Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 137 of 187
Found at i:41265738 original size:13 final size:13
Alignment explanation
Indices: 41265720--41265745 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41265710 ATAAGAGTTA
41265720 AAATATCAAATTT
1 AAATATCAAATTT
41265733 AAATATCAAATTT
1 AAATATCAAATTT
41265746 GAGTGAAATA
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:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATCAAATTT
Found at i:41268255 original size:9 final size:10
Alignment explanation
Indices: 41268237--41268266 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
41268227 AAAAGGCTAA
41268237 AAATATTTTT
1 AAATATTTTT
41268247 AAATATTTTT
1 AAATATTTTT
41268257 AAA-ATTTTT
1 AAATATTTTT
41268266 A
1 A
41268267 GAGTTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AAATATTTTT
Found at i:41268551 original size:30 final size:31
Alignment explanation
Indices: 41268510--41268568 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
41268500 TTTAGTGATT
* *
41268510 AAATTGAAAGAAATA-ATAGTTGGGTGACCA
1 AAATAGAAAGAAACACATAGTTGGGTGACCA
41268540 AAATAGAAAGAAACACATAGTTGGGTGAC
1 AAATAGAAAGAAACACATAGTTGGGTGAC
41268569 AATTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (31 bp):
AAATAGAAAGAAACACATAGTTGGGTGACCA
Found at i:41269243 original size:15 final size:15
Alignment explanation
Indices: 41269217--41269255 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
41269207 GTGGTATCAA
41269217 AACATA-TC-AATTC
1 AACATATTCAAATTC
*
41269230 AACTTATTCAAATTC
1 AACATATTCAAATTC
41269245 AACATATTCAA
1 AACATATTCAA
41269256 TCATTCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 5 0.23
14 2 0.09
15 15 0.68
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (15 bp):
AACATATTCAAATTC
Found at i:41279240 original size:19 final size:19
Alignment explanation
Indices: 41279216--41279256 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
41279206 TTCTTTTGGT
*
41279216 TTATGGTTCCAGAATTCAA
1 TTATGGTTCCAAAATTCAA
*
41279235 TTATGGTTCCAAAATTGAA
1 TTATGGTTCCAAAATTCAA
41279254 TTA
1 TTA
41279257 ATTGAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (19 bp):
TTATGGTTCCAAAATTCAA
Found at i:41281325 original size:40 final size:39
Alignment explanation
Indices: 41281269--41281392 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 39
41281259 CGTTTGGACA
* *
41281269 AAAAACCGCCACTAAAAATCAAGCATTAGCGGGGCTTTTAT-
1 AAAAA-CGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTT-TG
* * *
41281310 AAAAATGCCGCTAAAAGTTGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAA-ATAAGCATTAGCGGCGCTTTTTG
* *
41281350 GAAAACGCCGCTAAAAATAAGCATTAGCGGCGTTTTTTG
1 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTTG
41281389 AAAA
1 AAAA
41281393 GCGCTGCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 24 0.34
40 40 0.57
41 6 0.09
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTTG
Found at i:41281500 original size:41 final size:40
Alignment explanation
Indices: 41281443--41281765 Score: 439
Period size: 41 Copynumber: 7.9 Consensus size: 40
41281433 GTTATTGGGG
*
41281443 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGG
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GA
*** *
41281484 CCTTTAGCGATTTTTTTGAAGAAGCGCCGCTAATGCTCGGG
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GA
*
41281525 CCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGA
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GA
*
41281566 CCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGA
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GA
* ** *
41281607 CCTTTAGCGGCGTTTCTGAAGAAGCATCGCTAATGCTCGGG
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-GA
* *
41281648 CCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCGAA
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCG-A
* *
41281689 CCTTTAGCGGCGATTTTAAAGAAGCGCCGCTAATGCTCGAA
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCG-A
*
41281730 CCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGC
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
41281766 CCATTTTTGA
Statistics
Matches: 255, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 1 0.00
41 254 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (40 bp):
CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
Found at i:41281851 original size:38 final size:38
Alignment explanation
Indices: 41281806--41281881 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
41281796 TCTTTGATAT
41281806 ATTCTCAAGTAATGTTTCAATTATATTTTTTATTATAA
1 ATTCTCAAGTAATGTTTCAATTATATTTTTTATTATAA
41281844 ATTCTCAAGTAATGTTTCAATTATATTTTTTATTATAA
1 ATTCTCAAGTAATGTTTCAATTATATTTTTTATTATAA
41281882 GTTTAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (38 bp):
ATTCTCAAGTAATGTTTCAATTATATTTTTTATTATAA
Found at i:41282099 original size:36 final size:36
Alignment explanation
Indices: 41282052--41282120 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
41282042 CTTTAGTAGA
41282052 AAAATATATTAAATTATGAGTAAAATAAAATATCAT
1 AAAATATATTAAATTATGAGTAAAATAAAATATCAT
41282088 AAAATATATTAAATTATGAGTAAAATAAAATAT
1 AAAATATATTAAATTATGAGTAAAATAAAATAT
41282121 ATTAAAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.33
Consensus pattern (36 bp):
AAAATATATTAAATTATGAGTAAAATAAAATATCAT
Found at i:41282205 original size:14 final size:14
Alignment explanation
Indices: 41282188--41282224 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41282178 GGGTTTAATA
41282188 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
41282202 TATATGATTTAGGG
1 TATATGGTTTAGGG
41282216 TATATGGTT
1 TATATGGTT
41282225 AATTTAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:41282463 original size:20 final size:19
Alignment explanation
Indices: 41282438--41282476 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
41282428 TAAGGTGTAG
41282438 GGGTTAGGGGTTAGGGATTT
1 GGGTTAGGGGTTA-GGATTT
*
41282458 GGGTTAGGGTTTAGGATTT
1 GGGTTAGGGGTTAGGATTT
41282477 AGGATTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (19 bp):
GGGTTAGGGGTTAGGATTT
Found at i:41282550 original size:14 final size:14
Alignment explanation
Indices: 41282531--41282576 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
41282521 TAAATAAGAT
*
41282531 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
41282545 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
*
41282559 TTAGGGGTTAAGAG
1 TTAGGGGTTAGGAG
41282573 TTAG
1 TTAG
41282577 TGATTTAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:41282554 original size:7 final size:7
Alignment explanation
Indices: 41282531--41282568 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
41282521 TAAATAAGAT
41282531 TTAGGGG
1 TTAGGGG
**
41282538 TTAGTAG
1 TTAGGGG
41282545 TTAGGGG
1 TTAGGGG
41282552 TTAGGGG
1 TTAGGGG
41282559 TTAGGGG
1 TTAGGGG
41282566 TTA
1 TTA
41282569 AGAGTTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:41282575 original size:21 final size:21
Alignment explanation
Indices: 41282525--41282576 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
41282515 ATATATTAAA
* *
41282525 TAAGATTTAGGGGTTAGTAGT
1 TAAGAGTTAGGGGTTAGGAGT
* * *
41282546 TAGGGGTTAGGGGTTAGGGGT
1 TAAGAGTTAGGGGTTAGGAGT
41282567 TAAGAGTTAG
1 TAAGAGTTAG
41282577 TGATTTAGGG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (21 bp):
TAAGAGTTAGGGGTTAGGAGT
Found at i:41286066 original size:199 final size:198
Alignment explanation
Indices: 41285726--41286123 Score: 787
Period size: 199 Copynumber: 2.0 Consensus size: 198
41285716 GTCCGAGTAA
41285726 TATGGTTCTTTTCTTTTTCAAGTTCTAAATTGTTTAACAATAGGTTCTTTGTTTTCTTAAGCAGG
1 TATGGTTCTTTTCTTTTTCAAGTTCTAAATTGTTTAACAATAGGTTCTTTGTTTTCTTAAGCAGG
41285791 GATGATGAAGATGATTCTGTTGCCAAGATGAAGGCAGCTGAGGAAGCTTTGGAAGCAAAACAAAA
66 GATGATGAAGATGATTCTGTTGCCAAGATGAAGGCAGCTGAGGAAGCTTTGGAAGCAAAACAAAA
41285856 AGTAACAAATAGCTTGTCTGCTACCTGTTCTTTTTTTTTATCATGTTTTATAATTTTGTGACAAA
131 AGTAACAAATAGCTTGTCTGCTACCTGTTC-TTTTTTTTATCATGTTTTATAATTTTGTGACAAA
41285921 TTGT
195 TTGT
41285925 TATGGTTCTTTTCTTTTTCAAGTTCTAAATTGTTTAACAATAGGTTCTTTGTTTTCTTAAGCAGG
1 TATGGTTCTTTTCTTTTTCAAGTTCTAAATTGTTTAACAATAGGTTCTTTGTTTTCTTAAGCAGG
41285990 GATGATGAAGATGATTCTGTTGCCAAGATGAAGGCAGCTGAGGAAGCTTTGGAAGCAAAACAAAA
66 GATGATGAAGATGATTCTGTTGCCAAGATGAAGGCAGCTGAGGAAGCTTTGGAAGCAAAACAAAA
41286055 AGTAACAAATAGCTTGTCTGCTACCTGTTCTTTTTTTTATCATGTTTTATAATTTTGTGACAAAT
131 AGTAACAAATAGCTTGTCTGCTACCTGTTCTTTTTTTTATCATGTTTTATAATTTTGTGACAAAT
41286120 TGT
196 TGT
41286123 T
1 T
41286124 CTTGGTACTC
Statistics
Matches: 199, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
198 39 0.20
199 160 0.80
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (198 bp):
TATGGTTCTTTTCTTTTTCAAGTTCTAAATTGTTTAACAATAGGTTCTTTGTTTTCTTAAGCAGG
GATGATGAAGATGATTCTGTTGCCAAGATGAAGGCAGCTGAGGAAGCTTTGGAAGCAAAACAAAA
AGTAACAAATAGCTTGTCTGCTACCTGTTCTTTTTTTTATCATGTTTTATAATTTTGTGACAAAT
TGT
Found at i:41286243 original size:19 final size:19
Alignment explanation
Indices: 41286219--41286284 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
41286209 TAGTTTGATA
41286219 AATTTTATGTGTGGTGTTT
1 AATTTTATGTGTGGTGTTT
* * *
41286238 AATTTT-TCGTTACTGTTTGTGT
1 AATTTTAT-G-T-GTG-GTGTTT
41286260 AATTTTATGTGTGGTGTTT
1 AATTTTATGTGTGGTGTTT
41286279 AATTTT
1 AATTTT
41286285 TCATTACTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 1 0.03
19 17 0.47
20 3 0.08
21 3 0.08
22 11 0.31
23 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.21, T:0.59
Consensus pattern (19 bp):
AATTTTATGTGTGGTGTTT
Found at i:41286259 original size:24 final size:23
Alignment explanation
Indices: 41286232--41286311 Score: 57
Period size: 25 Copynumber: 3.6 Consensus size: 23
41286222 TTTATGTGTG
41286232 GTGTTTAATTTTTCGTTACTGTTT
1 GTGTTTAATTTTTC-TTACTGTTT
*
41286256 GTG--TAA---TT-TTA-TGTGTG
1 GTGTTTAATTTTTCTTACTGT-TT
*
41286273 GTGTTTAATTTTTCATTACTGTCT
1 GTGTTTAATTTTTC-TTACTGTTT
41286297 GTGTTTTAATTTTTC
1 GTG-TTTAATTTTTC
41286312 ATATGTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 19
0.66 0.05 0.29
Matches are distributed among these distances:
16 3 0.07
17 7 0.16
19 5 0.12
22 5 0.12
24 9 0.21
25 14 0.33
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.60
Consensus pattern (23 bp):
GTGTTTAATTTTTCTTACTGTTT
Found at i:41286268 original size:41 final size:41
Alignment explanation
Indices: 41286219--41286300 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
41286209 TAGTTTGATA
* *
41286219 AATTTTATGTGTGGTGTTTAATTTTTCGTTACTGTTTGTGT
1 AATTTTATGTGTGGTGTTTAATTTTTCATTACTGTCTGTGT
41286260 AATTTTATGTGTGGTGTTTAATTTTTCATTACTGTCTGTGT
1 AATTTTATGTGTGGTGTTTAATTTTTCATTACTGTCTGTGT
41286301 TTTAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.16, C:0.06, G:0.21, T:0.57
Consensus pattern (41 bp):
AATTTTATGTGTGGTGTTTAATTTTTCATTACTGTCTGTGT
Found at i:41286698 original size:43 final size:43
Alignment explanation
Indices: 41286621--41286747 Score: 193
Period size: 43 Copynumber: 3.0 Consensus size: 43
41286611 ATATTTTTAG
* *
41286621 AAGCGCCGCTAAAGGT-TTGTTCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAA
* *
41286663 AAGCGCTGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGTAA
1 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAA
* *
41286706 AAGCGCCGTTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGA
1 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGA
41286748 TAAGTGCCCT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
42 15 0.20
43 61 0.80
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.28
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAA
Found at i:41286822 original size:43 final size:43
Alignment explanation
Indices: 41286756--41286900 Score: 263
Period size: 43 Copynumber: 3.4 Consensus size: 43
41286746 GATAAGTGCC
*
41286756 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGT
41286799 CTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGT
* *
41286842 CTTTAGCGGCGTTTGTGGTAAAAGCACCGCTAAAGGCCTTGGT
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGT
41286885 CTTTAGCGGCGTTTGT
1 CTTTAGCGGCGTTTGT
41286901 TTCGAAAAAC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 99 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:41286849 original size:114 final size:114
Alignment explanation
Indices: 41286645--41286859 Score: 367
Period size: 114 Copynumber: 1.9 Consensus size: 114
41286635 GTTTGTTCTA
* *
41286645 TAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGTAAAAGC
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGTAAAAGC
*
41286710 GCCGTTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGATAAGTGCCCTT
66 GCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGATAAGTGCCCTT
* *
41286759 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGTAAAAGC
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGTAAAAGC
* *
41286824 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGG
66 GCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGG
41286860 TAAAAGCACC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (114 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGTAAAAGC
GCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGATAAGTGCCCTT
Found at i:41287023 original size:22 final size:21
Alignment explanation
Indices: 41286990--41287034 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
41286980 TTTAGCGGCA
*
41286990 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
41287011 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
41287033 CT
1 CT
41287035 GTTTTGGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:41290038 original size:21 final size:20
Alignment explanation
Indices: 41289997--41290042 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
41289987 TAAGTAGCTC
**
41289997 AAAAAATATTAAAAGGGTAT
1 AAAAAATATTAAAAGAATAT
*
41290017 AAAAAATAGTTAAAATAATAT
1 AAAAAATA-TTAAAAGAATAT
41290038 AAAAA
1 AAAAA
41290043 TAACCATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (20 bp):
AAAAAATATTAAAAGAATAT
Found at i:41290343 original size:24 final size:24
Alignment explanation
Indices: 41290264--41290390 Score: 81
Period size: 24 Copynumber: 5.5 Consensus size: 24
41290254 CACAAAAAAA
* * *
41290264 ATAGTACATGATAAA-TCTAAATA
1 ATAGTATATGATAAATTTTAAATT
* *
41290287 AT-G-ATATGATAAGTTTAAAATT
1 ATAGTATATGATAAATTTTAAATT
*
41290309 ATAGTACATGATAAATTTTAAATT
1 ATAGTATATGATAAATTTTAAATT
*
41290333 AT-GATATATGATAGA-TTTAAA-T
1 ATAG-TATATGATAAATTTTAAATT
* * *
41290355 AGTACT-TATGAT-AATTTAAAATA
1 A-TAGTATATGATAAATTTTAAATT
*
41290378 ATACTATATGATA
1 ATAGTATATGATA
41290391 TTAAAATAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
21 9 0.11
22 25 0.31
23 19 0.24
24 27 0.34
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (24 bp):
ATAGTATATGATAAATTTTAAATT
Found at i:41290367 original size:22 final size:23
Alignment explanation
Indices: 41290290--41290419 Score: 110
Period size: 24 Copynumber: 5.7 Consensus size: 23
41290280 CTAAATAATG
* *
41290290 ATATGATAAGTTTAAAATTATAGT
1 ATATGATAA-TTTAAAATAATACT
* * *
41290314 ACATGATAAATTTTAAATTATGA-T
1 ATATGAT-AATTTAAAATAAT-ACT
*
41290338 ATATGATAGATTT-AAATAGTACT
1 ATATGATA-ATTTAAAATAATACT
41290361 -TATGATAATTTAAAATAATACT
1 ATATGATAATTTAAAATAATACT
*
41290383 ATATGAT-A-TTAAAATAAAACT
1 ATATGATAATTTAAAATAATACT
41290404 A-ATGATAAATTTAAAA
1 ATATGAT-AATTTAAAA
41290420 CGATGTTAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
20 5 0.06
21 17 0.19
22 19 0.21
23 19 0.21
24 27 0.30
25 3 0.03
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATGATAATTTAAAATAATACT
Found at i:41290373 original size:21 final size:21
Alignment explanation
Indices: 41290339--41290418 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
41290329 AATTATGATA
*
41290339 TATGATAGATTTAAATAGTACT
1 TATGATA-ATTTAAATAATACT
41290361 TATGATAATTTAAAATAATACT
1 TATGATAATTT-AAATAATACT
* *
41290383 ATATGAT-ATTAAAATAAAACT
1 -TATGATAATTTAAATAATACT
*
41290404 AATGATAAATTTAAA
1 TATGAT-AATTTAAA
41290419 ACGATGTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.10
21 13 0.27
22 25 0.51
23 6 0.12
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (21 bp):
TATGATAATTTAAATAATACT
Found at i:41291935 original size:50 final size:50
Alignment explanation
Indices: 41291881--41292118 Score: 176
Period size: 50 Copynumber: 4.8 Consensus size: 50
41291871 AGATTCGCCA
* ** *
41291881 TTGTGGCTTTAATCTTTTTAACTGCAATGTTGGGGAAGCATTATTCGCTG
1 TTGTGGCTTTAATCTTTTCAACTGCAATGTTGGGGAAGCAAGATTCACTG
* * * * * *
41291931 TTGTGGCTTTAATCTATTCCACTGCACTGCCT-AGGAAGTAAGATTCACTG
1 TTGTGGCTTTAATCTTTTCAACTGCAATG-TTGGGGAAGCAAGATTCACTG
* * * * *
41291981 TTGTAGCTTTAATCTTTTGAAATGCAATGTCGGGGAAGCAAGATTCACCG
1 TTGTGGCTTTAATCTTTTCAACTGCAATGTTGGGGAAGCAAGATTCACTG
** * * ** * *
41292031 AAGTGGCTTTAATCTGTTCCACTGC-ATCACCT-GGGAGGTAAGATTCACTG
1 TTGTGGCTTTAATCTTTTCAACTGCAAT--GTTGGGGAAGCAAGATTCACTG
* * ** *
41292081 TTGTAGCTTTAATCTTTTGAACAACAATGTCGGGGAAG
1 TTGTGGCTTTAATCTTTTCAACTGCAATGTTGGGGAAG
41292119 TAAGGTCTTT
Statistics
Matches: 136, Mismatches: 46, Indels: 12
0.70 0.24 0.06
Matches are distributed among these distances:
49 2 0.01
50 131 0.96
51 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (50 bp):
TTGTGGCTTTAATCTTTTCAACTGCAATGTTGGGGAAGCAAGATTCACTG
Found at i:41292039 original size:100 final size:100
Alignment explanation
Indices: 41291866--41292118 Score: 312
Period size: 100 Copynumber: 2.5 Consensus size: 100
41291856 AACTTTTGGA
* ** * * * * ** * *
41291866 AAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAATGTTGGGGAAGCATTATTCGCTG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTGAAATGCAATGTCGGGGAAGCAAGATTCACCG
** *
41291931 TTGTGGCTTTAATCTATTCCACTGCA-CTGCCTAGG
66 AAGTGGCTTTAATCTATTCCACTGCATC-ACCTAGG
41291966 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTGAAATGCAATGTCGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTGAAATGCAATGTCGGGGAAGCAAGATTCACCG
* *
41292031 AAGTGGCTTTAATCTGTTCCACTGCATCACCTGGG
66 AAGTGGCTTTAATCTATTCCACTGCATCACCTAGG
* *
41292066 AGGTAAGATTCACTGTTGTAGCTTTAATCTTTTGAACA-ACAATGTCGGGGAAG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTGAA-ATGCAATGTCGGGGAAG
41292119 TAAGGTCTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
100 131 0.98
101 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (100 bp):
AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTGAAATGCAATGTCGGGGAAGCAAGATTCACCG
AAGTGGCTTTAATCTATTCCACTGCATCACCTAGG
Found at i:41292355 original size:44 final size:45
Alignment explanation
Indices: 41292306--41292545 Score: 147
Period size: 44 Copynumber: 5.2 Consensus size: 45
41292296 TAACTTCAAA
*
41292306 GAGATAAGATCCTTTATTTTAATTC-GCTCCACTGTAATCTCAGG
1 GAGATAAGATCCTTTACTTTAATTCTGCTCCACTGTAATCTCAGG
* * *
41292350 GAGATAGGAT--TACTAGCTTTAA-TCTGCTCCGCTGTAATCTCAGG
1 GAGATAAGATCCT-TTA-CTTTAATTCTGCTCCACTGTAATCTCAGG
* * * * *
41292394 GAGATAAGATTTCTGGCTTTAATCTGATGCGATCTGCTCTACTGTAA-CTTCAGA
1 GAGATAAGA--TC---CTTTACTTTAAT----TCTGCTCCACTGTAATC-TCAGG
* * *
41292448 GAGATAAGATCCTTTACTTTAA-TCCGCTGCACTGTAACCTCAGG
1 GAGATAAGATCCTTTACTTTAATTCTGCTCCACTGTAATCTCAGG
* * * *
41292492 GAGATATGAT--TACTAGCTTCAA-TCTGCTCCGCTGTAATCTCAGG
1 GAGATAAGATCCT-TTA-CTTTAATTCTGCTCCACTGTAATCTCAGG
41292536 GAGATAAGAT
1 GAGATAAGAT
41292546 TTCTGGCTTC
Statistics
Matches: 150, Mismatches: 27, Indels: 38
0.70 0.13 0.18
Matches are distributed among these distances:
42 2 0.01
43 6 0.04
44 97 0.65
45 1 0.01
46 1 0.01
49 11 0.07
50 2 0.01
51 1 0.01
52 2 0.01
53 1 0.01
54 26 0.17
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (45 bp):
GAGATAAGATCCTTTACTTTAATTCTGCTCCACTGTAATCTCAGG
Found at i:41292451 original size:142 final size:142
Alignment explanation
Indices: 41292191--41292703 Score: 839
Period size: 142 Copynumber: 3.6 Consensus size: 142
41292181 TTCGGTCTAT
* * * *
41292191 TCCACTGTAATCTCAGGGAAATAGGATTATTGGCTTCAATCTGCTTCGCTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
* *
41292256 TAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
41292321 ATTTTAATTCGC
131 ATTTTAATTCGC
*
41292333 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
* *
41292398 TAAGATTTCTGGCTTTAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
* *
41292463 ACTTTAATCCGC
131 ATTTTAATTCGC
* * *
41292475 TGCACTGTAACCTCAGGGAGATATGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
* * *
41292540 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTATTGTAACTTCAGAGAGGTAAGACCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
41292605 ATTTTAA-TCTGC
131 ATTTTAATTC-GC
* *
41292617 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCACAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
41292682 TAAGATTTCTGGCTTCAATCTG
66 TAAGATTTCTGGCTTCAATCTG
41292704 CTCCACTGTA
Statistics
Matches: 343, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 1 0.00
142 342 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (142 bp):
TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
ATTTTAATTCGC
Found at i:41292452 original size:98 final size:97
Alignment explanation
Indices: 41292331--41292517 Score: 216
Period size: 98 Copynumber: 1.9 Consensus size: 97
41292321 ATTTTAATTC
* * * * *
41292331 GCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGG
1 GCTCCACTGTAATCTCAGAGAGATAAGATCT-CTA-CTTTAATCCGCTCCACTGTAACCTCAGGG
* * *
41292395 AGATAAGATTTCTGGCTTTAATCTGATGCGATCT
64 AGATAAGATTACTAGCTTCAATCTGATGCGATCT
* * *
41292429 GCTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTACTTTAATCCGCTGCACTGTAACCTCAGGG
1 GCTCCACTGTAATC-TCAGAGAGATAAGAT-CTCTACTTTAATCCGCTCCACTGTAACCTCAGGG
*
41292493 AGATATGATTACTAGCTTCAATCTG
64 AGATAAGATTACTAGCTTCAATCTG
41292518 CTCCGCTGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 1 0.01
98 70 0.95
99 2 0.03
100 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (97 bp):
GCTCCACTGTAATCTCAGAGAGATAAGATCTCTACTTTAATCCGCTCCACTGTAACCTCAGGGAG
ATAAGATTACTAGCTTCAATCTGATGCGATCT
Found at i:41292555 original size:44 final size:44
Alignment explanation
Indices: 41292425--41292741 Score: 209
Period size: 44 Copynumber: 7.0 Consensus size: 44
41292415 ATCTGATGCG
* * * *
41292425 ATCTGCTCTACTGTAA-CTTCAGAGAGATAAGATCCTT-T-ACTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTCTGGCTTCA
* * * * * *
41292469 ATCCGCTGCACTGTAACCTCAGGGAGATATGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
*
41292513 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
* * * * *
41292557 ATCTGATGCGATCTACTCTATTGTAA-CTTCAGAGAGGTAAGACCCTTTAT---TTTA
1 ATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGA---TTTCTGGCTTCA
* * *
41292611 ATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
** *
41292655 ATCTGCTCTGCTGTAATCACAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
*
41292699 ATCTGCTCCACTGTAA-CATCAAGGAGATAAGATTTCTGGCTTC
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTTCTGGCTTC
41292742 CAGCCTATTC
Statistics
Matches: 213, Mismatches: 38, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
41 3 0.01
42 1 0.00
43 2 0.01
44 165 0.77
45 3 0.01
46 1 0.00
47 3 0.01
49 2 0.01
51 3 0.01
52 1 0.00
53 2 0.01
54 23 0.11
57 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
Found at i:41292839 original size:45 final size:43
Alignment explanation
Indices: 41292790--41292935 Score: 141
Period size: 45 Copynumber: 3.3 Consensus size: 43
41292780 AATCTTTGAT
*
41292790 CTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAAC
1 CTGCTCCACTG-C-ATGCAGGAAGGCAAGATCTGCTATCTTCAAC
** * * * * *
41292835 CTGCTCCACTGCAACCGAGGGAGGCAAG-GCTGGTATCTTCGAT
1 CTGCTCCACTGCATGC-AGGAAGGCAAGATCTGCTATCTTCAAC
** *
41292878 CTGCTTTACTGCCAGTGCAGGAAGGCAAGATCTGCTATCTTTAAC
1 CTGCTCCACTG-CA-TGCAGGAAGGCAAGATCTGCTATCTTCAAC
41292923 CTGCTCCACTGCA
1 CTGCTCCACTGCA
41292936 ACCGATGGAG
Statistics
Matches: 77, Mismatches: 20, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
43 22 0.29
44 25 0.32
45 30 0.39
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (43 bp):
CTGCTCCACTGCATGCAGGAAGGCAAGATCTGCTATCTTCAAC
Found at i:41292897 original size:88 final size:88
Alignment explanation
Indices: 41292781--41292952 Score: 283
Period size: 88 Copynumber: 2.0 Consensus size: 88
41292771 AGGACTTGTA
* *
41292781 ATCTTTGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTG
1 ATCTTCGATCTGCTTCACTGCCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTG
41292846 CAACCGAGGGAGGCAAGGCTGGT
66 CAACCGAGGGAGGCAAGGCTGGT
* *
41292869 ATCTTCGATCTGCTTTACTGCC-AGTGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACT
1 ATCTTCGATCTGCTTCACTGCCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
41292933 GCAACCGATGGAGGCAAGGC
65 GCAACCGAGGGAGGCAAGGC
41292953 AGGAAAGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 1 0.01
88 77 0.99
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (88 bp):
ATCTTCGATCTGCTTCACTGCCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTG
CAACCGAGGGAGGCAAGGCTGGT
Found at i:41292948 original size:44 final size:43
Alignment explanation
Indices: 41292812--41292950 Score: 145
Period size: 43 Copynumber: 3.2 Consensus size: 43
41292802 CGATGCAGGA
41292812 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGA-GG
* * * * ** * **
41292856 AGGCAAG-GCTGGTATCTTCGATCTGCTTTACTGCCAGTGCAGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCG-AGG
*
41292899 AAGGCAAGATCTGCTATCTTTAACCTGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGA-GG
41292944 AGGCAAG
1 AGGCAAG
41292951 GCAGGAAAGA
Statistics
Matches: 72, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
43 25 0.35
44 23 0.32
45 24 0.33
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.23
Consensus pattern (43 bp):
AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGG
Found at i:41292986 original size:57 final size:57
Alignment explanation
Indices: 41292894--41293006 Score: 181
Period size: 57 Copynumber: 2.0 Consensus size: 57
41292884 TACTGCCAGT
* * * *
41292894 GCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACTGCAACCGATGGAGGCAAG
1 GCAGGAAAGAAAGATCTGCCATCTTTAACCCGCTCCACTGCAACCGATGGAGGCAAG
*
41292951 GCAGGAAAGAAAGATCTGCCATCTTTAACCCGCTCCACTGGAACCGATGGAGGCAA
1 GCAGGAAAGAAAGATCTGCCATCTTTAACCCGCTCCACTGCAACCGATGGAGGCAA
41293007 TGCTTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.18
Consensus pattern (57 bp):
GCAGGAAAGAAAGATCTGCCATCTTTAACCCGCTCCACTGCAACCGATGGAGGCAAG
Found at i:41293054 original size:87 final size:87
Alignment explanation
Indices: 41292951--41293149 Score: 301
Period size: 87 Copynumber: 2.3 Consensus size: 87
41292941 TGGAGGCAAG
* * * *
41292951 GCAGGAAAGA-AAGATCTGCCATCTTTAACCCGCTCCACTGGAACCGATGGAGGCAATGCTTTAT
1 GCAGGAAA-ACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTAT
41293015 TTTCAATCTACTTCGCTGTCAAT
65 TTTCAATCTACTTCGCTGTCAAT
*
41293038 GCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTT
1 GCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATT
* *
41293103 TTCGATCTGCTTCGCTGTCAAT
66 TTCAATCTACTTCGCTGTCAAT
**
41293125 GCAGGAAGGCAAGATCTGCTATCTT
1 GCAGGAAAACAAGATCTGCTATCTT
41293150 CACTGATCTA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 101 0.99
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (87 bp):
GCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATT
TTCAATCTACTTCGCTGTCAAT
Found at i:41293083 original size:144 final size:145
Alignment explanation
Indices: 41292806--41293096 Score: 404
Period size: 144 Copynumber: 2.0 Consensus size: 145
41292796 CACTGTCGAT
* * * *
41292806 GCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTAT
1 GCAGGAAAGAAAGATCTGCCATCTTCAACCCGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTAT
* * * * ** *
41292871 CTTCGATCTGCTTTACTGCCAGTGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACTGCA
66 CTTCAATCTACTTCACTGCCAATGCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCA
41292936 ACCGATGGAGGCAAG
131 ACCGATGGAGGCAAG
* * * * *
41292951 GCAGGAAAGAAAGATCTGCCATCTTTAACCCGCTCCACTGGAACCGATGGAGGCAATGCT-TTAT
1 GCAGGAAAGAAAGATCTGCCATCTTCAACCCGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTAT
* * *
41293015 TTTCAATCTACTTCGCTGTCAATGCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCA
66 CTTCAATCTACTTCACTGCCAATGCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCA
41293080 ACCGATGGAGGCAAG
131 ACCGATGGAGGCAAG
41293095 GC
1 GC
41293097 TTTGTTTTCG
Statistics
Matches: 127, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
144 75 0.59
145 52 0.41
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (145 bp):
GCAGGAAAGAAAGATCTGCCATCTTCAACCCGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTAT
CTTCAATCTACTTCACTGCCAATGCAGGAAAACAAGATCTGCTATCTTTAACCAGCTCCACTGCA
ACCGATGGAGGCAAG
Found at i:41294354 original size:8 final size:8
Alignment explanation
Indices: 41294338--41294379 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
41294328 AGCCTCTCCA
41294338 TTTTT-AT
1 TTTTTCAT
41294345 TTTTTCAT
1 TTTTTCAT
41294353 TTTTTCA-
1 TTTTTCAT
41294360 TTTTTCA-
1 TTTTTCAT
*
41294367 CTTTTCAT
1 TTTTTCAT
41294375 TTTTT
1 TTTTT
41294380 TGACTTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCAT
Found at i:41295135 original size:12 final size:13
Alignment explanation
Indices: 41295118--41295191 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 13
41295108 TCTCCTTTTC
41295118 TTTTTTTTC-TCT
1 TTTTTTTTCTTCT
41295130 TTTTTTTTCCTTCT
1 TTTTTTTT-CTTCT
*
41295144 TTTTATTTCATT-T
1 TTTTTTTTC-TTCT
*
41295157 TTGATTTTTCTT-T
1 TT-TTTTTTCTTCT
*
41295170 TTCTTTTTCTTCT
1 TTTTTTTTCTTCT
41295183 TTTTGTTTT
1 TTTT-TTTT
41295192 TGATTTTGAC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
12 16 0.31
13 14 0.27
14 21 0.41
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:41295170 original size:6 final size:6
Alignment explanation
Indices: 41295113--41295180 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
41295103 TGACCTCTCC
* * *
41295113 TTTTCT TTTT-T TTCTCT TTTT-T TTTCCT TCTTT-T TATTTCAT TTTTGAT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT T-TTTC-T TTTT-CT
41295162 TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT T
41295181 CTTTTTGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
5 8 0.16
6 29 0.59
7 10 0.20
8 2 0.04
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:41295191 original size:6 final size:6
Alignment explanation
Indices: 41295183--41295216 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
41295173 TTTTTCTTCT
* *
41295183 TTTTGT TTTTGA TTTTGA CTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
41295217 TTTTTGAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:41295817 original size:12 final size:12
Alignment explanation
Indices: 41295800--41295826 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41295790 CCCATAGCAA
41295800 GTACAAAAGAAT
1 GTACAAAAGAAT
41295812 GTACAAAAGAAT
1 GTACAAAAGAAT
41295824 GTA
1 GTA
41295827 TAAATTCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (12 bp):
GTACAAAAGAAT
Found at i:41299865 original size:21 final size:20
Alignment explanation
Indices: 41299824--41299869 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
41299814 TAAGTAGCTC
**
41299824 AAAAAATATTAAAAGGGTAT
1 AAAAAATATTAAAAGAATAT
*
41299844 AAAAAATAGTTAAAATAATAT
1 AAAAAATA-TTAAAAGAATAT
41299865 AAAAA
1 AAAAA
41299870 TAACCATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (20 bp):
AAAAAATATTAAAAGAATAT
Found at i:41300184 original size:22 final size:23
Alignment explanation
Indices: 41300107--41300236 Score: 94
Period size: 24 Copynumber: 5.7 Consensus size: 23
41300097 CTAAATAATG
* **
41300107 ATATGATAAGTTTAAAATTATTGT
1 ATATGATAA-TTTAAAATAATACT
* * *
41300131 ACATGATAAATTTTAAATTATGA-T
1 ATATGAT-AATTTAAAATAAT-ACT
*
41300155 ATATGATAGATTT-AAATAGTACT
1 ATATGATA-ATTTAAAATAATACT
41300178 -TATGATAATTTAAAATAATACT
1 ATATGATAATTTAAAATAATACT
41300200 ATATGAT-A-TTAAAATAA-ATCT
1 ATATGATAATTTAAAATAATA-CT
41300221 A-ATGATAAATTTAAAA
1 ATATGAT-AATTTAAAA
41300237 CGATGTTAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.07
21 16 0.18
22 19 0.21
23 19 0.21
24 27 0.30
25 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATGATAATTTAAAATAATACT
Found at i:41300190 original size:21 final size:22
Alignment explanation
Indices: 41300154--41300235 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 22
41300144 TAAATTATGA
*
41300154 TATATGATAGATTTAAATAGTAC
1 TATATGATA-ATTTAAATAATAC
41300177 T-TATGATAATTTAAAATAATAC
1 TATATGATAATTT-AAATAATAC
*
41300199 TATATGAT-ATTAAAATAA-ATC
1 TATATGATAATTTAAATAATA-C
41300220 TA-ATGATAAATTTAAA
1 TATATGAT-AATTTAAA
41300236 ACGATGTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
20 6 0.12
21 13 0.25
22 25 0.49
23 7 0.14
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (22 bp):
TATATGATAATTTAAATAATAC
Found at i:41303715 original size:19 final size:17
Alignment explanation
Indices: 41303691--41303732 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
41303681 TACGCCATGT
41303691 TGGGCCAAAATGGGCTGTG
1 TGGGCC-AAATGGGCT-TG
*
41303710 TGGGCCCAATGGGCTTG
1 TGGGCCAAATGGGCTTG
41303727 TGGGCC
1 TGGGCC
41303733 TCACATGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 8 0.36
19 6 0.27
ACGTcount: A:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (17 bp):
TGGGCCAAATGGGCTTG
Found at i:41303741 original size:19 final size:18
Alignment explanation
Indices: 41303699--41303732 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41303689 GTTGGGCCAA
41303699 AATGGGCTGTGTGGGCCC
1 AATGGGCTGTGTGGGCCC
41303717 AATGGGCT-TGTGGGCC
1 AATGGGCTGTGTGGGCC
41303733 TCACATGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.21, G:0.44, T:0.24
Consensus pattern (18 bp):
AATGGGCTGTGTGGGCCC
Found at i:41304705 original size:33 final size:32
Alignment explanation
Indices: 41304668--41304729 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
41304658 TTACTGTCAC
*
41304668 TGTAATGGGCTAAGGCC-ACACTGATACTGATAT
1 TGTAATAGGCTAAGGCCTA-ACTGA-ACTGATAT
41304701 TGTAATAGGCTAAGGCCTAACTGAACTGA
1 TGTAATAGGCTAAGGCCTAACTGAACTGA
41304730 ACTATTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 5 0.19
33 21 0.78
34 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (32 bp):
TGTAATAGGCTAAGGCCTAACTGAACTGATAT
Found at i:41309519 original size:30 final size:31
Alignment explanation
Indices: 41309483--41309551 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
41309473 TTTTATAAAT
41309483 TATTTAAATAA-TGAAAAATAAT-TTTATTTA
1 TATTTAAATAATTGAAAAA-AATATTTATTTA
41309513 TATTTAAATAATTTGAAAAAAATACTTTATTTA
1 TATTTAAATAA-TTGAAAAAAATA-TTTATTTA
*
41309546 AATTTA
1 TATTTA
41309552 TCACCTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 11 0.32
31 3 0.09
32 7 0.21
33 13 0.38
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (31 bp):
TATTTAAATAATTGAAAAAAATATTTATTTA
Found at i:41309959 original size:16 final size:16
Alignment explanation
Indices: 41309938--41309970 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41309928 TTCGCTGTAT
41309938 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
41309954 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
41309970 T
1 T
41309971 AGCAAATCAA
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:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:41310054 original size:39 final size:43
Alignment explanation
Indices: 41309950--41310058 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
41309940 GAATAGAGGC
41309950 GTAATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTT--AT
* * *
41309995 GTAATGGAATAGAGGCGTAATAG-TATTC-ATGTGTTTGG-T-T
1 GTAATGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTAT
41310035 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGTGTAATAGCA
41310059 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 3 0.05
44 10 0.18
45 22 0.39
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
GTAATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTAT
Found at i:41310221 original size:16 final size:16
Alignment explanation
Indices: 41310184--41310225 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41310174 TTAATCATAT
*
41310184 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
41310200 TT-AAATATATTATAA
1 TTAAAATATATTATAA
41310215 TTAAAATATAT
1 TTAAAATATAT
41310226 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:41310232 original size:14 final size:15
Alignment explanation
Indices: 41310193--41310234 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41310183 TTTAAACATA
*
41310193 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41310208 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41310222 A-TATAATTTAATA
1 ATTATAATTAAATA
41310235 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41310353 original size:14 final size:15
Alignment explanation
Indices: 41310304--41310355 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41310294 ATAAAATATA
41310304 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
41310319 TATTAAATATATTAT
1 AATTAAATATATTAT
41310334 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
41310347 AATTTAATA
1 AATTAAATA
41310356 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:41310611 original size:120 final size:120
Alignment explanation
Indices: 41310182--41310600 Score: 714
Period size: 120 Copynumber: 3.5 Consensus size: 120
41310172 ATTTAATCAT
41310182 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
41310247 ATCAATATTCTTATATGAATTTACTCCAAATCATAATATATGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACT-CAAATCATAATATATGATACTATAAAAGATA
*
41310304 AATTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
41310369 TTAATATTCTTATATGAATTTGCTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
41310424 ATTTAACATAATTATTATTAAACATATTTTAATTAAAATCTATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
41310489 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
41310544 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
41310601 TAAAATAATT
Statistics
Matches: 283, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
120 195 0.69
121 85 0.30
122 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:41310697 original size:26 final size:25
Alignment explanation
Indices: 41310629--41310697 Score: 59
Period size: 26 Copynumber: 2.6 Consensus size: 25
41310619 TAAATTTTCT
41310629 TATATGAATTTGCATAATTTAAAATAA
1 TATAT-AATTT-CATAATTTAAAATAA
* * *
41310656 T-TATTATTACATATAATTTAATAATGA
1 TATATAATTTC--ATAATTTAA-AATAA
41310683 TATATAATTTCATAA
1 TATATAATTTCATAA
41310698 AATTCTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
24 1 0.03
25 3 0.09
26 16 0.48
27 6 0.18
28 7 0.21
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
TATATAATTTCATAATTTAAAATAA
Found at i:41316024 original size:33 final size:34
Alignment explanation
Indices: 41315959--41316025 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
41315949 TCGTAAATTT
*
41315959 TTTTTTAAATAAATTAAGATTTTGAGTTATTAGA
1 TTTTTTAAATAAATTAAGATTTTGAGTAATTAGA
* * * *
41315993 TTTTTTAAATTAATTGATATTTTTA-TAATTAGA
1 TTTTTTAAATAAATTAAGATTTTGAGTAATTAGA
41316026 ACTGTACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (34 bp):
TTTTTTAAATAAATTAAGATTTTGAGTAATTAGA
Found at i:41319125 original size:21 final size:20
Alignment explanation
Indices: 41319101--41319139 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41319091 AATTCCTCTT
41319101 TTATATATTATATTTAACTCA
1 TTATATATTAT-TTTAACTCA
*
41319122 TTATATGTTATTTTAACT
1 TTATATATTATTTTAACT
41319140 TGCTTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
TTATATATTATTTTAACTCA
Found at i:41319193 original size:27 final size:28
Alignment explanation
Indices: 41319154--41319212 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
41319144 TTGTAAAGGA
*
41319154 TTTATTTTAAGTTATTTTATATATT-AT
1 TTTATTTTAAGTTACTTTATATATTAAT
* *
41319181 TTTATTTTTAGTTGCTTTATATATTAAT
1 TTTATTTTAAGTTACTTTATATATTAAT
41319209 TTTA
1 TTTA
41319213 AAATTATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (28 bp):
TTTATTTTAAGTTACTTTATATATTAAT
Found at i:41323725 original size:45 final size:44
Alignment explanation
Indices: 41323661--41323759 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 44
41323651 TTTAGTTCGT
41323661 TGTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* * *
41323706 TGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
*
41323750 TGGAATGGAA
1 TGTAATGGAA
41323760 GTGTAATAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.02
44 24 0.49
45 24 0.49
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:41323936 original size:18 final size:17
Alignment explanation
Indices: 41323915--41323949 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41323905 TTATTATTAA
*
41323915 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41323933 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41323950 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41324058 original size:59 final size:59
Alignment explanation
Indices: 41323991--41324299 Score: 234
Period size: 59 Copynumber: 5.2 Consensus size: 59
41323981 CTCAAATCAT
*
41323991 AATATATGATACTATAAAATATAATTTGAAATTATTATTATTAAATATATTTTATTTAA
1 AATATATGATACTATAAAATATAATTTGAAATTATTATTATTAAATATATTTTAATTAA
* * * * * * * * ** * *
41324050 AATATATGAT-TTAATAAAATTCTTAATAAT-CAA-TATTCTTATATGAATTTACTCAAATCAT
1 AATATATGATACT-ATAAAA-T-ATAAT-TTGAAATTATTATTAT-TAAATATATTTTAATTAA
*
41324111 AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAAATTATTATTATTAAATATATTTTAATTAA
* * * * * * * * ** * *
41324170 AATATATGAT-TTAATAAAATTCTTAATAAT-CAA-TATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATACT-ATAAAA-T-ATAAT-TTGAAATTATTATTAT-TAAATATATTTTAATTAA
* *
41324231 AATATATGATACTATAAAATATATTTTGAAATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAAATTATTATTATTAAATATATTTTAATTAA
41324290 AATATATGAT
1 AATATATGAT
41324300 TTAATAAAAT
Statistics
Matches: 181, Mismatches: 53, Indels: 32
0.68 0.20 0.12
Matches are distributed among these distances:
58 4 0.02
59 75 0.41
60 33 0.18
61 65 0.36
62 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (59 bp):
AATATATGATACTATAAAATATAATTTGAAATTATTATTATTAAATATATTTTAATTAA
Found at i:41324117 original size:120 final size:120
Alignment explanation
Indices: 41323901--41324319 Score: 793
Period size: 120 Copynumber: 3.5 Consensus size: 120
41323891 ATATTTTAAC
*
41323901 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
41323966 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTGAA
* *
41324021 ATTATTATTATTAAATATATTTTATTTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
41324086 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTGAA
41324141 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
* *
41324206 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATATTTTGAA
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTGAA
41324261 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
41324320 TATTACTAAT
Statistics
Matches: 292, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 292 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:41324176 original size:18 final size:17
Alignment explanation
Indices: 41324153--41324189 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
41324143 AATTATTATT
41324153 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
41324169 AAATATATGATTTAATA
1 AAATATATGATTTAATA
41324186 AAAT
1 AAAT
41324190 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:41324248 original size:61 final size:61
Alignment explanation
Indices: 41323943--41324250 Score: 258
Period size: 61 Copynumber: 5.1 Consensus size: 61
41323933 ATATAATTTA
41323943 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * ** * * * *
41324004 ATAAAA-T-ATAAT-TTGAA-ATTATTATTATTAAATATATTTTATTTAAAATATATGAT-TT
1 ATAAAATTCTTAATAATCAATATTCTTA-TA-TGAATTTACTCAAATCATAATATATGATACT
41324062 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * ** * * *
41324124 ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAATTCTTAATAAT-CAAT-ATTCTTATATGAATTTACTCAAATCATAATATATGATACT
*
41324182 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
41324244 ATAAAAT
1 ATAAAAT
41324251 ATATTTTGAA
Statistics
Matches: 181, Mismatches: 50, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
57 6 0.03
58 8 0.04
59 64 0.35
60 18 0.10
61 71 0.39
62 8 0.04
63 6 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:41324296 original size:18 final size:17
Alignment explanation
Indices: 41324273--41324309 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
41324263 AATTATTATT
41324273 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
41324289 AAATATATGATTTAATA
1 AAATATATGATTTAATA
41324306 AAAT
1 AAAT
41324310 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:41324399 original size:44 final size:43
Alignment explanation
Indices: 41324351--41324503 Score: 130
Period size: 44 Copynumber: 3.4 Consensus size: 43
41324341 TATGAATTTT
41324351 TATAATTTAAAACAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAA-AATTATTATTAAATATAATTTAATAATAATA
* * * **
41324395 TATAATTTCATAAAATTCTT-TGATAATA-AATTTTCTTATATGAATTTA
1 TATAATTT-AAAAAATTATTATTA-AATATAA-TTTAATA-AT-AA--TA
* *
41324443 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAA-AATTATTATTAAATATAATTTAATAATAATA
*
41324487 TATAATTTCATAAAATT
1 TATAATTT-AAAAAATT
41324504 CTTAATAATA
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
43 4 0.05
44 37 0.44
45 8 0.09
46 3 0.04
47 5 0.06
48 24 0.28
49 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAAAATTATTATTAAATATAATTTAATAATAATA
Found at i:41324434 original size:92 final size:91
Alignment explanation
Indices: 41324317--41324533 Score: 353
Period size: 92 Copynumber: 2.4 Consensus size: 91
41324307 AATTCTTAAT
* * * *
41324317 AATTATTACTAATAAATTTTCTTATATGAATTTTTATAATTTAAAACAATTATTATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAACAATTAATATTAAATATAA
41324382 TTTAATAATAATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
* *
41324408 AATTCTTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATA
1 AATTC-TTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAACAATTAATATTAAATATA
*
41324473 ATTTAATAATGATATATAATTTCATAA
65 ATTTAATAATAATATATAATTTCATAA
*
41324500 AATTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTA
41324534 CTAAAATGAT
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 31 0.27
92 85 0.73
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (91 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAACAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:41328694 original size:19 final size:18
Alignment explanation
Indices: 41328652--41328696 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
41328642 GTAAACTCTT
41328652 TCAAAAAACAGCAGACTA
1 TCAAAAAACAGCAGACTA
*
41328670 TCAAAAAATAGCAGACTA
1 TCAAAAAACAGCAGACTA
41328688 TCAAAAAAC
1 TCAAAAAAC
41328697 TGTCTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.20, G:0.09, T:0.13
Consensus pattern (18 bp):
TCAAAAAACAGCAGACTA
Found at i:41337341 original size:47 final size:48
Alignment explanation
Indices: 41337243--41337346 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
41337233 TCACTTGAAG
* * * **
41337243 AAAAAAAGGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTTCTTA
1 AAAAAAAAGACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAA
*
41337291 AAAAAAAAGACCAATGTGAAAACCCGCAAAGGGCAC-TTGAGTCCAAA
1 AAAAAAAAGACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAA
41337338 AAAATAAAA
1 AAAA-AAAA
41337347 AATGAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 12 0.24
48 37 0.76
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (48 bp):
AAAAAAAAGACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAA
Found at i:41338825 original size:89 final size:88
Alignment explanation
Indices: 41338686--41339234 Score: 648
Period size: 89 Copynumber: 6.2 Consensus size: 88
41338676 AAGCTGCGAT
* * * *
41338686 GGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCA
1 GGAGCAGACTGAAGATAACAGATCTTGT-TTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCA
* *
41338751 GCCTTACCTCCCTGAGTTTGCAGT
65 GCCTTGCCTCCCTGAGTTTGCAGC
* * * * * *
41338775 GAAGTAGACTGAATATAACATATCTTGGTTTTCTGTATTGGCAGTGAAGCAGATCAAAGACACCA
1 GGAGCAGACTGAAGATAACAGATCTT-GTTTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCA
* * *
41338840 GCTTTGCCTCCCTGAGTTTGTAAC
65 GCCTTGCCTCCCTGAGTTTGCAGC
* * * *
41338864 GGAACAGACTGAAAATAACAGATCTTGTTTTCCTGTATTGGCAGTGAATCAGATCGAAGACACCA
1 GGAGCAGACTGAAGATAACAGATCTTGTTTT-CTGTATTGGCAGCGAAGCAGATCGAAGACACCA
* * * * *
41338929 GCTTTGCCTCCATAAATTTACAGC
65 GCCTTGCCTCCCTGAGTTTGCAGC
* ** * * * **
41338953 GGAGTAGACTGAAGATAGTAGATCTTGTCTTCCTGTATTGCCAGCGAAGCAGATTGAAGACAAAA
1 GGAGCAGACTGAAGATAACAGATCTTGT-TTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCA
* *
41339018 GTCTTGACTCCCTGAGTTTGCAGC
65 GCCTTGCCTCCCTGAGTTTGCAGC
* * *
41339042 GGAGCAGACTAAAGATAACATATCTTGTCTTTCTGTATTGGCAGCAAAGCAGATCGAAGACACCA
1 GGAGCAGACTGAAGATAACAGATCTTGT-TTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCA
*
41339107 GCCTTGCCTCCTTGAGTTTGCAGC
65 GCCTTGCCTCCCTGAGTTTGCAGC
* *
41339131 GGAGCAGACTAAAGATAACAGATCTTGTTTTCCTGTATTGGCAGCGAAGCAGATCAAAGACACCA
1 GGAGCAGACTGAAGATAACAGATCTTGTTTT-CTGTATTGGCAGCGAAGCAGATCGAAGACACCA
* * *
41339196 GCTTTGCCTCCCTGGGTTTGCAAC
65 GCCTTGCCTCCCTGAGTTTGCAGC
*
41339220 AGAGCAGACTGAAGA
1 GGAGCAGACTGAAGA
41339235 GAGCAAATTT
Statistics
Matches: 386, Mismatches: 70, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
88 8 0.02
89 374 0.97
90 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (88 bp):
GGAGCAGACTGAAGATAACAGATCTTGTTTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCAG
CCTTGCCTCCCTGAGTTTGCAGC
Found at i:41339048 original size:44 final size:44
Alignment explanation
Indices: 41338994--41339138 Score: 105
Period size: 44 Copynumber: 3.3 Consensus size: 44
41338984 CCTGTATTGC
41338994 CAGCGAAGCAGATTGAAGACAAAAGTCTTGACTCCCTGAGTTTG
1 CAGCGAAGCAGATTGAAGACAAAAGTCTTGACTCCCTGAGTTTG
* * * * * ** *
41339038 CAGCGGAGCAGACTAAAGATAACATA-TCTTGTCTTTCTGTA-TTGG
1 CAGCGAAGCAGATTGAAGACAA-A-AGTCTTGACTCCCTG-AGTTTG
* * ** * * *
41339083 CAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCTTGAGTTTG
1 CAGCGAAGCAGATTGAAGACAAAAGTCTTGACTCCCTGAGTTTG
*
41339127 CAGCGGAGCAGA
1 CAGCGAAGCAGA
41339139 CTAAAGATAA
Statistics
Matches: 72, Mismatches: 24, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
43 2 0.03
44 39 0.54
45 29 0.40
46 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (44 bp):
CAGCGAAGCAGATTGAAGACAAAAGTCTTGACTCCCTGAGTTTG
Found at i:41339172 original size:267 final size:267
Alignment explanation
Indices: 41338686--41339206 Score: 769
Period size: 267 Copynumber: 2.0 Consensus size: 267
41338676 AAGCTGCGAT
* **
41338686 GGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCA
1 GGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGCCAGCAAAGCAGATCGAAGACAAAA
* * * *
41338751 GCCTTACCTCCCTGAGTTTGCAGTGAAGTAGACTGAATATAACATATCTTGGTTTTCTGTATTGG
66 GCCTTACCTCCCTGAGTTTGCAGCGAAGCAGACTAAAGATAACATATCTTGGTTTTCTGTATTGG
** * *
41338816 CAGTGAAGCAGATCAAAGACACCAGCTTTGCCTCCCTGAGTTTGTAACGGAACAGACTGAAAATA
131 CAGCAAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGAGTTTGCAACGGAACAGACTGAAAATA
* * *
41338881 ACAGATCTTGTTTTCCTGTATTGGCAGTGAATCAGATCGAAGACACCAGCTTTGCCTCCATAAAT
196 ACAGATCTTGTTTTCCTGTATTGGCAGCGAAGCAGATCAAAGACACCAGCTTTGCCTCCATAAAT
41338946 TTACAGC
261 TTACAGC
* * * * *
41338953 GGAGTAGACTGAAGATAGTAGATCTTGTCTTCCTGTATTGCCAGCGAAGCAGATTGAAGACAAAA
1 GGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGCCAGCAAAGCAGATCGAAGACAAAA
* *
41339018 GTCTTGA-CTCCCTGAGTTTGCAGCGGAGCAGACTAAAGATAACATATCTT-GTCTTTCTGTATT
66 GCCTT-ACCTCCCTGAGTTTGCAGCGAAGCAGACTAAAGATAACATATCTTGGT-TTTCTGTATT
* * * *
41339081 GGCAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCTTGAGTTTGCAGCGGAGCAGACT-AAAG
129 GGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGAGTTTGCAACGGAACAGACTGAAA-
41339145 ATAACAGATCTTGTTTTCCTGTATTGGCAGCGAAGCAGATCAAAGACACCAGCTTTGCCTCC
193 ATAACAGATCTTGTTTTCCTGTATTGGCAGCGAAGCAGATCAAAGACACCAGCTTTGCCTCC
41339207 CTGGGTTTGC
Statistics
Matches: 226, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
266 5 0.02
267 220 0.97
268 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (267 bp):
GGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGCCAGCAAAGCAGATCGAAGACAAAA
GCCTTACCTCCCTGAGTTTGCAGCGAAGCAGACTAAAGATAACATATCTTGGTTTTCTGTATTGG
CAGCAAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGAGTTTGCAACGGAACAGACTGAAAATA
ACAGATCTTGTTTTCCTGTATTGGCAGCGAAGCAGATCAAAGACACCAGCTTTGCCTCCATAAAT
TTACAGC
Found at i:41339190 original size:45 final size:45
Alignment explanation
Indices: 41338704--41339192 Score: 177
Period size: 45 Copynumber: 11.0 Consensus size: 45
41338694 CTAAAGATAG
* * *
41338704 CAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACAC
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACAA
* ** * * * * * * *
41338749 CAG-CCTTACCTCCCTG-AGTTTGCAGTGAAGTAGA-CTGAATATAA
1 CAGATCTTGTCTTCCTGTA-TTGGCAGCGAAGCAGATC-AAAGACAA
* * * *
41338793 CATATCTTGGT-TTTCTGTATTGGCAGTGAAGCAGATCAAAGACAC
1 CAGATCTT-GTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACAA
* * * * * * * *
41338838 CAGCT-TTGCCTCCCTG-AGTTTGTAACGGAA-CAGACTGAAA-ATAA
1 CAGATCTTGTCTTCCTGTA-TTGGCAGC-GAAGCAGA-TCAAAGACAA
* * * * *
41338882 CAGATCTTGTTTTCCTGTATTGGCAGTGAATCAGATCGAAGACAC
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACAA
* * ** ** * * * * *
41338927 CAGCT-TTG-CCTCCATAAATTTACAGCGGAGTAGA-CTGAAGATAG
1 CAGATCTTGTCTTCC-TGTATTGGCAGCGAAGCAGATC-AAAGACAA
* * **
41338971 TAGATCTTGTCTTCCTGTATTGCCAGCGAAGCAGATTGAAGACAA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACAA
* * * * * *
41339016 AAG-TCTTGACTCCCTG-AGTTTGCAGCGGAGCAGA-CTAAAGATAA
1 CAGATCTTGTCTTCCTGTA-TTGGCAGCGAAGCAGATC-AAAGACAA
* * * * *
41339060 CATATCTTGTCTTTCTGTATTGGCAGCAAAGCAGATCGAAGACAC
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACAA
* * * * *
41339105 CAG-CCTTG-CCTCCT-TGAGTTTGCAGCGGAGCAGA-CTAAAGATAA
1 CAGATCTTGTCTTCCTGT-A-TTGGCAGCGAAGCAGATC-AAAGACAA
*
41339149 CAGATCTTGTTTTCCTGTATTGGCAGCGAAGCAGATCAAAGACA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACA
41339193 CCAGCTTTGC
Statistics
Matches: 305, Mismatches: 108, Indels: 62
0.64 0.23 0.13
Matches are distributed among these distances:
42 1 0.00
43 15 0.05
44 134 0.44
45 139 0.46
46 15 0.05
47 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCAAAGACAA
Found at i:41340890 original size:20 final size:21
Alignment explanation
Indices: 41340853--41340891 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41340843 AATTCCTCTT
41340853 TTATATATTATGTTTAACTCA
1 TTATATATTATGTTTAACTCA
*
41340874 TTATATGTTAT-TTTAACT
1 TTATATATTATGTTTAACT
41340892 TGCTTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (21 bp):
TTATATATTATGTTTAACTCA
Found at i:41341352 original size:17 final size:17
Alignment explanation
Indices: 41341330--41341362 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41341320 ATTGTAATGC
*
41341330 TTATTTGTATTGATTAA
1 TTATTTGTATTCATTAA
41341347 TTATTTGTATTCATTA
1 TTATTTGTATTCATTA
41341363 GTGTACTTTT
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:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (17 bp):
TTATTTGTATTCATTAA
Found at i:41345806 original size:31 final size:33
Alignment explanation
Indices: 41345771--41345843 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
41345761 TTATGATTTT
* *
41345771 AAAATAAAATC-A-TATCTATTATTTTAATATA
1 AAAATAAAATCAACAATCTATAATTTTAATATA
* * *
41345802 AAAATAGAATCAACAATCTGTAATTTTGATATA
1 AAAATAAAATCAACAATCTATAATTTTAATATA
41345835 AAAATAAAA
1 AAAATAAAA
41345844 AGGGTTTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 10 0.29
32 1 0.03
33 23 0.68
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (33 bp):
AAAATAAAATCAACAATCTATAATTTTAATATA
Found at i:41346229 original size:26 final size:24
Alignment explanation
Indices: 41346187--41346237 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
41346177 TTAATAAAAA
* *
41346187 TTTAAATATTTATATTTAATACATT
1 TTTAAATATCTAAATTTAAT-CATT
*
41346212 TTTAATATATCTAAATTTCATCATT
1 TTTAA-ATATCTAAATTTAATCATT
41346237 T
1 T
41346238 ATTTTAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAAATATCTAAATTTAATCATT
Found at i:41348625 original size:21 final size:21
Alignment explanation
Indices: 41348599--41348640 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41348589 CCTTATGTTA
41348599 AAGTTATGAAAGATTAAGTTG
1 AAGTTATGAAAGATTAAGTTG
*
41348620 AAGTTATGAAATATTAAGTTG
1 AAGTTATGAAAGATTAAGTTG
41348641 GAATAAGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
AAGTTATGAAAGATTAAGTTG
Found at i:41350367 original size:45 final size:45
Alignment explanation
Indices: 41350318--41350481 Score: 141
Period size: 45 Copynumber: 3.6 Consensus size: 45
41350308 CTCCATGGCT
*
41350318 TCTTTCAGCCATGGTCTTACTCATTTTAGTCATGATGCCATAACA
1 TCTTTCAGCCATAGTCTTACTCATTTTAGTCATGATGCCATAACA
* * ** * * * * * * *
41350363 TCTTTTAGCTATAGAATTAGTCCTATCTACT-ATGATTCCATGACG
1 TCTTTCAGCCATAGTCTTACTCAT-TTTAGTCATGATGCCATAACA
* * * *
41350408 TATTTCAACCATAGTCTTTACTCATTTTAGTCATGATGTCATATCA
1 TCTTTCAGCCATAGTC-TTACTCATTTTAGTCATGATGCCATAACA
* *
41350454 TCTTTCAGCTATGGTCTTACTCATTTTA
1 TCTTTCAGCCATAGTCTTACTCATTTTA
41350482 TAGCGTATAG
Statistics
Matches: 85, Mismatches: 31, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
45 54 0.64
46 31 0.36
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (45 bp):
TCTTTCAGCCATAGTCTTACTCATTTTAGTCATGATGCCATAACA
Found at i:41350414 original size:90 final size:91
Alignment explanation
Indices: 41350261--41350465 Score: 243
Period size: 90 Copynumber: 2.3 Consensus size: 91
41350251 GGACTACTAG
* * * * ** * * * *
41350261 GATGCCATAGCGTCTTTCAACTATGGTCTTAGTCCAGTCTACCATGACTCCATGGCTTCTTTCAG
1 GATGCCATAACATCTTTCAGCTATAGAATTAGTCCAGTCTACCATGACTCCATGACGTATTTCAA
*
41350326 CCATGGTC-TTACTCATTTTAGTCAT
66 CCATAGTCTTTACTCATTTTAGTCAT
* * *
41350351 GATGCCATAACATCTTTTAGCTATAGAATTAGTCCTA-TCTACTATGATTCCATGACGTATTTCA
1 GATGCCATAACATCTTTCAGCTATAGAATTAGTCC-AGTCTACCATGACTCCATGACGTATTTCA
41350415 ACCATAGTCTTTACTCATTTTAGTCAT
65 ACCATAGTCTTTACTCATTTTAGTCAT
* *
41350442 GATGTCATATCATCTTTCAGCTAT
1 GATGCCATAACATCTTTCAGCTAT
41350466 GGTCTTACTC
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
90 57 0.59
91 39 0.41
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (91 bp):
GATGCCATAACATCTTTCAGCTATAGAATTAGTCCAGTCTACCATGACTCCATGACGTATTTCAA
CCATAGTCTTTACTCATTTTAGTCAT
Found at i:41359509 original size:17 final size:16
Alignment explanation
Indices: 41359476--41359514 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
41359466 TCAAAAAAAA
*
41359476 ACGAAAATTTTGAAAC
1 ACGAAAATTTAGAAAC
41359492 ACGAAAACTTTAGAAAC
1 ACGAAAA-TTTAGAAAC
41359509 ACGAAA
1 ACGAAA
41359515 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (16 bp):
ACGAAAATTTAGAAAC
Found at i:41359529 original size:19 final size:19
Alignment explanation
Indices: 41359500--41359566 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
41359490 ACACGAAAAC
41359500 TTTAGAAACACGAAATTTTT
1 TTTA-AAACACGAAATTTTT
**
41359520 TTTAAAACACG--ACGTTT
1 TTTAAAACACGAAATTTTT
*
41359537 TTTGAAACACGAGAATTTTT
1 TTTAAAACACGA-AATTTTT
*
41359557 TTCAAAACAC
1 TTTAAAACAC
41359567 AAAAATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
17 14 0.38
19 7 0.19
20 16 0.43
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (19 bp):
TTTAAAACACGAAATTTTT
Found at i:41359530 original size:36 final size:36
Alignment explanation
Indices: 41359483--41359590 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
41359473 AAAACGAAAA
* *
41359483 TTTTGAAACACGAAAACTTTAGAAACACGAAATTTT
1 TTTTAAAACACGAAAATTTTAGAAACACGAAATTTT
*** *
41359519 TTTTAAAACACGACGTTTTTTGAAACACGAGAATTTT
1 TTTTAAAACACGAAAATTTTAGAAACACGA-AATTTT
* * *
41359556 TTTCAAAACACAAAAATTTTA-AAACATGAACATTT
1 TTTTAAAACACGAAAATTTTAGAAACACGAA-ATTT
41359591 GTGAAACACG
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
35 1 0.02
36 35 0.61
37 21 0.37
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (36 bp):
TTTTAAAACACGAAAATTTTAGAAACACGAAATTTT
Found at i:41359576 original size:53 final size:53
Alignment explanation
Indices: 41359519--41359636 Score: 141
Period size: 53 Copynumber: 2.2 Consensus size: 53
41359509 ACGAAATTTT
* *
41359519 TTTTAAAACACG-ACGTTTTTTGAAACACGAGAATTTTTTTCAAAACA-CAAAAA
1 TTTTAAAACACGAAC-ATTTGTGAAACACGAGAA-TTTTTTCAAAACATCAAAAA
* * * *
41359572 TTTTAAAACATGAACATTTGTGAAACACGAGAATTTTTTGAAAACATGAAAAT
1 TTTTAAAACACGAACATTTGTGAAACACGAGAATTTTTTCAAAACATCAAAAA
*
41359625 TTTTGAAACACG
1 TTTTAAAACACG
41359637 GGAATTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
52 12 0.22
53 41 0.75
54 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (53 bp):
TTTTAAAACACGAACATTTGTGAAACACGAGAATTTTTTCAAAACATCAAAAA
Found at i:41359616 original size:36 final size:37
Alignment explanation
Indices: 41359572--41359655 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 37
41359562 AACACAAAAA
*
41359572 TTTT-AAAACATGAACATTTGTGAAACACGAGAA-TT
1 TTTTGAAAACATGAAAATTTGTGAAACACGAGAATTT
* *
41359607 TTTTGAAAACATGAAAATTTTTGAAACACGGGAATTT
1 TTTTGAAAACATGAAAATTTGTGAAACACGAGAATTT
41359644 TTTTAGAAAACA
1 TTTT-GAAAACA
41359656 CAATTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 4 0.09
36 26 0.60
37 6 0.14
38 7 0.16
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (37 bp):
TTTTGAAAACATGAAAATTTGTGAAACACGAGAATTT
Found at i:41359645 original size:18 final size:18
Alignment explanation
Indices: 41359592--41359646 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
41359582 TGAACATTTG
*
41359592 TGAAACACGAGAATTTTT
1 TGAAACACGGGAATTTTT
* * *
41359610 TGAAA-ACATGAAAATTTT
1 TGAAACAC-GGGAATTTTT
41359628 TGAAACACGGGAATTTTT
1 TGAAACACGGGAATTTTT
41359646 T
1 T
41359647 TAGAAAACAC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (18 bp):
TGAAACACGGGAATTTTT
Found at i:41359664 original size:36 final size:35
Alignment explanation
Indices: 41359572--41359723 Score: 98
Period size: 36 Copynumber: 4.3 Consensus size: 35
41359562 AACACAAAAA
* *
41359572 TTTT-AAAACATGAACATTTGTGAAACACGAGAATT
1 TTTTGAAAACA-GAAAATTTTTGAAACACGAGAATT
*
41359607 TTTTGAAAACATGAAAATTTTTGAAACACGGGAATTT
1 TTTTGAAAACA-GAAAATTTTTGAAACACGAGAA-TT
* ** *
41359644 TTTTAGAAAACACAATTTTTTTTTAAATCACCG-GAA-T
1 TTTT-GAAAACAGAA-AATTTTTGAAA-CA-CGAGAATT
* * * *
41359681 TTTTCAAAACACG-AAATCTTTGAAACACCAAAATT
1 TTTTGAAAACA-GAAAATTTTTGAAACACGAGAATT
41359716 TTTT-AAAA
1 TTTTGAAAA
41359724 TTTTTTAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
33 1 0.01
34 8 0.09
35 16 0.17
36 33 0.35
37 13 0.14
38 15 0.16
39 5 0.05
40 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (35 bp):
TTTTGAAAACAGAAAATTTTTGAAACACGAGAATT
Found at i:41359757 original size:44 final size:44
Alignment explanation
Indices: 41359678--41359763 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
41359668 AAATCACCGG
41359678 AATTTTTCAAAACACGAAATCTTTGAAACACCAAAATTTTTTAA
1 AATTTTTCAAAACACGAAATCTTTGAAACACCAAAATTTTTTAA
* * *
41359722 AATTTTTTAAAACACGAGGATTTTTGAAACA-CAAAATTTTTT
1 AATTTTTCAAAACACGA-AATCTTTGAAACACCAAAATTTTTT
41359764 TGAAAATACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 27 0.71
45 11 0.29
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (44 bp):
AATTTTTCAAAACACGAAATCTTTGAAACACCAAAATTTTTTAA
Found at i:41359840 original size:35 final size:34
Alignment explanation
Indices: 41359796--41359867 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
41359786 TTTTTTTTGA
41359796 AAACACGGAAATTTTT-AAAACAC-AGGAATTATTG
1 AAACACGG-AATTTTTGAAAACACGAGG-ATTATTG
*
41359830 AAACACCGGAATTTTTGAAAACACGAGGATTTTTG
1 AAACA-CGGAATTTTTGAAAACACGAGGATTATTG
41359865 AAA
1 AAA
41359868 ACACAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
34 12 0.35
35 19 0.56
36 3 0.09
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (34 bp):
AAACACGGAATTTTTGAAAACACGAGGATTATTG
Found at i:41359941 original size:18 final size:18
Alignment explanation
Indices: 41359789--41360044 Score: 160
Period size: 18 Copynumber: 14.3 Consensus size: 18
41359779 TTGTTTTTTT
*
41359789 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
*
41359807 TTTTT-AAAACAC-AGGAA
1 TTTTTGAAAACACGA-AAA
* *
41359824 TTATTG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
**
41359841 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAA
*
41359859 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACACGAAAA
* * *
41359877 TTTTTTAAAACGCAAAAA
1 TTTTTGAAAACACGAAAA
41359895 TTTTT-AAAACACGAGAAAAA
1 TTTTTGAAAACAC--G-AAAA
*
41359915 TTTTTTTTGAAAACATGAAAA
1 ---TTTTTGAAAACACGAAAA
41359936 TTTTTG-AAACACCG-AAA
1 TTTTTGAAAACA-CGAAAA
*
41359953 -TCTTGAAAACAC-AAAGA
1 TTTTTGAAAACACGAAA-A
*
41359970 TTTTTGAAAACACGAAGAT
1 TTTTTGAAAACACGAA-AA
* *
41359989 TTTTTG-AAACATGAGAAT
1 TTTTTGAAAACACGA-AAA
* *
41360007 TTTTTGAAAACATGAGAA
1 TTTTTGAAAACACGAAAA
41360025 -TTTTGAAAA-ACG-AAA
1 TTTTTGAAAACACGAAAA
41360040 TTTTT
1 TTTTT
41360045 TTATTTTTAT
Statistics
Matches: 193, Mismatches: 22, Indels: 48
0.73 0.08 0.18
Matches are distributed among these distances:
15 2 0.01
16 13 0.07
17 57 0.30
18 83 0.43
19 17 0.09
20 5 0.03
21 4 0.02
22 1 0.01
23 5 0.03
24 6 0.03
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:41360010 original size:19 final size:19
Alignment explanation
Indices: 41359970--41360028 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
41359960 AACACAAAGA
*
41359970 TTTTTGAAAACACGA-AGAT
1 TTTTTGAAAACATGAGA-AT
41359989 TTTTTG-AAACATGAGAAT
1 TTTTTGAAAACATGAGAAT
41360007 TTTTTGAAAACATGAGAAT
1 TTTTTGAAAACATGAGAAT
41360026 TTT
1 TTT
41360029 GAAAAACGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 15 0.41
19 22 0.59
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTTTGAAAACATGAGAAT
Found at i:41360045 original size:17 final size:18
Alignment explanation
Indices: 41359483--41360045 Score: 151
Period size: 17 Copynumber: 31.2 Consensus size: 18
41359473 AAAACGAAAA
**
41359483 TTTTG-AAACACGAAAAC
1 TTTTGAAAACACGAAATT
*
41359500 TTTAG-AAACACGAAATTT
1 TTTTGAAAACACGAAA-TT
* **
41359518 TTTTTAAAACACGACGTT
1 TTTTGAAAACACGAAATT
41359536 TTTTG-AAACACGAGAATTT
1 TTTTGAAAACACGA-AA-TT
* **
41359555 TTTTCAAAACAC-AAAAA
1 TTTTGAAAACACGAAATT
*
41359572 TTTT-AAAACATGAACA-T
1 TTTTGAAAACACGAA-ATT
*
41359589 TTGTG-AAACACGAGAATT
1 TTTTGAAAACACGA-AATT
* *
41359607 TTTTGAAAACATGAAAAT
1 TTTTGAAAACACGAAATT
*
41359625 TTTTG-AAACACGGGAATTT
1 TTTTGAAAACAC--GAAATT
*
41359644 TTTTAGAAAACAC-AATTTT
1 TTTT-GAAAACACGAA-ATT
* * *
41359663 TTTTTAAATCACCGGAA-T
1 TTTTGAAAACA-CGAAATT
*
41359681 TTTTCAAAACACGAAA-T
1 TTTTGAAAACACGAAATT
* *
41359698 CTTTG-AAACACCAAAATT
1 TTTTGAAAACA-CGAAATT
41359716 TTTT------A--AAATT
1 TTTTGAAAACACGAAATT
*
41359726 TTTT-AAAACACGAGGA-T
1 TTTTGAAAACACGA-AATT
*
41359743 TTTTG-AAACACAAAATTT
1 TTTTGAAAACACGAAA-TT
*
41359761 TTTTGAAAATACGAAGATTTGTTTTTTTT
1 TTTTGAAAACACGAA-A----------TT
41359790 TTTTGAAAACACGGAAA-T
1 TTTTGAAAACAC-GAAATT
*
41359808 TTTT-AAAACACAGGAA-T
1 TTTTGAAAACAC-GAAATT
* *
41359825 TATTG-AAACACCGGAA-T
1 TTTTGAAAACA-CGAAATT
*
41359842 TTTTGAAAACACGAGGA-T
1 TTTTGAAAACACGA-AATT
*
41359860 TTTTGAAAACACAAAAATT
1 TTTTGAAAACAC-GAAATT
* * *
41359879 TTTT-AAAACGCAAAAAT
1 TTTTGAAAACACGAAATT
41359896 TTTT-AAAACACGAGAAAAATTTT
1 TTTTGAAAACAC--G--AAA--TT
* *
41359919 TTTTGAAAACATGAAAAT
1 TTTTGAAAACACGAAATT
41359937 TTTTG-AAACACCGAAA--
1 TTTTGAAAACA-CGAAATT
* *
41359953 TCTTGAAAACAC-AAAGAT
1 TTTTGAAAACACGAAA-TT
41359971 TTTTGAAAACACGAAGATT
1 TTTTGAAAACACGAA-ATT
*
41359990 TTTTG-AAACATGAGAATT
1 TTTTGAAAACACGA-AATT
*
41360008 TTTTGAAAACATGAGAA--
1 TTTTGAAAACACGA-AATT
41360025 TTTTGAAAA-ACGAAATT
1 TTTTGAAAACACGAAATT
41360042 TTTT
1 TTTT
41360046 TATTTTTATT
Statistics
Matches: 418, Mismatches: 61, Indels: 134
0.68 0.10 0.22
Matches are distributed among these distances:
10 9 0.02
13 1 0.00
15 6 0.01
16 20 0.05
17 137 0.33
18 122 0.29
19 71 0.17
20 13 0.03
21 9 0.02
22 1 0.00
23 5 0.01
24 6 0.01
29 15 0.04
30 3 0.01
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (18 bp):
TTTTGAAAACACGAAATT
Found at i:41360079 original size:19 final size:18
Alignment explanation
Indices: 41360058--41360119 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
41360048 TTTTTATTTT
41360058 ATTTTTTTAAAACACGAA
1 ATTTTTTTAAAACACGAA
* *
41360076 TATTTTTTGAAACCACGGAA
1 -ATTTTTTTAAAACAC-GAA
*
41360096 AGATTTTTTAAAACAC-AA
1 A-TTTTTTTAAAACACGAA
41360114 ATTTTT
1 ATTTTT
41360120 CGATTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.11
18 3 0.09
19 14 0.40
20 14 0.40
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.40
Consensus pattern (18 bp):
ATTTTTTTAAAACACGAA
Found at i:41360273 original size:22 final size:20
Alignment explanation
Indices: 41360223--41360331 Score: 66
Period size: 21 Copynumber: 5.4 Consensus size: 20
41360213 TGTTGTCGTA
* *
41360223 TTTTTGAAAACACGAATATAT
1 TTTTTG-AAACACGAAAAAAT
41360244 TTTTTGAAACACGAGAAAAAT
1 TTTTTGAAACACGA-AAAAAT
*
41360265 TATTTTGAAGCCACG--AAAA-
1 T-TTTTGAA-ACACGAAAAAAT
* * *
41360284 -TTTCGAAACACGGAAAATT
1 TTTTTGAAACACGAAAAAAT
*
41360303 TTTTGTGAAAACAC-AAAAATT
1 TTTT-TG-AAACACGAAAAAAT
41360324 TTTTTGAA
1 TTTTTGAA
41360332 TATTTACAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
16 4 0.06
17 6 0.08
18 3 0.04
19 2 0.03
20 17 0.24
21 22 0.31
22 13 0.18
23 4 0.06
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTTTGAAACACGAAAAAAT
Found at i:41360322 original size:38 final size:39
Alignment explanation
Indices: 41360249--41360324 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 39
41360239 TATATTTTTT
** *
41360249 GAAACACGAGAAAAATTATTTTGAAGCCACGAAAATTTC
1 GAAACACGAGAAAAATTATTTTGAAAACACAAAAATTTC
*
41360288 GAAACACG-G-AAAATTTTTTGTGAAAACACAAAAATTT
1 GAAACACGAGAAAAATTATTT-TGAAAACACAAAAATTT
41360325 TTTTGAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 9 0.28
38 15 0.47
39 8 0.25
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (39 bp):
GAAACACGAGAAAAATTATTTTGAAAACACAAAAATTTC
Found at i:41360505 original size:14 final size:13
Alignment explanation
Indices: 41360481--41360511 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
41360471 AAAATGGAAT
41360481 TAAATTAAAAATA
1 TAAATTAAAAATA
41360494 TAAATATAAAAATA
1 TAAAT-TAAAAATA
41360508 TAAA
1 TAAA
41360512 AATGCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAATTAAAAATA
Found at i:41360660 original size:9 final size:9
Alignment explanation
Indices: 41360646--41360735 Score: 73
Period size: 9 Copynumber: 9.9 Consensus size: 9
41360636 GAATTGAACC
41360646 TCTTTTTTT
1 TCTTTTTTT
41360655 TC-TTTTTT
1 TCTTTTTTT
41360663 TC---TTTT
1 TCTTTTTTT
*
41360669 TCTCTTTTT
1 TCTTTTTTT
41360678 TCTTTTTTT
1 TCTTTTTTT
41360687 TCCTTCTTTTT
1 T-CTT-TTTTT
41360698 TCCTTCTCTTTT
1 T-CTT-T-TTTT
*
41360710 TCTTCTTTT
1 TCTTTTTTT
41360719 TCTTTTCTTT
1 TCTTTT-TTT
41360729 T-TTTTTT
1 TCTTTTTT
41360736 CTCTGCTGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
6 6 0.08
8 10 0.14
9 28 0.39
10 7 0.10
11 15 0.21
12 5 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:41360696 original size:11 final size:10
Alignment explanation
Indices: 41360646--41360731 Score: 85
Period size: 11 Copynumber: 8.8 Consensus size: 10
41360636 GAATTGAACC
41360646 TCTTTTTT-T
1 TCTTTTTTCT
41360655 TC-TTTTT-T
1 TCTTTTTTCT
41360663 TC-TTTTTC-
1 TCTTTTTTCT
41360671 TCTTTTTTCT
1 TCTTTTTTCT
41360681 T-TTTTTTCCT
1 TCTTTTTT-CT
41360691 TCTTTTTTCCT
1 TCTTTTTT-CT
41360702 TCTCTTTTTCT
1 TCT-TTTTTCT
*
41360713 TCTTTTTCTTT
1 TCTTTTT-TCT
41360724 TCTTTTTT
1 TCTTTTTT
41360732 TTTTCTCTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
8 15 0.22
9 14 0.20
10 9 0.13
11 26 0.38
12 5 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TCTTTTTTCT
Found at i:41360738 original size:33 final size:32
Alignment explanation
Indices: 41360646--41360739 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
41360636 GAATTGAACC
*
41360646 TCTTTTTTTTCTTT-TTTTCTTTTTCTCTTTTT
1 TCTTTTTTTTCTTTCTTTTTTTTTTCTC-TTTT
* **
41360678 TCTTTTTTTTCCTTCTTTTTTCCTTCTCTTTT
1 TCTTTTTTTTCTTTCTTTTTTTTTTCTCTTTT
*
41360710 TCTTCTTTTTCTTTTCTTTTTTTTTTCTCT
1 TCTTTTTTTTC-TTTCTTTTTTTTTTCTCT
41360740 GCTGGGCCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
32 27 0.52
33 25 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (32 bp):
TCTTTTTTTTCTTTCTTTTTTTTTTCTCTTTT
Found at i:41361062 original size:3 final size:3
Alignment explanation
Indices: 41361054--41361083 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
41361044 TTTATTTCCT
*
41361054 TTC TTC TTC CTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
41361084 CTTTCCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:41361525 original size:29 final size:30
Alignment explanation
Indices: 41361420--41361592 Score: 138
Period size: 30 Copynumber: 5.8 Consensus size: 30
41361410 TTGTAAATAC
* ** *
41361420 AGAAAAAGTTTTGGGG-CTAAAACATAGTTT
1 AGAAAAAGTTTAGGGGTC-AAAATGTAATTT
* * *
41361450 TGAAGAAGTTTAGGGGCCAAAATGTAATTT
1 AGAAAAAGTTTAGGGGTCAAAATGTAATTT
* *
41361480 TGAAAAAG-TTACAGGGTCAAAATGTAATTT
1 AGAAAAAGTTTA-GGGGTCAAAATGTAATTT
**
41361510 AG-AAAAGTTTAGGGGTTGAAATGTAATTT
1 AGAAAAAGTTTAGGGGTCAAAATGTAATTT
* * * * *
41361539 TGAAAAAATTTAGGGGTTAAAATATACTTTT
1 AGAAAAAGTTTAGGGGTCAAAATGTA-ATTT
*
41361570 AGAAAAA-TTCAGGGGTCAAAATG
1 AGAAAAAGTTTAGGGGTCAAAATG
41361593 CAAATTTTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
29 24 0.21
30 82 0.71
31 10 0.09
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
AGAAAAAGTTTAGGGGTCAAAATGTAATTT
Found at i:41361561 original size:59 final size:60
Alignment explanation
Indices: 41361455--41361592 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 60
41361445 AGTTTTGAAG
* *
41361455 AAGTTTAGGGGCCAAAATGTAATTTTGAAAAAGTTACAGGGTCAAAATGTA-ATTTAGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTACAGGGTCAAAATATACATTTAGAA
** * * * *
41361514 AAGTTTAGGGGTTGAAATGTAATTTTGAAAAAATTTA-GGGGTTAAAATATACTTTTAGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTG-AAAAAGTTACAGGGTCAAAATATACATTTAGAA
* *
41361574 AAATTCAGGGGTCAAAATG
1 AAGTTTAGGGGTCAAAATG
41361593 CAAATTTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 35 0.54
60 30 0.46
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.31
Consensus pattern (60 bp):
AAGTTTAGGGGTCAAAATGTAATTTTGAAAAAGTTACAGGGTCAAAATATACATTTAGAA
Found at i:41362716 original size:78 final size:78
Alignment explanation
Indices: 41361767--41363060 Score: 1425
Period size: 78 Copynumber: 16.8 Consensus size: 78
41361757 GGTGTGTGGC
* * * * *
41361767 CCGACGCTGAACTCACCTCTAGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAG--ATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATA
41361830 CCTCGGCATGTGA
66 CCTCGGCATGTGA
* * *
41361843 CCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAAACTGAAATTTAAAAGGAA
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTTAAAAGAAA
* * *
41361908 TATCTCGGTATGTGT
64 TACCTCGGCATGTGA
* * * ***
41361923 CTGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAAAAACAGAAATTTAAAAGAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATA
**
41361988 CCTCGGCATGCAA
66 CCTCGGCATGTGA
* * * * * * *
41362001 CCCGAGACTCGACTCACTTCTCGCATTATGAATCGATTTTTGAAAAACAGAAA-TT--GA-AAAT
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAAT
* *
41362062 ACTTCGACATGTGA
65 ACCTCGGCATGTGA
* * * * * *
41362076 CCCGAGACTCGACTCACTTCTCGCATTATGAATCGATTTTTGAAAAAACAG-AATTTGAAAAG--
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTT-AAAAGAA
* *
41362138 -TACCTC--AACGTGA
63 ATACCTCGGCATGTGA
* *
41362151 CTCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAAACAGAAA-TT-GAA-AAA
1 C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTTAAAAGAAA
41362213 TACCTC-G-ATGTGA
64 TACCTCGGCATGTGA
* *
41362226 CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAATAC-GAAATTTATAA
1 C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAA-ACAGAAATTTAAAA
*
41362290 GAAATACCTCGACATGTGA
60 GAAATACCTCGGCATGTGA
* *
41362309 CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTTAAACGAAA
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAAAGAAA
* *
41362374 TACCTTGGCATGTGT
64 TACCTCGGCATGTGA
* * * *
41362389 CCGAGGCACAACTCACCTTTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAG--ATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATA
41362452 CCTCGGCATGTGA
66 CCTCGGCATGTGA
* *
41362465 CCCGGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT--GA-AAAT
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAAT
41362526 ACCTCGGCATGTGA
65 ACCTCGGCATGTGA
* ** * * *
41362540 CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTAAAAAAACATAAA-TT-GAA-AATT
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAAT
* *
41362602 A-CTCAGC--GTGG
65 ACCTCGGCATGTGA
* * *
41362613 CTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATATAAAAGAAGT
1 C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAAT
41362678 ACCTCGGCATGTGA
65 ACCTCGGCATGTGA
* *
41362692 CCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAACGAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATA
*
41362757 CCTCGGCATGTGT
66 CCTCGGCATGTGA
* ** *
41362770 CCGAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAGAACAGAAATTTAAACGAAAT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-AACAGAAATTTAAAAGAAAT
*
41362834 ACCTCGGCATGTGT
65 ACCTCGGCATGTGA
** *
41362848 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAGAACAGAAATTTAAACGAAAT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-AACAGAAATTTAAAAGAAAT
* *
41362912 ACCTCGGTATGTGT
65 ACCTCGGCATGTGA
*
41362926 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATA
41362991 CCTCGGCA--TGA
66 CCTCGGCATGTGA
* * * *
41363002 CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTAAAAAATAGAAATTGAAAA
1 -CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAA
41363061 ATATTTCTTG
Statistics
Matches: 1062, Mismatches: 113, Indels: 85
0.84 0.09 0.07
Matches are distributed among these distances:
72 1 0.00
73 52 0.05
74 3 0.00
75 225 0.21
76 60 0.06
77 135 0.13
78 355 0.33
79 132 0.12
80 51 0.05
81 9 0.01
83 38 0.04
84 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (78 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATA
CCTCGGCATGTGA
Found at i:41363940 original size:18 final size:17
Alignment explanation
Indices: 41363917--41364011 Score: 95
Period size: 17 Copynumber: 5.5 Consensus size: 17
41363907 TTCATCTTAA
*
41363917 TTTTTTTCTTTTTTTTG
1 TTTTTTTTTTTTTTTTG
*
41363934 TTTTTTTTGTTTTTTTG
1 TTTTTTTTTTTTTTTTG
*
41363951 --TTTTTTGTTTTTTTG
1 TTTTTTTTTTTTTTTTG
* *
41363966 TTTCTTTCTATTTTTTTG
1 TTT-TTTTTTTTTTTTTG
41363984 TTTTTTATTATTTTTTATTG
1 TTTTTT-TT-TTTTTT-TTG
41364004 TTTTTTTT
1 TTTTTTTT
41364012 GTCTCCTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
15 15 0.23
17 19 0.29
18 16 0.24
19 7 0.11
20 9 0.14
ACGTcount: A:0.04, C:0.03, G:0.07, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTTG
Found at i:41363992 original size:15 final size:16
Alignment explanation
Indices: 41363926--41364010 Score: 82
Period size: 15 Copynumber: 4.9 Consensus size: 16
41363916 ATTTTTTTCT
*
41363926 TTTTTTTGTTTTTTTTG
1 TTTTTTTG-TTTTTTTA
*
41363943 TTTTTTTG-TTTTTTG
1 TTTTTTTGTTTTTTTA
41363958 TTTTTTTGTTTCTTTCTA
1 TTTTTTTGTTT-TTT-TA
41363976 TTTTTTTGTTTTTTATTA
1 TTTTTTTG-TTTTT-TTA
41363994 TTTTTTATTGTTTTTTT
1 -TTTTT-TTGTTTTTTT
41364011 TGTCTCCTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
15 15 0.25
16 2 0.03
17 11 0.18
18 15 0.25
19 14 0.23
20 3 0.05
ACGTcount: A:0.05, C:0.02, G:0.08, T:0.85
Consensus pattern (16 bp):
TTTTTTTGTTTTTTTA
Found at i:41364013 original size:9 final size:9
Alignment explanation
Indices: 41363917--41364013 Score: 96
Period size: 9 Copynumber: 11.0 Consensus size: 9
41363907 TTCATCTTAA
*
41363917 TTTTTTTCT
1 TTTTTTTGT
41363926 TTTTTTTGT
1 TTTTTTTGT
41363935 TTTTTTTG-
1 TTTTTTTGT
41363943 TTTTTTTG-
1 TTTTTTTGT
41363951 -TTTTTTG-
1 TTTTTTTGT
41363958 TTTTTTTGT
1 TTTTTTTGT
* *
41363967 TTCTTTCT-A
1 TT-TTTTTGT
41363976 TTTTTTTGT
1 TTTTTTTGT
*
41363985 TTTTTATTAT
1 TTTTT-TTGT
41363995 TTTTTATTGT
1 TTTTT-TTGT
41364005 TTTTTTTGT
1 TTTTTTTGT
41364014 CTCCTTTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
7 7 0.09
8 19 0.25
9 29 0.38
10 21 0.28
ACGTcount: A:0.04, C:0.03, G:0.08, T:0.85
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:41364024 original size:1 final size:1
Alignment explanation
Indices: 41363917--41364011 Score: 64
Period size: 1 Copynumber: 95.0 Consensus size: 1
41363907 TTCATCTTAA
* * * * * * * * *
41363917 TTTTTTTCTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTGTTTTTTTGTTTCTTTCTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
41363982 TGTTTTTTATTATTTTTTATTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41364012 GTCTCCTTTT
Statistics
Matches: 66, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.04, C:0.03, G:0.07, T:0.85
Consensus pattern (1 bp):
T
Found at i:41372711 original size:4 final size:4
Alignment explanation
Indices: 41372702--41372728 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41372692 AATTTTTCTA
41372702 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
41372729 GGCAATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41375066 original size:23 final size:25
Alignment explanation
Indices: 41375039--41375089 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
41375029 TTAATATATA
41375039 TATATTAT-TTAGTTCAAA-TTT-TT
1 TATA-TATGTTAGTTCAAAGTTTGTT
*
41375062 TATATATGTTATTTCAAAGTTTGTT
1 TATATATGTTAGTTCAAAGTTTGTT
41375087 TAT
1 TAT
41375090 TTTTAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 13 0.54
24 3 0.12
25 5 0.21
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (25 bp):
TATATATGTTAGTTCAAAGTTTGTT
Found at i:41375166 original size:26 final size:27
Alignment explanation
Indices: 41375135--41375196 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
41375125 ATATTATATG
41375135 TTATTTTAACTTGCTTTGTAAATTA-T
1 TTATTTTAACTTGCTTTGTAAATTATT
*
41375161 TTATTTTAACTTGCTTTGTATATTATT
1 TTATTTTAACTTGCTTTGTAAATTATT
41375188 TTATTTTAA
1 TTATTTTAA
41375197 GTTTTTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 24 0.71
27 10 0.29
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (27 bp):
TTATTTTAACTTGCTTTGTAAATTATT
Found at i:41375209 original size:27 final size:28
Alignment explanation
Indices: 41375117--41375215 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 28
41375107 TTAAAATTCC
41375117 TCTTT-TATATATTATATGTTATTTTAACT
1 TCTTTGTATATATTAT-T-TTATTTTAACT
41375146 TGCTTTGTA-A-ATTA-TTTATTTTAACT
1 T-CTTTGTATATATTATTTTATTTTAACT
*
41375172 TGCTTTG--TATATTATTTTATTTTAAGT
1 T-CTTTGTATATATTATTTTATTTTAACT
41375199 T-TTTGTATATATTATTT
1 TCTTTGTATATATTATTT
41375216 GGTTTAAATA
Statistics
Matches: 62, Mismatches: 1, Indels: 16
0.78 0.01 0.20
Matches are distributed among these distances:
25 5 0.08
26 22 0.35
27 23 0.37
29 5 0.08
30 5 0.08
31 2 0.03
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (28 bp):
TCTTTGTATATATTATTTTATTTTAACT
Found at i:41375792 original size:17 final size:18
Alignment explanation
Indices: 41375760--41375793 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41375750 GTTCTTGTGT
41375760 GTATTGTATTGCTTATTG
1 GTATTGTATTGCTTATTG
*
41375778 GTATT-TATTGGTTATT
1 GTATTGTATTGCTTATT
41375794 TTTCGTTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (18 bp):
GTATTGTATTGCTTATTG
Found at i:41380567 original size:19 final size:18
Alignment explanation
Indices: 41380539--41380605 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 18
41380529 ACGTTAGCAA
41380539 TTAATTAATTTTTATATTT
1 TTAA-TAATTTTTATATTT
*
41380558 TTAATCAA-TTTTA-AATT
1 TTAAT-AATTTTTATATTT
* *
41380575 TAAAAATATTTTTATATTT
1 TTAATA-ATTTTTATATTT
41380594 TTAA-AATTTTTA
1 TTAATAATTTTTA
41380606 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.03
17 14 0.36
18 12 0.31
19 12 0.31
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATAATTTTTATATTT
Found at i:41380593 original size:36 final size:36
Alignment explanation
Indices: 41380546--41380617 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
41380536 CAATTAATTA
41380546 ATTTTTATATTTTTAATCAA-TTTT-AAATTTAAAAAT
1 ATTTTTATATTTTTAA--AATTTTTAAAATTTAAAAAT
41380582 ATTTTTATATTTTTAAAATTTTTAAAATTTAAAAAT
1 ATTTTTATATTTTTAAAATTTTTAAAATTTAAAAAT
41380618 TAATTAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 2 0.06
35 4 0.12
36 28 0.82
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (36 bp):
ATTTTTATATTTTTAAAATTTTTAAAATTTAAAAAT
Found at i:41380616 original size:17 final size:17
Alignment explanation
Indices: 41380566--41380618 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
41380556 TTTTAATCAA
41380566 TTTT-AAATTTAAAAATAT
1 TTTTAAAATTT-AAAA-AT
* * *
41380584 TTTTATATTTTTAAAAT
1 TTTTAAAATTTAAAAAT
41380601 TTTTAAAATTTAAAAAT
1 TTTTAAAATTTAAAAAT
41380618 T
1 T
41380619 AATTAATTGC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 17 0.61
18 7 0.25
19 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAAATTTAAAAAT
Found at i:41387886 original size:43 final size:43
Alignment explanation
Indices: 41387835--41388153 Score: 387
Period size: 43 Copynumber: 7.5 Consensus size: 43
41387825 GCTAAAGGTT
*
41387835 ATGACCTTTAGCGAG-GCTTTTCCCACAAACGTCGCTATAGACC
1 ATGACCTTTAGCG-GCGCTTTTCCCACAAACGCCGCTATAGACC
* *
41387878 ATAACCTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACC
* *
41387921 ATGACCTTTAGCGGTGATTTTCCCACAAACGCCGCTATAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACC
* * *
41387964 ATGACCTTTAGCGGCGCTTTTACCAAAAATGCCGCTATAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACC
* * * * * **
41388007 ATGACCTTTAGCGGTGATTTTGCCACAAATG-CGCTAAAGGTC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACC
* * *
41388049 ATGACCTTTAGCGGCGCCTTTTCCCACAAATGCCGTTATAGGCC
1 ATGACCTTTAGCGGCG-CTTTTCCCACAAACGCCGCTATAGACC
* * *
41388093 ATGACCTTTAGCGGTGCTTCT-CC-C-AATGCCGCTATAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACC
*
41388133 ATGACTTTTAGCGGCGCTTTT
1 ATGACCTTTAGCGGCGCTTTT
41388154 TTTACAAACG
Statistics
Matches: 241, Mismatches: 32, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
40 32 0.13
41 1 0.00
42 26 0.11
43 159 0.66
44 23 0.10
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACC
Found at i:41387925 original size:86 final size:86
Alignment explanation
Indices: 41387835--41388153 Score: 432
Period size: 86 Copynumber: 3.7 Consensus size: 86
41387825 GCTAAAGGTT
* * *
41387835 ATGACCTTTAGCGAG-GCTTTTCCCACAAACGTCGCTATAGACCATAACCTTTAGCGGCGCTTTT
1 ATGACCTTTAGCG-GTGATTTTCCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTT
*
41387899 ACCACAAACGCCGCTATAGACC
65 ACCACAAATGCCGCTATAGACC
41387921 ATGACCTTTAGCGGTGATTTTCCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTA
1 ATGACCTTTAGCGGTGATTTTCCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTA
*
41387986 CCAAAAATGCCGCTATAGACC
66 CCACAAATGCCGCTATAGACC
* * * **
41388007 ATGACCTTTAGCGGTGATTTTGCCACAAATG-CGCTAAAGGTCATGACCTTTAGCGGCGCCTTTT
1 ATGACCTTTAGCGGTGATTTTCCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCG-CTTTT
* * *
41388071 CCCACAAATGCCGTTATAGGCC
65 ACCACAAATGCCGCTATAGACC
* * * *
41388093 ATGACCTTTAGCGGTGCTTCT-CC-C-AATGCCGCTATAGACCATGACTTTTAGCGGCGCTTTT
1 ATGACCTTTAGCGGTGATTTTCCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTT
41388154 TTTACAAACG
Statistics
Matches: 210, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
83 9 0.04
84 24 0.11
85 27 0.13
86 150 0.71
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (86 bp):
ATGACCTTTAGCGGTGATTTTCCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTA
CCACAAATGCCGCTATAGACC
Found at i:41388498 original size:21 final size:21
Alignment explanation
Indices: 41388474--41388565 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
41388464 TTCTGCTCTG
41388474 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
41388495 CTCTGCTTCTCTCGCTGCTA-C
1 CTCTGCTTCCCTCGCTGC-AGC
* * * * *
41388516 CTTTACTTCTCTCGCTACTGC
1 CTCTGCTTCCCTCGCTGCAGC
*
41388537 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
41388558 ATCTGCTT
1 CTCTGCTT
41388566 TAAGCTACAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
21 57 0.98
22 1 0.02
ACGTcount: A:0.05, C:0.43, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Done.