 GAAAAA-AAAAATT
*
38017325 GAAAAAAGAAATT
1 GAAAAAAAAAATT
38017338 GAAA
1 GAAA
38017342 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 3 0.08
13 18 0.50
14 15 0.42
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.09
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:38017322 original size:27 final size:26
Alignment explanation
Indices: 38017285--38017341 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
38017275 AAAAGTGAGA
*
38017285 GAAAAAGAAAA-TGAAGAAAAAAAATT
1 GAAAAAGAAAAGCGAA-AAAAAAAATT
*
38017311 GAAAAAGAAAAAGCGAAAAAAGAAATT
1 GAAAAAG-AAAAGCGAAAAAAAAAATT
38017338 GAAA
1 GAAA
38017342 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 17 0.63
28 3 0.11
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.09
Consensus pattern (26 bp):
GAAAAAGAAAAGCGAAAAAAAAAATT
Found at i:38024062 original size:17 final size:18
Alignment explanation
Indices: 38024040--38024080 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
38024030 CGTTTCTTTT
38024040 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
38024057 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
38024075 T-TTTTG
1 TCTTTTG
38024081 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:38024064 original size:24 final size:25
Alignment explanation
Indices: 38024011--38024064 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
38024001 AACAAATTCT
* *
38024011 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
38024036 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
38024059 TTTTTT
1 TTTTTT
38024065 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:38026339 original size:14 final size:13
Alignment explanation
Indices: 38026315--38026342 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38026305 CTAGACCGTA
38026315 TGCAATTTTTTTT
1 TGCAATTTTTTTT
38026328 TGCAATTTTTTTT
1 TGCAATTTTTTTT
38026341 TG
1 TG
38026343 AAGCTACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.11, T:0.68
Consensus pattern (13 bp):
TGCAATTTTTTTT
Found at i:38029014 original size:10 final size:10
Alignment explanation
Indices: 38028998--38029055 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
38028988 CAACTCCGAC
38028998 CAGCTCAATT
1 CAGCTCAATT
* *
38029008 GAGCTCATTT
1 CAGCTCAATT
38029018 CAGCTCAATT
1 CAGCTCAATT
*
38029028 GAGCTCAATT
1 CAGCTCAATT
*
38029038 TAGCTACAATT
1 CAGCT-CAATT
38029049 CAGCTCA
1 CAGCTCA
38029056 TTTATTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 31 0.77
11 9 0.22
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:38029021 original size:20 final size:20
Alignment explanation
Indices: 38028998--38029058 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
38028988 CAACTCCGAC
38028998 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
38029018 CAGCTCAATTGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
38029039 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
38029059 ATTTTATTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:38031281 original size:10 final size:11
Alignment explanation
Indices: 38031251--38031280 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38031241 GTTCGTAACG
*
38031251 AAAAAAAAGTC
1 AAAAAAAAATC
38031262 AAAAAAAAATC
1 AAAAAAAAATC
38031273 AAAAAAAA
1 AAAAAAAA
38031281 TTTGAGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:38032620 original size:39 final size:36
Alignment explanation
Indices: 38032569--38032642 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 36
38032559 GAGAAAAGGA
38032569 GAAAGAGATTGAAAAAGAAA-AAGTGAAAAAAGAAATT
1 GAAAGAGATTG-AAAAGAAACAAGTG-AAAAAGAAATT
38032606 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAAGAAA
1 GAAAGAGA--TTGAAAAGAAA-CAAGTGAAAAAGAAA
38032643 GAGAGTCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
37 8 0.24
38 8 0.24
39 12 0.36
40 5 0.15
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.12
Consensus pattern (36 bp):
GAAAGAGATTGAAAAGAAACAAGTGAAAAAGAAATT
Found at i:38032643 original size:33 final size:33
Alignment explanation
Indices: 38032606--38032668 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38032596 AAAAGAAATT
38032606 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
38032639 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
38032669 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:38034291 original size:20 final size:20
Alignment explanation
Indices: 38034268--38034321 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38034258 AGTTTTTCCC
*
38034268 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
38034288 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
38034308 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
38034322 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:38034303 original size:30 final size:30
Alignment explanation
Indices: 38034268--38034341 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38034258 AGTTTTTCCC
38034268 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
38034298 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
38034328 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
38034342 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:38034331 original size:20 final size:20
Alignment explanation
Indices: 38034268--38034332 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38034258 AGTTTTTCCC
* * * *
38034268 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
38034288 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
38034307 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
38034328 AGCTC
1 AGCTC
38034333 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:38036881 original size:15 final size:16
Alignment explanation
Indices: 38036861--38036892 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38036851 AGAAAATGAA
38036861 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
38036876 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
38036892 A
1 A
38036893 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:38037007 original size:17 final size:18
Alignment explanation
Indices: 38036975--38037008 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38036965 AAAAGAGAGT
*
38036975 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
38036993 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
38037009 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:38038296 original size:20 final size:20
Alignment explanation
Indices: 38038273--38038326 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38038263 AGTTTTTCCC
*
38038273 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
38038293 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
38038313 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
38038327 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:38038308 original size:30 final size:30
Alignment explanation
Indices: 38038273--38038346 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38038263 AGTTTTTCCC
38038273 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
38038303 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
38038333 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
38038347 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:38038336 original size:20 final size:20
Alignment explanation
Indices: 38038273--38038337 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38038263 AGTTTTTCCC
* * * *
38038273 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
38038293 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
38038312 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
38038333 AGCTC
1 AGCTC
38038338 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:38040026 original size:30 final size:30
Alignment explanation
Indices: 38039981--38040054 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
38039971 AGTTTTTCCC
38039981 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
38040011 AGGTCGATTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
38040041 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
38040055 TGGCTTAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:38048439 original size:30 final size:30
Alignment explanation
Indices: 38048418--38048483 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
38048408 GCTCACTCCT
38048418 AGCTCATA-TTTAGCTCACGAGCTAAACCTC
1 AGCTCA-ACTTTAGCTCACGAGCTAAACCTC
* *
38048448 AGCTCAACTTTAGCTCACGAGCTAAAACTT
1 AGCTCAACTTTAGCTCACGAGCTAAACCTC
38048478 AGCTCA
1 AGCTCA
38048484 TTTTAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.26
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTC
Found at i:38050207 original size:12 final size:12
Alignment explanation
Indices: 38050190--38050220 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38050180 AGGAAATTTG
38050190 AAAAAAAAATTC
1 AAAAAAAAATTC
38050202 AAAAAAAAATTC
1 AAAAAAAAATTC
38050214 AAAAAAA
1 AAAAAAA
38050221 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:38051183 original size:37 final size:37
Alignment explanation
Indices: 38051132--38051202 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
38051122 CATTCTTGTA
38051132 AAGAGAAAACAAAG-AAAAGAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAAAG-AAAGAAAAAGAAAAAGC
*
38051169 AAGAGAAGAA-AAAGAAAAAGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAAAGAAAGAAAAAGAAAA
38051203 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.01
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAAAGAAAGAAAAAGAAAAAGC
Found at i:38051190 original size:15 final size:16
Alignment explanation
Indices: 38051131--38051202 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
38051121 ACATTCTTGT
*
38051131 AAAGAGAAAACAAAG-A
1 AAAGA-AAAAGAAAGAA
*
38051147 AAAGAAAAGAAAAAGAA
1 AAAGAAAA-AGAAAGAA
* *
38051164 AAAGCAAGAG-AAGAA
1 AAAGAAAAAGAAAGAA
*
38051179 AAAGAAAAAGAAATAA
1 AAAGAAAAAGAAAGAA
38051195 AAAGAAAA
1 AAAGAAAA
38051203 GAGAGGCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 16 0.35
16 23 0.50
17 7 0.15
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:38051202 original size:6 final size:6
Alignment explanation
Indices: 38051142--38051191 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
38051132 AAGAGAAAAC
38051142 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
38051191 A
1 A
38051192 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.22
6 23 0.56
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:38051204 original size:21 final size:21
Alignment explanation
Indices: 38051142--38051202 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
38051132 AAGAGAAAAC
38051142 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAAA-AAAAGAAAAAGAA
* * *
38051164 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAAAAAAGAAAAAGAA
38051185 AAAGAAATAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
38051203 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:38051284 original size:11 final size:12
Alignment explanation
Indices: 38051252--38051282 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38051242 TTGAGAGAAC
38051252 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38051264 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38051276 TTGAAAA
1 TTGAAAA
38051283 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:38053483 original size:30 final size:30
Alignment explanation
Indices: 38053462--38053527 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
38053452 GCTCACTCCT
38053462 AGCTCATA-TTTAGCTCACGAGCTAAACCTC
1 AGCTCA-ACTTTAGCTCACGAGCTAAACCTC
* *
38053492 AGCTCAACTTTAGCTCACGAGCTAAAACTT
1 AGCTCAACTTTAGCTCACGAGCTAAACCTC
38053522 AGCTCA
1 AGCTCA
38053528 TTTTAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.26
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTC
Found at i:38061525 original size:11 final size:10
Alignment explanation
Indices: 38061509--38061548 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
38061499 TGCAATATAT
38061509 TTTTTTTTCAA
1 TTTTTTTTC-A
38061520 TTTTTTTTCGA
1 TTTTTTTTC-A
38061531 TTTTTTTT-A
1 TTTTTTTTCA
38061540 TTTTTTTTC
1 TTTTTTTTC
38061549 GAAAACTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:38061536 original size:20 final size:20
Alignment explanation
Indices: 38061511--38061550 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38061501 CAATATATTT
38061511 TTTTTTCAATTTTTTTTCGA
1 TTTTTTCAATTTTTTTTCGA
**
38061531 TTTTTTTTATTTTTTTTCGA
1 TTTTTTCAATTTTTTTTCGA
38061551 AAACTACAAT
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:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTTCAATTTTTTTTCGA
Found at i:38068402 original size:24 final size:25
Alignment explanation
Indices: 38068349--38068402 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
38068339 AACAAATTCT
* *
38068349 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
38068374 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
38068397 TTTTTT
1 TTTTTT
38068403 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:38073680 original size:28 final size:29
Alignment explanation
Indices: 38073643--38073704 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
38073633 GGACTTATCT
38073643 TTTA-TTCTTGCTG-TTCAATTTCT-TTTC
1 TTTATTTCTTGCTGTTTC-ATTTCTATTTC
*
38073670 TTTATTTCTTGCTGTTTCATTTTTATTTC
1 TTTATTTCTTGCTGTTTCATTTCTATTTC
38073699 TTTATT
1 TTTATT
38073705 CCTACTTGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 4 0.13
28 14 0.45
29 13 0.42
ACGTcount: A:0.11, C:0.15, G:0.06, T:0.68
Consensus pattern (29 bp):
TTTATTTCTTGCTGTTTCATTTCTATTTC
Found at i:38085540 original size:17 final size:18
Alignment explanation
Indices: 38085518--38085551 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38085508 ACAACACTCC
*
38085518 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
38085535 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
38085552 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:38086623 original size:29 final size:27
Alignment explanation
Indices: 38086588--38086660 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 27
38086578 CTCGCAAGAC
*
38086588 TTTTCACTTTTTTTTAACTTGATTTTT
1 TTTTCACTTTTTTTTAACTCGATTTTT
**
38086615 TTTGGTCACCTTTTTTTTTTGCTCGATTTTT
1 TTT--TCA-C-TTTTTTTTAACTCGATTTTT
38086646 TTTTCACTTTTTTTT
1 TTTTCACTTTTTTTT
38086661 TTGAATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 11 0.28
28 1 0.03
29 6 0.15
30 1 0.03
31 20 0.51
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.70
Consensus pattern (27 bp):
TTTTCACTTTTTTTTAACTCGATTTTT
Found at i:38086657 original size:13 final size:13
Alignment explanation
Indices: 38086641--38086679 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
38086631 TTTTGCTCGA
*
38086641 TTTTTTTTTCACT
1 TTTTTTTTTCAAT
*
38086654 TTTTTTTTTGAAT
1 TTTTTTTTTCAAT
38086667 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
38086680 CAATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:38089579 original size:23 final size:22
Alignment explanation
Indices: 38089527--38089579 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38089517 TCCACGTCTT
*
38089527 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38089549 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38089572 TTTCTTTT
1 TTTCTTTT
38089580 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:38094662 original size:28 final size:28
Alignment explanation
Indices: 38094608--38094670 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
38094598 GCACAAGTAG
38094608 GAATAAAGAAATAAAAATGAAACAGCAA
1 GAATAAAGAAATAAAAATGAAACAGCAA
*
38094636 GAAATAAAGAAA-AGAAATTG-AACAGCAA
1 G-AATAAAGAAATA-AAAATGAAACAGCAA
38094664 GAATAAA
1 GAATAAA
38094671 AGATAAGTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.19
28 11 0.34
29 15 0.47
ACGTcount: A:0.67, C:0.06, G:0.16, T:0.11
Consensus pattern (28 bp):
GAATAAAGAAATAAAAATGAAACAGCAA
Found at i:38099940 original size:24 final size:25
Alignment explanation
Indices: 38099913--38099969 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
38099903 ATGAGTGATA
*
38099913 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
38099937 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
38099961 AAAAAAGAA
1 AAAAAAGAA
38099970 TTTGTTGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 13 0.46
24 7 0.25
25 8 0.29
ACGTcount: A:0.63, C:0.04, G:0.23, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:38106468 original size:10 final size:10
Alignment explanation
Indices: 38106453--38106514 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38106443 TTTGAACCAT
*
38106453 TACCAATTCG
1 TACCAATTCA
*
38106463 TACCAAATACCA
1 TACC-AAT-TCA
*
38106475 TACCATTTCA
1 TACCAATTCA
38106485 TACCAATTCCA
1 TACCAATT-CA
* *
38106496 TACCATTTCG
1 TACCAATTCA
38106506 TACCAATTC
1 TACCAATTC
38106515 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38106498 original size:21 final size:21
Alignment explanation
Indices: 38106453--38106515 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38106443 TTTGAACCAT
* *
38106453 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38106475 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38106496 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
38106516 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38106833 original size:13 final size:13
Alignment explanation
Indices: 38106817--38106851 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
38106807 TAAAAAAAAT
*
38106817 AAAAAAAACTT-G
1 AAAAAAAAATTCG
38106829 AAAAAAAAATTCG
1 AAAAAAAAATTCG
38106842 AAAAAAAAAT
1 AAAAAAAAAT
38106852 AAAAAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:38107869 original size:17 final size:15
Alignment explanation
Indices: 38107849--38107887 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
38107839 GCGAGCGAGA
38107849 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
38107866 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
38107881 AAGATGA
1 AA-ATGA
38107888 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:38110695 original size:15 final size:16
Alignment explanation
Indices: 38110656--38110696 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
38110646 AATAACACTC
38110656 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
38110672 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
38110686 CTTTCTTTTTC
1 CTTTCTTTTTC
38110697 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:38110891 original size:17 final size:15
Alignment explanation
Indices: 38110854--38110892 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
38110844 TATCTCCCAC
38110854 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
38110870 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
38110887 TCATTT
1 TCATTT
38110893 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:38111775 original size:28 final size:30
Alignment explanation
Indices: 38111743--38111810 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
38111733 TTTCAATCAC
38111743 TCTTTTTTTTCAATT-TCG-A-TTTTTTTCT
1 TCTTTTTTTTCAATTCT-GAATTTTTTTTCT
38111771 TCTTTTTTTT-AATTCTGAATTTTTTTTCT
1 TCTTTTTTTTCAATTCTGAATTTTTTTTCT
38111800 TCTTTTTTTTC
1 TCTTTTTTTTC
38111811 CTTCAATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 5 0.14
28 12 0.33
29 19 0.53
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (30 bp):
TCTTTTTTTTCAATTCTGAATTTTTTTTCT
Found at i:38111778 original size:13 final size:13
Alignment explanation
Indices: 38111762--38111814 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
38111752 TCAATTTCGA
38111762 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
**
38111775 TTTTTTAATTCTGAAT
1 TTTTTTTCTTCT---T
38111791 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
38111804 TTTTTTCCTTC
1 TTTTTTTCTTC
38111815 AATACTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 21 0.66
16 11 0.34
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:38111872 original size:12 final size:12
Alignment explanation
Indices: 38111855--38111886 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
38111845 GAATACAAAC
38111855 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
38111867 TTTTTTTCGAAT
1 TTTTTTTTGAAT
38111879 TTTTTTTT
1 TTTTTTTT
38111887 TCAAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:38111873 original size:13 final size:13
Alignment explanation
Indices: 38111855--38111898 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
38111845 GAATACAAAC
38111855 TTTTTTTTGAA-T
1 TTTTTTTTGAATT
*
38111867 TTTTTTTCGAATT
1 TTTTTTTTGAATT
*
38111880 TTTTTTTTCAAGTT
1 TTTTTTTTGAA-TT
38111894 TTTTT
1 TTTTT
38111899 ATTTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 10 0.37
14 7 0.26
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.75
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:38113797 original size:20 final size:19
Alignment explanation
Indices: 38113774--38113838 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38113764 AAGCTCAAAC
38113774 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
38113794 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
38113814 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
38113834 GAGCT
1 GAGCT
38113839 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:38115703 original size:21 final size:21
Alignment explanation
Indices: 38115674--38115729 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
38115664 CAAGCTCTCT
*
38115674 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
38115695 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
38115716 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
38115730 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:38115722 original size:14 final size:14
Alignment explanation
Indices: 38115673--38115729 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
38115663 TCAAGCTCTC
38115673 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
38115686 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
38115700 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
38115714 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
38115728 TT
1 TT
38115730 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:38115783 original size:18 final size:18
Alignment explanation
Indices: 38115691--38115793 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
38115681 TCTTTTTTCG
38115691 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
38115710 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* ** *
38115730 CTCTCACTTTTTGA-TTT
1 CTTTTTCTTTTTCATTTT
* *
38115747 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
38115765 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
38115783 CTTTTTGTTTT
1 CTTTTTCTTTT
38115794 CTTTCAATTT
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 12 0.19
18 33 0.52
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:38115810 original size:6 final size:6
Alignment explanation
Indices: 38115691--38115797 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
38115681 TCTTTTTTCG
* * * **
38115691 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
38115742 -GATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
38115789 -GTTTT CTTT
1 CTTTTT CTTT
38115798 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
5 7 0.10
6 53 0.74
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:38116894 original size:31 final size:31
Alignment explanation
Indices: 38116829--38116894 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
38116819 TTAAACTTGA
*
38116829 TTTTTTTTGCTCACCTTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCACCTTTTTTTTTCCTTTCT
*
38116860 TTTTTTTTGCTCGA-TTTTTTTTTTCACTTT-T
1 TTTTTTTTGCTC-ACCTTTTTTTTTC-CTTTCT
38116891 TTTT
1 TTTT
38116895 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (31 bp):
TTTTTTTTGCTCACCTTTTTTTTTCCTTTCT
Found at i:38116938 original size:10 final size:12
Alignment explanation
Indices: 38116876--38116942 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 12
38116866 TTGCTCGATT
*
38116876 TTTTTTTTC-AC
1 TTTTTTTTCGAA
38116887 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
38116898 TTTTTTTTCAATCAA
1 TTTTTTTTC---GAA
38116913 TTTTTTTTTCGAA
1 -TTTTTTTTCGAA
38116926 TTTTTTTT-G-A
1 TTTTTTTTCGAA
38116936 TTTTTTT
1 TTTTTTT
38116943 ACTCCAATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
10 8 0.17
11 18 0.38
12 8 0.17
13 2 0.04
15 2 0.04
16 9 0.19
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:38127249 original size:10 final size:11
Alignment explanation
Indices: 38127226--38127294 Score: 64
Period size: 10 Copynumber: 6.9 Consensus size: 11
38127216 AGCTAATAAC
38127226 GAGCTC-AA-T
1 GAGCTCGAATT
38127235 GAGCT-GAATT
1 GAGCTCGAATT
38127245 GAGCTCGAA-T
1 GAGCTCGAATT
*
38127255 GAGCT-GACTT
1 GAGCTCGAATT
38127265 GAGCTCGAA-T
1 GAGCTCGAATT
38127275 GAGCT--AATTT
1 GAGCTCGAA-TT
38127285 GAGCTCGAAT
1 GAGCTCGAAT
38127295 GAACTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 30 0.61
11 6 0.12
12 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (11 bp):
GAGCTCGAATT
Found at i:38127255 original size:20 final size:20
Alignment explanation
Indices: 38127226--38127296 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
38127216 AGCTAATAAC
38127226 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
*
38127245 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
38127265 GAGCTCGAATGAGCT-AATTT
1 GAGCTCGAATGAGCTGAA-TT
38127285 GAGCTCGAATGA
1 GAGCTCGAATGA
38127297 ACTAAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 7 0.15
20 41 0.85
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:38129769 original size:20 final size:20
Alignment explanation
Indices: 38129744--38129798 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
38129734 TGTGGTTCAA
* *
38129744 CTCATTCGAGCTTAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
38129764 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
38129784 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
38129799 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:38129890 original size:13 final size:13
Alignment explanation
Indices: 38129869--38129903 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
38129859 ATAAGTTGCT
* *
38129869 GTTAGTTAAATTA
1 GTTAATTAAATAA
38129882 GTTAATTAAATAA
1 GTTAATTAAATAA
38129895 GTTAATTAA
1 GTTAATTAA
38129904 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:38130153 original size:23 final size:24
Alignment explanation
Indices: 38130123--38130184 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
38130113 ATTTTCCAGA
38130123 CGAATTTAATGTATGTCTT-TGGC
1 CGAATTTAATGTATGTCTTCTGGC
* *
38130146 CGAATTTAAAGTAT-TTTTCTGGC
1 CGAATTTAATGTATGTCTTCTGGC
*
38130169 CGAATTTAATGCATGT
1 CGAATTTAATGTATGT
38130185 TTTAAATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 3 0.09
23 29 0.88
24 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (24 bp):
CGAATTTAATGTATGTCTTCTGGC
Found at i:38132945 original size:15 final size:16
Alignment explanation
Indices: 38132906--38132946 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
38132896 AACAACACTC
38132906 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
38132922 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
38132936 CTTTCTTTTTC
1 CTTTCTTTTTC
38132947 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:38133140 original size:17 final size:15
Alignment explanation
Indices: 38133104--38133142 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
38133094 TATCTCCCAC
38133104 TCATCTTCTTTTTCGT
1 TCAT-TTCTTTTTCGT
38133120 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC--GT
38133137 TCATTT
1 TCATTT
38133143 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 8 0.38
ACGTcount: A:0.10, C:0.21, G:0.05, T:0.64
Consensus pattern (15 bp):
TCATTTCTTTTTCGT
Found at i:38134028 original size:13 final size:13
Alignment explanation
Indices: 38134012--38134065 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
38134002 TCAATTTCGA
38134012 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
38134025 TTTTTTTAATTCTGAAT
1 TTTTTTT-CTTCT---T
38134042 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
38134055 TTTTTTCCTTC
1 TTTTTTTCTTC
38134066 AATACTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 18 0.53
14 4 0.12
16 4 0.12
17 8 0.24
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:38134030 original size:30 final size:30
Alignment explanation
Indices: 38133992--38134060 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 30
38133982 TTTCAATCAC
38133992 TCTTTTTTTTTCAATT-TCG-A-TTTTTTTCT
1 TCTTTTTTTTT-AATTCT-GAATTTTTTTTCT
38134021 TCTTTTTTTTTAATTCTGAATTTTTTTTCT
1 TCTTTTTTTTTAATTCTGAATTTTTTTTCT
38134051 TCTTTTTTTT
1 TCTTTTTTTT
38134061 CCTTCAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
28 5 0.14
29 13 0.35
30 19 0.51
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (30 bp):
TCTTTTTTTTTAATTCTGAATTTTTTTTCT
Found at i:38134123 original size:12 final size:12
Alignment explanation
Indices: 38134106--38134163 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
38134096 GAATACAAAC
*
38134106 TTTTTTTTTGAA
1 TTTTTTTTTCAA
38134118 -TTTTTTTTCAA
1 TTTTTTTTTCAA
*
38134129 ATTTTTTTTCAA
1 TTTTTTTTTCAA
*
38134141 GTTTTTTTT--A
1 TTTTTTTTTCAA
*
38134151 TTTTTTTTACAA
1 TTTTTTTTTCAA
38134163 T
1 T
38134164 ACCGTAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 8 0.21
11 10 0.26
12 21 0.54
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:38138933 original size:27 final size:27
Alignment explanation
Indices: 38138903--38138954 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
38138893 ACAAGTGAGG
38138903 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
38138930 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
38138955 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:38143312 original size:11 final size:11
Alignment explanation
Indices: 38143296--38143329 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
38143286 AATAATTAAT
38143296 TTTTTTTCGAA
1 TTTTTTTCGAA
*
38143307 TTTTTTTCAAA
1 TTTTTTTCGAA
*
38143318 TTTTTTTAGAA
1 TTTTTTTCGAA
38143329 T
1 T
38143330 CTCGTAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:38145265 original size:20 final size:20
Alignment explanation
Indices: 38145242--38145288 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38145232 GGGTTAAAAT
*
38145242 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
38145262 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
38145282 TGAGCTG
1 TGAGCTG
38145289 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:38147014 original size:18 final size:17
Alignment explanation
Indices: 38146993--38147120 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
38146983 CACACTTTTG
38146993 TTCAATCTCAATTTCTTT
1 TTCAATCTC-ATTTCTTT
*
38147011 TTCAATTTC-TTTCTCTT
1 TTCAATCTCATTTCT-TT
*
38147028 TTC-A---CA-TCCTTT
1 TTCAATCTCATTTCTTT
38147040 TTCAATCTCAATTTCTTT
1 TTCAATCTC-ATTTCTTT
* *
38147058 TTCCATGACACTCGTTTCTTT
1 TT-CA--A-TCTCATTTCTTT
* * *
38147079 TACACTCTCGTTTCTTT
1 TTCAATCTCATTTCTTT
*
38147096 CTTCAATCTCACTCTCTTT
1 -TTCAATCTCA-TTTCTTT
38147115 TTCAAT
1 TTCAAT
38147121 TTCTTGTTCC
Statistics
Matches: 84, Mismatches: 12, Indels: 28
0.68 0.10 0.23
Matches are distributed among these distances:
12 5 0.06
13 5 0.06
16 7 0.08
17 17 0.20
18 28 0.33
19 8 0.10
20 2 0.02
21 9 0.11
22 3 0.04
ACGTcount: A:0.17, C:0.27, G:0.02, T:0.53
Consensus pattern (17 bp):
TTCAATCTCATTTCTTT
Found at i:38147044 original size:47 final size:47
Alignment explanation
Indices: 38146956--38147060 Score: 142
Period size: 47 Copynumber: 2.2 Consensus size: 47
38146946 TTGTCTTTTC
* *
38146956 TTTCTTTTTCAATTTTCTCTTTTTCCTCACACTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTCTTT-CTCACACCTTTGTTCAATCTCAA
*
38147004 TTTCTTTTTCAATTTCTTTCTCTTT-TCACATCCTTT-TTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCTCTTTCTCACA-CCTTTGTTCAATCTCAA
38147051 TTTCTTTTTC
1 TTTCTTTTTC
38147061 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
47 26 0.50
48 19 0.37
49 7 0.13
ACGTcount: A:0.15, C:0.25, G:0.01, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTTCTCTCTTTCTCACACCTTTGTTCAATCTCAA
Found at i:38147451 original size:20 final size:21
Alignment explanation
Indices: 38147416--38147454 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38147406 CAGCTCGTTG
38147416 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
38147437 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
38147455 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:38147862 original size:13 final size:13
Alignment explanation
Indices: 38147844--38147869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38147834 TGTGTCCTAA
38147844 TATGAATTAAATT
1 TATGAATTAAATT
38147857 TATGAATTAAATT
1 TATGAATTAAATT
38147870 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:38151242 original size:20 final size:19
Alignment explanation
Indices: 38151202--38151254 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
38151192 TTTTCACTTT
*
38151202 TTTTTGTTCTTTTTT-TTAC
1 TTTTT-TTCTTTTTTGTCAC
38151221 TTTTTTTCTTTTTTGCTCAC
1 TTTTTTTCTTTTTTG-TCAC
*
38151241 TTCTTTT-TTTTTTG
1 TTTTTTTCTTTTTTG
38151255 AATTTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 9 0.30
19 12 0.40
20 9 0.30
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTTTTTGTCAC
Found at i:38151367 original size:14 final size:13
Alignment explanation
Indices: 38151348--38151373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38151338 GATTTTTTGA
38151348 TTTTTTTTAAAAC
1 TTTTTTTTAAAAC
38151361 TTTTTTTTAAAAC
1 TTTTTTTTAAAAC
38151374 CTATCTTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTTAAAAC
Found at i:38154249 original size:20 final size:20
Alignment explanation
Indices: 38154226--38154272 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38154216 GGGTTAAGAT
*
38154226 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
38154246 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
38154266 TGAGCTG
1 TGAGCTG
38154273 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:38155633 original size:10 final size:11
Alignment explanation
Indices: 38155610--38155678 Score: 64
Period size: 10 Copynumber: 6.9 Consensus size: 11
38155600 AGCTAATAAC
38155610 GAGCTC-AA-T
1 GAGCTCGAATT
38155619 GAGCT-GAATT
1 GAGCTCGAATT
38155629 GAGCTCGAA-T
1 GAGCTCGAATT
*
38155639 GAGCT-GACTT
1 GAGCTCGAATT
38155649 GAGCTCGAA-T
1 GAGCTCGAATT
38155659 GAGCT--AATTT
1 GAGCTCGAA-TT
38155669 GAGCTCGAAT
1 GAGCTCGAAT
38155679 GAACTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 30 0.61
11 6 0.12
12 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (11 bp):
GAGCTCGAATT
Found at i:38155639 original size:20 final size:20
Alignment explanation
Indices: 38155610--38155680 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
38155600 AGCTAATAAC
38155610 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
*
38155629 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
38155649 GAGCTCGAATGAGCT-AATTT
1 GAGCTCGAATGAGCTGAA-TT
38155669 GAGCTCGAATGA
1 GAGCTCGAATGA
38155681 ACTAAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 7 0.15
20 41 0.85
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:38161544 original size:55 final size:55
Alignment explanation
Indices: 38161429--38161545 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
38161419 TGCATGTTTT
* * *
38161429 CATT-AATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCC
1 CATTAAATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
* * * *
38161483 CTTTAAATGCCGTTCCATGCATGGGAACATCTCCTT-AATTCGTGGCTTTGCTGCA
1 CATTAAATGCCG-TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
38161538 CATTAAAT
1 CATTAAAT
38161546 CAGCAAGCAG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 3 0.06
55 28 0.53
56 22 0.42
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (55 bp):
CATTAAATGCCGTCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCA
Found at i:38162873 original size:21 final size:21
Alignment explanation
Indices: 38162828--38162890 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
38162818 TTTCAACCAT
* *
38162828 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
38162850 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
38162871 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
38162891 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38163269 original size:23 final size:22
Alignment explanation
Indices: 38163235--38163299 Score: 103
Period size: 23 Copynumber: 2.9 Consensus size: 22
38163225 GACACCATTT
*
38163235 AAAACATGCATTAAATTCGGCC
1 AAAACATACATTAAATTCGGCC
38163257 AGAAACATACATTAAATTCGGCC
1 A-AAACATACATTAAATTCGGCC
38163280 AAAGACATACATTAAATTCG
1 AAA-ACATACATTAAATTCG
38163300 TCTGGAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.08
23 37 0.93
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (22 bp):
AAAACATACATTAAATTCGGCC
Found at i:38163536 original size:13 final size:13
Alignment explanation
Indices: 38163514--38163554 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
38163504 CAAAATTTTA
38163514 AACTAA-TTAATT
1 AACTAATTTAATT
*
38163526 AACTTATTTAATT
1 AACTAATTTAATT
*
38163539 AACTAATTTAACT
1 AACTAATTTAATT
38163552 AAC
1 AAC
38163555 AGCAACTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
AACTAATTTAATT
Found at i:38166629 original size:23 final size:22
Alignment explanation
Indices: 38166578--38166629 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
38166568 CCTCGTCTTT
*
38166578 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
38166600 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
38166623 TTCTTTT
1 TTCTTTT
38166630 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:38168805 original size:20 final size:20
Alignment explanation
Indices: 38168776--38168846 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
38168766 AGCTAATAAC
38168776 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
* *
38168795 AAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
38168815 GAGCTCGAATGAGCT-AATTT
1 GAGCTCGAATGAGCTGAA-TT
38168835 GAGCTCGAATGA
1 GAGCTCGAATGA
38168847 ACTAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 6 0.13
20 40 0.87
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:38168809 original size:10 final size:10
Alignment explanation
Indices: 38168776--38168846 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
38168766 AGCTAATAAC
38168776 GAGCTC-AAT
1 GAGCTCGAAT
38168785 GAGCT-GAATT
1 GAGCTCGAA-T
*
38168795 AAGCTCGAAT
1 GAGCTCGAAT
*
38168805 GAGCT-GACTT
1 GAGCTCGA-AT
38168815 GAGCTCGAAT
1 GAGCTCGAAT
38168825 GAGCT--AATTT
1 GAGCTCGAA--T
38168835 GAGCTCGAAT
1 GAGCTCGAAT
38168845 GA
1 GA
38168847 ACTAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 31 0.63
11 5 0.10
12 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (10 bp):
GAGCTCGAAT
Found at i:38170297 original size:28 final size:29
Alignment explanation
Indices: 38170241--38170298 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
38170231 CAATCACTCT
**
38170241 TTTTTTTTCTTTTTTTTTTCAATTTTGAA
1 TTTTTTTTCTTTTTTTTTTCAATACTGAA
38170270 TTTTTTTTC-TTTTTTTTTCAATACTGAA
1 TTTTTTTTCTTTTTTTTTTCAATACTGAA
38170298 T
1 T
38170299 ACTATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (29 bp):
TTTTTTTTCTTTTTTTTTTCAATACTGAA
Found at i:38172200 original size:20 final size:20
Alignment explanation
Indices: 38172171--38172241 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
38172161 AGCTAATAAC
38172171 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
* *
38172190 AAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
38172210 GAGCTCGAATGAGCT-AATTT
1 GAGCTCGAATGAGCTGAA-TT
38172230 GAGCTCGAATGA
1 GAGCTCGAATGA
38172242 ACTAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 6 0.13
20 40 0.87
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:38172204 original size:10 final size:10
Alignment explanation
Indices: 38172171--38172241 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
38172161 AGCTAATAAC
38172171 GAGCTC-AAT
1 GAGCTCGAAT
38172180 GAGCT-GAATT
1 GAGCTCGAA-T
*
38172190 AAGCTCGAAT
1 GAGCTCGAAT
*
38172200 GAGCT-GACTT
1 GAGCTCGA-AT
38172210 GAGCTCGAAT
1 GAGCTCGAAT
38172220 GAGCT--AATTT
1 GAGCTCGAA--T
38172230 GAGCTCGAAT
1 GAGCTCGAAT
38172240 GA
1 GA
38172242 ACTAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 31 0.63
11 5 0.10
12 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (10 bp):
GAGCTCGAAT
Found at i:38172204 original size:40 final size:39
Alignment explanation
Indices: 38172160--38172246 Score: 88
Period size: 40 Copynumber: 2.2 Consensus size: 39
38172150 ATGAGCTAGA
38172160 GAGCTAATAACGAGCTC-AATGAGCTGAA-TTAAGCTCGAAT
1 GAGCTAAT--CGAGCTCGAATGAGCT-AATTTAAGCTCGAAT
* * *
38172200 GAGCTGACTTGAGCTCGAATGAGCTAATTTGAGCTCGAAT
1 GAGCT-AATCGAGCTCGAATGAGCTAATTTAAGCTCGAAT
*
38172240 GAACTAA
1 GAGCTAA
38172247 AAAAAAAGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
39 9 0.23
40 28 0.72
41 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (39 bp):
GAGCTAATCGAGCTCGAATGAGCTAATTTAAGCTCGAAT
Found at i:38176858 original size:21 final size:21
Alignment explanation
Indices: 38176832--38176894 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38176822 TTGGTATTTG
38176832 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
38176853 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
38176874 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
38176895 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:38184174 original size:27 final size:27
Alignment explanation
Indices: 38184144--38184195 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
38184134 ACAAGTGAGG
38184144 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
38184171 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
38184196 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:38189577 original size:21 final size:21
Alignment explanation
Indices: 38189532--38189594 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
38189522 TTTCAACCAT
*
38189532 TACCAATTCGTACCAAATACCA
1 TACCAATTCGTACC-AATTCCA
*
38189554 TACCATTTCGTACCAATTCCA
1 TACCAATTCGTACCAATTCCA
* * *
38189575 TACTACTTCGAACCAATTCC
1 TACCAATTCGTACCAATTCC
38189595 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCAATTCGTACCAATTCCA
Found at i:38189922 original size:12 final size:12
Alignment explanation
Indices: 38189893--38189944 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 12
38189883 ATAGGTACGT
38189893 AAAAAAAAGAGTTCG
1 AAAAAAAA-A-TT-G
38189908 AAAAAAAAATTG
1 AAAAAAAAATTG
38189920 AAAAAAAAAATTG
1 -AAAAAAAAATTG
38189933 AAAAAAAAATTG
1 AAAAAAAAATTG
38189945 CATACGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 13 0.36
13 14 0.39
14 1 0.03
15 8 0.22
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:38189923 original size:25 final size:25
Alignment explanation
Indices: 38189893--38189944 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
38189883 ATAGGTACGT
*
38189893 AAAAAAAAGAGTTCGAAAAAAAAATTG
1 AAAAAAAA-AATT-GAAAAAAAAATTG
38189920 AAAAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAAAATTGAAAAAAAAATTG
38189945 CATACGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.54
26 3 0.12
27 8 0.33
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (25 bp):
AAAAAAAAAATTGAAAAAAAAATTG
Found at i:38190606 original size:20 final size:20
Alignment explanation
Indices: 38190583--38190636 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38190573 AGTTTTTCCC
*
38190583 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
38190603 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
38190623 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
38190637 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:38190618 original size:30 final size:30
Alignment explanation
Indices: 38190583--38190656 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38190573 AGTTTTTCCC
38190583 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
38190613 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
38190643 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
38190657 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:38190646 original size:20 final size:20
Alignment explanation
Indices: 38190583--38190647 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38190573 AGTTTTTCCC
* * * *
38190583 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
38190603 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
38190622 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
38190643 AGCTC
1 AGCTC
38190648 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:38192256 original size:10 final size:10
Alignment explanation
Indices: 38192241--38192268 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
38192231 TGGAGTAACA
38192241 AAAAAAAATC
1 AAAAAAAATC
38192251 AAAAAAAATC
1 AAAAAAAATC
38192261 AAAAAAAA
1 AAAAAAAA
38192269 AATTTGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:38194566 original size:30 final size:29
Alignment explanation
Indices: 38194532--38194628 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
38194522 TAAACTAAAA
38194532 TGAGCTAAGTTTCAGCTCGTGAGCTAAAGT
1 TGAGCTAAGTTT-AGCTCGTGAGCTAAAGT
* * * * * * *
38194562 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGTTTAGCTCGTGAGCTAAAGT
38194592 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAA-GTTTAGCTCGTGAGCTAAAGT
38194621 ATGAGCTA
1 -TGAGCTA
38194629 GGAGTGATCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 45 0.90
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (29 bp):
TGAGCTAAGTTTAGCTCGTGAGCTAAAGT
Found at i:38199008 original size:12 final size:12
Alignment explanation
Indices: 38198993--38199023 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38198983 TTCTTTTTGC
38198993 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38199005 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38199017 TTTTCAA
1 TTTTCAA
38199024 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:38199100 original size:6 final size:6
Alignment explanation
Indices: 38199084--38199133 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
38199074 TTTCTTTTTA
*
38199084 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
38199133 T
1 T
38199134 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:38199116 original size:37 final size:37
Alignment explanation
Indices: 38199073--38199143 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
38199063 CTTGCCTCTC
38199073 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
38199110 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
38199144 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:38199144 original size:16 final size:16
Alignment explanation
Indices: 38199069--38199129 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
38199059 GCCTCTTGCC
*
38199069 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
38199085 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
38199101 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
38199117 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
38199130 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:38200075 original size:12 final size:12
Alignment explanation
Indices: 38200054--38200106 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
38200044 TATACTTCGA
38200054 TTTTTCAATTTT
1 TTTTTCAATTTT
*
38200066 TTTTTAAATTTTT
1 TTTTTCAA-TTTT
*
38200079 TTTTTCGATTTT
1 TTTTTCAATTTT
*
38200091 TGTTTCAATTTT
1 TTTTTCAATTTT
38200103 TTTT
1 TTTT
38200107 CAAATTTCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 24 0.71
13 10 0.29
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTTCAATTTT
Found at i:38200082 original size:25 final size:25
Alignment explanation
Indices: 38200054--38200106 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
38200044 TATACTTCGA
*
38200054 TTTTTCAATTTTTTTTTAAATTTTT
1 TTTTTCAATTTTTGTTTAAATTTTT
* *
38200079 TTTTTCGATTTTTGTTTCAATTTTT
1 TTTTTCAATTTTTGTTTAAATTTTT
38200104 TTT
1 TTT
38200107 CAAATTTCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTTCAATTTTTGTTTAAATTTTT
Done.