Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 39 of 64
Found at i:6124438 original size:15 final size:15
Alignment explanation
Indices: 6124418--6124448 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6124408 ATTTTATTTG
6124418 TATTTTTGTATTTTT
1 TATTTTTGTATTTTT
6124433 TATTTTTGTATTTTT
1 TATTTTTGTATTTTT
6124448 T
1 T
6124449 TTCGATTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (15 bp):
TATTTTTGTATTTTT
Found at i:6125519 original size:11 final size:11
Alignment explanation
Indices: 6125503--6125527 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6125493 ATTTTTCAAC
6125503 AAAAAAATATA
1 AAAAAAATATA
6125514 AAAAAAATATA
1 AAAAAAATATA
6125525 AAA
1 AAA
6125528 TGGGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATATA
Found at i:6129979 original size:10 final size:10
Alignment explanation
Indices: 6129964--6129991 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6129954 ATAATGGGAG
6129964 AAAGAAAAAA
1 AAAGAAAAAA
6129974 AAAGAAAAAA
1 AAAGAAAAAA
6129984 AAAGAAAA
1 AAAGAAAA
6129992 TGGAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:6130817 original size:48 final size:49
Alignment explanation
Indices: 6130727--6130822 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 49
6130717 TAAGAAGCCC
* *
6130727 ATGAACGATGATCAAGTGATGAAAGATGAAATTTTTATTGAGA-GGCTT
1 ATGAACGATGATCAAATGATGAAAGATGAAATTTTTACTGAGATGGCTT
*
6130775 ATGAGCGATGATCAAATGAT-AGAAGAT-AGAATTTATT-CTGAGATGGCT
1 ATGAACGATGATCAAATGATGA-AAGATGA-AATTT-TTACTGAGATGGCT
6130823 AGTGCTAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
47 2 0.05
48 33 0.80
49 6 0.15
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (49 bp):
ATGAACGATGATCAAATGATGAAAGATGAAATTTTTACTGAGATGGCTT
Found at i:6131239 original size:20 final size:20
Alignment explanation
Indices: 6131214--6131251 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6131204 TTGAGATTTA
6131214 TTGAATAAGAACCTTTGAGT
1 TTGAATAAGAACCTTTGAGT
* *
6131234 TTGAATGAGAAGCTTTGA
1 TTGAATAAGAACCTTTGA
6131252 ATTTTTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGAATAAGAACCTTTGAGT
Found at i:6131951 original size:20 final size:20
Alignment explanation
Indices: 6131926--6131969 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
6131916 AATTAGCCCA
6131926 TTTTA-TTTGTATTTTTGTAT
1 TTTTATTTTGTA-TTTTGTAT
6131946 TTTTATTTTGTATTTTGTAT
1 TTTTATTTTGTATTTTGTAT
6131966 TTTT
1 TTTT
6131970 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTTATTTTGTATTTTGTAT
Found at i:6131959 original size:7 final size:7
Alignment explanation
Indices: 6131931--6131968 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
6131921 GCCCATTTTA
6131931 TTTGTATT
1 TTTGTA-T
6131939 TTTGTAT
1 TTTGTAT
6131946 TTT-TAT
1 TTTGTAT
6131952 TTTGTAT
1 TTTGTAT
6131959 TTTGTAT
1 TTTGTAT
6131966 TTT
1 TTT
6131969 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (7 bp):
TTTGTAT
Found at i:6131963 original size:28 final size:27
Alignment explanation
Indices: 6131931--6131983 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
6131921 GCCCATTTTA
6131931 TTTGTATTTTTGTATTTTTATTTTGTAT
1 TTTGTATTTTTGTATTTTT-TTTTGTAT
*
6131959 TTTGTATTTTTTTATTTTTTTTTGT
1 TTTGTATTTTTGTATTTTTTTTTGT
6131984 TAACTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.79
Consensus pattern (27 bp):
TTTGTATTTTTGTATTTTTTTTTGTAT
Found at i:6131981 original size:20 final size:19
Alignment explanation
Indices: 6131926--6131983 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
6131916 AATTAGCCCA
6131926 TTTTATTTGTATTTTTGTAT
1 TTTTATTT-TATTTTTGTAT
*
6131946 TTTTATTTTGTATTTTGTATTT
1 TTTTATTTTAT-TTTTGTA--T
6131968 TTTTATTTT-TTTTTGT
1 TTTTATTTTATTTTTGT
6131984 TAACTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 21 0.62
21 1 0.03
22 10 0.29
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (19 bp):
TTTTATTTTATTTTTGTAT
Found at i:6133015 original size:9 final size:9
Alignment explanation
Indices: 6132991--6133024 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
6132981 AAAAAAATAT
6132991 ATATAAAAA
1 ATATAAAAA
*
6133000 AT-GAAAAA
1 ATATAAAAA
6133008 ATATAAAAA
1 ATATAAAAA
6133017 ATATAAAA
1 ATATAAAA
6133025 TGGGAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
ATATAAAAA
Found at i:6135956 original size:25 final size:25
Alignment explanation
Indices: 6135886--6135958 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
6135876 ATACTACGTA
* ****
6135886 CAGAAACACCATTCAACAATGTGCT
1 CAGAAACACCATTTAACAAACCACT
* * *
6135911 CAGACACACCCTTTAATAAACCACT
1 CAGAAACACCATTTAACAAACCACT
*
6135936 CAGAAACACCATTTAGCAAACCA
1 CAGAAACACCATTTAACAAACCA
6135959 TTCAACATAT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.32, G:0.08, T:0.18
Consensus pattern (25 bp):
CAGAAACACCATTTAACAAACCACT
Found at i:6136092 original size:80 final size:78
Alignment explanation
Indices: 6135950--6136198 Score: 320
Period size: 80 Copynumber: 3.1 Consensus size: 78
6135940 AACACCATTT
* *
6135950 AGCAAACCATTCAACATATGATTCAGCCCTCCAATATCATACAAAACCATTCAGCAAAACAATAT
1 AGCAAACCATTCAACATATGATTCAGCCCTCTAATATCATACAATACCATTCA-C-AAACAATAT
6136015 CAGACAATAAGGTTC
64 CAGACAATAAGGTTC
* * *
6136030 AGCAAACCATTTAGCATATGATTCAATCCC-CTAATATCATACAATACCATTCGACAATACAATA
1 AGCAAACCATTCAACATATGATTC-AGCCCTCTAATATCATACAATACCATTC-ACAA-ACAATA
* *
6136094 TCATACAACAAGGTTC
63 TCAGACAATAAGGTTC
* * * * *
6136110 AGCAAACCATTCAACACACGATTCAGCCCTCTAATATCATACAATACCATTCAATAAAAAAAATC
1 AGCAAACCATTCAACATATGATTCAGCCCTCTAATATCATACAATACCATTC-ACAAACAATATC
*
6136175 AGATAATAAGGTTC
65 AGACAATAAGGTTC
6136189 AGCAAACCAT
1 AGCAAACCAT
6136199 AATATTTAAG
Statistics
Matches: 146, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
79 33 0.23
80 108 0.74
81 5 0.03
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (78 bp):
AGCAAACCATTCAACATATGATTCAGCCCTCTAATATCATACAATACCATTCACAAACAATATCA
GACAATAAGGTTC
Found at i:6137723 original size:165 final size:166
Alignment explanation
Indices: 6137523--6137845 Score: 377
Period size: 165 Copynumber: 2.0 Consensus size: 166
6137513 AAAATTTATT
* * ** **
6137523 TATTGAAGGCGTTTGTCAGTAAAAGATGACTTTAATAAT-TTCAAAATTTTTTTAAGGGAAAATT
1 TATTGAAGGCGTTTGTCAATAAAAGACGACTTTAATAATCTT-AAAAAATTTTTAAGAAAAAATT
* * * * * *
6137587 ATTGAAGGC-ATGTATTAT-TAACAAATGCCTTCAATAATTATGTACTAAGTTT-AAAGGAATTA
65 ATTGAAGGCGGT-TATTATCTAA-AAACGCCTTCAATAATTATCTACAAAATTTAAAAAGAATTA
6137649 TTAAAGGTATTTTTATAGAATAAACGCCTTCTATAACCA
128 TTAAAGGTATTTTTATAGAATAAACGCCTTCTATAACCA
* *
6137688 TATTGAAGGCGTTT-TCCAATAGAAGACGCCTTTAATAATCTTAAAAAATTTTTAAGAAAAAATT
1 TATTGAAGGCGTTTGT-CAATAAAAGACGACTTTAATAATCTTAAAAAATTTTTAAGAAAAAATT
* * * * *
6137752 ATTGACGGCGGTTGTTATCTAAAAACGTCTTTATTAATTATCTACAAAATTTAAAAAGAATTATT
65 ATTGAAGGCGGTTATTATCTAAAAACGCCTTCAATAATTATCTACAAAATTTAAAAAGAATTATT
* * *
6137817 AAAGGTATTTTTCTTGAATATACGCCTTC
130 AAAGGTATTTTTATAGAATAAACGCCTTC
6137846 AATTACCGTG
Statistics
Matches: 131, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
164 1 0.01
165 87 0.66
166 43 0.33
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (166 bp):
TATTGAAGGCGTTTGTCAATAAAAGACGACTTTAATAATCTTAAAAAATTTTTAAGAAAAAATTA
TTGAAGGCGGTTATTATCTAAAAACGCCTTCAATAATTATCTACAAAATTTAAAAAGAATTATTA
AAGGTATTTTTATAGAATAAACGCCTTCTATAACCA
Found at i:6140115 original size:9 final size:9
Alignment explanation
Indices: 6140101--6140161 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
6140091 AAATTTTCCA
6140101 AAAAATTTT
1 AAAAATTTT
*
6140110 AAAAATTCTA
1 AAAAATT-TT
6140120 AAAAATCTTT
1 AAAAAT-TTT
6140130 CAAAAATCTTT
1 -AAAAAT-TTT
*
6140141 -AAAATTAT
1 AAAAATTTT
*
6140149 AAAAAATTT
1 AAAAATTTT
6140158 AAAA
1 AAAA
6140162 TTTAAAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 2 0.05
9 22 0.51
10 8 0.19
11 11 0.26
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATTTT
Found at i:6140123 original size:10 final size:9
Alignment explanation
Indices: 6140100--6140262 Score: 55
Period size: 10 Copynumber: 16.6 Consensus size: 9
6140090 GAAATTTTCC
6140100 AAAAAATTT
1 AAAAAATTT
*
6140109 TAAAAATTCT
1 AAAAAATT-T
6140119 AAAAAATCTTT
1 AAAAAA--TTT
*
6140130 CAAAAATCTT
1 AAAAAAT-TT
*
6140140 -TAAAATTAT
1 AAAAAATT-T
6140149 AAAAAATTT
1 AAAAAATTT
6140158 --AAAATTT
1 AAAAAATTT
*
6140165 AAAACAA-TA
1 AAAA-AATTT
*
6140174 AAAAAATTCA
1 AAAAAATT-T
6140184 AAAACAATTTTT
1 AAAA-AA--TTT
* *
6140196 TAAAAATTCA
1 AAAAAATT-T
6140206 AAAAAATTCT
1 AAAAAATT-T
*
6140216 AAAATAATTAA
1 AAAA-AATT-T
6140227 AAAACAATTTT
1 AAAA-AA-TTT
*
6140238 AGAAAATTT
1 AAAAAATTT
6140247 GAAAAAAATTT
1 --AAAAAATTT
6140258 AAAAA
1 AAAAA
6140263 TTCAAAACAA
Statistics
Matches: 118, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
7 7 0.06
8 3 0.03
9 33 0.28
10 35 0.30
11 31 0.26
12 7 0.06
13 2 0.02
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAAATTT
Found at i:6140198 original size:32 final size:32
Alignment explanation
Indices: 6140162--6140224 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
6140152 AAATTTAAAA
6140162 TTTAAAACAAT-AAAAAAATTCAAAAACAATTT
1 TTTAAAA-AATCAAAAAAATTCAAAAACAATTT
* * *
6140194 TTTAAAAATTCAAAAAAATTCTAAAATAATT
1 TTTAAAAAATCAAAAAAATTCAAAAACAATT
6140225 AAAAAACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (32 bp):
TTTAAAAAATCAAAAAAATTCAAAAACAATTT
Found at i:6140219 original size:43 final size:42
Alignment explanation
Indices: 6140172--6140269 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 42
6140162 TTTAAAACAA
**
6140172 TAAAAAAATTCAAAAACAATTTTTTAAAAATTCAAAAAAATT
1 TAAAAAAATTCAAAAACAATTTTAGAAAAATTCAAAAAAATT
* * * *
6140214 CTAAAATAATTAAAAAACAATTTTAGAAAATTTGAAAAAAATT
1 -TAAAAAAATTCAAAAACAATTTTAGAAAAATTCAAAAAAATT
6140257 T--AAAAATTCAAAA
1 TAAAAAAATTCAAAA
6140270 CAACAATCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 10 0.21
42 1 0.02
43 36 0.77
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (42 bp):
TAAAAAAATTCAAAAACAATTTTAGAAAAATTCAAAAAAATT
Found at i:6140254 original size:11 final size:10
Alignment explanation
Indices: 6140158--6140262 Score: 70
Period size: 10 Copynumber: 10.2 Consensus size: 10
6140148 TAAAAAATTT
6140158 AAAATTTAAA
1 AAAATTTAAA
*
6140168 ACAA--TAAA
1 AAAATTTAAA
*
6140176 AAAATTCAAA
1 AAAATTTAAA
**
6140186 AACAATTTTTTA
1 AA-AA-TTTAAA
*
6140198 AAAATTCAAA
1 AAAATTTAAA
6140208 AAAATTCTAAA
1 AAAATT-TAAA
* *
6140219 ATAATTAAAA
1 AAAATTTAAA
* *
6140229 AACAATTTTAG
1 AA-AATTTAAA
6140240 AAAATTTGAAA
1 AAAATTT-AAA
6140251 AAAATTTAAA
1 AAAATTTAAA
6140261 AA
1 AA
6140263 TTCAAAACAA
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
8 7 0.10
10 31 0.44
11 27 0.39
12 5 0.07
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:6140398 original size:9 final size:9
Alignment explanation
Indices: 6140337--6140526 Score: 125
Period size: 9 Copynumber: 19.7 Consensus size: 9
6140327 ACAATTTTTC
6140337 AAAAATTCTA
1 AAAAATT-TA
* *
6140347 AAAAGTCTA
1 AAAAATTTA
6140356 AAAAACTTTCA
1 AAAAA-TTT-A
6140367 AAAAATTTTTA
1 AAAAA--TTTA
*
6140378 GAAAAA-TAA
1 -AAAAATTTA
6140387 AAAAATTTA
1 AAAAATTTA
*
6140396 AAAATTTTA
1 AAAAATTTA
6140405 AAAAATTTTA
1 AAAAA-TTTA
6140415 AAAAATTTA
1 AAAAATTTA
6140424 AAAGAATTTAA
1 AAA-AATTT-A
*
6140435 AAAACATATA
1 AAAA-ATTTA
6140445 AAAAA-TTA
1 AAAAATTTA
6140453 CAAAAATTCTTA
1 -AAAAA-T-TTA
*
6140465 AAAAAATTA
1 AAAAATTTA
*
6140474 TAAAATTCTA
1 AAAAATT-TA
*
6140484 AAAACTTTAA
1 AAAAATTT-A
6140494 AAAAATATTA
1 AAAAAT-TTA
*
6140504 AGAAA-TTA
1 AAAAATTTA
*
6140512 AAAAATTTT
1 AAAAATTTA
6140521 AAAAAT
1 AAAAAT
6140527 GCTTGAAATT
Statistics
Matches: 143, Mismatches: 20, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
8 14 0.10
9 52 0.36
10 45 0.31
11 21 0.15
12 11 0.08
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTTA
Found at i:6140399 original size:10 final size:10
Alignment explanation
Indices: 6140354--6140525 Score: 96
Period size: 10 Copynumber: 17.6 Consensus size: 10
6140344 CTAAAAAGTC
*
6140354 TAAAAAACTT
1 TAAAAAAATT
*
6140364 TCAAAAAATTTT
1 T-AAAAAA-ATT
*
6140376 TAGAAAAA--
1 TAAAAAAATT
6140384 TAAAAAAATT
1 TAAAAAAATT
6140394 T--AAAAATT
1 TAAAAAAATT
*
6140402 TTAAAAAATT
1 TAAAAAAATT
*
6140412 TTAAAAAATT
1 TAAAAAAATT
*
6140422 TAAAAGAATT
1 TAAAAAAATT
*
6140432 TAAAAAACATA
1 TAAAAAA-ATT
6140443 T-AAAAAA-T
1 TAAAAAAATT
*
6140451 TACAAAAATTCT
1 TA-AAAAAAT-T
6140463 TAAAAAAA-T
1 TAAAAAAATT
*
6140472 T-ATAAAATT
1 TAAAAAAATT
*
6140481 CT-AAAAACTT
1 -TAAAAAAATT
6140491 TAAAAAAATAT
1 TAAAAAAAT-T
*
6140502 T-AAGAAA-T
1 TAAAAAAATT
*
6140510 TAAAAAATTT
1 TAAAAAAATT
6140520 TAAAAA
1 TAAAAA
6140526 TGCTTGAAAT
Statistics
Matches: 127, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
8 23 0.18
9 9 0.07
10 68 0.54
11 21 0.17
12 6 0.05
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:6140408 original size:20 final size:19
Alignment explanation
Indices: 6140384--6140525 Score: 101
Period size: 19 Copynumber: 7.3 Consensus size: 19
6140374 TTTAGAAAAA
6140384 TAAAAAAATTTAAAAATTT
1 TAAAAAAATTTAAAAATTT
* *
6140403 TAAAAAATTTTAAAAAATT
1 TAAAAAAATTTAAAAATTT
* ***
6140422 TAAAAGAATTTAAAAAACA
1 TAAAAAAATTTAAAAATTT
*
6140441 TATAAAAAATTACAAAAATTCT
1 TA-AAAAAATT-TAAAAATT-T
*
6140463 TAAAAAAA-TTATAAAATTC
1 TAAAAAAATTTA-AAAATTT
* *
6140482 T-AAAAACTTTAAAAAAATAT
1 TAAAAAAATTT--AAAAATTT
* *
6140502 T-AAGAAATTAAAAAATTT
1 TAAAAAAATTTAAAAATTT
6140520 TAAAAA
1 TAAAAA
6140526 TGCTTGAAAT
Statistics
Matches: 94, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
18 13 0.14
19 41 0.44
20 26 0.28
21 12 0.13
22 2 0.02
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (19 bp):
TAAAAAAATTTAAAAATTT
Found at i:6140426 original size:38 final size:39
Alignment explanation
Indices: 6140356--6140525 Score: 134
Period size: 38 Copynumber: 4.4 Consensus size: 39
6140346 AAAAAGTCTA
* *
6140356 AAAAACTTTCAAAAAATTTTTAGAAAA-A-TAAAAAAATTT
1 AAAAA-TTTTAAAAAA-TTTTAAAAAATATTAAAAAAATTT
*
6140395 AAAAATTTTAAAAAATTTTAAAAAAT-TTAAAAGAATTT
1 AAAAATTTTAAAAAATTTTAAAAAATATTAAAAAAATTT
* * ** * *
6140433 AAAAAACATATAAAAAATTACAAAAATTCTTAAAAAAA-TT
1 -AAAAA-TTTTAAAAAATTTTAAAAAATATTAAAAAAATTT
* * * * *
6140473 ATAAAATTCTAAAAACTTTAAAAAAATATT-AAGAAATTA
1 A-AAAATTTTAAAAAATTTTAAAAAATATTAAAAAAATTT
6140512 AAAAATTTTAAAAA
1 AAAAATTTTAAAAA
6140526 TGCTTGAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 15
0.76 0.14 0.11
Matches are distributed among these distances:
37 9 0.09
38 36 0.34
39 30 0.29
40 22 0.21
41 8 0.08
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (39 bp):
AAAAATTTTAAAAAATTTTAAAAAATATTAAAAAAATTT
Found at i:6140739 original size:17 final size:17
Alignment explanation
Indices: 6140701--6140744 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
6140691 AAAACTAAAA
**
6140701 TAAAAAATA-AATCTTT
1 TAAAAAATATAATAATT
6140717 TGAAAAAATATAATAATT
1 T-AAAAAATATAATAATT
6140735 TAAAAAATAT
1 TAAAAAATAT
6140745 TTAAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 17 0.71
18 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAAAATATAATAATT
Found at i:6141114 original size:10 final size:10
Alignment explanation
Indices: 6141099--6141177 Score: 52
Period size: 10 Copynumber: 8.0 Consensus size: 10
6141089 TCCAAATTTA
6141099 AAAATTTTTT
1 AAAATTTTTT
*
6141109 AAAATTTGTT
1 AAAATTTTTT
* *
6141119 ATAATTTTTC
1 AAAATTTTTT
***
6141129 AAAAAAATTT
1 AAAATTTTTT
*
6141139 AGAATTTTTT
1 AAAATTTTTT
* *
6141149 ACATTTTTTT
1 AAAATTTTTT
**
6141159 TGAA-TTTTT
1 AAAATTTTTT
6141168 AAAATTTTTT
1 AAAATTTTTT
6141178 GAGAAATTTG
Statistics
Matches: 48, Mismatches: 20, Indels: 2
0.69 0.29 0.03
Matches are distributed among these distances:
9 7 0.15
10 41 0.85
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:6141155 original size:49 final size:49
Alignment explanation
Indices: 6141102--6141232 Score: 115
Period size: 49 Copynumber: 2.7 Consensus size: 49
6141092 AAATTTAAAA
6141102 ATTTTTTAAAATTTGTTATAATTTTTCAAAAAAATTT-AG-AATTTTTTAC
1 ATTTTTTAAAATTT-TTATAATTTTTCAAAAAAATTTGAGAAATTTTTT-C
** * ** * *
6141151 ATTTTTTTTGAATTTTTAAAATTTTT-TGAGAAATTTGAGAAATTTTTTG
1 A-TTTTTTAAAATTTTTATAATTTTTCAAAAAAATTTGAGAAATTTTTTC
* * *
6141200 GTTATTTAAATTTTTTTATAATTTTTCAAAAAA
1 ATTTTTTAAA-ATTTTTATAATTTTTCAAAAAA
6141233 TGTTTTATTA
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
48 13 0.21
49 26 0.43
50 22 0.36
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (49 bp):
ATTTTTTAAAATTTTTATAATTTTTCAAAAAAATTTGAGAAATTTTTTC
Found at i:6141163 original size:20 final size:20
Alignment explanation
Indices: 6141140--6141177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6141130 AAAAAATTTA
* *
6141140 GAATTTTTTACATTTTTTTT
1 GAATTTTTAAAATTTTTTTT
6141160 GAATTTTTAAAATTTTTT
1 GAATTTTTAAAATTTTTT
6141178 GAGAAATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
GAATTTTTAAAATTTTTTTT
Found at i:6141687 original size:23 final size:23
Alignment explanation
Indices: 6141661--6141704 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
6141651 TCACTTAGAT
6141661 ATTC-TATGTTTGGTTTTTATTCC
1 ATTCATATGTTT-GTTTTTATTCC
* *
6141684 ATTCATTTGTTTTTTTTTATT
1 ATTCATATGTTTGTTTTTATT
6141705 AAAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (23 bp):
ATTCATATGTTTGTTTTTATTCC
Found at i:6142878 original size:11 final size:11
Alignment explanation
Indices: 6142861--6142913 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 11
6142851 GTTTACAAAG
6142861 CTTAAAAATTT
1 CTTAAAAATTT
*
6142872 TTTAAAAATATT
1 CTTAAAAAT-TT
6142884 CTTAAAAA-TT
1 CTTAAAAATTT
*
6142894 C-TAAAAAATT
1 CTTAAAAATTT
6142904 C-TAAAAATTT
1 CTTAAAAATTT
6142914 AAAATAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 6 0.16
10 14 0.38
11 8 0.22
12 9 0.24
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
CTTAAAAATTT
Found at i:6142904 original size:20 final size:19
Alignment explanation
Indices: 6142872--6142917 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
6142862 TTAAAAATTT
6142872 TTTAAAAATATTCTTAAAAA
1 TTTAAAAATATTC-TAAAAA
6142892 TTCTAAAAA-ATTCTAAAAA
1 TT-TAAAAATATTCTAAAAA
6142911 TTTAAAA
1 TTTAAAA
6142918 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 6 0.24
21 6 0.24
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTAAAAATATTCTAAAAA
Found at i:6142922 original size:20 final size:19
Alignment explanation
Indices: 6142872--6142929 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
6142862 TTAAAAATTT
*
6142872 TTTAAAAATATTCTTAAAAA
1 TTTAAAAAAATTC-TAAAAA
6142892 TTCT-AAAAAATTCTAAAAA
1 TT-TAAAAAAATTCTAAAAA
6142911 TTTAAAATAAATT-TAAAAA
1 TTTAAAA-AAATTCTAAAAA
6142930 AATTCTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 17 0.50
20 15 0.44
21 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTAAAAAAATTCTAAAAA
Found at i:6142980 original size:10 final size:10
Alignment explanation
Indices: 6142874--6142986 Score: 89
Period size: 10 Copynumber: 11.5 Consensus size: 10
6142864 AAAAATTTTT
6142874 TAAAAATATTC
1 TAAAAA-ATTC
*
6142885 TTAAAAATTC
1 TAAAAAATTC
6142895 TAAAAAATTC
1 TAAAAAATTC
6142905 T-AAAAATT-
1 TAAAAAATTC
6142913 TAAAATAAATT-
1 T-AAA-AAATTC
6142924 TAAAAAAATTC
1 T-AAAAAATTC
*
6142935 TAGAAAA-T-
1 TAAAAAATTC
6142943 TAAAAAATTC
1 TAAAAAATTC
6142953 ---AAAATTC
1 TAAAAAATTC
*
6142960 AAAACAAAATTC
1 -TAA-AAAATTC
6142972 TAAAAAATTC
1 TAAAAAATTC
6142982 TAAAA
1 TAAAA
6142987 TTTTTCATTT
Statistics
Matches: 86, Mismatches: 5, Indels: 23
0.75 0.04 0.20
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 9 0.10
10 38 0.44
11 18 0.21
12 7 0.08
ACGTcount: A:0.61, C:0.08, G:0.01, T:0.30
Consensus pattern (10 bp):
TAAAAAATTC
Found at i:6143054 original size:39 final size:37
Alignment explanation
Indices: 6142965--6143055 Score: 92
Period size: 39 Copynumber: 2.4 Consensus size: 37
6142955 AATTCAAAAC
* * *
6142965 AAAATTCTAAAAAATTCTAAAATTTTTCATTTTTCTA
1 AAAATTCTAAAAAATTCTAAAATTTTACAATTTTCCA
* * *
6143002 AATAACTTTTAAAAATTTGTAAAATTTCTAACAATTTTCCA
1 AA-AA-TTCTAAAAAATTCTAAAATTT-T-ACAATTTTCCA
6143043 AAAATTCTAAAAA
1 AAAATTCTAAAAA
6143056 GTATAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
37 2 0.05
38 2 0.05
39 26 0.60
40 3 0.07
41 10 0.23
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (37 bp):
AAAATTCTAAAAAATTCTAAAATTTTACAATTTTCCA
Found at i:6143112 original size:18 final size:18
Alignment explanation
Indices: 6143085--6143124 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6143075 ACATTTTTAG
*
6143085 AAAAATAAAAAAGATT-AA
1 AAAAACAAAAAA-ATTGAA
6143103 AAAAACAAAAAAATTGAA
1 AAAAACAAAAAAATTGAA
6143121 AAAA
1 AAAA
6143125 GAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAACAAAAAAATTGAA
Found at i:6143189 original size:19 final size:19
Alignment explanation
Indices: 6143164--6143239 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
6143154 TAAAATATTC
6143164 TTAAAAAATTTATAA-AAT
1 TTAAAAAATTTATAAGAAT
*
6143182 TATAAAAACTTTA-AAGAAT
1 T-TAAAAAATTTATAAGAAT
*
6143201 TTAACAAAATTTAAAAGAAT
1 TTAA-AAAATTTATAAGAAT
*
6143221 TTTAAAAATTT-TAA-AAT
1 TTAAAAAATTTATAAGAAT
6143238 TT
1 TT
6143240 TCTAAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
17 5 0.10
18 8 0.16
19 28 0.56
20 9 0.18
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAAAAATTTATAAGAAT
Found at i:6143240 original size:8 final size:9
Alignment explanation
Indices: 6143154--6143266 Score: 82
Period size: 10 Copynumber: 11.7 Consensus size: 9
6143144 AAATAAAGAA
6143154 TAAAATATTCT
1 TAAAA-ATT-T
*
6143165 TAAAAAATT
1 TAAAAATTT
*
6143174 TATAAAATTA
1 TA-AAAATTT
*
6143184 TAAAAACTT
1 TAAAAATTT
6143193 TAAAGAATTT
1 TAAA-AATTT
*
6143203 AACAAAATTT
1 TA-AAAATTT
*
6143213 AAAAGAATTT
1 TAAA-AATTT
6143223 TAAAAATTT
1 TAAAAATTT
*
6143232 TAAAATTTT
1 TAAAAATTT
*
6143241 CTAAAAATTC
1 -TAAAAATTT
6143251 TAGAAAATTT
1 TA-AAAATTT
*
6143261 GAAAAA
1 TAAAAA
6143267 AAATTCAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
9 33 0.40
10 43 0.52
11 7 0.08
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (9 bp):
TAAAAATTT
Found at i:6143266 original size:9 final size:8
Alignment explanation
Indices: 6143167--6143239 Score: 56
Period size: 9 Copynumber: 8.0 Consensus size: 8
6143157 AATATTCTTA
6143167 AAAAATTT
1 AAAAATTT
6143175 ATAAAATTAT
1 A-AAAATT-T
6143185 AAAAACTTT
1 AAAAA-TTT
6143194 AAAGAATTT
1 AAA-AATTT
6143203 AACAAAATTT
1 -A-AAAATTT
6143213 AAAAGAATTTT
1 -AAA-AA-TTT
6143224 AAAAATTT
1 AAAAATTT
*
6143232 TAAAATTT
1 AAAAATTT
6143240 TCTAAAAATT
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
8 11 0.20
9 21 0.38
10 19 0.34
11 5 0.09
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (8 bp):
AAAAATTT
Found at i:6143577 original size:10 final size:11
Alignment explanation
Indices: 6143549--6143576 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
6143539 AATGTTTTTG
6143549 CATTTTTATTA
1 CATTTTTATTA
6143560 CATTTTTATTA
1 CATTTTTATTA
6143571 CATTTT
1 CATTTT
6143577 AAAGTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (11 bp):
CATTTTTATTA
Found at i:6143903 original size:20 final size:19
Alignment explanation
Indices: 6143850--6143951 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 19
6143840 AATGTTTCAT
*
6143850 ATTTTTA-ATTTTTTAATAA
1 ATTTTTATAATTTTTAA-AA
*
6143869 A-TTTTA-AAATTTTAAAA
1 ATTTTTATAATTTTTAAAA
6143886 ATTTGTTATAATTTTTAAAAA
1 ATTT-TTATAATTTTT-AAAA
* * *
6143907 AATTTTATAGTTTTTAAGA
1 ATTTTTATAATTTTTAAAA
**
6143926 ATTATTT-TGAATTTTGCAAA
1 ATT-TTTAT-AATTTTTAAAA
6143946 ATTTTT
1 ATTTTT
6143952 TGAGAAATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
17 3 0.05
18 14 0.21
19 13 0.20
20 29 0.44
21 7 0.11
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTTTATAATTTTTAAAA
Found at i:6143910 original size:22 final size:20
Alignment explanation
Indices: 6143850--6143923 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
6143840 AATGTTTCAT
* *
6143850 ATTTT-TAATTTTTTAATAA
1 ATTTTATAATTTTTAAAAAA
*
6143869 ATTTTA-AAATTTT-AAAAA
1 ATTTTATAATTTTTAAAAAA
*
6143887 TTTGTTATAATTTTTAAAAAA
1 ATT-TTATAATTTTTAAAAAA
*
6143908 ATTTTATAGTTTTTAA
1 ATTTTATAATTTTTAA
6143924 GAATTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.13
19 14 0.31
20 18 0.40
21 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTATAATTTTTAAAAAA
Found at i:6143932 original size:21 final size:20
Alignment explanation
Indices: 6143849--6143968 Score: 63
Period size: 20 Copynumber: 6.0 Consensus size: 20
6143839 AAATGTTTCA
6143849 TATTTT-TAATTTTTTAATAA-
1 TATTTTATAA-TTTTTAA-AAT
* *
6143869 -ATTTTAAAATTTTAAAAAT
1 TATTTTATAATTTTTAAAAT
* *
6143888 T-TGTTATAATTTTTAAAAA
1 TATTTTATAATTTTTAAAAT
* *
6143907 AATTTTATAGTTTTTAAGAAT
1 TATTTTATAATTTTTAA-AAT
* *
6143928 TATTTT-GAATTTTGCAAAAT
1 TATTTTATAATTTT-TAAAAT
* *
6143948 T-TTTTGAGAAATTTTAAAAT
1 TATTTT-ATAATTTTTAAAAT
6143968 T
1 T
6143969 TTGTTAGTTA
Statistics
Matches: 76, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.03
19 29 0.38
20 30 0.39
21 15 0.20
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (20 bp):
TATTTTATAATTTTTAAAAT
Found at i:6147503 original size:23 final size:21
Alignment explanation
Indices: 6147456--6147515 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
6147446 TACTTAAAAT
6147456 AAATAAATTATAAAAACCAATA
1 AAATAAATTATAAAAA-CAATA
6147478 AAATAGAATTATAAAAA-AACTAA
1 AAATA-AATTATAAAAACAA-T-A
*
6147501 AAATAAAATA-AAAAA
1 AAATAAATTATAAAAA
6147516 TCTCAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 7 0.21
22 10 0.29
23 17 0.50
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATAAATTATAAAAACAATA
Found at i:6147513 original size:20 final size:22
Alignment explanation
Indices: 6147488--6147534 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
6147478 AAATAGAATT
6147488 ATAAAAAAACT-AAAA-ATAAA
1 ATAAAAAAACTCAAAATATAAA
* *
6147508 ATAAAAAATCTCAAAATGTAAA
1 ATAAAAAAACTCAAAATATAAA
6147530 ATAAA
1 ATAAA
6147535 TCAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 4 0.17
22 9 0.39
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.19
Consensus pattern (22 bp):
ATAAAAAAACTCAAAATATAAA
Found at i:6147559 original size:18 final size:17
Alignment explanation
Indices: 6147538--6147588 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
6147528 AAATAAATCA
6147538 AAAATGAAATCAAAAATT
1 AAAATGAAAT-AAAAATT
* *
6147556 AAAATTAAAATTAAAATT
1 AAAA-TGAAATAAAAATT
6147574 AAAATAGAAA-AAAAA
1 AAAAT-GAAATAAAAA
6147589 AACCTACGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 5 0.19
18 17 0.63
19 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAATGAAATAAAAATT
Found at i:6147561 original size:6 final size:6
Alignment explanation
Indices: 6147550--6147578 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6147540 AATGAAATCA
6147550 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
6147579 AGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:6148360 original size:3 final size:3
Alignment explanation
Indices: 6148354--6148453 Score: 69
Period size: 3 Copynumber: 33.3 Consensus size: 3
6148344 AAAAATAAAA
* * * * *
6148354 AAT AAT AAT GAT GAT GAT AAT AAT AAT AAT AAT AAC AGT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
6148401 ATAT TAT ACT -AT AAT ACT AGT AAT AAT AAC AAT AAT AAT AAC ACAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
6148447 AAT AAT A
1 AAT AAT A
6148454 GAAATCGACT
Statistics
Matches: 76, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
2 3 0.04
3 69 0.91
4 4 0.05
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6148848 original size:55 final size:54
Alignment explanation
Indices: 6148789--6149047 Score: 189
Period size: 55 Copynumber: 4.7 Consensus size: 54
6148779 ACAGATATTG
*
6148789 AACCATAAGTCTAAAAAATGATTTGAACTGAGCAGAGATCAAATAACTAGGATTA
1 AACCATAAGTCTAAAAAATGATTTGGACTGAGCA-AGATCAAATAACTAGGATTA
** * ** * * *
6148844 AACCATAAGTCTAAAAAACAATTTGGACTAAGCCAAGATGTAATGATTGGGATTA
1 AACCATAAGTCTAAAAAATGATTTGGACTGAG-CAAGATCAAATAACTAGGATTA
* * * * * * * * * * * *
6148899 AACCACAAGTCAAAAAAATGATCTAGATTAAGCCGAGATCGAATGATTGGGATTG
1 AACCATAAGTCTAAAAAATGATTTGGACTGAG-CAAGATCAAATAACTAGGATTA
* * * *
6148954 AACCATAAGT-TAAAAAAATGATCTGGATTGAGCTAAGATCAAATAACTAAGATTG
1 AACCATAAGTCT-AAAAAATGATTTGGACTGAGC-AAGATCAAATAACTAGGATTA
* * *
6149009 AACTACAAGTC-AGAAGAATGATTTGGACTGAGCCAAGAT
1 AACCATAAGTCTA-AAAAATGATTTGGACTGAG-CAAGAT
6149048 TGAAAATGAG
Statistics
Matches: 163, Mismatches: 35, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
54 2 0.01
55 158 0.97
56 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (54 bp):
AACCATAAGTCTAAAAAATGATTTGGACTGAGCAAGATCAAATAACTAGGATTA
Found at i:6149856 original size:18 final size:18
Alignment explanation
Indices: 6149833--6149871 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6149823 TGTCTCCTTC
6149833 TTTTTCTACTTTTT-ATTT
1 TTTTTC-ACTTTTTCATTT
*
6149851 TTTTTCATTTTTTCATTT
1 TTTTTCACTTTTTCATTT
6149869 TTT
1 TTT
6149872 ATTTGCACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCACTTTTTCATTT
Found at i:6150195 original size:16 final size:15
Alignment explanation
Indices: 6150174--6150224 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 15
6150164 TTTTCTTTCA
6150174 TTTTTTCTTTGTTTTT
1 TTTTTTCTTT-TTTTT
6150190 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
6150205 CTCCTTTTTCTTTTTCTTT
1 -T--TTTTTCTTTTT-TTT
6150224 T
1 T
6150225 CATCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.16
16 11 0.35
18 12 0.39
19 3 0.10
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:6150200 original size:9 final size:9
Alignment explanation
Indices: 6150174--6150219 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
6150164 TTTTCTTTCA
6150174 TTTTTTC-T
1 TTTTTTCTT
*
6150182 TTGTTT-TT
1 TTTTTTCTT
6150190 TTTTTTCTT
1 TTTTTTCTT
*
6150199 TTTTTTCTC
1 TTTTTTCTT
*
6150208 CTTTTTCTT
1 TTTTTTCTT
6150217 TTT
1 TTT
6150220 CTTTTCATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
8 11 0.37
9 19 0.63
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:6150223 original size:12 final size:11
Alignment explanation
Indices: 6150164--6150224 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
6150154 CCCCGTCAAC
*
6150164 TTTTCTTTCATT
1 TTTTTTTTC-TT
6150176 TTTTCTTTGT-TT
1 TTTT-TTT-TCTT
6150188 TTTTTTTTCTT
1 TTTTTTTTCTT
*
6150199 TTTTTTCTCCTT
1 TTTTTT-TTCTT
6150211 TTTCTTTTTCTT
1 TTT-TTTTTCTT
6150223 TT
1 TT
6150225 CATCATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
10 1 0.02
11 11 0.27
12 23 0.56
13 5 0.12
14 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:6154893 original size:19 final size:18
Alignment explanation
Indices: 6154863--6154956 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 18
6154853 AATAAAATAG
*
6154863 AATAATAAAAAAAACTCAA
1 AATAAAAAAAAAAACT-AA
*
6154882 AATAAAATAAAAAACTCAA
1 AATAAAAAAAAAAACT-AA
*
6154901 AATGTAAAATAAAAAAA-TGA
1 AA--TAAAA-AAAAAAACTAA
*
6154921 AATAAAAAAATAAAAGTAA
1 AATAAAAAAA-AAAACTAA
6154940 AATAAAAAAGAAAAACT
1 AATAAAAAA-AAAAACT
6154957 TACGATCAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.05
18 9 0.14
19 35 0.56
20 4 0.06
21 6 0.10
22 6 0.10
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.16
Consensus pattern (18 bp):
AATAAAAAAAAAAACTAA
Found at i:6154923 original size:13 final size:13
Alignment explanation
Indices: 6154905--6154954 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
6154895 ACTCAAAATG
6154905 TAAAATAAAAAAA
1 TAAAATAAAAAAA
*
6154918 TGAAATAAAAAAA
1 TAAAATAAAAAAA
*
6154931 TAAAAGTAAAATAA
1 TAAAA-TAAAAAAA
*
6154945 -AAAAGAAAAA
1 TAAAATAAAAA
6154955 CTTACGATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 4 0.13
13 20 0.65
14 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:6162287 original size:28 final size:30
Alignment explanation
Indices: 6162255--6162312 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
6162245 AAATAATTGT
*
6162255 AGACTTATAAGTC-AA-GAATTTGAATATA
1 AGACTTACAAGTCAAACGAATTTGAATATA
*
6162283 AGACTTACAATTCATAACGAATTTGAATAT
1 AGACTTACAAGTCA-AACGAATTTGAATAT
6162313 GATATGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
30 2 0.08
31 12 0.48
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (30 bp):
AGACTTACAAGTCAAACGAATTTGAATATA
Found at i:6178363 original size:10 final size:10
Alignment explanation
Indices: 6178350--6178380 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
6178340 ATTATTTAAC
6178350 ATTAAAAAAA
1 ATTAAAAAAA
6178360 ATT-AAAAAA
1 ATTAAAAAAA
6178369 ATTAAAAAAA
1 ATTAAAAAAA
6178379 AT
1 AT
6178381 AATGATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:6178368 original size:9 final size:9
Alignment explanation
Indices: 6178354--6178378 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6178344 TTTAACATTA
6178354 AAAAAAATT
1 AAAAAAATT
6178363 AAAAAAATT
1 AAAAAAATT
6178372 AAAAAAA
1 AAAAAAA
6178379 ATAATGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:6178582 original size:47 final size:47
Alignment explanation
Indices: 6178491--6178584 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
6178481 AGAGTTTCTA
*
6178491 TTTTAAAAAATATTGATACTTTCAACTTTTTCCTAAAACGTTTTTTT
1 TTTTAAAAAATATTGATACTTTCAACTTTTTCCTAAAACATTTTTTT
*
6178538 TTTTAAGAAAA-ATTGATAC-TTCTAACTTTTT-CTCAAAATATTTTTTT
1 TTTTAA-AAAATATTGATACTTTC-AACTTTTTCCT-AAAACATTTTTTT
6178585 GAAAATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
46 5 0.12
47 33 0.79
48 4 0.10
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (47 bp):
TTTTAAAAAATATTGATACTTTCAACTTTTTCCTAAAACATTTTTTT
Found at i:6178711 original size:3 final size:3
Alignment explanation
Indices: 6178703--6178747 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
6178693 CAAATTATTC
*
6178703 TAA TAA TAA TAA TAA TAA TAA -AA GAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
6178748 ATAAGAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:6179500 original size:3 final size:3
Alignment explanation
Indices: 6179492--6179534 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
6179482 TGAAGTCAAA
* *
6179492 AAT AAT AAT AAT AAT TAT AAT AAT AAAT AAC AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
6179535 TGTATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:6179571 original size:20 final size:20
Alignment explanation
Indices: 6179537--6179575 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6179527 ATAAAATATG
6179537 TATATTAATAAATAAATAAA
1 TATATTAATAAATAAATAAA
**
6179557 TATATTAATTGATAAATAA
1 TATATTAATAAATAAATAA
6179576 TAATAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TATATTAATAAATAAATAAA
Found at i:6179571 original size:24 final size:25
Alignment explanation
Indices: 6179526--6179583 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
6179516 AAATAACAAT
6179526 AATAAAATATGTATATTAATAAATA
1 AATAAAATATGTATATTAATAAATA
*
6179551 AATAAATATAT-TA-ATTGATAAAT-
1 AATAAA-ATATGTATATTAATAAATA
6179574 AATAATAATA
1 AATAA-AATA
6179584 AAAATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.27
24 10 0.33
25 8 0.27
26 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (25 bp):
AATAAAATATGTATATTAATAAATA
Found at i:6179963 original size:44 final size:44
Alignment explanation
Indices: 6179829--6180083 Score: 288
Period size: 44 Copynumber: 5.9 Consensus size: 44
6179819 TTGATTAAGT
** *
6179829 TCCTCTAAGTAGAGGTTCAACGACTTTG-AAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAACAAAGC
* * *
6179872 TCTTCTAATA-AGAGGCTC-ACAACTTTG-GAAAAT-AACTAAAGC
1 TCCTCTAA-ACAGAGGCTCAACGACTTTGAAAAAATAAAC-AAAGC
** *
6179914 TCCTCTAATTAGAGGCTCAACGACTTTGAAAAAATAAATACAA-C
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAACA-AAGC
* * *
6179958 TCCTCTAAGCAGAGGCTCAACGACTTTGGAACAATAAACAAAGC
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAACAAAGC
* * **
6180002 TCCTTTAAACAGAGGTTCAATAACTTTGAAAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAACAAAGC
*
6180046 TCCTCTAAACAGAAGCTCAACGACTTTGAAAAAATAAA
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAA
6180084 TTACTCTTTA
Statistics
Matches: 177, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.02
42 33 0.19
43 24 0.14
44 113 0.64
45 4 0.02
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (44 bp):
TCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAACAAAGC
Found at i:6180065 original size:132 final size:129
Alignment explanation
Indices: 6179829--6180084 Score: 356
Period size: 132 Copynumber: 2.0 Consensus size: 129
6179819 TTGATTAAGT
* *
6179829 TCCTCTAAGTAGAGGTTCAACGACTTTGAAAAATAAACAAAGCTCTTCTAATAAGAGGCTCACAA
1 TCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCTTCTAATAAGAGGCTCACAA
* ** *
6179894 CTTTGGAAAATAACTAAAGCTCCTCTAATTAGAGGCTCAACGACTTTGAAAAAATAAATACAAC
66 CTTTGAAAAATAACTAAAGCTCCTCTAAACAGAAGCTCAACGACTTTGAAAAAATAAATACAAC
* *
6179958 TCCTCTAAGCAGAGGCTCAACGACTTTGGAACAATAAACAAAGCTCCTT-TAA-ACAGAGGTTCA
1 TCCTCTAAGCAGAGGCTCAACGACTTT-GAAAAATAAACAAAGCT-CTTCTAATA-AGAGGCTC-
*
6180021 ATAACTTTGAAAAAATAAAC-AAAGCTCCTCTAAACAGAAGCTCAACGACTTTGAAAAAATAAAT
62 ACAACTTTG-AAAAAT-AACTAAAGCTCCTCTAAACAGAAGCTCAACGACTTTGAAAAAATAAAT
6180085 TACTCTTTAA
Statistics
Matches: 112, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
129 26 0.23
130 26 0.23
131 11 0.10
132 46 0.41
133 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (129 bp):
TCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCTTCTAATAAGAGGCTCACAA
CTTTGAAAAATAACTAAAGCTCCTCTAAACAGAAGCTCAACGACTTTGAAAAAATAAATACAAC
Found at i:6181087 original size:11 final size:12
Alignment explanation
Indices: 6181057--6181134 Score: 62
Period size: 11 Copynumber: 6.8 Consensus size: 12
6181047 TTATCTTGAG
6181057 TTTTCCTTTTTCA
1 TTTT-CTTTTTCA
*
6181070 TTCTCTTTTTC-
1 TTTTCTTTTTCA
6181081 TTTTCTTTTTCA
1 TTTTCTTTTTCA
*
6181093 TATT-TTTTT-A
1 TTTTCTTTTTCA
6181103 -TTT-TTTTTCA
1 TTTTCTTTTTCA
6181113 TTTT-TTCATTTCA
1 TTTTCTT--TTTCA
6181126 TTTT-TTTTT
1 TTTTCTTTTT
6181135 TTTTTTTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.12
10 2 0.04
11 23 0.41
12 10 0.18
13 14 0.25
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:6190825 original size:43 final size:43
Alignment explanation
Indices: 6190737--6190826 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
6190727 AGAGTTTCTA
** *
6190737 TTTTAAGAAAAATTAATACTTTCAACTTTTTCTTAAATTTTTT
1 TTTTAAGAAAAATTAATACTTTCAACTTTTTCTTAAAAATATT
*
6190780 TTTTAAGAAAAATTGATACTTTCAAC-TTTTCTTCAAAAATATT
1 TTTTAAGAAAAATTAATACTTTCAACTTTTTCTT-AAAAATATT
6190823 TTTT
1 TTTT
6190827 TAAAATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 7 0.17
43 35 0.83
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (43 bp):
TTTTAAGAAAAATTAATACTTTCAACTTTTTCTTAAAAATATT
Found at i:6190865 original size:5 final size:5
Alignment explanation
Indices: 6190855--6190889 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
6190845 AAATCATTTA
6190855 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAA
6190890 AATACCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:6190867 original size:11 final size:11
Alignment explanation
Indices: 6190853--6190890 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
6190843 AAAAATCATT
6190853 TAAAAATAAAA
1 TAAAAATAAAA
6190864 T-AAAATAAAA
1 TAAAAATAAAA
6190874 TAAAAATAAAA
1 TAAAAATAAAA
6190885 TAAAAA
1 TAAAAA
6190891 ATACCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:6190937 original size:19 final size:19
Alignment explanation
Indices: 6190905--6190942 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
6190895 CAAATTATTC
6190905 TAATATAATCAATAAATAA
1 TAATATAATCAATAAATAA
6190924 TAATAATAAT-AATAAATAA
1 TAAT-ATAATCAATAAATAA
6190943 GAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATATAATCAATAAATAA
Found at i:6194917 original size:20 final size:19
Alignment explanation
Indices: 6194894--6194941 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
6194884 TATTTATATA
6194894 ATATAAAATATTAAAATTTT
1 ATATAAAAT-TTAAAATTTT
* * *
6194914 ATATATTAATTTTATATTTT
1 ATATA-AAATTTAAAATTTT
6194934 ATATAAAA
1 ATATAAAA
6194942 GTTATATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAAAATTTAAAATTTT
Found at i:6195012 original size:22 final size:23
Alignment explanation
Indices: 6194966--6195023 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
6194956 TTTATTTAGA
* *
6194966 TATAAAATATATAAAATATATTTTT
1 TATAAAATTTAT-ATATA-ATTTTT
*
6194991 TATTAAATTTATATATAATTTTT
1 TATAAAATTTATATATAATTTTT
6195014 TATAAAATTT
1 TATAAAATTT
6195024 TAAATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 15 0.52
24 4 0.14
25 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATAAAATTTATATATAATTTTT
Found at i:6195039 original size:25 final size:23
Alignment explanation
Indices: 6194979--6195039 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
6194969 AAAATATATA
*
6194979 AAATATATTTTTTATTAAA-TTT
1 AAATATATTTTTTATAAAATTTT
*
6195001 ATATATAATTTTTTATAAAATTTT
1 AAATAT-ATTTTTTATAAAATTTT
6195025 AAATTATATTATTTT
1 AAA-TATATT-TTTT
6195040 TTTATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 5 0.16
23 12 0.38
24 8 0.25
25 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATATATTTTTTATAAAATTTT
Found at i:6195051 original size:27 final size:28
Alignment explanation
Indices: 6194984--6195060 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 28
6194974 ATATAAAATA
*
6194984 TATTTTTTATTAAATTTATATATAATTTTT
1 TATTATTT-TTAAA-TTATATATAATTTTT
* * *
6195014 TATAAAATTTTAAATTATAT-TATTTTTT
1 TAT-TATTTTTAAATTATATATAATTTTT
**
6195042 TATTATTTTTGTATTATAT
1 TATTATTTTTAAATTATAT
6195061 CACTATATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
27 12 0.32
28 10 0.26
29 6 0.16
30 8 0.21
31 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTATTTTTAAATTATATATAATTTTT
Found at i:6204608 original size:3 final size:3
Alignment explanation
Indices: 6204602--6204635 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6204592 ATAATAATAA
6204602 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6204636 CTATTTGTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6206205 original size:14 final size:14
Alignment explanation
Indices: 6206188--6206218 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6206178 CTTTTTTCTT
*
6206188 TTTTATAAAATGTA
1 TTTTATAAAATATA
6206202 TTTTATAAAATATA
1 TTTTATAAAATATA
6206216 TTT
1 TTT
6206219 AAAAAGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTTATAAAATATA
Found at i:6206533 original size:31 final size:30
Alignment explanation
Indices: 6206498--6206558 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
6206488 GAAATATATG
* *
6206498 AAATTTTGAAATAATTTCATCTTTGATCTCT
1 AAATTTTGAAAGAATTTCAT-TTTAATCTCT
*
6206529 AAATTTTGAAAGAATTTTATTTTAATCTCT
1 AAATTTTGAAAGAATTTCATTTTAATCTCT
6206559 CATCTATCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (30 bp):
AAATTTTGAAAGAATTTCATTTTAATCTCT
Found at i:6206863 original size:25 final size:26
Alignment explanation
Indices: 6206835--6206884 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
6206825 TATCTTGATG
*
6206835 ATTTTTT-ATAAATATATATTAATAT
1 ATTTTTTAATAAAAATATATTAATAT
6206860 ATTTTTTCAATAAAAATATATTAAT
1 ATTTTTT-AATAAAAATATATTAAT
6206885 TCTAGTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTTTAATAAAAATATATTAATAT
Found at i:6207191 original size:14 final size:14
Alignment explanation
Indices: 6207172--6207198 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6207162 ATGATTTTAT
6207172 AAATAAAATAATTA
1 AAATAAAATAATTA
6207186 AAATAAAATAATT
1 AAATAAAATAATT
6207199 TTAAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAAATAATTA
Found at i:6207224 original size:31 final size:29
Alignment explanation
Indices: 6207167--6207254 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
6207157 TTTAGATGAT
* * *
6207167 TTTATAAATAAAATAATTAAAATAAAATAA
1 TTTAAAAATTAAA-AATCAAAATAAAATAA
* * *
6207197 TTTTAAATAATTAAGAATCAAATTAAAATTA
1 -TTTAAA-AATTAAAAATCAAAATAAAATAA
*
6207228 TTTAAAATTTAAAAATCAAAATAAAAT
1 TTTAAAAATTAAAAATCAAAATAAAAT
6207255 TTGAATCAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 18 0.38
30 6 0.13
31 18 0.38
32 5 0.11
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (29 bp):
TTTAAAAATTAAAAATCAAAATAAAATAA
Found at i:6207244 original size:29 final size:31
Alignment explanation
Indices: 6207185--6207255 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
6207175 TAAAATAATT
* *
6207185 AAAATAAAATAATTTTAAATAATTAAGAATC
1 AAAATAAAATTATTTTAAATAATTAAAAATC
* *
6207216 AAATTAAAATTA-TTTAAA-ATTTAAAAATC
1 AAAATAAAATTATTTTAAATAATTAAAAATC
6207245 AAAATAAAATT
1 AAAATAAAATT
6207256 TGAATCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 19 0.54
30 6 0.17
31 10 0.29
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (31 bp):
AAAATAAAATTATTTTAAATAATTAAAAATC
Found at i:6207726 original size:2 final size:2
Alignment explanation
Indices: 6207719--6207749 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6207709 AGTAAAAATA
6207719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6207750 AATACATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6208959 original size:3 final size:3
Alignment explanation
Indices: 6208951--6209003 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
6208941 AAGTTTTAAT
*
6208951 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6208999 TTA TT
1 TTA TT
6209004 GTTCTTAGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6210405 original size:3 final size:3
Alignment explanation
Indices: 6210397--6210424 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6210387 TGAAGATGAA
6210397 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6210425 GAACATGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6210631 original size:14 final size:14
Alignment explanation
Indices: 6210612--6210648 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
6210602 TGTGTTTCTT
6210612 CTGTTTGGTATATG
1 CTGTTTGGTATATG
*
6210626 CTGTTT-ATATATG
1 CTGTTTGGTATATG
6210639 CTGTTTGGTA
1 CTGTTTGGTA
6210649 AATAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.51
Consensus pattern (14 bp):
CTGTTTGGTATATG
Found at i:6214835 original size:28 final size:29
Alignment explanation
Indices: 6214781--6214840 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
6214771 AAAATTATAG
*
6214781 TAAAATATTTAATATGATACTTTAACT-T
1 TAAAAAATTTAATATGATACTTTAACTAT
6214809 TAAAAAATTTAATAT-AGTA-TTTAAACTAT
1 TAAAAAATTTAATATGA-TACTTT-AACTAT
6214838 TAA
1 TAA
6214841 TCTGTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.14
28 20 0.71
29 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAAATTTAATATGATACTTTAACTAT
Found at i:6216655 original size:3 final size:3
Alignment explanation
Indices: 6216647--6216677 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6216637 TTAATCTAAA
6216647 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6216678 TATTTGGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6217660 original size:21 final size:21
Alignment explanation
Indices: 6217634--6217681 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6217624 TGGACCGGTA
*
6217634 TTGACTCACCATTAATGGACG
1 TTGACTCACCATTAATCGACG
** *
6217655 TTGACTCACTGTTGATCGACG
1 TTGACTCACCATTAATCGACG
6217676 TTGACT
1 TTGACT
6217682 TGTCACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (21 bp):
TTGACTCACCATTAATCGACG
Found at i:6217866 original size:20 final size:19
Alignment explanation
Indices: 6217841--6217882 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6217831 TAAAATTTAT
* *
6217841 AATAATGAATGAATAAAATA
1 AATAATGAA-AAATAAAAAA
6217861 AATAATGAAAAATAAAAAA
1 AATAATGAAAAATAAAAAA
6217880 AAT
1 AAT
6217883 CACAAGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (19 bp):
AATAATGAAAAATAAAAAA
Found at i:6218676 original size:13 final size:15
Alignment explanation
Indices: 6218635--6218679 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
6218625 AATTTTCAAT
*
6218635 ATTCAAATAACAAAA
1 ATTCAAATAATAAAA
6218650 ATTCAAATAATAAAA
1 ATTCAAATAATAAAA
6218665 ATT-AAA-AATAAAA
1 ATTCAAATAATAAAA
6218678 AT
1 AT
6218680 AATAAGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 9 0.31
14 3 0.10
15 17 0.59
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
ATTCAAATAATAAAA
Found at i:6219042 original size:13 final size:13
Alignment explanation
Indices: 6219024--6219051 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6219014 TCTAGTTTTC
6219024 TTTATTCATTCAT
1 TTTATTCATTCAT
6219037 TTTATTCATTCAT
1 TTTATTCATTCAT
6219050 TT
1 TT
6219052 CTCCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTCATTCAT
Found at i:6227162 original size:44 final size:44
Alignment explanation
Indices: 6227070--6227164 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 44
6227060 GGACAGAATA
* * * * *
6227070 TTTTAAATTTTTTAAAAGTTGTTGAGCTTCTACTTAGAGGAGCC
1 TTTTAAATGTTTCAAAAGTTGTTGAGCCTCTACTTAAAGAAGCC
* **
6227114 TTTTAAATGTTTCAAAAGTTGTTGAGCCTCTGCTTAAAGAAGTT
1 TTTTAAATGTTTCAAAAGTTGTTGAGCCTCTACTTAAAGAAGCC
6227158 TTTTAAA
1 TTTTAAA
6227165 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (44 bp):
TTTTAAATGTTTCAAAAGTTGTTGAGCCTCTACTTAAAGAAGCC
Found at i:6227270 original size:36 final size:36
Alignment explanation
Indices: 6227185--6227270 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
6227175 TTATGGGGCT
* * *
6227185 TCTACTTAAAAGAATTTTTTTTTAAATTGTTAAGCC
1 TCTACTTAAATGAGTTTTTTTTTAAATTATTAAGCC
* * *
6227221 TCTACTTAGATGAGTTTTTTTTTTAATTATTGAGCC
1 TCTACTTAAATGAGTTTTTTTTTAAATTATTAAGCC
**
6227257 TCTGTTTAAATGAG
1 TCTACTTAAATGAG
6227271 CATTTATTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (36 bp):
TCTACTTAAATGAGTTTTTTTTTAAATTATTAAGCC
Found at i:6227885 original size:12 final size:13
Alignment explanation
Indices: 6227853--6227885 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6227843 CTAAAAAAAC
6227853 AAAAAAAAGTTTG
1 AAAAAAAAGTTTG
*
6227866 CAAAAAAA-TTTG
1 AAAAAAAAGTTTG
6227878 AAAAAAAA
1 AAAAAAAA
6227886 AAACTCTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAAAAAAGTTTG
Found at i:6228961 original size:114 final size:110
Alignment explanation
Indices: 6228782--6228997 Score: 317
Period size: 114 Copynumber: 1.9 Consensus size: 110
6228772 TGTTAGAAAT
*
6228782 ATTTTAGAATTTTTTTCAAATATAAGAAAAATTATTAATAAAAAATAAAATCACAAGTAGTGATT
1 ATTTTAGAATTTTTTTCAAACATAAGAAAAATTATTAATAAAAAATAAAATCACAAGTAGTGATT
* *
6228847 TTATTAAAAATATTTACATAATGAAATTTTTTAAAATATTGTAAAAGC
66 TTATT-AAAA-ATTTACATAAAGAAATTTTCT-AAATATTGTAAAAGC
* * *
6228895 ATTTTAGAATTTTTTTCAAACATAA-AAAAATAATATTAATAAAAAATAAAGTCATAAGTGGTGA
1 ATTTTAGAATTTTTTTCAAACATAAGAAAAAT--TATTAATAAAAAATAAAATCACAAGTAGTGA
*
6228959 TTTTATTGAAAATTTACATAAAGAAATTTTCTAAATATT
64 TTTTATTAAAAATTTACATAAAGAAATTTTCTAAATATT
6228998 TAGAATTTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
111 7 0.07
112 25 0.27
113 27 0.29
114 35 0.37
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (110 bp):
ATTTTAGAATTTTTTTCAAACATAAGAAAAATTATTAATAAAAAATAAAATCACAAGTAGTGATT
TTATTAAAAATTTACATAAAGAAATTTTCTAAATATTGTAAAAGC
Found at i:6241508 original size:16 final size:16
Alignment explanation
Indices: 6241481--6241524 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
6241471 TTTTTTCATT
6241481 TTTAAA-AATATTAAA
1 TTTAAATAATATTAAA
6241496 TTTAAATAATATTAAA
1 TTTAAATAATATTAAA
*
6241512 TTCAAATAATATT
1 TTTAAATAATATT
6241525 TCTTTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAATAATATTAAA
Found at i:6241704 original size:29 final size:28
Alignment explanation
Indices: 6241641--6241704 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
6241631 TTTAAAAAAA
6241641 TATAAATTTTTCTAAAAATTACAAAATTT
1 TATAAATTTTTCTAAAAATTA-AAAATTT
* *
6241670 TA-AAATTTTTTTAAAAAATT-ATAATTT
1 TATAAATTTTTCT-AAAAATTAAAAATTT
6241697 TATTAAAT
1 TA-TAAAT
6241705 AAATTCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 8 0.27
28 9 0.30
29 13 0.43
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
TATAAATTTTTCTAAAAATTAAAAATTT
Found at i:6241879 original size:36 final size:37
Alignment explanation
Indices: 6241820--6241907 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 37
6241810 GTTAAGAAAT
* *
6241820 ATTATTTTTTTAAAAAAGTAAATATCAAA-AAAT-AAA
1 ATTAATTTTTTAAAAAAGAAAATAT-AAATAAATCAAA
*
6241856 ATTAATTTTTTAAAATAA-AAAATATAAATAATTCAAA
1 ATTAATTTTTTAAAA-AAGAAAATATAAATAAATCAAA
*
6241893 ATTGATTATTTTAAA
1 ATTAATT-TTTTAAA
6241908 TTTGAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
35 3 0.07
36 23 0.52
37 11 0.25
38 7 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (37 bp):
ATTAATTTTTTAAAAAAGAAAATATAAATAAATCAAA
Found at i:6241968 original size:20 final size:18
Alignment explanation
Indices: 6241938--6241981 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6241928 AAATTTTAGG
* *
6241938 AAATTAATATTTTAAAAA
1 AAATTAAAATATTAAAAA
*
6241956 AAATTAAAATATTCAAAA
1 AAATTAAAATATTAAAAA
6241974 AAATTAAA
1 AAATTAAA
6241982 TGTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTAAAATATTAAAAA
Found at i:6249593 original size:2 final size:2
Alignment explanation
Indices: 6249586--6249621 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
6249576 TTTCATTGTA
6249586 AT AT AT AT AT AT AT AT AT AT AT AT ACT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
6249622 TTTTCAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6250665 original size:35 final size:35
Alignment explanation
Indices: 6250626--6250697 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
6250616 TTCGTTTTTG
* * *
6250626 AAAAATCTCAAAGTTTT-TCGAATATTTATTTTCAA
1 AAAAAACTCAAA-TTTTCTCAAATATCTATTTTCAA
6250661 AAAAAACTCAAATTTTCTCAAATATCTATTTTCAA
1 AAAAAACTCAAATTTTCTCAAATATCTATTTTCAA
6250696 AA
1 AA
6250698 GGCCTTAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (35 bp):
AAAAAACTCAAATTTTCTCAAATATCTATTTTCAA
Found at i:6252910 original size:142 final size:142
Alignment explanation
Indices: 6252654--6252929 Score: 498
Period size: 142 Copynumber: 1.9 Consensus size: 142
6252644 AGAATGAATC
* *
6252654 TTGTATTTTTTCATTAAGTGTTTTTTTAATGTGTTATAGTATTTGATTATCTTGAATACTCTATT
1 TTGTATTCTTTCATTAAGTGTTTTTTTAATGTGTTATAGTATTTGATTATCTTCAATACTCTATT
* * *
6252719 AGTCTTTGGTAAGTGTCACAAACTGACTTAAGTGTATTTAAATAATAATTTTTCACCTAAAGTCA
66 AATCTTTGGTAAGTGTCACAAACTGACTTAAGTATATTTAAATAATAATTTCTCACCTAAAGTCA
6252784 TACAATGATAAA
131 TACAATGATAAA
6252796 TTGTATTCTTTCATTAAGTGTTTTTTTAATGTGTTATAGTATTTGATTATCTTCAATACTCTATT
1 TTGTATTCTTTCATTAAGTGTTTTTTTAATGTGTTATAGTATTTGATTATCTTCAATACTCTATT
*
6252861 AATCTTTGGTAAGTGTCACGAACTGACTTAAGTATATTTAAATAATAATTTCTCACCTAAAGTCA
66 AATCTTTGGTAAGTGTCACAAACTGACTTAAGTATATTTAAATAATAATTTCTCACCTAAAGTCA
6252926 TACA
131 TACA
6252930 GTGACAAAGT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 128 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (142 bp):
TTGTATTCTTTCATTAAGTGTTTTTTTAATGTGTTATAGTATTTGATTATCTTCAATACTCTATT
AATCTTTGGTAAGTGTCACAAACTGACTTAAGTATATTTAAATAATAATTTCTCACCTAAAGTCA
TACAATGATAAA
Found at i:6252972 original size:142 final size:142
Alignment explanation
Indices: 6252684--6252973 Score: 341
Period size: 142 Copynumber: 2.0 Consensus size: 142
6252674 TTTTTTTAAT
* *
6252684 GTGTTATAGTATTTGATTATCTTGAATACTCTATTAGTCTTTGGTAAGTGTCACAAACTGACTTA
1 GTGTTATAGTATTTGATTATCTTCAATACTCTATTAATCTTTGGTAAGTGTCACAAACTGACTTA
* * * ** *** **
6252749 AGTGTATTTAAATAATAATTTTTCACCTAAAGTCATACAATGATAAATTGTATTCTTTCATTAAG
66 AGTATATTTAAATAATAATTTCTCACCTAAAGTCATACAATGACAAATTGTAGACTCGAAGCAAG
****** *
6252814 TGTTTTTTTAAT
131 TGACACAATAAG
*
6252826 GTGTTATAGTATTTGATTATCTTCAATACTCTATTAATCTTTGGTAAGTGTCACGAACTGACTTA
1 GTGTTATAGTATTTGATTATCTTCAATACTCTATTAATCTTTGGTAAGTGTCACAAACTGACTTA
*
6252891 AGTATATTTAAATAATAATTTCTCACCTAAAGTCATACAGTGACAAAGTT-TAAGAC-CGAAGCA
66 AGTATATTTAAATAATAATTTCTCACCTAAAGTCATACAATGACAAA-TTGT-AGACTCGAAGCA
* *
6252954 CGTGACACAATCAG
129 AGTGACACAATAAG
6252968 GTGTTA
1 GTGTTA
6252974 ATAGCATGGA
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
142 119 0.97
143 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (142 bp):
GTGTTATAGTATTTGATTATCTTCAATACTCTATTAATCTTTGGTAAGTGTCACAAACTGACTTA
AGTATATTTAAATAATAATTTCTCACCTAAAGTCATACAATGACAAATTGTAGACTCGAAGCAAG
TGACACAATAAG
Found at i:6255193 original size:35 final size:35
Alignment explanation
Indices: 6255147--6255216 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
6255137 AAATTTTGTT
6255147 TCCTTTACTTTCTTTTCCTTTCGCTCCCCTCGATC
1 TCCTTTACTTTCTTTTCCTTTCGCTCCCCTCGATC
* *
6255182 TCCTTTACTTTCTTTTTCTTTCGCTCCCTTCGATC
1 TCCTTTACTTTCTTTTCCTTTCGCTCCCCTCGATC
6255217 AAAATACACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.06, C:0.37, G:0.06, T:0.51
Consensus pattern (35 bp):
TCCTTTACTTTCTTTTCCTTTCGCTCCCCTCGATC
Found at i:6257083 original size:17 final size:17
Alignment explanation
Indices: 6257050--6257088 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6257040 AGGTAAAAGA
6257050 AAATACAAAAAATAAAT
1 AAATACAAAAAATAAAT
*
6257067 AAATGACAAATAA-AAAT
1 AAAT-ACAAAAAATAAAT
6257084 AAATA
1 AAATA
6257089 ATGAAGAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.60
18 7 0.35
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATACAAAAAATAAAT
Found at i:6261487 original size:49 final size:49
Alignment explanation
Indices: 6261414--6261515 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
6261404 TAACTCTGAT
* *
6261414 CTTTATTTTTTATGGATCTTCATTCTCCCTTAATTTTCAAATCTTTAAC
1 CTTTATTTTTTAGGGATCTCCATTCTCCCTTAATTTTCAAATCTTTAAC
*
6261463 CTTTATTTTTTAGGGATCTCCATTCTCCCTTGATTTTCAAATCTTTAAC
1 CTTTATTTTTTAGGGATCTCCATTCTCCCTTAATTTTCAAATCTTTAAC
6261512 CTTT
1 CTTT
6261516 CAAGTTAAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.52
Consensus pattern (49 bp):
CTTTATTTTTTAGGGATCTCCATTCTCCCTTAATTTTCAAATCTTTAAC
Found at i:6262343 original size:16 final size:16
Alignment explanation
Indices: 6262324--6262359 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6262314 AAATTAAAAT
6262324 AATTAAAAAAACTGAA
1 AATTAAAAAAACTGAA
* *
6262340 AATTAAAAAATCTTAA
1 AATTAAAAAAACTGAA
6262356 AATT
1 AATT
6262360 TTCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (16 bp):
AATTAAAAAAACTGAA
Found at i:6262529 original size:17 final size:16
Alignment explanation
Indices: 6262506--6262553 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
6262496 TAAAACTACA
*
6262506 AAAAAATTCCAAAATTT
1 AAAAAATT-AAAAATTT
*
6262523 TAAAAATATAAAAATTT
1 AAAAAAT-TAAAAATTT
6262540 AAAAAATTTAAAAA
1 AAAAAA-TTAAAAA
6262554 GTAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 24 0.92
18 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATTAAAAATTT
Found at i:6264391 original size:11 final size:11
Alignment explanation
Indices: 6264375--6264409 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6264365 TTAATATTTT
*
6264375 TATAAAATATG
1 TATAAAATATA
*
6264386 TATAAAAAATA
1 TATAAAATATA
6264397 TATAAAATATA
1 TATAAAATATA
6264408 TA
1 TA
6264410 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
TATAAAATATA
Found at i:6272589 original size:24 final size:25
Alignment explanation
Indices: 6272541--6272602 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
6272531 TATTGATAAA
*
6272541 AATTATTATAATATTTTTATATCAT
1 AATTATTAAAATATTTTTATATCAT
* *
6272566 AATTATAAAAATATTTTT-TCTCAT
1 AATTATTAAAATATTTTTATATCAT
6272590 AATTGATTAAAAT
1 AATT-ATTAAAAT
6272603 TATTATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (25 bp):
AATTATTAAAATATTTTTATATCAT
Found at i:6272603 original size:59 final size:59
Alignment explanation
Indices: 6272509--6272643 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 59
6272499 CTTATTATTG
* * *
6272509 AATTGTAAAAATA-ATTTTCTATTATTGATAAAAATTATTATAAT-AT-TTTTATATCAT
1 AATTATAAAAATATTTTTTCTATAATTGATAAAAATTATTATAATAATGTTTT-TATCAT
*
6272566 AATTATAAAAATATTTTTTCTCATAATTGATTAAAATTATTATAATAATGTTTTTATCAT
1 AATTATAAAAATATTTTTTCT-ATAATTGATAAAAATTATTATAATAATGTTTTTATCAT
* *
6272626 AATTTTGAAAATATTTTT
1 AATTATAAAAATATTTTT
6272644 ATGAATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 12 0.18
58 6 0.09
59 22 0.32
60 24 0.35
61 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (59 bp):
AATTATAAAAATATTTTTTCTATAATTGATAAAAATTATTATAATAATGTTTTTATCAT
Found at i:6272664 original size:60 final size:59
Alignment explanation
Indices: 6272539--6272664 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 59
6272529 ATTATTGATA
** *
6272539 AAAATTATTATAATATTTTTATATCATAATTATAAAAATATTTTTTCTCATAATTGATT
1 AAAATTATTATAATATTTTTATATCATAATTATAAAAATATTTTTTCGAATAATTGAAT
* * *
6272598 AAAATTATTATAATAATGTTTT-TATCATAATTTTGAAAATATTTTTAT-GAAT-ATTTAAT
1 AAAATTATTATAAT-AT-TTTTATATCATAATTATAAAAATATTTTT-TCGAATAATTGAAT
6272657 AAGAATTA
1 AA-AATTA
6272665 GACATGTGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
59 21 0.37
60 31 0.54
61 5 0.09
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (59 bp):
AAAATTATTATAATATTTTTATATCATAATTATAAAAATATTTTTTCGAATAATTGAAT
Found at i:6272879 original size:14 final size:14
Alignment explanation
Indices: 6272851--6272898 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
6272841 CATAAGATAT
**
6272851 TTATTAATTTTAAA
1 TTATTAATTAAAAA
6272865 TTATTAATTAAAAA
1 TTATTAATTAAAAA
6272879 TATATT--TTAAAAA
1 T-TATTAATTAAAAA
6272892 TTATTAA
1 TTATTAA
6272899 ATTATCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 4 0.14
13 8 0.28
14 13 0.45
15 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATTAATTAAAAA
Found at i:6275696 original size:16 final size:16
Alignment explanation
Indices: 6275677--6275712 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6275667 AATTTAAAAT
6275677 AATTAAAAAAACTGAA
1 AATTAAAAAAACTGAA
* *
6275693 AATTAAAAAATCTTAA
1 AATTAAAAAAACTGAA
6275709 AATT
1 AATT
6275713 TTCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (16 bp):
AATTAAAAAAACTGAA
Found at i:6286059 original size:24 final size:25
Alignment explanation
Indices: 6286011--6286072 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
6286001 TATTGATAAA
*
6286011 AATTATTATAATATTTTTATATCAT
1 AATTATTAAAATATTTTTATATCAT
* *
6286036 AATTATAAAAATATTTTT-TCTCAT
1 AATTATTAAAATATTTTTATATCAT
6286060 AATTGATTAAAAT
1 AATT-ATTAAAAT
6286073 TATTATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (25 bp):
AATTATTAAAATATTTTTATATCAT
Found at i:6286073 original size:59 final size:59
Alignment explanation
Indices: 6285979--6286113 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 59
6285969 CTTATTATTG
* * *
6285979 AATTGTAAAAATA-ATTTTCTATTATTGATAAAAATTATTATAAT-AT-TTTTATATCAT
1 AATTATAAAAATATTTTTTCTATAATTGATAAAAATTATTATAATAATGTTTT-TATCAT
*
6286036 AATTATAAAAATATTTTTTCTCATAATTGATTAAAATTATTATAATAATGTTTTTATCAT
1 AATTATAAAAATATTTTTTCT-ATAATTGATAAAAATTATTATAATAATGTTTTTATCAT
* *
6286096 AATTTTGAAAATATTTTT
1 AATTATAAAAATATTTTT
6286114 ATGAATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 12 0.18
58 6 0.09
59 22 0.32
60 24 0.35
61 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (59 bp):
AATTATAAAAATATTTTTTCTATAATTGATAAAAATTATTATAATAATGTTTTTATCAT
Found at i:6286134 original size:60 final size:59
Alignment explanation
Indices: 6286009--6286134 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 59
6285999 ATTATTGATA
** *
6286009 AAAATTATTATAATATTTTTATATCATAATTATAAAAATATTTTTTCTCATAATTGATT
1 AAAATTATTATAATATTTTTATATCATAATTATAAAAATATTTTTTCGAATAATTGAAT
* * *
6286068 AAAATTATTATAATAATGTTTT-TATCATAATTTTGAAAATATTTTTAT-GAAT-ATTTAAT
1 AAAATTATTATAAT-AT-TTTTATATCATAATTATAAAAATATTTTT-TCGAATAATTGAAT
6286127 AAGAATTA
1 AA-AATTA
6286135 GACATGTGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
59 21 0.37
60 31 0.54
61 5 0.09
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (59 bp):
AAAATTATTATAATATTTTTATATCATAATTATAAAAATATTTTTTCGAATAATTGAAT
Found at i:6289120 original size:25 final size:27
Alignment explanation
Indices: 6289082--6289131 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
6289072 ACAAAAAATA
6289082 AAAAAAATAAA-TTTTT-AAAATTTTT
1 AAAAAAATAAATTTTTTGAAAATTTTT
**
6289107 AAAAAAATTTATTTTTTGAAAATTT
1 AAAAAAATAAATTTTTTGAAAATTT
6289132 AAAATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 5 0.24
27 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAAAAATAAATTTTTTGAAAATTTTT
Found at i:6289156 original size:16 final size:16
Alignment explanation
Indices: 6289137--6289172 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6289127 AATTTAAAAT
6289137 AATTAAAAAAACTGAA
1 AATTAAAAAAACTGAA
* *
6289153 AATTAAAAAATCTTAA
1 AATTAAAAAAACTGAA
6289169 AATT
1 AATT
6289173 TTCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (16 bp):
AATTAAAAAAACTGAA
Found at i:6289672 original size:15 final size:15
Alignment explanation
Indices: 6289631--6289671 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
6289621 ACAAAATTGA
*
6289631 AAAAATTAAAATGTC
1 AAAAATTAAAAAGTC
*
6289646 AAAACTTAAAAAGT-
1 AAAAATTAAAAAGTC
6289660 AAAAATTAAAAA
1 AAAAATTAAAAA
6289672 AAATCTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (15 bp):
AAAAATTAAAAAGTC
Found at i:6290268 original size:19 final size:18
Alignment explanation
Indices: 6290245--6290289 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
6290235 AATTGTTTTG
6290245 ATTTTTTTT-AATTGTTCA
1 ATTTTTTTTGAATT-TTCA
*
6290263 ATTTTTTCTTGAATTTTTA
1 ATTTTTT-TTGAATTTTCA
6290282 ATTTTTTT
1 ATTTTTTT
6290290 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (18 bp):
ATTTTTTTTGAATTTTCA
Found at i:6298364 original size:25 final size:26
Alignment explanation
Indices: 6298321--6298374 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
6298311 AAATAATTAT
*
6298321 AATATTTTTATATCGTAATT-ATAAA
1 AATATTTTTATATCATAATTGATAAA
* * *
6298346 AATATTTTTTTCTCATAATTGATTAA
1 AATATTTTTATATCATAATTGATAAA
6298372 AAT
1 AAT
6298375 TATTATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (26 bp):
AATATTTTTATATCATAATTGATAAA
Found at i:6298377 original size:35 final size:35
Alignment explanation
Indices: 6298337--6298409 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
6298327 TTTATATCGT
* * *
6298337 AATTATAAAAAT-ATTTTTTTCTCATAATTGATTAA
1 AATTATAAAAATAATATTTTTATCATAATT-ATGAA
* *
6298372 AATTATTATAATAATATTTTTATCATAATTATGAA
1 AATTATAAAAATAATATTTTTATCATAATTATGAA
6298407 AAT
1 AAT
6298410 ATTTTTATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (35 bp):
AATTATAAAAATAATATTTTTATCATAATTATGAA
Done.