Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007973.1 Hibiscus syriacus cultivar Beakdansim tig00110410_pilon, 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: 1299094
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:378533 original size:5 final size:5
Alignment explanation
Indices: 378525--378562 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
378515 TAGATTAGGG
* *
378525 AGGTT AGGTT AGGTT AGGTT AGGTT AGGAT AGGAT AGG
1 AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT AGG
378563 GTGGTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32
Consensus pattern (5 bp):
AGGTT
Found at i:379669 original size:38 final size:38
Alignment explanation
Indices: 379608--379726 Score: 213
Period size: 38 Copynumber: 3.2 Consensus size: 38
379598 TTTATTTTGT
*
379608 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
379645 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
*
379683 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
379721 TCGGGT
1 TCGGGT
379727 TTAGGGTGAA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
37 10 0.13
38 69 0.87
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
Found at i:380322 original size:17 final size:17
Alignment explanation
Indices: 380300--380363 Score: 110
Period size: 17 Copynumber: 3.7 Consensus size: 17
380290 TATGGAATTG
380300 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
380317 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
380334 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
380352 GATTCCAATTCC
1 GATTCCAATTCC
380364 ATCATAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 29 0.64
18 16 0.36
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:392206 original size:21 final size:21
Alignment explanation
Indices: 392174--392234 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
392164 AGTCACTCGT
*
392174 CAGAAATGATCGATCCCTT-A
1 CAGAAAGGATCGATCCCTTAA
* * *
392194 GAGAAAAGGATCGGTCCCTCAA
1 CAG-AAAGGATCGATCCCTTAA
392216 CAGAAAGGATCGATCCCTT
1 CAGAAAGGATCGATCCCTT
392235 CTCTGTTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.84
22 3 0.09
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (21 bp):
CAGAAAGGATCGATCCCTTAA
Found at i:392231 original size:42 final size:41
Alignment explanation
Indices: 392136--392234 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
392126 TCTGTCAAGT
* **
392136 AAAGGATTGATCCCTTAGAGAAATAATCAGTCACTCGTCAG
1 AAAGGATCGATCCCTTAGAGAAATAATCAGTCACTCAACAG
* * *
392177 AAATGATCGATCCCTTAGAGAAA-AGGATCGGTCCCTCAACAG
1 AAAGGATCGATCCCTTAGAGAAATA--ATCAGTCACTCAACAG
392219 AAAGGATCGATCCCTT
1 AAAGGATCGATCCCTT
392235 CTCTGTTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.02
41 21 0.43
42 27 0.55
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (41 bp):
AAAGGATCGATCCCTTAGAGAAATAATCAGTCACTCAACAG
Found at i:401493 original size:37 final size:40
Alignment explanation
Indices: 401438--401536 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 40
401428 GATCGACCCC
* * *
401438 TTTTCGAAATGATCGATCTTTCGGGA-T-T-AACGATCCA
1 TTTTCAAAAGGATCGATCTCTCGGGAGTATGAACGATCCA
* * *
401475 TTTTCAAAAGGATTGATCTCTCGGGAGTAATGATCGATCCC
1 TTTTCAAAAGGATCGATCTCTCGGGAGT-ATGAACGATCCA
*
401516 TTTTCAAAAGGATCAATCTCT
1 TTTTCAAAAGGATCGATCTCT
401537 TGGAGAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 22 0.44
38 1 0.02
40 1 0.02
41 26 0.52
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (40 bp):
TTTTCAAAAGGATCGATCTCTCGGGAGTATGAACGATCCA
Found at i:401513 original size:41 final size:41
Alignment explanation
Indices: 401468--401555 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
401458 TCGGGATTAA
** *
401468 CGATCCATTTTCAAAAGGATTGATCTCTCGGGAG-TAATGAT
1 CGATCCATTTTCAAAAGGATCAATCTCT-GGGAGAAAATGAT
* *
401509 CGATCCCTTTTCAAAAGGATCAATCTCTTGGAGAAAATGAT
1 CGATCCATTTTCAAAAGGATCAATCTCTGGGAGAAAATGAT
401550 CGATCC
1 CGATCC
401556 TCGACAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 4 0.10
41 37 0.90
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
CGATCCATTTTCAAAAGGATCAATCTCTGGGAGAAAATGAT
Found at i:404970 original size:24 final size:24
Alignment explanation
Indices: 404938--404987 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
404928 TTAACGAATG
*
404938 TCCCGTTCTTCTTTCGGACAGAGT
1 TCCCGTTCTTCTTCCGGACAGAGT
404962 TCCCGTTCTTCTTCCGGACAGAGT
1 TCCCGTTCTTCTTCCGGACAGAGT
404986 TC
1 TC
404988 GAACAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.32, G:0.20, T:0.36
Consensus pattern (24 bp):
TCCCGTTCTTCTTCCGGACAGAGT
Found at i:414556 original size:113 final size:113
Alignment explanation
Indices: 414406--414638 Score: 376
Period size: 113 Copynumber: 2.1 Consensus size: 113
414396 GGTAAGTAGT
* **
414406 GTTGCGAAAACGAAATTCGTGTTGCGAATTTAAAGAATCGCGTTTTGAATTTAAAAACTGAGTTG
1 GTTGCGAAAACGAAATTCGCGTTGCGAATTTAAAGAATCGCGTTACGAATTTAAAAACTGAGTTG
* *
414471 TGAATAGTTGTGTTTACCTATATTGGTAATTAGCGTTGCGAAATTCGA
66 CGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGA
* ** *
414519 GTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAACTGAGTTG
1 GTTGCGAAAACGAAATTCGCGTTGCGAATTTAAAGAATCGCGTTACGAATTTAAAAACTGAGTTG
*
414584 CGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGT
66 CGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGA
414632 GTTGCGA
1 GTTGCGA
414639 TTTTGGAGAA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (113 bp):
GTTGCGAAAACGAAATTCGCGTTGCGAATTTAAAGAATCGCGTTACGAATTTAAAAACTGAGTTG
CGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGA
Found at i:417368 original size:32 final size:30
Alignment explanation
Indices: 417332--417400 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 30
417322 TTAAAGGTAC
417332 AAAATAGAAAAAAAATATAAACTTAAGGGACT
1 AAAATAGAAAAAAAA-A-AAACTTAAGGGACT
417364 AAAATAG---AAAAAAAAACTTAAGGGACT
1 AAAATAGAAAAAAAAAAAACTTAAGGGACT
417391 AAAATAGAAA
1 AAAATAGAAA
417401 TTACAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 21 0.62
28 1 0.03
29 5 0.15
32 7 0.21
ACGTcount: A:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (30 bp):
AAAATAGAAAAAAAAAAAACTTAAGGGACT
Found at i:418980 original size:18 final size:18
Alignment explanation
Indices: 418957--418994 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
418947 TGTGAATTGT
418957 TAATGATAATAATAATAA
1 TAATGATAATAATAATAA
* *
418975 TAATGATATTATTAATAA
1 TAATGATAATAATAATAA
418993 TA
1 TA
418995 TAAATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
TAATGATAATAATAATAA
Found at i:419023 original size:20 final size:20
Alignment explanation
Indices: 418968--419025 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
418958 AATGATAATA
* *
418968 ATAATAATAATGATATTATTA
1 ATAATAATAAT-ATAATATTT
418989 ATAAT-ATAA-AT-ATATTT
1 ATAATAATAATATAATATTT
419006 ATAATAATAATATAATATTT
1 ATAATAATAATATAATATTT
419026 TTGTAGACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 9 0.28
18 6 0.19
19 2 0.06
20 10 0.31
21 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATAATAATATAATATTT
Found at i:419058 original size:14 final size:14
Alignment explanation
Indices: 419039--419068 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
419029 TAGACTCGGA
419039 TAAAAACGAGTGTC
1 TAAAAACGAGTGTC
419053 TAAAAACGAGTGTC
1 TAAAAACGAGTGTC
419067 TA
1 TA
419069 CAAGGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (14 bp):
TAAAAACGAGTGTC
Found at i:422875 original size:18 final size:17
Alignment explanation
Indices: 422836--422878 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
422826 ATTATATGGA
422836 TATT-TTATTCACTTAT
1 TATTATTATTCACTTAT
* *
422852 TTTTATTATTCATGTTAT
1 TATTATTATTCA-CTTAT
422870 TATTATTAT
1 TATTATTAT
422879 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATTATTCACTTAT
Found at i:426521 original size:11 final size:11
Alignment explanation
Indices: 426507--426551 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
426497 AATAAAAAGG
426507 GCAAAAAAAAA
1 GCAAAAAAAAA
*
426518 GCAAAAAAAAG
1 GCAAAAAAAAA
426529 GCAAAAAAAGAA
1 GCAAAAAAA-AA
426541 -CAAAAAGAAAA
1 GCAAAAA-AAAA
426552 AAGAAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 27 0.90
12 3 0.10
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (11 bp):
GCAAAAAAAAA
Found at i:426523 original size:10 final size:9
Alignment explanation
Indices: 426510--426553 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
426500 AAAAAGGGCA
426510 AAAAAAAAG
1 AAAAAAAAG
426519 CAAAAAAAAGG
1 -AAAAAAAA-G
*
426530 CAAAAAAAG
1 AAAAAAAAG
*
426539 AACAAAAAG
1 AAAAAAAAG
426548 AAAAAA
1 AAAAAA
426554 GAAAAAGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 13 0.45
10 15 0.52
11 1 0.03
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:426526 original size:22 final size:22
Alignment explanation
Indices: 426500--426546 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
426490 TAATCAGAAT
*
426500 AAAAAGGGCAAAAAAA-AAGCAA
1 AAAAAAGGCAAAAAAAGAA-CAA
426522 AAAAAAGGCAAAAAAAGAACAA
1 AAAAAAGGCAAAAAAAGAACAA
426544 AAA
1 AAA
426547 GAAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAGGCAAAAAAAGAACAA
Found at i:427185 original size:22 final size:22
Alignment explanation
Indices: 427157--427200 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
427147 AGCTACCCCA
427157 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCGTTT-AGCATCAAATG
427179 TCAAACCGTTTAGCATCAAATG
1 TCAAACCGTTTAGCATCAAATG
427201 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (22 bp):
TCAAACCGTTTAGCATCAAATG
Found at i:428273 original size:36 final size:36
Alignment explanation
Indices: 428165--428288 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
428155 ATTGAAAACA
* * *
428165 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
428201 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
428238 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
428274 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
428289 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:428372 original size:66 final size:66
Alignment explanation
Indices: 428264--428420 Score: 210
Period size: 66 Copynumber: 2.4 Consensus size: 66
428254 TTTCGTCTAT
* **
428264 CTTGAGACAGTTTCCCTTGAAACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TTCT
1 CTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT-T
428327 CC
65 CC
* * *
428329 CTTGAGACAGTTACTCTTGAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTTT
1 CTTGAGACAGTTTCTCTTGAA-ACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTTT
428394 CC
65 CC
* *
428396 CTTGAGACCGTTTCTCATGAAACAA
1 CTTGAGACAGTTTCTCTTGAAACAA
428421 CATATATCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 19 0.24
66 32 0.40
67 27 0.34
68 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (66 bp):
CTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTTTC
C
Found at i:429248 original size:105 final size:105
Alignment explanation
Indices: 429063--429883 Score: 1181
Period size: 105 Copynumber: 8.0 Consensus size: 105
429053 GCACTCGAGG
* * * *
429063 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
429128 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
429169 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCATGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
429234 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
429274 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAATAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
429339 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
429379 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
**
429444 GCCAA--T----TT--C-A--AAGGATATTGGACTTTAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
429473 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCAGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
429538 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
429578 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
429643 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
429683 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
429743 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * ** *
429783 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCA
* * * *
429847 GAACCAATTTCAACTTCACGACGGAGGATATTAGACT
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
429884 TGGAACAATG
Statistics
Matches: 652, Mismatches: 45, Indels: 36
0.89 0.06 0.05
Matches are distributed among these distances:
94 84 0.13
96 1 0.00
97 1 0.00
99 4 0.01
100 82 0.13
101 3 0.00
102 4 0.01
103 6 0.01
104 3 0.00
105 389 0.60
106 75 0.12
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:429646 original size:304 final size:307
Alignment explanation
Indices: 429063--429883 Score: 1127
Period size: 304 Copynumber: 2.6 Consensus size: 307
429053 GCACTCGAGG
* * * *
429063 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
429128 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
65 AG-C-----CAACTTCACAAC-AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
429193 AAGGGACCGCTGCATGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
123 AAGGGACCGCTGCTTGTCAACAACAACTTCCCAA-TTCAGAGCCAATTTCAACTTCACAACGAAG
* * *
429258 GATATTGGACTTCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAATA
187 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACA
* * * *
429323 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
252 ACTTCCCAATCTAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
429379 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* **
429444 GCCAA-TT-TC-A-AAGGATATTGGACTTTAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
66 GCCAACTTCACAACAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
*
429505 GCAGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
131 GCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
429570 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
195 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
429635 ATCTAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
260 ATCTAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
429683 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AATTTCATTCAGA-TTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC--TCA-ATTTC
** * * *
429746 A-ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
63 AGA-GCCAACTTCACAAC-AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * ** * * *
429810 GGA-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAACCAATTTCAACTTCACGACGGAGG
126 GGACCG-CTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCAATTTCAACTTCACAACGAAGG
*
429874 ATATTAGACT
188 ATATTGGACT
429884 TGGAACAATG
Statistics
Matches: 456, Mismatches: 36, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
303 6 0.01
304 261 0.57
305 10 0.02
306 4 0.01
307 2 0.00
308 3 0.01
309 5 0.01
310 56 0.12
311 46 0.10
314 1 0.00
315 21 0.05
316 41 0.09
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (307 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAACTTCACAACAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
GCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAA
TCTAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:429826 original size:205 final size:211
Alignment explanation
Indices: 429454--429883 Score: 615
Period size: 205 Copynumber: 2.1 Consensus size: 211
429444 GCCAATTTCA
**
429454 AAGGATATTGGACTTTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCAGCTTGTCAACA
1 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCAGCTTGTCAACA
**
429519 ACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGC
66 ACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAC
* *
429584 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TCTAAGAGCCA
131 AAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTC-AAGAACCA
429647 ATTTCAACTTCACAACG
195 ATTTCAACTTCACAACG
*
429664 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACA
1 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCAGCTTGTCAACA
* ** *
429729 A-AA-TT-TC-AT-TCAGATTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACAC
66 ACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAC
* * ** *
429789 AAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAACCA
131 AAGTTCAACTTCACAACGAAGGGACCG-CTGCTTGTCAACAAACAACTTCCCAATTCAAGAACCA
*
429853 ATTTCAACTTCACGACG
195 ATTTCAACTTCACAACG
* *
429870 GAGGATATTAGACT
1 AAGGATATTGGACT
429884 TGGAACAATG
Statistics
Matches: 198, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
204 2 0.01
205 80 0.40
206 46 0.23
207 3 0.02
208 2 0.01
209 2 0.01
210 63 0.32
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (211 bp):
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCAGCTTGTCAACA
ACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAC
AAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTCAAGAACCAA
TTTCAACTTCACAACG
Found at i:430516 original size:37 final size:36
Alignment explanation
Indices: 430431--430532 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
430421 TTTCGTCCTA
430431 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
430466 -TAGGATTCAAACTCCTAAAGATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
430501 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
430533 GTTATACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 28 0.47
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:430961 original size:18 final size:17
Alignment explanation
Indices: 430922--430964 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
430912 ATTATATGGA
430922 TATT-TTATTCACTTAT
1 TATTATTATTCACTTAT
* *
430938 TTTTATTATTCATGTTAT
1 TATTATTATTCA-CTTAT
430956 TATTATTAT
1 TATTATTAT
430965 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATTATTCACTTAT
Found at i:431048 original size:41 final size:39
Alignment explanation
Indices: 430970--431050 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 39
430960 ATTATATGTA
* *
430970 TATATTTATATATTAAATTATTTTCATTTGATTTTTTAC
1 TATATTTATATATTAAATTATTTTCATTTAATATTTTAC
* *
431009 TATATTTAT-TATTATTATTATATATTTATTTAATATTTTAC
1 TATATTTATATATTA-AATTAT-T-TTCATTTAATATTTTAC
431050 T
1 T
431051 TACAAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 5 0.14
39 14 0.40
40 1 0.03
41 15 0.43
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (39 bp):
TATATTTATATATTAAATTATTTTCATTTAATATTTTAC
Found at i:431453 original size:2 final size:2
Alignment explanation
Indices: 431446--431471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
431436 TAATACTTTG
431446 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
431472 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:432155 original size:29 final size:29
Alignment explanation
Indices: 432121--432176 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
432111 CCTAACAACG
432121 AAATATTATCTG-TCAAGCACCCTTTCTTC
1 AAATATTATC-GATCAAGCACCCTTTCTTC
*
432150 AAATATTATCGATCTAGCACCCTTTCT
1 AAATATTATCGATCAAGCACCCTTTCT
432177 GACACAGCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (29 bp):
AAATATTATCGATCAAGCACCCTTTCTTC
Found at i:432616 original size:44 final size:45
Alignment explanation
Indices: 432538--432708 Score: 228
Period size: 44 Copynumber: 3.9 Consensus size: 45
432528 CAACTCAAAC
* *
432538 AATTAAATAATAAAAATATTAAGAAACAATATAAATAAAA-TCCAT
1 AATTAAATAAT-AAAACATTAAGAAACAAAATAAATAAAATTCCAT
*
432583 AATTAAATAATAAAACATTAAGAAACAAAATAAATAAAAAGTCCAT
1 AATTAAATAATAAAACATTAAGAAACAAAATAAAT-AAAATTCCAT
* *
432629 AATT--A-AATAAAATATTAAGAAACAAAATAAATAAAATTTTCAT
1 AATTAAATAATAAAACATTAAGAAACAAAATAAATAAAA-TTCCAT
432672 AATTAAAT-A-AAAACATTAAGAAACAAAATAAATAAAA
1 AATTAAATAATAAAACATTAAGAAACAAAATAAATAAAA
432709 ACATTAAGAA
Statistics
Matches: 114, Mismatches: 6, Indels: 13
0.86 0.05 0.10
Matches are distributed among these distances:
42 4 0.04
43 34 0.30
44 50 0.44
45 17 0.15
46 9 0.08
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (45 bp):
AATTAAATAATAAAACATTAAGAAACAAAATAAATAAAATTCCAT
Found at i:432652 original size:87 final size:86
Alignment explanation
Indices: 432550--432709 Score: 268
Period size: 87 Copynumber: 1.8 Consensus size: 86
432540 TTAAATAATA
*
432550 AAAATATTAAGAAACAATATAAATAAAA-TCCATAATTAAATAATAAAACATTAAGAAACAAAAT
1 AAAATATTAAGAAACAAAATAAATAAAATTCCATAATTAAAT-A-AAAACATTAAGAAACAAAAT
432614 AAATAAAAAGTCCATAATTAAAT
64 AAATAAAAAGTCCATAATTAAAT
*
432637 AAAATATTAAGAAACAAAATAAATAAAATTTTCATAATTAAATAAAAACATTAAGAAACAAAATA
1 AAAATATTAAGAAACAAAATAAATAAAA-TTCCATAATTAAATAAAAACATTAAGAAACAAAATA
432702 AATAAAAA
65 AATAAAAA
432710 CATTAAGAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
87 56 0.81
88 1 0.01
89 12 0.17
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (86 bp):
AAAATATTAAGAAACAAAATAAATAAAATTCCATAATTAAATAAAAACATTAAGAAACAAAATAA
ATAAAAAGTCCATAATTAAAT
Found at i:432705 original size:25 final size:25
Alignment explanation
Indices: 432675--432736 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
432665 TTTTCATAAT
432675 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
432700 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
432725 TAAATAAAAACA
1 TAAATAAAAACA
432737 AGTTTATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.73, C:0.08, G:0.03, T:0.16
Consensus pattern (25 bp):
TAAATAAAAACATTAAGAAACAAAA
Found at i:433163 original size:21 final size:22
Alignment explanation
Indices: 433139--433179 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
433129 CATTTGAAAT
*
433139 GGTTGTCGTGGCATC-GAAAAC
1 GGTTGTCGTGCCATCTGAAAAC
*
433160 GGTTGTGGTGCCATCTGAAA
1 GGTTGTCGTGCCATCTGAAA
433180 TGGCTACGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (22 bp):
GGTTGTCGTGCCATCTGAAAAC
Found at i:433958 original size:21 final size:21
Alignment explanation
Indices: 433932--433971 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
433922 TATTTAGTGT
433932 AAAAAAATTCA-TTATATACTC
1 AAAAAAATT-ATTTATATACTC
433953 AAAAAAATTATTTATATAC
1 AAAAAAATTATTTATATAC
433972 AAACCTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAAATTATTTATATACTC
Found at i:441076 original size:23 final size:22
Alignment explanation
Indices: 441022--441076 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
441012 CTATTCATGC
441022 TAAAAAAATCCTAAAAGATAAAA
1 TAAAAAAAT-CTAAAAGATAAAA
**
441045 TAACTAAAT-TATAAAGATAAATA
1 TAAAAAAATCTA-AAAGATAAA-A
441068 TAAAAAAAT
1 TAAAAAAAT
441077 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 9 0.35
23 15 0.58
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.24
Consensus pattern (22 bp):
TAAAAAAATCTAAAAGATAAAA
Found at i:441907 original size:2 final size:2
Alignment explanation
Indices: 441896--441951 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
441886 TAGGTAAGGG
441896 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
441937 TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA
441952 ATGTTAACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:450550 original size:20 final size:21
Alignment explanation
Indices: 450527--450567 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
450517 TGAGAAATTG
450527 TTTTT-AAAATAT-AAAAATGA
1 TTTTTCAAAAT-TGAAAAATGA
450547 TTTTTCAAAATTGAAAAATGA
1 TTTTTCAAAATTGAAAAATGA
450568 AAACAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTCAAAATTGAAAAATGA
Found at i:460380 original size:22 final size:22
Alignment explanation
Indices: 460355--460397 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
460345 ATAAGTAAAG
460355 AAGAAAAAGAAGCAG-CAGACAC
1 AAGAAAAAGAAG-AGACAGACAC
*
460377 AAGAAGAAGAAGAGACAGACA
1 AAGAAAAAGAAGAGACAGACA
460398 AGAGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.60, C:0.14, G:0.26, T:0.00
Consensus pattern (22 bp):
AAGAAAAAGAAGAGACAGACAC
Found at i:467317 original size:21 final size:21
Alignment explanation
Indices: 467293--467336 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
467283 CCGGTGCCGG
*
467293 AGGAGGAGCACAAGAAGAGCT
1 AGGAGCAGCACAAGAAGAGCT
* **
467314 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACAAGAAGAGCT
467335 AG
1 AG
467337 CTCCTGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACAAGAAGAGCT
Found at i:474740 original size:55 final size:57
Alignment explanation
Indices: 474672--474789 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 57
474662 AGTGCAACGA
* * *
474672 TGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGT-GG
1 TGCATCAAATGCATTCGATGTTTTCATAAA-AACCACAGTGCATCGATGCATGGTAGG
* *
474727 TGCATCAAATGCATTCGATGTTTTCATAAAAACCTCAGTGCATCGATGCATGGTATG
1 TGCATCAAATGCATTCGATGTTTTCATAAAAACCACAGTGCATCGATGCATGGTAGG
474784 TGCATC
1 TGCATC
474790 GATGCATGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 19 0.35
56 26 0.47
57 10 0.18
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (57 bp):
TGCATCAAATGCATTCGATGTTTTCATAAAAACCACAGTGCATCGATGCATGGTAGG
Found at i:476678 original size:23 final size:25
Alignment explanation
Indices: 476642--476687 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
476632 TAATTATATA
476642 TATATATTGAAATT-TTAAGTTAAAT
1 TATATATTGAAATTATT-AGTTAAAT
476667 TATAT-TTG-AATTATTAGTTAA
1 TATATATTGAAATTATTAGTTAA
476688 TTGTTACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (25 bp):
TATATATTGAAATTATTAGTTAAAT
Found at i:477032 original size:16 final size:16
Alignment explanation
Indices: 477011--477045 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
477001 TGAGTCAATT
477011 ACATGCCAGGTTCATA
1 ACATGCCAGGTTCATA
* *
477027 ACATGCCCGGTTGATA
1 ACATGCCAGGTTCATA
477043 ACA
1 ACA
477046 GGTCGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (16 bp):
ACATGCCAGGTTCATA
Found at i:477897 original size:10 final size:10
Alignment explanation
Indices: 477882--477955 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
477872 CATTTAATAA
477882 ATAAACGAAC
1 ATAAACGAAC
477892 ATAAACGAAC
1 ATAAACGAAC
477902 ----ACGAAC
1 ATAAACGAAC
477908 ATAAACGAA-
1 ATAAACGAAC
** *
477917 ACGAAC-ATAA
1 ATAAACGA-AC
477927 ATGAACACGAAC
1 AT-AA-ACGAAC
477939 ATAAACGAAC
1 ATAAACGAAC
477949 ATAAACG
1 ATAAACG
477956 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
6 6 0.12
8 1 0.02
9 5 0.10
10 29 0.58
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:477907 original size:16 final size:16
Alignment explanation
Indices: 477886--477949 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
477876 TAATAAATAA
477886 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
477902 ACGAACATAAACGAA-
1 ACGAACATAAACGAAC
*
477917 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
477933 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
477949 A
1 A
477950 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.31
16 31 0.69
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:477919 original size:31 final size:31
Alignment explanation
Indices: 477884--477947 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
477874 TTTAATAAAT
477884 AAACGAACATAAACGAACACGAACATAAACG
1 AAACGAACATAAACGAACACGAACATAAACG
*
477915 AAACGAACATAAATGAACACGAACATAAACG
1 AAACGAACATAAACGAACACGAACATAAACG
477946 AA
1 AA
477948 CATAAACGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.08
Consensus pattern (31 bp):
AAACGAACATAAACGAACACGAACATAAACG
Found at i:478720 original size:14 final size:14
Alignment explanation
Indices: 478703--478758 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
478693 AATGAACATA
*
478703 AACGAACATAATCG
1 AACGAACATAACCG
478717 AACGAACAT-A---
1 AACGAACATAACCG
478727 AACGAACATAACCG
1 AACGAACATAACCG
478741 AACGAACATAACCG
1 AACGAACATAACCG
478755 AACG
1 AACG
478759 TTCACGAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:478723 original size:24 final size:24
Alignment explanation
Indices: 478683--478757 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
478673 GGTTGAGTTA
*
478683 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
478707 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
478731 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
478755 AAC
1 AAC
478758 GTTCACGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:478757 original size:10 final size:10
Alignment explanation
Indices: 478696--478743 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
478686 ATAAATGAAT
478696 GAACATAAAC
1 GAACATAAAC
478706 GAACATAATCGAAC
1 GAACAT-A---AAC
478720 GAACATAAAC
1 GAACATAAAC
*
478730 GAACATAACC
1 GAACATAAAC
478740 GAAC
1 GAAC
478744 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:479361 original size:21 final size:20
Alignment explanation
Indices: 479335--479404 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
479325 GTTATTGATA
479335 ATTTTAATAATATAATATTAT
1 ATTTTAAT-ATATAATATTAT
* *
479356 ATTTTATTGTTATAAT-TATATT
1 ATTTTAAT-ATATAATAT-TA-T
*
479378 ATTATAATATATAATATTAT
1 ATTTTAATATATAATATTAT
479398 ACTTTTA
1 A-TTTTA
479405 TTTTAATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 3 0.08
21 27 0.71
22 8 0.21
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (20 bp):
ATTTTAATATATAATATTAT
Found at i:479372 original size:35 final size:36
Alignment explanation
Indices: 479340--479428 Score: 75
Period size: 35 Copynumber: 2.6 Consensus size: 36
479330 TGATAATTTT
* * *
479340 AATAATATAATAT-T-ATATTTTATTGTTATAATTAT
1 AATAATATAATATATAATATTATACT-TTATAATTTT
* *
479375 ATTATTATAATATATAATATTATACTTT-T-ATTTT
1 AATAATATAATATATAATATTATACTTTATAATTTT
479409 AATAATAT-ATA-ATAA-ATTAT
1 AATAATATAATATATAATATTAT
479429 TAAAAAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
31 5 0.11
32 4 0.09
33 3 0.07
34 10 0.22
35 12 0.27
36 3 0.07
37 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
AATAATATAATATATAATATTATACTTTATAATTTT
Found at i:479397 original size:29 final size:29
Alignment explanation
Indices: 479365--479422 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
479355 TATTTTATTG
479365 TTATAATTATATTATT-ATAATATATAATA
1 TTATAATTATATT-TTAATAATATATAATA
* *
479394 TTATACTTTTATTTTAATAATATATAATA
1 TTATAATTATATTTTAATAATATATAATA
479423 AATTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATAATTATATTTTAATAATATATAATA
Found at i:479537 original size:17 final size:17
Alignment explanation
Indices: 479515--479551 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
479505 AAAATATAAT
*
479515 ATATTATTTTTATTTTA
1 ATATTATTATTATTTTA
479532 ATATTATTATTATTTTA
1 ATATTATTATTATTTTA
479549 ATA
1 ATA
479552 AATAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATTATTATTTTA
Found at i:479570 original size:33 final size:32
Alignment explanation
Indices: 479532--479613 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 32
479522 TTTTATTTTA
479532 ATATTATTATTATTTTAATAAATAATTAATAAT
1 ATATTATTATTATTTTAATAAATAATTAAT-AT
* *
479565 ATATTATTCTCATTTTAATAAATAATTAATAT
1 ATATTATTATTATTTTAATAAATAATTAATAT
479597 A-ATTATTATTAATTTTA
1 ATATTATTATT-ATTTTA
479614 TTTTAGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 7 0.16
32 9 0.20
33 28 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATTATTATTATTTTAATAAATAATTAATAT
Found at i:479868 original size:13 final size:14
Alignment explanation
Indices: 479846--479880 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
479836 CAAATACCGT
479846 AAAATAATTTT-CAA
1 AAAAT-ATTTTCCAA
479860 AAAATATTTTCCAA
1 AAAATATTTTCCAA
479874 AAAATAT
1 AAAATAT
479881 AATTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATATTTTCCAA
Found at i:494656 original size:22 final size:22
Alignment explanation
Indices: 494608--494657 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
494598 CATGAAGGTA
*
494608 ATTATTTCTAGGGAAAGAATAT
1 ATTATTTCTAGGAAAAGAATAT
* *
494630 TTTATTTTTAGGAAAAGAA-AGT
1 ATTATTTCTAGGAAAAGAATA-T
494652 ATTATT
1 ATTATT
494658 ACTATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (22 bp):
ATTATTTCTAGGAAAAGAATAT
Found at i:507267 original size:5 final size:5
Alignment explanation
Indices: 507259--507283 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
507249 GATGAGAATG
507259 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
507284 GGTGGAGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:522992 original size:17 final size:17
Alignment explanation
Indices: 522972--523088 Score: 116
Period size: 17 Copynumber: 6.8 Consensus size: 17
522962 AGAATGAATA
*
522972 AAAAAAATGAAAAAGTG
1 AAAAAAATGAAAAAATG
*
522989 AAAAAAAAAGGAAAAAA--
1 --AAAAAAATGAAAAAATG
*
523006 AAAAAAA-AAAAAAATG
1 AAAAAAATGAAAAAATG
523022 AAAAAAAAATGAAAAAAAATG
1 --AAAAAAATG--AAAAAATG
523043 AAAAAAATGAAAAAATG
1 AAAAAAATGAAAAAATG
*
523060 AAAAAAATAAAAAAATG
1 AAAAAAATGAAAAAATG
523077 -AAAAAATGAAAA
1 AAAAAAATGAAAA
523089 GTGAAAAGAA
Statistics
Matches: 85, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
14 6 0.07
15 7 0.08
16 11 0.13
17 24 0.28
18 7 0.08
19 22 0.26
21 8 0.09
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (17 bp):
AAAAAAATGAAAAAATG
Found at i:522993 original size:9 final size:9
Alignment explanation
Indices: 522972--523088 Score: 115
Period size: 8 Copynumber: 13.4 Consensus size: 9
522962 AGAATGAATA
522972 AAAAAAATG
1 AAAAAAATG
*
522981 -AAAAAGTG
1 AAAAAAATG
*
522989 AAAAAAAAAG
1 -AAAAAAATG
*
522999 GAAAAAA--
1 AAAAAAATG
523006 AAAAAAA--
1 AAAAAAATG
523013 AAAAAAATG
1 AAAAAAATG
523022 AAAAAAAAATG
1 --AAAAAAATG
523033 AAAAAAAATG
1 -AAAAAAATG
523043 AAAAAAATG
1 AAAAAAATG
523052 -AAAAAATG
1 AAAAAAATG
523060 AAAAAAAT-
1 AAAAAAATG
523068 AAAAAAATG
1 AAAAAAATG
523077 -AAAAAATG
1 AAAAAAATG
523085 AAAA
1 AAAA
523089 GTGAAAAGAA
Statistics
Matches: 94, Mismatches: 5, Indels: 18
0.80 0.04 0.15
Matches are distributed among these distances:
7 13 0.14
8 31 0.33
9 25 0.27
10 16 0.17
11 9 0.10
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:522995 original size:11 final size:11
Alignment explanation
Indices: 522981--523082 Score: 102
Period size: 11 Copynumber: 9.3 Consensus size: 11
522971 AAAAAAAATG
*
522981 AAAAAGTGAAA
1 AAAAAATGAAA
*
522992 AAAAAAGGAAA
1 AAAAAATGAAA
**
523003 AAAAAAAAAAA
1 AAAAAATGAAA
523014 AAAAAATGAAA
1 AAAAAATGAAA
523025 AAAAAATG-AA
1 AAAAAATGAAA
523035 AAAAAATG--A
1 AAAAAATGAAA
523044 AAAAAATGAAA
1 AAAAAATGAAA
**
523055 AAATGAAAAAAATA
1 AAA--AAATGAA-A
523069 AAAAAATGAAA
1 AAAAAATGAAA
523080 AAA
1 AAA
523083 TGAAAAGTGA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
9 9 0.12
10 10 0.13
11 43 0.57
12 5 0.07
13 5 0.07
14 4 0.05
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:522995 original size:21 final size:20
Alignment explanation
Indices: 522964--523111 Score: 85
Period size: 19 Copynumber: 7.9 Consensus size: 20
522954 GGTGAAAAAG
*
522964 AATGAATAAAAAAAATGAAA
1 AATGAAAAAAAAAAATGAAA
*
522984 AAGTG--AAAAAAAAA-GGAA
1 AA-TGAAAAAAAAAAATGAAA
523002 AA--AAAAAAAAAAA--AAA
1 AATGAAAAAAAAAAATGAAA
523018 AATG--AAAAAAAAATGAAA
1 AATGAAAAAAAAAAATGAAA
*
523036 AA--AAATGAAAAAAATGAAAA
1 AATGAAA-AAAAAAAATG-AAA
*
523056 AATG-AAAAAAATAA--AAA
1 AATGAAAAAAAAAAATGAAA
*
523073 AATGAAAAAATGAAAAGTG-AA
1 AATGAAAAAA--AAAAATGAAA
523094 AA-GAAAAAAGAAAAATGA
1 AATGAAAAAA-AAAAATGA
523112 GGGTTCGAGA
Statistics
Matches: 100, Mismatches: 9, Indels: 38
0.68 0.06 0.26
Matches are distributed among these distances:
16 13 0.13
17 16 0.16
18 16 0.16
19 24 0.24
20 23 0.23
21 8 0.08
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (20 bp):
AATGAAAAAAAAAAATGAAA
Found at i:523034 original size:52 final size:53
Alignment explanation
Indices: 522971--523108 Score: 157
Period size: 52 Copynumber: 2.6 Consensus size: 53
522961 AAGAATGAAT
*
522971 AAAAAAAATGAAAAAGTGAAAAAAAAAGGAAAAAA-AAAAAAA-AAAAAAATG
1 AAAAAAAATGAAAAAGTGAAAAAAAAAAGAAAAAAGAAAAAAATAAAAAAATG
523022 AAAAAAAAATGAAAAA---AAATGAAAAAAATGAAAAAATGAAAAAAATAAAAAAATG
1 -AAAAAAAATGAAAAAGTGAAA--AAAAAAA-GAAAAAA-GAAAAAAATAAAAAAATG
523077 --AAAAAATG-AAAAGTGAAAAGAAAAAAGAAAAA
1 AAAAAAAATGAAAAAGTGAAAA-AAAAAAGAAAAA
523109 TGAGGGTTCG
Statistics
Matches: 75, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
49 3 0.04
51 10 0.13
52 37 0.49
53 6 0.08
54 10 0.13
55 9 0.12
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (53 bp):
AAAAAAAATGAAAAAGTGAAAAAAAAAAGAAAAAAGAAAAAAATAAAAAAATG
Found at i:523082 original size:1 final size:1
Alignment explanation
Indices: 522989--523074 Score: 55
Period size: 1 Copynumber: 86.0 Consensus size: 1
522979 TGAAAAAGTG
** ** ** ** **
522989 AAAAAAAAAGGAAAAAAAAAAAAAAAAAAAATGAAAAAAAAATGAAAAAAAATGAAAAAAATGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *
523054 AAAATGAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
523075 TGAAAAAATG
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.07
Consensus pattern (1 bp):
A
Found at i:523101 original size:6 final size:7
Alignment explanation
Indices: 522992--523108 Score: 53
Period size: 8 Copynumber: 15.7 Consensus size: 7
522982 AAAAGTGAAA
522992 AAAAAAGG
1 AAAAAA-G
*
523000 AAAAAAA
1 AAAAAAG
*
523007 AAAAAAA
1 AAAAAAG
523014 AAAAAATG
1 AAAAAA-G
523022 AAAAAA-
1 AAAAAAG
523028 AAATGAAA-
1 AAA--AAAG
*
523036 AAAAATG
1 AAAAAAG
523043 AAAAAAATG
1 -AAAAAA-G
523052 AAAAAATG
1 AAAAAA-G
*
523060 AAAAAAATA
1 -AAAAAA-G
523069 AAAAAATG
1 AAAAAA-G
523077 AAAAAATG
1 AAAAAA-G
523085 --AAAAG
1 AAAAAAG
**
523090 TGAAAAG
1 AAAAAAG
523097 AAAAAAG
1 AAAAAAG
523104 AAAAA
1 AAAAA
523109 TGAGGGTTCG
Statistics
Matches: 92, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
5 1 0.01
6 9 0.10
7 28 0.30
8 46 0.50
9 8 0.09
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (7 bp):
AAAAAAG
Found at i:524200 original size:105 final size:105
Alignment explanation
Indices: 524018--524500 Score: 822
Period size: 105 Copynumber: 4.6 Consensus size: 105
524008 TCAACAACAA
*
524018 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
524083 CCTAAAGGAGAAGGTTCGTAATGAAAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* *
524123 TCAAATCCACCACAGAATGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
524188 CCTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
524228 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
524293 CCTAAATGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
*
524333 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
524398 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * * * * * *
524438 TTAAATTCACCAAAGAATGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAAAACTC
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
524501 ATCCGAAAAA
Statistics
Matches: 358, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 358 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
Found at i:527993 original size:20 final size:20
Alignment explanation
Indices: 527964--528008 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
527954 TACCAACCAA
527964 GGGAAATATCGGTACTGTTG
1 GGGAAATATCGGTACTGTTG
*
527984 GGGAAGTATCGGTACTGTTG
1 GGGAAATATCGGTACTGTTG
528004 GGGAA
1 GGGAA
528009 TTACCGATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (20 bp):
GGGAAATATCGGTACTGTTG
Found at i:528019 original size:20 final size:20
Alignment explanation
Indices: 527976--528019 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
527966 GAAATATCGG
* *
527976 TACTGTTGGGGAAGTATCGG
1 TACTGTTGGGGAAGTACCGA
*
527996 TACTGTTGGGGAATTACCGA
1 TACTGTTGGGGAAGTACCGA
528016 TACT
1 TACT
528020 ATTAAATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.32
Consensus pattern (20 bp):
TACTGTTGGGGAAGTACCGA
Found at i:528589 original size:24 final size:24
Alignment explanation
Indices: 528561--528613 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
528551 TTCGGGATAT
528561 TTCTACGTC-GTCCTTAT-GGACAAA
1 TTCTACG-CGGTCCTT-TGGGACAAA
528585 TTCTACGCGGTCCTTTGGGACAAA
1 TTCTACGCGGTCCTTTGGGACAAA
528609 TTCTA
1 TTCTA
528614 TGTAGCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (24 bp):
TTCTACGCGGTCCTTTGGGACAAA
Found at i:529909 original size:20 final size:20
Alignment explanation
Indices: 529884--529957 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
529874 TTTTCCCAAT
529884 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
529904 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
529924 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
529945 TCGCAATGCGAAT
1 TCGCAATGCGAAT
529958 TGGGAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:529926 original size:41 final size:42
Alignment explanation
Indices: 529881--529976 Score: 169
Period size: 41 Copynumber: 2.3 Consensus size: 42
529871 CGATTTTCCC
529881 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGG-A
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
*
529922 AATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
529964 AATT-GCAATGCGA
1 AATTCGCAATGCGA
529977 TACTGACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
41 48 0.91
42 5 0.09
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (42 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:529971 original size:21 final size:20
Alignment explanation
Indices: 529884--529976 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
529874 TTTTCCCAAT
** *
529884 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATTGGGAAA
*
529904 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATTGGGAAA
** *
529924 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATTGGGAAA
529945 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGG-AAA
*
529966 TTGCAATGCGA
1 TCGCAATGCGA
529977 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 30 0.51
21 29 0.49
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATTGGGAAA
Found at i:529993 original size:20 final size:20
Alignment explanation
Indices: 529968--530059 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
529958 TGGGAAAATT
*
529968 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* * * ** *
529988 GCAATGCGATAATAAAAAATT
1 GCAACGCGATACT-GACTATC
* * *
530009 GCAACGAGATACTTACTTTC
1 GCAACGCGATACTGACTATC
* *
530029 ACAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
530049 GCAACGCGATA
1 GCAACGCGATA
530060 ATACATAATC
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 41 0.76
21 13 0.24
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:530007 original size:41 final size:41
Alignment explanation
Indices: 529962--530039 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
529952 GCGAATTGGG
* * * *
529962 AAAATTGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATTGCAACGAGATACTGACTATCACAACGCGATAATAA
* *
530003 AAAATTGCAACGAGATACTTACTTTCACAACGCGATA
1 AAAATTGCAACGAGATACTGACTATCACAACGCGATA
530040 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAATTGCAACGAGATACTGACTATCACAACGCGATAATAA
Found at i:530275 original size:22 final size:22
Alignment explanation
Indices: 530247--530290 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
530237 CACTCTCTCA
530247 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
530269 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
530291 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:530521 original size:19 final size:19
Alignment explanation
Indices: 530497--530547 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
530487 ATCAACCAAG
530497 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
530516 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
530535 AATCGCAACGCGA
1 AATCGCAACGCGA
530548 TTTTAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGCA
Found at i:530599 original size:20 final size:20
Alignment explanation
Indices: 530574--530611 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
530564 CGATTCTCTC
530574 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
530594 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
530612 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:531952 original size:18 final size:18
Alignment explanation
Indices: 531931--531975 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
531921 TCCACTTCGG
*
531931 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
531949 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
531967 GAGCCATCA
1 GAGCCATCA
531976 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:532501 original size:14 final size:14
Alignment explanation
Indices: 532482--532571 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
532472 ATGCGAAATG
532482 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
532496 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
532512 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
532528 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
532544 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
532560 AAAATCGCAACG
1 AAAATCGCAACG
532572 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:532524 original size:32 final size:33
Alignment explanation
Indices: 532466--532588 Score: 223
Period size: 32 Copynumber: 3.8 Consensus size: 33
532456 CGAAATGGCT
*
532466 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
532499 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
532531 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
532563 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
532589 TGCGATTTGT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
32 64 0.73
33 24 0.27
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:532624 original size:14 final size:14
Alignment explanation
Indices: 532605--532662 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
532595 TTGTGTTTCG
532605 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
532619 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
532635 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
532651 CGTTGCGATTTT
1 CGTTGCGATTTT
532663 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:532639 original size:32 final size:33
Alignment explanation
Indices: 532600--532678 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
532590 GCGATTTGTG
532600 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
532632 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
532665 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
532679 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:532677 original size:19 final size:19
Alignment explanation
Indices: 532619--532736 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
532609 GCGATTTTGT
532619 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
532637 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
532651 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
532670 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
532690 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
532709 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
532729 TGTTGCGA
1 CGTTGCGA
532737 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:534596 original size:14 final size:14
Alignment explanation
Indices: 534577--534612 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
534567 ATTGTTTAAT
534577 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
534591 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
534605 TGATTTGT
1 TGATTTGT
534613 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:534738 original size:14 final size:16
Alignment explanation
Indices: 534719--534795 Score: 54
Period size: 18 Copynumber: 4.7 Consensus size: 16
534709 CGAAATGGCT
534719 ATCGCAA-CG-ATAAA
1 ATCGCAAGCGAATAAA
*
534733 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCG-AATAAA
534751 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AAT-AAA
*
534770 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAATAAA
534784 ATCGCAATGCGA
1 ATCGCAA-GCGA
534796 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
14 17 0.33
15 1 0.02
16 4 0.08
17 2 0.04
18 19 0.37
19 9 0.17
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (16 bp):
ATCGCAAGCGAATAAA
Found at i:534754 original size:18 final size:18
Alignment explanation
Indices: 534731--534795 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
534721 CGCAACGATA
534731 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
534749 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
534767 AAAATCGCAA--CGAGA--
1 -AAATCGCAATGCGAAATG
534782 AAATCGCAATGCGA
1 AAATCGCAATGCGA
534796 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 9 0.21
16 3 0.07
17 4 0.09
18 18 0.42
19 9 0.21
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:534871 original size:20 final size:20
Alignment explanation
Indices: 534821--534871 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
534811 GCGATATTCT
* *
534821 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
534841 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
534861 CGTTGCGATAG
1 CGTTGCGATAG
534872 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:535256 original size:14 final size:14
Alignment explanation
Indices: 535237--535272 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
535227 ATTGTTTAAT
535237 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
535251 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
535265 TGATTTGT
1 TGATTTGT
535273 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:536573 original size:24 final size:24
Alignment explanation
Indices: 536517--536575 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
536507 AGTCAGTATT
* *
536517 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
536541 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
536565 CGAATTTTGAT
1 CGAAATTTGAT
536576 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:536767 original size:12 final size:12
Alignment explanation
Indices: 536750--536774 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
536740 ATATAATCCT
536750 GAAGAAGAAAAA
1 GAAGAAGAAAAA
536762 GAAGAAGAAAAA
1 GAAGAAGAAAAA
536774 G
1 G
536775 TCCTCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:539095 original size:19 final size:19
Alignment explanation
Indices: 539073--539167 Score: 84
Period size: 19 Copynumber: 5.5 Consensus size: 19
539063 AATTACTATT
539073 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
539092 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
539106 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
**
539125 GCAA--CG--A-GGGAATC
1 GCAATGCGAAATGAAAATC
539139 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
539158 GCAACGCGAA
1 GCAATGCGAA
539168 TTTAATTTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:539115 original size:33 final size:33
Alignment explanation
Indices: 539073--539163 Score: 173
Period size: 33 Copynumber: 2.8 Consensus size: 33
539063 AATTACTATT
539073 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
*
539106 GCAATGCGAAATGAAAATCGCAACGAGGGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
539139 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
539164 CGAATTTAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:539185 original size:19 final size:20
Alignment explanation
Indices: 539163--539205 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
539153 AAATCGCAAC
539163 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
539182 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
539202 GCGA
1 GCGA
539206 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:539190 original size:14 final size:14
Alignment explanation
Indices: 539191--539224 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
539181 TGCGATTTTC
539191 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
539205 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
539219 ATTTTC
1 ATTTTC
539225 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:539365 original size:14 final size:14
Alignment explanation
Indices: 539346--539382 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
539336 CATCAATTAA
539346 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
539360 ACAAATCACCTTTT
1 ACAAATCAACTTTT
539374 ACAAATCAA
1 ACAAATCAA
539383 TTAAACAATC
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:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:540806 original size:21 final size:21
Alignment explanation
Indices: 540740--540806 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
540730 GTGAATCGGG
*
540740 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
540760 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
540782 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
540803 CTCT
1 CTCT
540807 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:540825 original size:42 final size:41
Alignment explanation
Indices: 540740--540862 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
540730 GTGAATCGGG
* * * * *
540740 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
540782 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
540824 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
540863 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:541070 original size:29 final size:29
Alignment explanation
Indices: 541037--541095 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
541027 AACAGACATG
* ** *
541037 ATATTTAAACAGTGAAAACAAAGATAAAT
1 ATATTCAAACAGACAAAACAAAGACAAAT
541066 ATATTCAAACAGACAAAACAAAGACAAAT
1 ATATTCAAACAGACAAAACAAAGACAAAT
541095 A
1 A
541096 CTAACTTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.61, C:0.12, G:0.08, T:0.19
Consensus pattern (29 bp):
ATATTCAAACAGACAAAACAAAGACAAAT
Found at i:542969 original size:19 final size:19
Alignment explanation
Indices: 542852--543036 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
542842 TCTTTTGGTT
*
542852 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
542871 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
542891 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
542909 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
542925 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
542943 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
542958 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
542978 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
542997 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
543016 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
543035 GA
1 GA
543037 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:542990 original size:39 final size:38
Alignment explanation
Indices: 542852--543036 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
542842 TCTTTTGGTT
* *
542852 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
542891 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
542925 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
542958 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
542997 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
543035 GA
1 GA
543037 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
33 42 0.33
34 16 0.13
35 2 0.02
38 24 0.19
39 28 0.22
40 14 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:543065 original size:19 final size:19
Alignment explanation
Indices: 543032--543076 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
543022 AAAATCGCAA
**
543032 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
543051 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
543070 TGCGATT
1 TGCGATT
543077 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:543658 original size:20 final size:20
Alignment explanation
Indices: 543630--543681 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
543620 CGCTAAGTAA
* *
543630 ATCGCGTTGCGAAAGTCAGT
1 ATCGTGTTGCGAAAGTAAGT
543650 ATCGTGTTGCGAAAGTAAGT
1 ATCGTGTTGCGAAAGTAAGT
543670 ATC-TCGTTGCGA
1 ATCGT-GTTGCGA
543682 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGTGTTGCGAAAGTAAGT
Found at i:543756 original size:20 final size:20
Alignment explanation
Indices: 543712--543804 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
543702 ATAGTCAGTA
* **
543712 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
543733 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
543753 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
543774 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
543794 TCGCATTGCGA
1 TCGCATTGCGA
543805 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:543757 original size:41 final size:41
Alignment explanation
Indices: 543712--543807 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
543702 ATAGTCAGTA
*
543712 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
543753 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
543794 TCGCATTGCGAATT
1 TCGCATTGCGAATT
543808 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:549432 original size:41 final size:41
Alignment explanation
Indices: 549406--549520 Score: 194
Period size: 41 Copynumber: 2.8 Consensus size: 41
549396 GCCCACTGAT
549406 CCGCGCTATACGCCACGTAGGGGTATAGCGCGGATCAGGGG
1 CCGCGCTATACGCCACGTAGGGGTATAGCGCGGATCAGGGG
* *
549447 CCGCGTTATACGCCACGTAGGGGTATATCGCGGATCAGGGG
1 CCGCGCTATACGCCACGTAGGGGTATAGCGCGGATCAGGGG
* *
549488 CCGCGCTATACGCCACGTAGGGCTAGAGCGCGG
1 CCGCGCTATACGCCACGTAGGGGTATAGCGCGG
549521 CTGCGCTATA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.19, C:0.28, G:0.37, T:0.16
Consensus pattern (41 bp):
CCGCGCTATACGCCACGTAGGGGTATAGCGCGGATCAGGGG
Found at i:551416 original size:134 final size:134
Alignment explanation
Indices: 551176--551444 Score: 520
Period size: 134 Copynumber: 2.0 Consensus size: 134
551166 CAGATTTGTT
*
551176 AACACAAATAAATCGGAATGCATGCACGAGCTAGTAAGCTCCTAACTATCCAACCATTAGCTAAG
1 AACACAAATAAATCAGAATGCATGCACGAGCTAGTAAGCTCCTAACTATCCAACCATTAGCTAAG
551241 CTTCATAGGACGAGTTCCCTAGAACCCATAATTAATCGTACATTAAAACAGGATGCAACGAATCA
66 CTTCATAGGACGAGTTCCCTAGAACCCATAATTAATCGTACATTAAAACAGGATGCAACGAATCA
551306 CATA
131 CATA
551310 AACACAAATAAATCAGAATGCATGCACGAGCTAGTAAGCTCCTAACTATCCAACCATTAGCTAAG
1 AACACAAATAAATCAGAATGCATGCACGAGCTAGTAAGCTCCTAACTATCCAACCATTAGCTAAG
*
551375 CTTCATAGGACGAGTTCCCTAGAACCCATAATTAATCGTACATTAAAACATGATGCAACGAATCA
66 CTTCATAGGACGAGTTCCCTAGAACCCATAATTAATCGTACATTAAAACAGGATGCAACGAATCA
551440 CATA
131 CATA
551444 A
1 A
551445 GCACGAGGGT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (134 bp):
AACACAAATAAATCAGAATGCATGCACGAGCTAGTAAGCTCCTAACTATCCAACCATTAGCTAAG
CTTCATAGGACGAGTTCCCTAGAACCCATAATTAATCGTACATTAAAACAGGATGCAACGAATCA
CATA
Found at i:560100 original size:13 final size:12
Alignment explanation
Indices: 560082--560110 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
560072 GCTTTTTTTG
560082 TTTTTTTTGCCT
1 TTTTTTTTGCCT
560094 TTTTTTTTGCCT
1 TTTTTTTTGCCT
560106 TTTTT
1 TTTTT
560111 GTTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:560934 original size:43 final size:46
Alignment explanation
Indices: 560886--560991 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 46
560876 ATAACTAGAG
560886 AATAAAATAATAATAAACT-AAACA-TGTTTTAACT-C-TAATTCCT
1 AATAAAATAATAATAAA-TAAAACATTGTTTTAACTACTTAATTCCT
*
560929 AATAAAATAATAATAAATAAAAATATTGTTTTAACTCAACCTTAATTCCT
1 AATAAAATAATAATAAAT-AAAACATTGTTTTAACT--A-CTTAATTCCT
560979 AATAAAATAATAA
1 AATAAAATAATAA
560992 ATCTGATCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
42 1 0.02
43 17 0.31
44 4 0.07
45 10 0.19
49 1 0.02
50 21 0.39
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (46 bp):
AATAAAATAATAATAAATAAAACATTGTTTTAACTACTTAATTCCT
Found at i:568425 original size:19 final size:19
Alignment explanation
Indices: 568401--568438 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
568391 TGGATAAGAT
568401 AGTTTCTGAATCTTATAGA
1 AGTTTCTGAATCTTATAGA
568420 AGTTTCTGAATCTTATAGA
1 AGTTTCTGAATCTTATAGA
568439 TTGTACACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
AGTTTCTGAATCTTATAGA
Found at i:575185 original size:24 final size:24
Alignment explanation
Indices: 575149--575204 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
575139 GCCAACCAAA
*
575149 CATGAGAATGTGGGATTCTCATCC
1 CATGAGAACGTGGGATTCTCATCC
*
575173 CATGGGAACGTGGGATTCTCATCC
1 CATGAGAACGTGGGATTCTCATCC
575197 CATGAGAA
1 CATGAGAA
575205 TCCCACAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (24 bp):
CATGAGAACGTGGGATTCTCATCC
Found at i:575918 original size:22 final size:23
Alignment explanation
Indices: 575878--575923 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
575868 TCTTCGTCGC
**
575878 ATTATTTTAATATCCAAA-TAAT
1 ATTATTTTAATATAAAAATTAAT
*
575900 ATTATTTTAATTTAAAAATTAAT
1 ATTATTTTAATATAAAAATTAAT
575923 A
1 A
575924 AATATCTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATTTTAATATAAAAATTAAT
Found at i:576510 original size:17 final size:17
Alignment explanation
Indices: 576488--576527 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
576478 TATAAATTTG
576488 ATATACTAATTATATTA
1 ATATACTAATTATATTA
576505 ATATACTAATTATATTA
1 ATATACTAATTATATTA
576522 ACTATA
1 A-TATA
576528 TGCTAAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATACTAATTATATTA
Found at i:577210 original size:24 final size:24
Alignment explanation
Indices: 577165--577224 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
577155 ATTTTAAAAA
577165 ATATTATTTAT--AATATAGTTAT
1 ATATTATTTATAAAATATAGTTAT
*
577187 ATGATT-TTTATAAAATATATTTAT
1 AT-ATTATTTATAAAATATAGTTAT
577211 ATATTATTTATAAA
1 ATATTATTTATAAA
577225 TAATTAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.21
23 6 0.18
24 20 0.61
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
ATATTATTTATAAAATATAGTTAT
Found at i:584342 original size:42 final size:42
Alignment explanation
Indices: 584295--584459 Score: 199
Period size: 42 Copynumber: 4.0 Consensus size: 42
584285 GAAAGGTGAA
* *
584295 TAAAGTAGAACAAAAAGAAGCATCGCACTTTCGATTCTCATC
1 TAAAGTAGAACGAAAAGAAGCATCGCACTTTCGATTCTCGTC
* * * * *
584337 TAAAGTAGAACGGAAGGAGGCATCACATTTTCGATTCTCGTC
1 TAAAGTAGAACGAAAAGAAGCATCGCACTTTCGATTCTCGTC
* *
584379 TAAAGTAGAACG-GAAGAAGGCATTGCACTTTCGATTCTCGTC
1 TAAAGTAGAACGAAAAGAA-GCATCGCACTTTCGATTCTCGTC
* * *
584421 TAAAGTAGAACGAAAGGAGGCATTGCAC-TTCGATTCTCG
1 TAAAGTAGAACGAAAAGAAGCATCGCACTTTCGATTCTCG
584460 ATTACAAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 14 0.13
42 88 0.84
43 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (42 bp):
TAAAGTAGAACGAAAAGAAGCATCGCACTTTCGATTCTCGTC
Found at i:590361 original size:3 final size:3
Alignment explanation
Indices: 590353--590382 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
590343 ATTAATAAAA
590353 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
590383 AAGTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:594450 original size:23 final size:24
Alignment explanation
Indices: 594412--594468 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
594402 AATAAAAAAG
594412 TATT-TAAAAAACTATA-TGA-AA
1 TATTATAAAAAACTATATTGATAA
* *
594433 TCATTATAAAAAAGTATATTTATAA
1 T-ATTATAAAAAACTATATTGATAA
594458 TATTATAAAAA
1 TATTATAAAAA
594469 TATTTGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 3 0.10
23 11 0.37
24 12 0.40
25 3 0.10
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
TATTATAAAAAACTATATTGATAA
Found at i:594697 original size:24 final size:24
Alignment explanation
Indices: 594647--594713 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
594637 AACAATATTA
**
594647 TTTCAAATAAATAAATAATTCTTT
1 TTTCAAATAAATAAATAATTCGAT
594671 TTTCAAATAAATAAATAATAT-GAT
1 TTTCAAATAAATAAATAAT-TCGAT
*
594695 TTTAAACATTAAATAAATA
1 TTTCAA-A-TAAATAAATA
594714 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 25 0.68
25 2 0.05
26 10 0.27
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (24 bp):
TTTCAAATAAATAAATAATTCGAT
Found at i:594800 original size:23 final size:23
Alignment explanation
Indices: 594728--594790 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
594718 TAAAATATTT
* *
594728 TTTTAT-AATATTATAA-ATACAC
1 TTTTATAAATAATATAATATA-AA
*
594750 TTTT-TAGAATAATTTAATATAAA
1 TTTTATA-AATAATATAATATAAA
594773 TTTTATAAATAATATAAT
1 TTTTATAAATAATATAAT
594791 TAATTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 1 0.03
22 4 0.12
23 23 0.70
24 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTATAAATAATATAATATAAA
Found at i:596196 original size:16 final size:16
Alignment explanation
Indices: 596177--596209 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
596167 TATTTTGTTT
596177 TTATTTATT-TTTTAAA
1 TTATTT-TTATTTTAAA
596193 TTATTTTTATTTTAAA
1 TTATTTTTATTTTAAA
596209 T
1 T
596210 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTTATTTTAAA
Found at i:599880 original size:28 final size:27
Alignment explanation
Indices: 599840--599896 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
599830 TCAACTTATA
*
599840 TTTTTTTTCCAGTTTGGTGCCTAATGT
1 TTTTTTTTCCAGTTTGGTGCCTAACGT
* *
599867 TTTTTCTTTTCAGTTTGTTGCCTAACGT
1 TTTTT-TTTCCAGTTTGGTGCCTAACGT
599895 TT
1 TT
599897 CATTCTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.58
Consensus pattern (27 bp):
TTTTTTTTCCAGTTTGGTGCCTAACGT
Found at i:599902 original size:29 final size:29
Alignment explanation
Indices: 599844--599902 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
599834 CTTATATTTT
* *
599844 TTTTCCAGTTTGGTGCCTAATGTTTTTTC
1 TTTTCCAGTTTGGTGCCTAACGTTTATTC
*
599873 TTTT-CAGTTTGTTGCCTAACGTTTCATTC
1 TTTTCCAGTTTGGTGCCTAACGTTT-ATTC
599902 T
1 T
599903 GTAACTCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.12, C:0.19, G:0.15, T:0.54
Consensus pattern (29 bp):
TTTTCCAGTTTGGTGCCTAACGTTTATTC
Found at i:600022 original size:24 final size:25
Alignment explanation
Indices: 599995--600042 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
599985 ATGAATTTTC
*
599995 TAATT-AAAATAATAAAAAATTAAT
1 TAATTGAAAATAAAAAAAAATTAAT
*
600019 TAATTGAAATTAAAAAAAAATTAA
1 TAATTGAAAATAAAAAAAAATTAA
600043 AAAAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TAATTGAAAATAAAAAAAAATTAAT
Found at i:600050 original size:12 final size:11
Alignment explanation
Indices: 600025--600049 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
600015 TAATTAATTG
600025 AAATTAAAAAA
1 AAATTAAAAAA
600036 AAATTAAAAAA
1 AAATTAAAAAA
600047 AAA
1 AAA
600050 AGATAAAAAC
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):
AAATTAAAAAA
Done.