Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 39
Found at i:3620728 original size:54 final size:53
Alignment explanation
Indices: 3620670--3620790 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 53
3620660 ACCTATTTGT
* ** *
3620670 TATGAATTTCTTATGTTGCATAGGTAATTCCCATACGAAAATTCATACACTTAG
1 TATGAATTTCTTAT-TTGCACACATAATGCCCATACGAAAATTCATACACTTAG
* **
3620724 TATGAATTTCTTAATTTGCACACATAGTGCCCATACGGGAATTCATACACTTAG
1 TATGAATTTCTT-ATTTGCACACATAATGCCCATACGAAAATTCATACACTTAG
3620778 TATGAATTTCTTA
1 TATGAATTTCTTA
3620791 ACTTGTTGCA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.02
54 56 0.95
55 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (53 bp):
TATGAATTTCTTATTTGCACACATAATGCCCATACGAAAATTCATACACTTAG
Found at i:3620791 original size:54 final size:56
Alignment explanation
Indices: 3620699--3620809 Score: 172
Period size: 54 Copynumber: 2.0 Consensus size: 56
3620689 ATAGGTAATT
*
3620699 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAA-T-TTGCACACATAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAACTGTTGCACACAAAGTG
**
3620753 CCCATACGGGAATTCATACACTTAGTATGAATTTCTTAACTTGTTGCACACAAAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAAC-TGTTGCACACAAAGTG
3620810 TCATTTGGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
54 37 0.73
56 1 0.02
57 13 0.25
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (56 bp):
CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAACTGTTGCACACAAAGTG
Found at i:3620974 original size:18 final size:18
Alignment explanation
Indices: 3620951--3620987 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3620941 GAACTTGGCC
3620951 TTTGCCTTTTGCTTTGCT
1 TTTGCCTTTTGCTTTGCT
3620969 TTTGCCTTTTGCTTTGCT
1 TTTGCCTTTTGCTTTGCT
3620987 T
1 T
3620988 GACTCTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.16, T:0.62
Consensus pattern (18 bp):
TTTGCCTTTTGCTTTGCT
Found at i:3621287 original size:20 final size:20
Alignment explanation
Indices: 3621241--3621287 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3621231 ATTTTGTTTT
* *
3621241 TAATGGTATCGATACCTTCC
1 TAATAGTATCGATACCTCCC
*
3621261 TTATAGTATCGATACC-CCC
1 TAATAGTATCGATACCTCCC
3621280 TAACTAGT
1 TAA-TAGT
3621288 TGATTCTTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (20 bp):
TAATAGTATCGATACCTCCC
Found at i:3630949 original size:111 final size:111
Alignment explanation
Indices: 3630812--3631144 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
3630802 ATTACAAAAA
3630812 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
3630877 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
3630923 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
3630988 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
3631034 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
3631099 AATTAAAAGGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
3631145 ATGATTTCCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:3631979 original size:6 final size:6
Alignment explanation
Indices: 3631968--3632000 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3631958 TATATGTGAA
3631968 TTATAT TTATAT TTATAT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTA
3632001 GTTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:3642644 original size:2 final size:2
Alignment explanation
Indices: 3642639--3642663 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3642629 GGAAGACGTG
3642639 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3642664 GTCTCGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3645289 original size:20 final size:20
Alignment explanation
Indices: 3645252--3645306 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
3645242 TTTAAACTTA
* * *
3645252 GGGAACAAAATCCTCAGGAG
1 GGGAACAGATTCCCCAGGAG
*
3645272 GGGAACCGATTCCCCAGGAG
1 GGGAACAGATTCCCCAGGAG
*
3645292 GGGTACAGATTCCCC
1 GGGAACAGATTCCCC
3645307 CCACGCTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.31, T:0.13
Consensus pattern (20 bp):
GGGAACAGATTCCCCAGGAG
Found at i:3650574 original size:22 final size:21
Alignment explanation
Indices: 3650547--3650629 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 21
3650537 TATAGGGCAG
3650547 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* *
3650568 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAATCGATACCCCC-TTGA
*
3650591 ATGGGAA-CTGATTCCCTCCTTG-
1 A-GGGAATC-GATACCC-CCTTGA
*
3650613 AGGAAATCGATACCCCC
1 AGGGAATCGATACCCCC
3650630 AATGGGTTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 11 0.21
22 17 0.33
23 20 0.38
24 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:3650613 original size:23 final size:22
Alignment explanation
Indices: 3650548--3650613 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
3650538 ATAGGGCAGA
* *
3650548 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
3650570 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-TTGAAG
*
3650593 GGGAACTGATTCCCTCCTTGA
1 GGGAACCGATTCCC-CCTTGA
3650614 GGAAATCGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 14 0.37
23 22 0.58
24 2 0.05
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:3654311 original size:366 final size:362
Alignment explanation
Indices: 3653575--3654478 Score: 1361
Period size: 366 Copynumber: 2.5 Consensus size: 362
3653565 ATTATGTGGA
*
3653575 CATTCTTCAATGAATTGAGAAGAT--AATCCCAAAGGACTTGACTCTTCACATGTATTATAATTA
1 CATTCTTCAATGAATTGAGAAGATGAAATGCCAAAGGACTTGACTCTTCACATGTATTATAATTA
* * *
3653638 TTAGAGAGCATTCTTCACCCCTATATATATGAGGTTCATGTAATCATCAAAATATAAATATCAAT
66 TTAGAGAGCATTCTTTACCCCTATATATATG-GGTTCATGTACTCATCAAAATATGAATAT-AAT
* * * *
3653703 ACA-ACTATCTCTATTTTTTCTCCCAAATCTCTCCTTTATTTTAAAACATTTAATGAGGTAGCAT
129 ACATA-TATCTCTATTTTCTCTCTCATATCTCTCCTTTATTTTAAAACATTTAATGAGGCAGCAT
* ** * * *
3653767 GTCAAGCATATAATTATGTACTCTTTTCTTTCATTAGGTTTTTGTCCCACTGGGTTTTTTTAGTA
193 GCCAAGCATATAATTATGTACAATTTTCATTCACTAGGTTTTTGTCCCACTGGGTTTTTCTAGTA
* *
3653832 AAGTTTTTAATGAGGCACAATTAGATAATGAACATCCAAGGGGAAGTGTTATGAATATATTATGT
258 AAGTTTTTAACGAGGCACAATTAGATAAGGAACATCCAAGGGGAAGTGTTATGAATATATTATGT
* * * *
3653897 GCATGCCACTATTACTCCTATTAGTTAATGTGGCTTTTGG
323 GAATGCCACTATTACTCCTATTAGTTAATATGACTTTTAG
* * *
3653937 CATTCTTCAATGAATTGAGAAGATGAAATGTCAAGGGACTTGATTCTTCACATGTATTATAATTA
1 CATTCTTCAATGAATTGAGAAGATGAAATGCCAAAGGACTTGACTCTTCACATGTATTATAATTA
*
3654002 TTAGAGAGCATTCTTTACCCCTATATATATATGGGTTCATGTACTCATCAAAACATGAATATAGA
66 TTAGAGAGCATTCTTTACCCC--TATATATATGGGTTCATGTACTCATCAAAATATGAATATA-A
* *
3654067 TACATATATCTCTATTTTCTCTCTCATATCTCTCATTTATTTTAAAATATTTAATGAGGCAGCAT
128 TACATATATCTCTATTTTCTCTCTCATATCTCTCCTTTATTTTAAAACATTTAATGAGGCAGCAT
*
3654132 GCCAAGCATATAATTATGTACAATTTTCATTCACTATGTTTTTGTCCCACTGGGTTTTTCCTAGT
193 GCCAAGCATATAATTATGTACAATTTTCATTCACTAGGTTTTTGTCCCACTGGGTTTTT-CTAGT
* *
3654197 AAAGTTTTTAACGAGGCACAATTAGATAACGGAA-ATCCAAGGGGGATTGTTATGAATATATTAT
257 AAAGTTTTTAACGAGGCACAATTAGATAA-GGAACATCCAAGGGGAAGTGTTATGAATATATTAT
* *
3654261 GTGAATGTCATTATTACTCCTATTAGTTAATATGACTTTTAG
321 GTGAATGCCACTATTACTCCTATTAGTTAATATGACTTTTAG
* *
3654303 CATTCTTCAATGAATTGAAAAGATGAAATGCCAAAGGACTTGACTCTTCATATGTATTATAATTA
1 CATTCTTCAATGAATTGAGAAGATGAAATGCCAAAGGACTTGACTCTTCACATGTATTATAATTA
*
3654368 TTAGAGAGCATTCTTTACACCTATATATATGGGTT-ATGTACTCATCAAAATATGAATATATATA
66 TTAGAGAGCATTCTTTACCCCTATATATATGGGTTCATGTACTCATCAAAATATGAATATA-ATA
*
3654432 CATCTATCTCTATTTTCTCTCTCATA-CATCTCCTTTATTTTAAAACA
130 CATATATCTCTATTTTCTCTCTCATATC-TCTCCTTTATTTTAAAACA
3654479 CGTTATCAAC
Statistics
Matches: 491, Mismatches: 42, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
362 25 0.05
363 69 0.14
364 70 0.14
365 137 0.28
366 187 0.38
367 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (362 bp):
CATTCTTCAATGAATTGAGAAGATGAAATGCCAAAGGACTTGACTCTTCACATGTATTATAATTA
TTAGAGAGCATTCTTTACCCCTATATATATGGGTTCATGTACTCATCAAAATATGAATATAATAC
ATATATCTCTATTTTCTCTCTCATATCTCTCCTTTATTTTAAAACATTTAATGAGGCAGCATGCC
AAGCATATAATTATGTACAATTTTCATTCACTAGGTTTTTGTCCCACTGGGTTTTTCTAGTAAAG
TTTTTAACGAGGCACAATTAGATAAGGAACATCCAAGGGGAAGTGTTATGAATATATTATGTGAA
TGCCACTATTACTCCTATTAGTTAATATGACTTTTAG
Found at i:3655101 original size:45 final size:46
Alignment explanation
Indices: 3655037--3655161 Score: 207
Period size: 45 Copynumber: 2.7 Consensus size: 46
3655027 CGGCTTTGAG
3655037 TTTTTGAAGCAAATTACTGTTACCTTTTATCAGGCATGTC-TTAAA
1 TTTTTGAAGCAAATTACTGTTACCTTTTATCAGGCATGTCTTTAAA
3655082 TTTTTGAAGCAAATTACTGTTACCTTTTATCAGGCATGTCTTTAAA
1 TTTTTGAAGCAAATTACTGTTACCTTTTATCAGGCATGTCTTTAAA
* **
3655128 TTTTTGAAGCAACTTACTAATACCTTTTTATCAG
1 TTTTTGAAGCAAATTACTGTTACC-TTTTATCAG
3655162 TCAACTAGCT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
45 40 0.53
46 26 0.35
47 9 0.12
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (46 bp):
TTTTTGAAGCAAATTACTGTTACCTTTTATCAGGCATGTCTTTAAA
Found at i:3658948 original size:3 final size:3
Alignment explanation
Indices: 3658942--3658984 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3658932 AATAATAATA
*
3658942 ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3658985 AATAATAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3662869 original size:364 final size:364
Alignment explanation
Indices: 3661873--3663293 Score: 2012
Period size: 364 Copynumber: 3.9 Consensus size: 364
3661863 AGGTAAGATT
* * * * * *
3661873 TTTAATGAGCCAGTATATCAAGCGTATAACTATGTACTCTTTT-TTT-ACTA-GTTTTTTTCTCT
1 TTTAATGAGGCAGCATGTCAAGCATATAATTATGTACTCTTTTCTTTCACTAGGTTTTTGTC-C-
* *
3661935 CACTGGGTATTTCCTAGTAAAGTTTTTAACGAGGCATAATTAGATAAT-ACACATCCAATGGGGA
64 CACTGGGTATTTCCTAGTAAAGTTTTTAACGAGGCACAATTAGATAATGA-ACATCCAAGGGGGA
* * *
3661999 GTGTTATAAATATATTATGTGGATGCCATTATTACTCCTATTAGTTAATGTGGGTTTAAGCATTC
128 GTGTTATGAATATATTATGTGGATGCCATTATTACTCCTATTAGTTAATGTGGCTTTTAGCATTC
* * *
3662064 TTCAATGAATTGAGAAAATGAAATGTCAAAGGAATTGACTCTTCACATGTATTGTAATTATTAGA
193 TTCAATGAATTGAGAAGATGAAATG-CAAAGGACTTGACTCTTCACATGTATTATAATTATTAGA
* * * *
3662129 TAACATTTTTTACCTCTATATATATGGGGTTCATGTACTCATCAAAATATGAATATAGATACATC
257 GAGCATTCTTTACCCCTATATATATGGGGTTCATGTACTCATCAAAATATGAATATAGATACATC
3662194 TATCTCTATTTTCTCTCCCATATCTCTCATTTATTTTAAAACA
322 TATCTCTATTTTCTCTCCCATATCTCTCATTTATTTTAAAACA
* * * * *
3662237 TTTAATGAGGCAGCATGTCAAGCGTATAATTATGTATTCTTTTCTTTCATTAAGTTTTTATCCCA
1 TTTAATGAGGCAGCATGTCAAGCATATAATTATGTACTCTTTTCTTTCACTAGGTTTTTGTCCCA
* *
3662302 CTAGGTATTTCCTAGTAAA-TTTTTAATGAGGCACAATTAGATAATGAACATCCAAGGGGGGAGT
66 CTGGGTATTTCCTAGTAAAGTTTTTAACGAGGCACAATTAGATAATGAACATCCAA-GGGGGAGT
*
3662366 GTTATGAATATATTATGTGGATGTCATTATTACTCCTATTAGTTAATGTGGCTTTTAGCATTCTT
130 GTTATGAATATATTATGTGGATGCCATTATTACTCCTATTAGTTAATGTGGCTTTTAGCATTCTT
*
3662431 CAATGAATTGAGAAGATGAAATTGTAAAGGACTTGACTCTTCACATGTATTATAATTATTAGAGA
195 CAATGAATTGAGAAGATGAAA-TGCAAAGGACTTGACTCTTCACATGTATTATAATTATTAGAGA
* * * *
3662496 GCATTCTTTACCCCTATATATATGGGGTTTATTTACTTATCGAAATATGAATATAGATACATCTA
259 GCATTCTTTACCCCTATATATATGGGGTTCATGTACTCATCAAAATATGAATATAGATACATCTA
* * * * *
3662561 TCTCTATTTTCTCTCCCATATTTCTCCTTTATTTCAGAATA
324 TCTCTATTTTCTCTCCCATATCTCTCATTTATTTTAAAACA
*
3662602 TTTAATGAGGTAGCATGTCAAGCATATAATTATGTACTCTTTTCTTTCACTAGGTTTTTGTCCCA
1 TTTAATGAGGCAGCATGTCAAGCATATAATTATGTACTCTTTTCTTTCACTAGGTTTTTGTCCCA
* * * *
3662667 CTGGGT-TTGTCCTAGTAAAGTTTTTAACGAGACACAATTAGATAATGGACATCCAA-TGTGAGT
66 CTGGGTATT-TCCTAGTAAAGTTTTTAACGAGGCACAATTAGATAATGAACATCCAAGGGGGAGT
* * * *
3662730 GTTATGTATATATTATGTAGATGCCATTATTACTCATATTAGTTAATGTAGCTTTTAGCATTCTT
130 GTTATGAATATATTATGTGGATGCCATTATTACTCCTATTAGTTAATGTGGCTTTTAGCATTCTT
*
3662795 CAATGAATTGAGAATATGAAATGACAAAGGACTTGACTCTTCACATGTATTATAATTATTAGAGA
195 CAATGAATTGAGAAGATGAAATG-CAAAGGACTTGACTCTTCACATGTATTATAATTATTAGAGA
* *
3662860 GCATTCTTTACCCGTATATATATGGGGTTCATGTACTCATCAAAACATGAATATAGATACATCTA
259 GCATTCTTTACCCCTATATATATGGGGTTCATGTACTCATCAAAATATGAATATAGATACATCTA
* *
3662925 TCTCTATTTTCTCTCCCATGTCTCTCTTTTATTTTAAAACA
324 TCTCTATTTTCTCTCCCATATCTCTCATTTATTTTAAAACA
* * *
3662966 TTTAATGAGGCAACATGACAAGCATATAATTATGTATTCTTTTCTTTCACTAGGTTTTTGTCCCA
1 TTTAATGAGGCAGCATGTCAAGCATATAATTATGTACTCTTTTCTTTCACTAGGTTTTTGTCCCA
* * * * * *
3663031 -TTGGTTTTTTCTAGTAAAGTTTTTAACGAGGCACAATTAGTTAATGTACATCCAAGGGGGGGTG
66 CTGGGTATTTCCTAGTAAAGTTTTTAACGAGGCACAATTAGATAATGAACATCCAAGGGGGAGTG
** * *
3663095 TTATGAATATATTATGTGGATTACATTAATACTCCTATTAGTTAATGTGGCTTTTAGCATTCTTT
131 TTATGAATATATTATGTGGATGCCATTATTACTCCTATTAGTTAATGTGGCTTTTAGCATTCTTC
* * *
3663160 AATGAATTGAGAAGATGAAATGCTAAAGGACTTGACTCTTCACTTGCATTATAATTATTATAGAG
196 AATGAATTGAGAAGATGAAATGC-AAAGGACTTGACTCTTCACATGTATTATAATTATTAGAGAG
****
3663225 CATTCCTCACTCTTATATATATATATATGGGGGTTCATGTACTCATCAAAATATGAATATAGATA
260 CA-T--T--CT-TTACCCCTATATATAT-GGGGTTCATGTACTCATCAAAATATGAATATAGATA
3663290 CATC
318 CATC
3663294 AACTTTAATG
Statistics
Matches: 946, Mismatches: 92, Indels: 31
0.88 0.09 0.03
Matches are distributed among these distances:
363 50 0.05
364 477 0.50
365 318 0.34
366 39 0.04
367 9 0.01
369 2 0.00
370 12 0.01
371 39 0.04
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (364 bp):
TTTAATGAGGCAGCATGTCAAGCATATAATTATGTACTCTTTTCTTTCACTAGGTTTTTGTCCCA
CTGGGTATTTCCTAGTAAAGTTTTTAACGAGGCACAATTAGATAATGAACATCCAAGGGGGAGTG
TTATGAATATATTATGTGGATGCCATTATTACTCCTATTAGTTAATGTGGCTTTTAGCATTCTTC
AATGAATTGAGAAGATGAAATGCAAAGGACTTGACTCTTCACATGTATTATAATTATTAGAGAGC
ATTCTTTACCCCTATATATATGGGGTTCATGTACTCATCAAAATATGAATATAGATACATCTATC
TCTATTTTCTCTCCCATATCTCTCATTTATTTTAAAACA
Found at i:3663969 original size:14 final size:14
Alignment explanation
Indices: 3663952--3663996 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3663942 TCATTTATTT
3663952 TTATGTAAATCTTA
1 TTATGTAAATCTTA
3663966 TTATGT--AT-TT-
1 TTATGTAAATCTTA
3663976 TTCATGTAAATCTTA
1 TT-ATGTAAATCTTA
3663991 TTATGT
1 TTATGT
3663997 CTGGATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
10 2 0.08
11 6 0.23
12 2 0.08
13 2 0.08
14 12 0.46
15 2 0.08
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.56
Consensus pattern (14 bp):
TTATGTAAATCTTA
Found at i:3663982 original size:25 final size:24
Alignment explanation
Indices: 3663947--3663996 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
3663937 TTAAGTCATT
3663947 TATTTTTATGTAAATCTTATTATG
1 TATTTTTATGTAAATCTTATTATG
3663971 TATTTTTCATGTAAATCTTATTATG
1 TATTTTT-ATGTAAATCTTATTATG
3663996 T
1 T
3663997 CTGGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (24 bp):
TATTTTTATGTAAATCTTATTATG
Found at i:3666245 original size:21 final size:21
Alignment explanation
Indices: 3666220--3666263 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3666210 AATTTAGTTA
3666220 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
3666241 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
3666262 AT
1 AT
3666264 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:3666273 original size:28 final size:28
Alignment explanation
Indices: 3666240--3666293 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3666230 TAGTATAAAT
3666240 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
3666268 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGTTAGTTTAAGTTATAT
3666294 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:3670177 original size:13 final size:12
Alignment explanation
Indices: 3670097--3670236 Score: 62
Period size: 11 Copynumber: 11.5 Consensus size: 12
3670087 TTTGGTTTAG
3670097 TAATGATTTGATAA
1 TAATGA-TT-ATAA
*
3670111 TCATGATT-TAA
1 TAATGATTATAA
*
3670122 TAATGATTTTATATT
1 TAATGA--TTATA-A
*
3670137 TAA-AATTATAA
1 TAATGATTATAA
*
3670148 TAATGATT-TAG
1 TAATGATTATAA
3670159 TAATGATTAGTAA
1 TAATGATTA-TAA
*
3670172 TAATGACTTATTAT
1 TAATGA-TTA-TAA
3670186 TAAT-ATT-TAA
1 TAATGATTATAA
* *
3670196 T-AT-TTTGATAT
1 TAATGATT-ATAA
3670207 TAATGATT-TAA
1 TAATGATTATAA
*
3670218 TAATGATTAGTTA
1 TAATGATTA-TAA
3670231 TAATGA
1 TAATGA
3670237 AATTATTATT
Statistics
Matches: 96, Mismatches: 16, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 34 0.35
12 12 0.12
13 23 0.24
14 17 0.18
15 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.47
Consensus pattern (12 bp):
TAATGATTATAA
Found at i:3670272 original size:60 final size:59
Alignment explanation
Indices: 3670132--3670334 Score: 295
Period size: 60 Copynumber: 3.4 Consensus size: 59
3670122 TAATGATTTT
* * *
3670132 ATATTTAA-AATT-ATAATAATGATTTAGTAATGATTAGTAATAATG-ACTTATTATTA
1 ATATTTAATATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
* * *
3670188 ATATTTAATATTTTGATATTAATGATTTAATAATGATTAGTTATAATGAAATTATTATTA
1 ATATTTAATA-TTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
*
3670248 ATATCTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
1 ATATTTAAT-ATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
3670308 ATATTTAATCATTTGATAGTAATGATT
1 ATATTTAAT-ATTTGATAGTAATGATT
3670335 AATGGATGTG
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
56 8 0.06
57 1 0.01
58 2 0.02
59 30 0.23
60 89 0.68
61 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.46
Consensus pattern (59 bp):
ATATTTAATATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
Found at i:3670510 original size:13 final size:12
Alignment explanation
Indices: 3670474--3670738 Score: 71
Period size: 11 Copynumber: 21.9 Consensus size: 12
3670464 TATATTTAAA
3670474 ATTATAATAATG
1 ATTATAATAATG
*
3670486 ATT-TAGTAATG
1 ATTATAATAATG
3670497 ATTAGTAATAATG
1 ATTA-TAATAATG
*
3670510 ATTTATTATTAAT-
1 A-TTA-TAATAATG
*
3670523 ATT-TAAT-GT-
1 ATTATAATAATG
* *
3670532 TTTGATATTAATG
1 ATT-ATAATAATG
3670545 ATT-TAATAATG
1 ATTATAATAATG
*
3670556 ATTAGTTATAATG
1 ATTA-TAATAATG
*
3670569 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
3670583 ATT-TAATGAT-
1 ATTATAATAATG
*
3670593 -TTGATAGTAATG
1 ATT-ATAATAATG
3670605 ATTAGTAATAATG
1 ATTA-TAATAATG
*
3670618 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
3670632 ATT-TAATCAT-
1 ATTATAATAATG
*
3670642 -TTGATAGTAATG
1 ATT-ATAATAATG
3670654 ATTAATAATAATG
1 ATT-ATAATAATG
3670667 AAATTATAATAATG
1 --ATTATAATAATG
* *
3670681 ATTTTATACTTATG
1 A--TTATAATAATG
*
3670695 ATT-TAATAATT
1 ATTATAATAATG
*
3670706 A-T-TACTAATG
1 ATTATAATAATG
*
3670716 ATT-TAATAATT
1 ATTATAATAATG
3670727 ATTACTAATAAT
1 ATTA-TAATAAT
3670739 TATGGAATAA
Statistics
Matches: 187, Mismatches: 37, Indels: 57
0.67 0.13 0.20
Matches are distributed among these distances:
9 7 0.04
10 21 0.11
11 49 0.26
12 16 0.09
13 44 0.24
14 28 0.15
15 22 0.12
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:3670556 original size:59 final size:60
Alignment explanation
Indices: 3670481--3670618 Score: 206
Period size: 60 Copynumber: 2.3 Consensus size: 60
3670471 AAAATTATAA
* * * *
3670481 TAATGATTTAGTAATGATTAGTAATAATG-ATTTATTATTAATATTTAATGTTTTGATAT
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
*
3670540 TAATGATTTAATAATGATTAGTTATAATGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
3670600 TAATGATTAGTAATAATGA
1 TAATGATT--TAATAATGA
3670619 AATTATTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 27 0.38
60 35 0.49
62 9 0.13
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:3670608 original size:28 final size:28
Alignment explanation
Indices: 3670577--3670660 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
3670567 TGAAATTATT
3670577 ATTAATATTTAATGATTTGATAGTAATG
1 ATTAATATTTAATGATTTGATAGTAATG
* * * *
3670605 ATTAGTA-ATAATGA----A-A-TTATT
1 ATTAATATTTAATGATTTGATAGTAATG
*
3670626 ATTAATATTTAATCATTTGATAGTAATG
1 ATTAATATTTAATGATTTGATAGTAATG
3670654 ATTAATA
1 ATTAATA
3670661 ATAATGAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 1 0.03
26 1 0.03
27 7 0.17
28 16 0.40
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (28 bp):
ATTAATATTTAATGATTTGATAGTAATG
Found at i:3670609 original size:49 final size:49
Alignment explanation
Indices: 3670539--3670673 Score: 222
Period size: 49 Copynumber: 2.8 Consensus size: 49
3670529 TGTTTTGATA
*
3670539 TTAATGATTT-A-A-TAATGATTAGTTATAATGAAATTATTATTAATAT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATAT
3670585 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATAT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATAT
* *
3670634 TTAATCATTTGATAGTAATGATTAATAATAATGAAATTAT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTAT
3670674 AATAATGATT
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
46 10 0.12
47 1 0.01
48 1 0.01
49 71 0.86
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (49 bp):
TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATAT
Found at i:3670707 original size:14 final size:14
Alignment explanation
Indices: 3670635--3670704 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
3670625 TATTAATATT
* * *
3670635 TAATCATTTGATAG
1 TAATGATTTAATAA
3670649 TAATGA-TTAATAA
1 TAATGATTTAATAA
*
3670662 TAATGAAATT-ATAA
1 TAATG-ATTTAATAA
* *
3670676 TAATGATTTTATAC
1 TAATGATTTAATAA
*
3670690 TTATGATTTAATAA
1 TAATGATTTAATAA
3670704 T
1 T
3670705 TATTACTAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 13 0.29
14 30 0.67
15 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:3670738 original size:24 final size:21
Alignment explanation
Indices: 3670687--3670735 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3670677 AATGATTTTA
*
3670687 TACTTATGATTTAATAATTAT
1 TACTAATGATTTAATAATTAT
3670708 TACTAATGATTTAATAATTAT
1 TACTAATGATTTAATAATTAT
3670729 TACTAAT
1 TACTAAT
3670736 AATTATGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
TACTAATGATTTAATAATTAT
Found at i:3671043 original size:13 final size:12
Alignment explanation
Indices: 3671007--3671045 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
3670997 TATATTTAAA
3671007 ATTATAATAATG
1 ATTATAATAATG
*
3671019 ATT-TAGTAATG
1 ATTATAATAATG
3671030 ATTAATAATAATG
1 ATT-ATAATAATG
3671043 ATT
1 ATT
3671046 TATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 10 0.43
12 3 0.13
13 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:3671173 original size:17 final size:17
Alignment explanation
Indices: 3671148--3671209 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
3671138 TTTAGTAATG
*
3671148 ATTAGTAATAATGATTT
1 ATTAGTAATAATGAATT
* * * *
3671165 ATTATTAATATTTAATG
1 ATTAGTAATAATGAATT
3671182 ATTAGTAATAATGAAATT
1 ATTAGTAATAATG-AATT
*
3671200 ATTATTAATA
1 ATTAGTAATA
3671210 TTTAATCATT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
ATTAGTAATAATGAATT
Found at i:3671183 original size:59 final size:59
Alignment explanation
Indices: 3671019--3671184 Score: 278
Period size: 59 Copynumber: 2.8 Consensus size: 59
3671009 TATAATAATG
* * *
3671019 ATTTAGTAATGATTAATAATAATGATTTATTATTATTATTTAATGAATTGATATTAAAA
1 ATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATTTGATATTAAAA
* * *
3671078 CTTTAGTAATTATTAGTAATATTGATTTATTATTAATATTTAATGATTTGATATTAAAA
1 ATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATTTGATATTAAAA
3671137 ATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATT
1 ATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATT
3671185 AGTAATAATG
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 98 1.00
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (59 bp):
ATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATTTGATATTAAAA
Found at i:3671184 original size:21 final size:21
Alignment explanation
Indices: 3671030--3671134 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
3671020 TTTAGTAATG
*
3671030 ATTAATA-ATAATGATTTATT
1 ATTAATATTTAATGATTTATT
* *
3671050 ATTATTATTTAATGAATTGA-T
1 ATTAATATTTAATG-ATTTATT
* * *
3671071 ATTAAAACTTTAGT-AATTATT
1 ATTAATA-TTTAATGATTTATT
*
3671092 AGTAATA--T--TGATTTATT
1 ATTAATATTTAATGATTTATT
3671109 ATTAATATTTAATGATTTGA-T
1 ATTAATATTTAATGATTT-ATT
3671130 ATTAA
1 ATTAA
3671135 AAATTTAGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 19
0.67 0.13 0.20
Matches are distributed among these distances:
16 1 0.02
17 12 0.19
18 1 0.02
19 1 0.02
20 9 0.14
21 29 0.46
22 10 0.16
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (21 bp):
ATTAATATTTAATGATTTATT
Found at i:3671186 original size:34 final size:35
Alignment explanation
Indices: 3671143--3671215 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
3671133 AAAAATTTAG
*
3671143 TAATGATTAGTAATAATG-ATTTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
3671177 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
3671212 TAAT
1 TAAT
3671216 CATTTTGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 18 0.49
35 19 0.51
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:3672355 original size:23 final size:23
Alignment explanation
Indices: 3672328--3672371 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3672318 AAATTAAAAT
*
3672328 AATAATAAAATTGATTTAAATCA
1 AATAATAAAATTAATTTAAATCA
* *
3672351 AATAATATAGTTAATTTAAAT
1 AATAATAAAATTAATTTAAAT
3672372 AATAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATAATAAAATTAATTTAAATCA
Found at i:3674461 original size:29 final size:29
Alignment explanation
Indices: 3674424--3674484 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3674414 GCATCTCACG
*
3674424 TACAAGGTCACCCAGAAGGCATGGCGACC
1 TACAAGGTCACCCAGAAGGCATGGCAACC
* ** **
3674453 TACAGGGTCGTCTGGAAGGCATGGCAACC
1 TACAAGGTCACCCAGAAGGCATGGCAACC
3674482 TAC
1 TAC
3674485 TGCCAACACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.15
Consensus pattern (29 bp):
TACAAGGTCACCCAGAAGGCATGGCAACC
Found at i:3674952 original size:45 final size:45
Alignment explanation
Indices: 3674901--3674986 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
3674891 TCGGTAAAGT
*
3674901 GCTACCTAAAACATTATTTTTCTA-CCGAAAATGTTAATATTGGAC
1 GCTACCTAAAACATTATTTTTCTACCCG-AAATATTAATATTGGAC
3674946 GCTACCTAAAACATTATTTTTCTACCCGAAATATTAATATT
1 GCTACCTAAAACATTATTTTTCTACCCGAAATATTAATATT
3674987 AGGCGATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 36 0.92
46 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (45 bp):
GCTACCTAAAACATTATTTTTCTACCCGAAATATTAATATTGGAC
Found at i:3675000 original size:45 final size:45
Alignment explanation
Indices: 3674903--3675011 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
3674893 GGTAAAGTGC
* *
3674903 TACCTAAAACATTATTTTTCTACCGAAAATGTTAATATTGGACGC
1 TACCTAAAACATTATTTTTCTACCGAAAATATTAATATTGGACGA
3674948 TACCTAAAACATTATTTTTCTACCCG-AAATATTAATATTAGG-CGA
1 TACCTAAAACATTATTTTTCTA-CCGAAAATATTAATATT-GGACGA
* **
3674993 TATCTAAAATGTTATTTTT
1 TACCTAAAACATTATTTTT
3675012 TTCTATCGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 52 0.91
46 5 0.09
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (45 bp):
TACCTAAAACATTATTTTTCTACCGAAAATATTAATATTGGACGA
Found at i:3680174 original size:3 final size:3
Alignment explanation
Indices: 3680160--3680194 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3680150 AAAGAAAATA
*
3680160 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3680195 ATATATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3680284 original size:34 final size:34
Alignment explanation
Indices: 3680246--3680343 Score: 90
Period size: 36 Copynumber: 2.8 Consensus size: 34
3680236 CACGTTTTCA
*
3680246 AAAAATTATATTGTATATGTTTTCAAAAGTA-TTT
1 AAAAACTATATT-TATATGTTTTCAAAAGTATTTT
* ** *
3680280 AAAAACTATATATTATACTTTTTTTTAAATTATTTT
1 AAAAACTATAT-TTATA-TGTTTTCAAAAGTATTTT
* *
3680316 AAAAACTATATACTATAAGTTTTCAAAA
1 AAAAACTATAT-TTATATGTTTTCAAAA
3680344 CCATTTTTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
34 14 0.27
35 18 0.35
36 19 0.37
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (34 bp):
AAAAACTATATTTATATGTTTTCAAAAGTATTTT
Found at i:3680370 original size:77 final size:76
Alignment explanation
Indices: 3680280--3680453 Score: 198
Period size: 77 Copynumber: 2.3 Consensus size: 76
3680270 AAAAGTATTT
* ****
3680280 AAAAACTATATATTATACTTTTTTTTAAAT-TATTTT-AAAAACTATATACTATA-AGTTTTCAA
1 AAAAACTATATATTATACGTTTCAAAAAATAT-TTTTAAAAAACTATATACTATATA-TTTTCAA
3680342 AACCATT-TTTTAAA
64 AA--ATTATTTTAAA
*
3680356 AAAAGACTATATATTATACGTTTCAAAAAATATTTTTAAAAAATTATATACTATATATTTTCAAA
1 AAAA-ACTATATATTATACGTTTCAAAAAATATTTTTAAAAAACTATATACTATATATTTTCAAA
3680421 AATTATTTT--A
65 AATTATTTTAAA
*
3680431 AAAAATTATATATTATACGTTTC
1 AAAAACTATATATTATACGTTTC
3680454 CAAATTAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
74 18 0.21
75 5 0.06
76 7 0.08
77 29 0.34
78 26 0.30
79 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (76 bp):
AAAAACTATATATTATACGTTTCAAAAAATATTTTTAAAAAACTATATACTATATATTTTCAAAA
ATTATTTTAAA
Found at i:3680397 original size:39 final size:37
Alignment explanation
Indices: 3680280--3680453 Score: 133
Period size: 37 Copynumber: 4.6 Consensus size: 37
3680270 AAAAGTATTT
* ****
3680280 AAAAACTATATATTATACTTTTTTTTAAAT-TATTTT-
1 AAAAACTATATATTATACGTTTCAAAAAATAT-TTTTA
* * *
3680316 AAAAACTATATACTATAAGTTTTCAAAACCAT-TTTTTAAA
1 AAAAACTATATATTATACG-TTTCAAAA-AATATTTTT--A
3680356 AAAAGACTATATATTATACGTTTCAAAAAATATTTTTA
1 AAAA-ACTATATATTATACGTTTCAAAAAATATTTTTA
* * *
3680394 AAAAATTATATACTATATA-TTTTCAAAAATTA-TTTTA
1 AAAAACTATATA-T-TATACGTTTCAAAAAATATTTTTA
*
3680431 AAAAATTATATATTATACGTTTC
1 AAAAACTATATATTATACGTTTC
3680454 CAAATTAAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
35 4 0.04
36 21 0.19
37 32 0.28
38 20 0.18
39 6 0.05
40 17 0.15
41 13 0.12
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (37 bp):
AAAAACTATATATTATACGTTTCAAAAAATATTTTTA
Found at i:3680422 original size:37 final size:37
Alignment explanation
Indices: 3680226--3680447 Score: 129
Period size: 37 Copynumber: 5.9 Consensus size: 37
3680216 ATAAACTATG
* * ** *
3680226 TTTTCAAAAACACGTTTTCAAAAAATTATATTGTATATG
1 TTTTCAAAAATA--TTTTTAAAAAATTATATACTATATA
* * * *
3680265 TTTTCAAAAGTA--TTT-AAAAACTATATATTATACTT
1 TTTTCAAAAATATTTTTAAAAAATTATATACTATA-TA
** * *
3680300 TTTTTTAAATTA-TTTT-AAAAACTATATACTATA-A
1 TTTTCAAAAATATTTTTAAAAAATTATATACTATATA
**
3680334 GTTTTCAAAACCAT-TTTTTAAAAAAAGACTATA-TATTATA
1 -TTTTCAAAA--ATATTTTTAAAAAATTA-TATACTA-TATA
*
3680374 CGTTTCAAAAAATATTTTTAAAAAATTATATACTATATA
1 -TTTTC-AAAAATATTTTTAAAAAATTATATACTATATA
*
3680413 TTTTCAAAAAT-TATTTTAAAAAATTATATATTATA
1 TTTTCAAAAATAT-TTTTAAAAAATTATATACTATA
3680448 CGTTTCCAAA
Statistics
Matches: 146, Mismatches: 23, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
34 14 0.10
35 19 0.13
36 20 0.14
37 32 0.22
38 12 0.08
39 26 0.18
40 19 0.13
41 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAATATTTTTAAAAAATTATATACTATATA
Found at i:3681613 original size:14 final size:14
Alignment explanation
Indices: 3681594--3681628 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3681584 TTAAATTTAA
* *
3681594 AAAAAATGTTATAT
1 AAAAAATGTTAAAG
3681608 AAAAAATGTTAAAG
1 AAAAAATGTTAAAG
3681622 AAAAAAT
1 AAAAAAT
3681629 AAAATAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (14 bp):
AAAAAATGTTAAAG
Found at i:3681671 original size:5 final size:5
Alignment explanation
Indices: 3681661--3681746 Score: 57
Period size: 5 Copynumber: 15.6 Consensus size: 5
3681651 AATTTCTAAA
* *
3681661 AAAAT AAAAT ATAAA- AAAAGTT AAAAG AGAAAA AAAAT CAAAAT AAAAT
1 AAAAT AAAAT A-AAAT AAAA--T AAAAT A-AAAT AAAAT -AAAAT AAAAT
*
3681710 AAAAT AAAAGT GGGAAAAT AAAAT AAAAC AAAAT AAA
1 AAAAT AAAA-T ---AAAAT AAAAT AAAAT AAAAT AAA
3681747 TTTTAAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
4 3 0.05
5 41 0.62
6 13 0.20
7 4 0.06
8 1 0.02
9 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:3681837 original size:18 final size:18
Alignment explanation
Indices: 3681816--3681858 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3681806 AGGGATTTTA
*
3681816 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
3681834 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
3681852 AAATAAA
1 AAATAAA
3681859 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:3683107 original size:198 final size:200
Alignment explanation
Indices: 3682731--3683109 Score: 462
Period size: 201 Copynumber: 1.9 Consensus size: 200
3682721 AAAGTGGCTT
* * * ** *
3682731 CTTGTTGCCAAATCGTAGTCAACCTTGGTCTTCTTTTTGGTTTAAAGACCTCGGTTTAAAAATTC
1 CTTGTTGCCAAATCGCAGTCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAAAATTC
* ** * *
3682796 AATCAGAAAGTAGTTTCTCGATGCTACTATATGGTTGATATTCCTCGAACTAAATGGAATCGAAC
66 AATCAGAAAGTAGTTTCTCGATGCTACCATACAGTTGATAGTCCTCGAACTAAATGGAATCAAAC
*
3682861 TCGAAGGTTTTCGTTGACAGATAACCCTTATCGCCTTGAGCTATGTTGTAAATTCGGCTGGGAGA
131 TCGAA-GTTTTCGTTGACAAATAACCCTTATCGCCTTGAGCTATGTTGTAAATTCGGCTGGGAGA
3682926 TAGTTC
195 TAGTTC
* *
3682932 CTTGTTGCTAAATCGCA-TCTAACCTAGGTCTTCTTCTTGACTTAAAGACC-CAGTTT-AAACTT
1 CTTGTTGCCAAATCGCAGTC-AACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAAAATT
* * * * *
3682994 CAATCAGAAAGTAG-TTCTTTGCTGCTACCATACAGTTGATACGTCTTCGAGCTGAATGGAATCA
65 CAATCAGAAAGTAGTTTC-TCGATGCTACCATACAGTTGATA-GTCCTCGAACTAAATGGAATCA
** * * * *
3683058 AACTCGAA-TTTTTTTTTATAAATAACCCTTCTTGCCTTGAGCTATGTTGTAA
128 AACTCGAAGTTTTCGTTGACAAATAACCCTTATCGCCTTGAGCTATGTTGTAA
3683110 TGGGTTGGGA
Statistics
Matches: 150, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
198 40 0.27
199 37 0.25
200 32 0.21
201 41 0.27
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (200 bp):
CTTGTTGCCAAATCGCAGTCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAAAATTC
AATCAGAAAGTAGTTTCTCGATGCTACCATACAGTTGATAGTCCTCGAACTAAATGGAATCAAAC
TCGAAGTTTTCGTTGACAAATAACCCTTATCGCCTTGAGCTATGTTGTAAATTCGGCTGGGAGAT
AGTTC
Found at i:3683949 original size:123 final size:123
Alignment explanation
Indices: 3683745--3683974 Score: 318
Period size: 123 Copynumber: 1.9 Consensus size: 123
3683735 GCTCCTTTGA
* * *
3683745 TGTGAAGTTGAACTTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTTGTATATTGA
1 TGTGAAGTTGAACTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTGA
* ** * *
3683810 ATCGCTTTGAGATTAATATTTTTCGCTGTGAAGTTGAAATTGTGGATGGCTCATTCGC
66 ATCGCTTCGAGATTAATATCCTTCACCGTGAAGTTGAAATTGTGGATGGCTCATTCGC
* *
3683868 TGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTGC
1 TGTGAAGTTGAACTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTG-
* * * *
3683933 ATTGGC-TCGAGTTTAATATCCTTCACCGTGAAGTTGACATTG
65 AATCGCTTCGAGATTAATATCCTTCACCGTGAAGTTGAAATTG
3683975 ACTCTAACAA
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
123 88 0.96
124 4 0.04
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (123 bp):
TGTGAAGTTGAACTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTGA
ATCGCTTCGAGATTAATATCCTTCACCGTGAAGTTGAAATTGTGGATGGCTCATTCGC
Found at i:3690509 original size:18 final size:18
Alignment explanation
Indices: 3690466--3690512 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
3690456 GTTATTTTTA
*
3690466 AAATAAAAAATAAGAATT
1 AAATAAATAATAAGAATT
*
3690484 AAATAAATAATAATAATT
1 AAATAAATAATAAGAATT
3690502 AAATAAATAAT
1 AAATAAATAAT
3690513 CTAAAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AAATAAATAATAAGAATT
Found at i:3691109 original size:12 final size:13
Alignment explanation
Indices: 3691094--3691122 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3691084 AAAGATTAAA
3691094 TAAAATAATAT-T
1 TAAAATAATATCT
3691106 TAAAATAATATCT
1 TAAAATAATATCT
3691119 TAAA
1 TAAA
3691123 TCTTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:3691541 original size:19 final size:19
Alignment explanation
Indices: 3691513--3691551 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3691503 TTTAATTATG
3691513 TATTTAA-TTTAAATATTT
1 TATTTAATTTTAAATATTT
3691531 TATTATAATTTTAAATATTT
1 TATT-TAATTTTAAATATTT
3691551 T
1 T
3691552 CTCATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 3 0.16
20 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAATTTTAAATATTT
Found at i:3691775 original size:2 final size:2
Alignment explanation
Indices: 3691768--3691820 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
3691758 TATTTGATTA
*
3691768 AT AT AT AT AC AT AT AT 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 AT AT AT AT AT AT AT AT
3691810 AT AT AT AT AT A
1 AT AT AT AT AT A
3691821 AGGTTTAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3700331 original size:46 final size:46
Alignment explanation
Indices: 3700268--3700355 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
3700258 TGATTTAAGA
* *
3700268 CTCTACAAAAATGAATATTCCATGTGATCAAGAGAAATTAAAGACC
1 CTCTACAAAAATAAATATTCCATGTAATCAAGAGAAATTAAAGACC
* **
3700314 CTCTACAAGAATAAATATTCTTTGTAATCAAGAGAAATTAAA
1 CTCTACAAAAATAAATATTCCATGTAATCAAGAGAAATTAAA
3700356 TTATATGCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (46 bp):
CTCTACAAAAATAAATATTCCATGTAATCAAGAGAAATTAAAGACC
Found at i:3701648 original size:2 final size:2
Alignment explanation
Indices: 3701641--3701675 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3701631 AATTAAAGTG
3701641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3701676 TTAGGGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3708981 original size:20 final size:20
Alignment explanation
Indices: 3708956--3708995 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3708946 TTTTGGTGCA
3708956 GAGGGAA-TCGATCCCCCCTT
1 GAGGGAACT-GATCCCCCCTT
*
3708976 GAGGGAACTGATTCCCCCTT
1 GAGGGAACTGATCCCCCCTT
3708996 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAACTGATCCCCCCTT
Found at i:3708993 original size:21 final size:23
Alignment explanation
Indices: 3708958--3709017 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
3708948 TTGGTGCAGA
*
3708958 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
* *
3708978 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
3709001 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
3709018 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 9 0.28
22 1 0.03
23 15 0.47
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:3709025 original size:21 final size:21
Alignment explanation
Indices: 3708999--3709038 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3708989 CCCCCTTTGA
*
3708999 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3709020 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3709039 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3711825 original size:20 final size:20
Alignment explanation
Indices: 3711800--3711854 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3711790 TTTACACTTA
3711800 GGGAACCGATTCCCCATAGG
1 GGGAACCGATTCCCCATAGG
3711820 GGGAACCGATTCCCCATAGG
1 GGGAACCGATTCCCCATAGG
*
3711840 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
3711855 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCATAGG
Found at i:3713712 original size:177 final size:176
Alignment explanation
Indices: 3713414--3713999 Score: 881
Period size: 177 Copynumber: 3.3 Consensus size: 176
3713404 GATAAAATTT
*
3713414 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATCAAGAAACCC
1 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGAT-GCCCTTAGGACTTACAAATCAAGAAACCC
* * *
3713479 CCAAAGGCTTAGTTTCTTAGTTGTCAA-ATAACCCCTTTGTTAGGCTTAGATTCCTTTAACAACT
65 CCGAAGGCTTAGTTTCTTAGTTGTCAAGA-AACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCT
*
3713543 CTTTTGAGATAATTACTAAACCCCCAAAGGCTTCGTTTCTATAATCTC
129 CTTTTGAGATAATTACTAAACCCCCAAAGGCTTGGTTTCTATAATCTC
* * * **
3713591 ATTTGAAAACATCATGCACTAAAGGTCTTATGGATAACCCTTATAACTTACAAATCAAGAAACCC
1 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGAT-GCCCTTAGGACTTACAAATCAAGAAACCC
3713656 CCGAAGGCTTAGTTTCTTAGTTGTCAAGAAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTC
65 CCGAAGGCTTAGTTTCTTAGTTGTCAAGAAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTC
* *
3713721 TTTTGAGATAATTACTAAACCCCCGAAGGCTTGGTTTCTAAAATCTC
130 TTTTGAGATAATTACTAAACCCCCAAAGGCTTGGTTTCTATAATCTC
* *
3713768 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCTGTAGGATTTACAAATCAAGAAACCC
1 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGCCCT-TAGGACTTACAAATCAAGAAACCC
* * * *
3713833 CCGAAGGCTTAGTTTCTTAGTTGTCAATG-AACCCCTTTTTTAAGCTTAACTTCCGTTAACAGCT
65 CCGAAGGCTTAGTTTCTTAGTTGTCAA-GAAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCT
* * *
3713897 CTTTTTAGATAATTAATAAACCCCCAAAGTCTTGGTTTCT-TAAATCTC
129 CTTTTGAGATAATTACTAAACCCCCAAAGGCTTGGTTTCTAT-AATCTC
* *
3713945 ATTTGAAAACATCCTGCACTGAGGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGAT-GCCCTTAGGACTTACAAAT
3714000 TTGGGAAATA
Statistics
Matches: 371, Mismatches: 33, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
176 3 0.01
177 363 0.98
178 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (176 bp):
ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGCCCTTAGGACTTACAAATCAAGAAACCCC
CGAAGGCTTAGTTTCTTAGTTGTCAAGAAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCT
TTTGAGATAATTACTAAACCCCCAAAGGCTTGGTTTCTATAATCTC
Found at i:3714708 original size:22 final size:22
Alignment explanation
Indices: 3714640--3714708 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
3714630 GTAGAAATCC
*
3714640 AATAAATCTTTCATCTTTGAA-
1 AATAAATCTATCATCTTTGAAG
*
3714661 AAGAGAATCTATCATCTTTGAAG
1 AATA-AATCTATCATCTTTGAAG
*
3714684 AATAAATCTATCATTTTTGAAG
1 AATAAATCTATCATCTTTGAAG
3714706 AAT
1 AAT
3714709 GTAGATGTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.07
22 36 0.86
23 3 0.07
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
AATAAATCTATCATCTTTGAAG
Found at i:3715136 original size:54 final size:53
Alignment explanation
Indices: 3715073--3715189 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 53
3715063 ATAATCACTA
*
3715073 GTTCGTAAAACATTTGACAACACATTAATTCTTTAT-TGTGGTTTCTGCACAGAT
1 GTTCGTAAAACAATTGACAACACATTAA-TCTTT-TCTGTGGTTTCTGCACAGAT
*
3715127 GTTCGTAAAACAATTGACAACACATTCATCTTTTCCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACAATTGACAACACATTAATCTTTT-CTGTGGTTTCTGCACAGAT
3715181 GTTCGTAAA
1 GTTCGTAAA
3715190 TAAAGCTCTT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
52 1 0.02
53 5 0.08
54 53 0.90
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (53 bp):
GTTCGTAAAACAATTGACAACACATTAATCTTTTCTGTGGTTTCTGCACAGAT
Found at i:3716565 original size:16 final size:16
Alignment explanation
Indices: 3716544--3716577 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3716534 TTATTGCATA
3716544 TAATAGTATAATAGGC
1 TAATAGTATAATAGGC
3716560 TAATAGTATAATAGGC
1 TAATAGTATAATAGGC
3716576 TA
1 TA
3716578 GCTGAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (16 bp):
TAATAGTATAATAGGC
Found at i:3716610 original size:100 final size:100
Alignment explanation
Indices: 3716472--3716661 Score: 328
Period size: 100 Copynumber: 1.9 Consensus size: 100
3716462 CACCTTTATC
* * * *
3716472 AGGCTAGTTGAAACTTATCCATAAAGCTGGGGCTATTAACCAATTGCTTTAGAGGGACAACTTTA
1 AGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGAGGGACAACTTTA
3716537 TTGCATATAATAGTATAATAGGCTAATAGTATAAT
66 TTGCATATAATAGTATAATAGGCTAATAGTATAAT
3716572 AGGCTAGCTGAATA-TTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGAGGGACAACTTT
1 AGGCTAGCTGAA-ACTTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGAGGGACAACTTT
3716636 ATTGCATATAATAGTATAATAGGCTA
65 ATTGCATATAATAGTATAATAGGCTA
3716662 GCTGAATATT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
100 84 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (100 bp):
AGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGAGGGACAACTTTA
TTGCATATAATAGTATAATAGGCTAATAGTATAAT
Found at i:3716707 original size:84 final size:84
Alignment explanation
Indices: 3716560--3716717 Score: 291
Period size: 84 Copynumber: 1.9 Consensus size: 84
3716550 TATAATAGGC
3716560 TAATAGTATAATAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGA
1 TAATAGTATAATAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGA
3716625 GGGACAACTTTATTGCATA
66 GGGACAACTTTATTGCATA
3716644 TAATAGTATAATAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATT-ACTTTAG
1 TAATAGTATAATAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGA-TTTAG
*
3716708 AGGGATAACT
65 AGGGACAACT
3716718 CAAGCTTTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
83 1 0.01
84 71 0.99
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (84 bp):
TAATAGTATAATAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGATTTAGA
GGGACAACTTTATTGCATA
Found at i:3723052 original size:3 final size:3
Alignment explanation
Indices: 3723044--3723089 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
3723034 TGAAATTATT
*
3723044 TAA TAA TAA T-A TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3723090 AATGGGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3724007 original size:15 final size:15
Alignment explanation
Indices: 3723974--3724014 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3723964 CCGTCTACCC
3723974 GACCCGTTGA-C-TG
1 GACCCGTTGACCGTG
*
3723987 GACCCGTTGACCGTT
1 GACCCGTTGACCGTG
3724002 GACCCGTTGACCG
1 GACCCGTTGACCG
3724015 GAGTTGACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
15 14 0.56
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTG
Found at i:3726580 original size:24 final size:24
Alignment explanation
Indices: 3726491--3726592 Score: 89
Period size: 24 Copynumber: 4.2 Consensus size: 24
3726481 TTATCTAATT
* * *
3726491 TCTGATTTGAATTATGTTTTGACA
1 TCTGATCTGAATTATGTTCTGATA
* *
3726515 TCTGATCTGAAATCTGTTCTGAT-
1 TCTGATCTGAATTATGTTCTGATA
* * * *
3726538 TCCTAACCTGGATTCTGTTCTGATA
1 T-CTGATCTGAATTATGTTCTGATA
* *
3726563 TCTGATCTGAATTATGTTTTGATT
1 TCTGATCTGAATTATGTTCTGATA
3726587 TCTGAT
1 TCTGAT
3726593 ATCTCCGTTT
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 59 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATCTGAATTATGTTCTGATA
Found at i:3728732 original size:13 final size:13
Alignment explanation
Indices: 3728714--3728781 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
3728704 GTCACAACCC
3728714 GACCCGACCCGTT
1 GACCCGACCCGTT
3728727 GACCCGACCC---
1 GACCCGACCCGTT
3728737 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
3728750 TACCCGACCTGTT
1 GACCCGACCCGTT
*
3728763 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
3728778 GACC
1 GACC
3728782 GGAGTTGACC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
10 10 0.22
13 24 0.53
15 11 0.24
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3728736 original size:23 final size:23
Alignment explanation
Indices: 3728710--3728758 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
3728700 ACCGGTCACA
3728710 ACCCGACCCGACCCGTTGACCCG
1 ACCCGACCCGACCCGTTGACCCG
*
3728733 ACCCGACCCGACCCGTTTACCCG
1 ACCCGACCCGACCCGTTGACCCG
3728756 ACC
1 ACC
3728759 TGTTGACCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.53, G:0.18, T:0.10
Consensus pattern (23 bp):
ACCCGACCCGACCCGTTGACCCG
Found at i:3731346 original size:24 final size:24
Alignment explanation
Indices: 3731250--3731358 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
3731240 GAATATTTTA
* *
3731250 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
3731274 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
3731298 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
3731322 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
3731346 TTTGATTTCTGAT
1 TCTGATATCTGAT
3731359 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:3733186 original size:24 final size:24
Alignment explanation
Indices: 3733159--3733206 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3733149 TGGCCGTAGG
*
3733159 TCGCCATACACTCCTGGCGACCTA
1 TCGCCATACACTCCGGGCGACCTA
*
3733183 TCGCCATGCACTCCGGGCGACCTA
1 TCGCCATACACTCCGGGCGACCTA
3733207 CACTTGCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.19
Consensus pattern (24 bp):
TCGCCATACACTCCGGGCGACCTA
Found at i:3733391 original size:33 final size:33
Alignment explanation
Indices: 3733305--3733416 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 33
3733295 GCTTGGCTTC
* * * *
3733305 CCTCGAATTCCCTCGCATAGCTCGCTCGGTTGC
1 CCTCGGATGCCCTCGCATAGCTCGCTCGGATGG
*
3733338 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
1 CCTCGGATGCCCTCGCATAGCTCGCTCGGATGG
* *
3733371 CCTCGGATGCTCTCAG-ATAGCCTCGGTCGGATGG
1 CCTCGGATGCCCTC-GCATAG-CTCGCTCGGATGG
*
3733405 CCTCAGATGCCC
1 CCTCGGATGCCC
3733417 AGCGTGTTGG
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
33 45 0.66
34 23 0.34
ACGTcount: A:0.13, C:0.36, G:0.27, T:0.24
Consensus pattern (33 bp):
CCTCGGATGCCCTCGCATAGCTCGCTCGGATGG
Found at i:3739073 original size:243 final size:243
Alignment explanation
Indices: 3738637--3739099 Score: 592
Period size: 243 Copynumber: 1.9 Consensus size: 243
3738627 TGTCTGAAGG
* * * * * *
3738637 ATTATTGTCAAAAGACTGCACTATCCTTCCCAAGAATACTATCAGCTGTGCATCTTCAGTGGTGT
1 ATTATTATCAAAAGACTGCACTATCCTTCCCAAGAATACCATCAGCTGCGCATCTTCACTGGAGA
* * * **
3738702 ATTCGCTGATCCTTTCATTTAGGCCCTCAATGAATCCAAGTAAAAGTTCCCTATCCATTGACAAC
66 ACTCACTGATCCTGTCACCTAGGCCCTCAATGAATCCAAGTAAAAGTTCCCTATCCATTGACAAC
* * * *** *
3738767 TTCATGATGTCTTCGAGCAAATTTGTTTTTTCACTCTTAAGCTCATCGATTGAAGCTTCTGATGC
131 TTCATGATATCTTCGAGCAAATTTGTTTTTTCACTCTTAAGATCATCAACCAAAGCCTCTGATG-
3738832 TT-TCAGCCTTGCCTCCATATGATCACAGCCTTTAAAATCTGAAGGGTT
195 TTCTCAGCCTTGCCTCCATATGATCACAGCCTTTAAAATCTGAAGGGTT
* * * *
3738880 ATTATTATCAAAAGACTGCACTATCCTTTCCAAGAATCCCATCAGCTGCGCGTCTTCCCTGGAGA
1 ATTATTATCAAAAGACTGCACTATCCTTCCCAAGAATACCATCAGCTGCGCATCTTCACTGGAGA
** *
3738945 ACTCACTGATCCTGTCACCTAGGCCCTCAATGAATCC-AG-ACAGATTTTCCCTATGCATTGACA
66 ACTCACTGATCCTGTCACCTAGGCCCTCAATGAATCCAAGTA-A-AAGTTCCCTATCCATTGACA
* * * *
3739008 GCTTCATGATATCTTCGAGCAAATTT-TTCTTTTCATTCTTAAGATTATCAACCAAATCCTCTGA
129 ACTTCATGATATCTTCGAGCAAATTTGTT-TTTTCACTCTTAAGATCATCAACCAAAGCCTCTGA
*
3739072 TGTTCTCAGCCTTGCCTCCATCTGATCA
193 TGTTCTCAGCCTTGCCTCCATATGATCA
3739100 GTCAAATTCT
Statistics
Matches: 186, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
241 1 0.01
242 7 0.04
243 178 0.96
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (243 bp):
ATTATTATCAAAAGACTGCACTATCCTTCCCAAGAATACCATCAGCTGCGCATCTTCACTGGAGA
ACTCACTGATCCTGTCACCTAGGCCCTCAATGAATCCAAGTAAAAGTTCCCTATCCATTGACAAC
TTCATGATATCTTCGAGCAAATTTGTTTTTTCACTCTTAAGATCATCAACCAAAGCCTCTGATGT
TCTCAGCCTTGCCTCCATATGATCACAGCCTTTAAAATCTGAAGGGTT
Found at i:3743242 original size:31 final size:28
Alignment explanation
Indices: 3743202--3743259 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3743192 ATCATTTTTT
3743202 TTATAATTTTTGTTTTCATATATCAAACAAA
1 TTATAA-TTTT-TTTT-ATATATCAAACAAA
*
3743233 TTATCATTTTTTTTATATATCAAACAA
1 TTATAATTTTTTTTATATATCAAACAA
3743260 TAATAATGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 4 0.15
30 4 0.15
31 5 0.19
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (28 bp):
TTATAATTTTTTTTATATATCAAACAAA
Found at i:3744215 original size:18 final size:18
Alignment explanation
Indices: 3744192--3744235 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
3744182 TCACGGAATG
*
3744192 TAAGATTATCGGCGGGAA
1 TAAGATTATCGGAGGGAA
3744210 TAAGATTATCGGAGGGAA
1 TAAGATTATCGGAGGGAA
3744228 TAAGATTA
1 TAAGATTA
3744236 CTGGGAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.30, T:0.25
Consensus pattern (18 bp):
TAAGATTATCGGAGGGAA
Found at i:3748453 original size:3 final size:3
Alignment explanation
Indices: 3748445--3748497 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3748435 ATCCTCTGAA
3748445 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3748493 TTC TT
1 TTC TT
3748498 GTGACTGGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3752086 original size:14 final size:14
Alignment explanation
Indices: 3752067--3752114 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
3752057 CGTTCGGTAA
3752067 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
3752081 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
* *
3752095 TATGTGCATTCATT
1 TATGTTCGTTCATT
3752109 TATGTT
1 TATGTT
3752115 TAGCTCAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:3752226 original size:21 final size:21
Alignment explanation
Indices: 3752202--3752242 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3752192 TCAATTAATT
*
3752202 TTAAATACAAATAAAAAAAAA
1 TTAAAAACAAATAAAAAAAAA
* *
3752223 TTAAAAACAATTAAATAAAA
1 TTAAAAACAAATAAAAAAAA
3752243 TATAATCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
TTAAAAACAAATAAAAAAAAA
Found at i:3752304 original size:10 final size:10
Alignment explanation
Indices: 3752282--3752317 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3752272 AAAATCTATT
3752282 TTCATTTATG
1 TTCATTTATG
* *
3752292 TTCGTTTACG
1 TTCATTTATG
3752302 TTCATTTATG
1 TTCATTTATG
3752312 TTCATT
1 TTCATT
3752318 ATTGTGTTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (10 bp):
TTCATTTATG
Found at i:3752363 original size:24 final size:24
Alignment explanation
Indices: 3752319--3752364 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3752309 ATGTTCATTA
* *
3752319 TTGTGTTCGTTTACGTCCGTTCAT
1 TTGTGTTCGTTTACATACGTTCAT
3752343 TTGTGTTCGTTTACATACGTTC
1 TTGTGTTCGTTTACATACGTTC
3752365 GTTTATGTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (24 bp):
TTGTGTTCGTTTACATACGTTCAT
Found at i:3752377 original size:24 final size:24
Alignment explanation
Indices: 3752326--3752377 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3752316 TTATTGTGTT
* * * *
3752326 CGTTTACGTCCGTTCATTTGTGTT
1 CGTTTACATACGTTCATTTATGTC
*
3752350 CGTTTACATACGTTCGTTTATGTC
1 CGTTTACATACGTTCATTTATGTC
3752374 CGTT
1 CGTT
3752378 CATTTGTGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (24 bp):
CGTTTACATACGTTCATTTATGTC
Found at i:3763467 original size:73 final size:73
Alignment explanation
Indices: 3763345--3763624 Score: 332
Period size: 73 Copynumber: 3.8 Consensus size: 73
3763335 GTTAAAAACG
* * * * * *
3763345 GCTAATAATGTAAACGGTAAAAAAAAAATAAGCGCTACTTATTATATTAAACTGCATACCGGTTT
1 GCTAATAATGTAAACAGT--AAAAAAAATAAGCGCTACCTATTACATTAAAATACCTACCGGTTT
3763410 TTTTGAAGGTT
64 TTTT-AAGGTT
*
3763421 GCTAATAATGTAAACAGT-AAAAAAATAAGCGCTACCTATTACATTAAAATACCTACCGATTTGT
1 GCTAATAATGTAAACAGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACCTACCGGTTT-T
* *
3763485 TTAAAGATT
65 TTTAAGGTT
* * *
3763494 GCTAATAATGTAAA-AGATAAAATAAAATAGGTGTTACCTATTACATTAAAATACCTACCGGTTT
1 GCTAATAATGTAAACAG-TAAAA-AAAATAAGCGCTACCTATTACATTAAAATACCTACCGGTTT
3763558 TTTTAAGGTT
64 TTTTAAGGTT
* * * * *
3763568 GTTAATAATGTAAACGGT-AAAAAAATAGGCGATACCTATTACATTAAACTACCTACC
1 GCTAATAATGTAAACAGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACCTACC
3763625 TGATATGTTG
Statistics
Matches: 179, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
72 35 0.20
73 61 0.34
74 28 0.16
75 38 0.21
76 17 0.09
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (73 bp):
GCTAATAATGTAAACAGTAAAAAAAATAAGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
TTAAGGTT
Found at i:3763588 original size:147 final size:150
Alignment explanation
Indices: 3763345--3763638 Score: 405
Period size: 147 Copynumber: 2.0 Consensus size: 150
3763335 GTTAAAAACG
* * * * * *
3763345 GCTAATAATGTAAACGGTAAAAAAAAAATAAGCGCTACTTATTATATTAAACTGCATACCGGTTT
1 GCTAATAATGTAAAAGATAAAAAAAAAATAAGCGCTACCTATTACATTAAAATACATACCGGTTT
*
3763410 TTTTGAAGGTTGCTAATAATGTAAACAGTAAAAAAATAAGCGCTACCTATTACATTAAAATACCT
66 TTTTGAAGGTTGCTAATAATGTAAACAGTAAAAAAATAAGCGATACCTATTACATTAAAATACCT
* *
3763475 ACC-GATTTGTTTAAAGATT
131 ACCTGATATGTTGAAAGATT
* * * * *
3763494 GCTAATAATGTAAAAGAT-AAAATAAAATAGGTGTTACCTATTACATTAAAATACCTACCGGTTT
1 GCTAATAATGTAAAAGATAAAAAAAAAATAAGCGCTACCTATTACATTAAAATACATACCGGTTT
* * * *
3763558 TTTT-AAGGTTGTTAATAATGTAAACGGTAAAAAAATAGGCGATACCTATTACATTAAACTACCT
66 TTTTGAAGGTTGCTAATAATGTAAACAGTAAAAAAATAAGCGATACCTATTACATTAAAATACCT
3763622 ACCTGATATGTTGAAAG
131 ACCTGATATGTTGAAAG
3763639 TATCAATTCC
Statistics
Matches: 126, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
147 58 0.46
148 52 0.41
149 16 0.13
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (150 bp):
GCTAATAATGTAAAAGATAAAAAAAAAATAAGCGCTACCTATTACATTAAAATACATACCGGTTT
TTTTGAAGGTTGCTAATAATGTAAACAGTAAAAAAATAAGCGATACCTATTACATTAAAATACCT
ACCTGATATGTTGAAAGATT
Found at i:3763903 original size:112 final size:112
Alignment explanation
Indices: 3763706--3764016 Score: 518
Period size: 112 Copynumber: 2.8 Consensus size: 112
3763696 TAACACCTAT
* *
3763706 AAAGTATCAATAATTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
* **
3763771 ACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
66 ACCAGTTTCATTATGACAAAACCGATAAAGAGCTACAAGATATGTTG
*
3763818 AAAGTATCGATACTTTATAAAAATATATCGATACATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
*
3763883 ATCAGTTTCATTATGACAAAACCGATAAAGAGCTACAAGATATGTTG
66 ACCAGTTTCATTATGACAAAACCGATAAAGAGCTACAAGATATGTTG
*
3763930 AAAGTATCGATACTTTATAAAAATGTATCAATACATATA-AA-ATAACAGGTAAAAATATGACAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACATA-ACAATATAACAGGTAAAAATATGACAA
*
3763993 AACCAGTTTCATTATTACAAAACC
65 AACCAGTTTCATTATGACAAAACC
3764017 TGTTGAAAAC
Statistics
Matches: 187, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
111 44 0.24
112 142 0.76
113 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAACCGATAAAGAGCTACAAGATATGTTG
Found at i:3764311 original size:21 final size:21
Alignment explanation
Indices: 3764282--3764334 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3764272 ATGCAAAAAT
*
3764282 GTACTGATACCTAAACCAGAG
1 GTACCGATACCTAAACCAGAG
3764303 GTACCGATACCTAAACCAGAG
1 GTACCGATACCTAAACCAGAG
3764324 GTACCGATACC
1 GTACCGATACC
3764335 CTTGTGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (21 bp):
GTACCGATACCTAAACCAGAG
Found at i:3770164 original size:21 final size:22
Alignment explanation
Indices: 3770114--3770173 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
3770104 ATTTTTGTGC
*
3770114 ACAGTGTATCGATACCCCTAAA
1 ACAGTGTATCGATACTCCTAAA
**
3770136 ACAG-GTATCGATACTCCTTCA
1 ACAGTGTATCGATACTCCTAAA
3770157 AC-GTGTATCGATA-TCCT
1 ACAGTGTATCGATACTCCT
3770174 CTTTGAATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.15
21 25 0.74
22 4 0.12
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (22 bp):
ACAGTGTATCGATACTCCTAAA
Found at i:3770619 original size:19 final size:19
Alignment explanation
Indices: 3770596--3770633 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3770586 ATTTTCGAAA
3770596 TAAAAAAATGTT-TTGTTT
1 TAAAAAAATGTTGTTGTTT
*
3770614 TAAAAAATTGTTGTTGTTT
1 TAAAAAAATGTTGTTGTTT
3770633 T
1 T
3770634 TATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TAAAAAAATGTTGTTGTTT
Found at i:3770887 original size:12 final size:12
Alignment explanation
Indices: 3770867--3770903 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
3770857 TCTAGTCGTT
3770867 CAAATCGACCTC
1 CAAATCGACCTC
*
3770879 CAAACCGACCTC
1 CAAATCGACCTC
3770891 CAAATCGACCTC
1 CAAATCGACCTC
3770903 C
1 C
3770904 TATTCAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.46, G:0.08, T:0.14
Consensus pattern (12 bp):
CAAATCGACCTC
Found at i:3772462 original size:13 final size:14
Alignment explanation
Indices: 3772431--3772464 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3772421 TAAGGGGGTA
3772431 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
3772445 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
3772457 ATTTTCAA
1 ATTTTCAA
3772465 TAAGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 15 0.79
14 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:3774028 original size:111 final size:112
Alignment explanation
Indices: 3773775--3774011 Score: 386
Period size: 112 Copynumber: 2.1 Consensus size: 112
3773765 TGGCGCCTAT
* * * *
3773775 AAAGTATTGATACTTTATAAAAATATATCGAAACATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTGTATAAAAATGTATCGAAACATAACAATATAACAGGTAAAAATATGAAAAA
*
3773840 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCGTATATGTTG
66 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCGAATATGTTG
*
3773887 AAAGTATCGATACTGTATAAAAATGTATCGAAGCATAACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTATCGATACTGTATAAAAATGTATCGAAACATAACAATATAACAGGTAAAAATATGAAAAA
* * *
3773952 ATCAGTTTCATTATGA-AAAACCGGTAAAGAGCTACTGAATATGTTG
66 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCGAATATGTTG
3773998 AAAGTATCGATACT
1 AAAGTATCGATACT
3774012 TTTTTTACAT
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
111 42 0.36
112 74 0.64
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (112 bp):
AAAGTATCGATACTGTATAAAAATGTATCGAAACATAACAATATAACAGGTAAAAATATGAAAAA
ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCGAATATGTTG
Found at i:3775123 original size:18 final size:17
Alignment explanation
Indices: 3775069--3775117 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3775059 TTGGACCCTT
* *
3775069 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3775087 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3775105 AGTGCATTCGATG
1 AGTGCA-TCGATG
3775118 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3775222 original size:65 final size:64
Alignment explanation
Indices: 3775089--3775298 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 64
3775079 TGCACTAAGA
* *
3775089 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * * *
3775153 GTGCATCGATGGATCAAATGCATTCGATATTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGAT-GTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
3775216 AT
64 -G
* ** ** ** *
3775218 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-AGCCACAGTGCATCGATGCATGG-CT
3775282 G
64 G
*
3775283 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3775299 CTCTGAAAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.38
65 64 0.54
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:3781962 original size:19 final size:20
Alignment explanation
Indices: 3781928--3781967 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3781918 TAAATCCTTC
* *
3781928 TTCAAGATTTCATTTTGATT
1 TTCAAGATTCCATTTTCATT
3781948 TTCAA-ATTCCATTTTCATT
1 TTCAAGATTCCATTTTCATT
3781967 T
1 T
3781968 CTAGAAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (20 bp):
TTCAAGATTCCATTTTCATT
Found at i:3783609 original size:65 final size:64
Alignment explanation
Indices: 3783411--3783620 Score: 209
Period size: 65 Copynumber: 3.2 Consensus size: 64
3783401 TGCACTAAGA
* * *
3783411 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA--AATAGCCA-GAGTGCATCGATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAA-A-TCATG-GTGCATCGATGCATGGT
3783473 TG
63 TG
* * * *
3783475 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCATCAGTGCATTGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATTAAATCAT-GGTGCATCGATGCATGGT-
3783539 T-
63 TG
* *
3783540 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TTAAATCATGGTGCATCGATGCATGG-TT
3783604 G
64 G
3783605 GTGCATC-AGTGCATCA
1 GTGCATCGA-TGCATCA
3783621 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 21
0.78 0.08 0.13
Matches are distributed among these distances:
63 3 0.02
64 48 0.39
65 68 0.56
66 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATGGTGCATCGATGCATGGTTG
Found at i:3785419 original size:6 final size:6
Alignment explanation
Indices: 3785408--3785483 Score: 125
Period size: 6 Copynumber: 12.7 Consensus size: 6
3785398 GAAATCGGTG
* * *
3785408 GAAGAA GAAGAA GAAGAA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
3785456 GAAGGA GAAGGA GAAGGA GAAGGA GAAG
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAG
3785484 AAGAGAAACG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:3785550 original size:73 final size:73
Alignment explanation
Indices: 3785467--3785611 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
3785457 AAGGAGAAGG
* *
3785467 AGAAGGAGAAGGAGAAGAAGAGAAACGTTGATTATTTAAAAGAAGAGACACAATGATTTTTTTAA
1 AGAAGAAGAAGAAGAAGAAGAGAAACGTTGATTATTTAAAAGAAGAGACACAATGATTTTTTTAA
3785532 ACAATTGA
66 ACAATTGA
3785540 AGAAGAAGAAGAAGAAGAAGAGAAACGTTGATTATTTAAAAGAAGAGACACAATGATTTTTTTAA
1 AGAAGAAGAAGAAGAAGAAGAGAAACGTTGATTATTTAAAAGAAGAGACACAATGATTTTTTTAA
*
3785605 ATAATTG
66 ACAATTG
3785612 CCGACTCAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (73 bp):
AGAAGAAGAAGAAGAAGAAGAGAAACGTTGATTATTTAAAAGAAGAGACACAATGATTTTTTTAA
ACAATTGA
Found at i:3788199 original size:15 final size:15
Alignment explanation
Indices: 3788166--3788216 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
3788156 TCAAGTTATA
* **
3788166 ATGATGATGATGATA
1 ATGATGACGATGACG
3788181 ATGATGACGATGACG
1 ATGATGACGATGACG
* *
3788196 ATGAAGACGACGACG
1 ATGATGACGATGACG
3788211 ATGATG
1 ATGATG
3788217 GTGGTTGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.31, T:0.22
Consensus pattern (15 bp):
ATGATGACGATGACG
Found at i:3788994 original size:14 final size:13
Alignment explanation
Indices: 3788955--3789002 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
3788945 ATTTTTATTT
* *
3788955 TTAAAATAAAATA
1 TTAAAAGAATATA
3788968 TTAAAAGAATATA
1 TTAAAAGAATATA
*
3788981 TTAATAGTAATATA
1 TTAAAAG-AATATA
3788995 TTAAAAGA
1 TTAAAAGA
3789003 TAATTGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
TTAAAAGAATATA
Found at i:3790031 original size:2 final size:2
Alignment explanation
Indices: 3790026--3790059 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3790016 TCTTTCTCTC
3790026 AT AT AT AT 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 AT AT AT AT
3790060 TAAGATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3791246 original size:80 final size:80
Alignment explanation
Indices: 3791118--3791320 Score: 318
Period size: 80 Copynumber: 2.5 Consensus size: 80
3791108 AAAAGGGGAG
* *
3791118 CCAACCTAAGGATATACCTTGGGGCCTACTCAAGGATATCCCTAGATCCGTAGGGTTACCTTAAG
1 CCAACCTAAGGATATACCTT-GGGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTAAG
*
3791183 AACACAGCAAAAGAAA
65 AACACAACAAAAGAAA
* * *
3791199 CCAATCTAAGGATATACCTTGGGTCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTAAGC
1 CCAACCTAAGGATATACCTTGGGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTAAGA
*
3791264 ACACAACAAAGGAAA
66 ACACAACAAAAGAAA
*
3791279 CCAACCTAAGGATATGCCTTGGGCCTACCCAA-GATATCCTTA
1 CCAACCTAAGGATATACCTTGGGCCTACCCAAGGATATCCTTA
3791321 CGTCCTTAAG
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 10 0.09
80 83 0.74
81 19 0.17
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (80 bp):
CCAACCTAAGGATATACCTTGGGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTAAGA
ACACAACAAAAGAAA
Found at i:3799492 original size:16 final size:17
Alignment explanation
Indices: 3799455--3799500 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
3799445 GTTTATGAGA
3799455 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
*
3799473 GAATTAGAATCTGT-AG
1 GAATTGGAATCTGTAAG
3799489 GAATTGGAATCT
1 GAATTGGAATCT
3799501 AATTCCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 13 0.50
18 13 0.50
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:3800160 original size:37 final size:38
Alignment explanation
Indices: 3800075--3800164 Score: 148
Period size: 38 Copynumber: 2.4 Consensus size: 38
3800065 CCCTAAACCC
3800075 AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
3800113 AAACCCGACCCGA-CTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
*
3800150 AAACCGGACCCGACC
1 AAACCCGACCCGACC
3800165 CGAAGAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
37 17 0.35
38 32 0.65
ACGTcount: A:0.38, C:0.39, G:0.12, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:3800339 original size:27 final size:28
Alignment explanation
Indices: 3800277--3800343 Score: 109
Period size: 29 Copynumber: 2.4 Consensus size: 28
3800267 ACTTAATCCG
*
3800277 ACCCGACCCGAATATCACACTTAAAAAAA
1 ACCCGACCCGAACATCACACTT-AAAAAA
3800306 ACCCGACCCGAACATCACACTT-AAAAA
1 ACCCGACCCGAACATCACACTTAAAAAA
3800333 ACCCGACCCGA
1 ACCCGACCCGA
3800344 CCTGACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 16 0.43
29 21 0.57
ACGTcount: A:0.43, C:0.37, G:0.09, T:0.10
Consensus pattern (28 bp):
ACCCGACCCGAACATCACACTTAAAAAA
Found at i:3801432 original size:23 final size:23
Alignment explanation
Indices: 3801386--3801428 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3801376 AAAATGCATC
3801386 ATGTAGTAAATAATATTATATAT
1 ATGTAGTAAATAATATTATATAT
3801409 ATGT-GTATAATAATA-TATAT
1 ATGTAGTA-AATAATATTATAT
3801429 TATACTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (23 bp):
ATGTAGTAAATAATATTATATAT
Found at i:3802315 original size:33 final size:34
Alignment explanation
Indices: 3802240--3802361 Score: 201
Period size: 33 Copynumber: 3.6 Consensus size: 34
3802230 CTCGAAGGTC
*
3802240 TTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGG--TTTT
3802276 TTTGTGTTTCAAGAGAAACAATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
3802309 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
*
3802343 TTTGTGTTTCGAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
3802362 TGTCTCCAGG
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
33 33 0.40
34 21 0.25
36 29 0.35
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
Found at i:3802506 original size:36 final size:36
Alignment explanation
Indices: 3802414--3802694 Score: 285
Period size: 36 Copynumber: 7.9 Consensus size: 36
3802404 CAAAGATTGG
3802414 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
3802451 TGTTTCAAGGGAAAATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
3802487 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
3802524 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
3802560 TGTTTCAAG-GAAAACATAT-TC---AGAG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* * * * *
3802589 TGTTCCAAGGGAAACTGTCTTAAGATAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
3802625 TGTTTCAAGGGAAACT-TCCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGT-CTCAAGAGAGACAAAATT
*
3802661 TGTTTCAAGAGAAACTGTCTCAAGACAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
3802695 CCTTGTTTTG
Statistics
Matches: 201, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 1 0.00
32 3 0.01
33 3 0.01
35 2 0.01
36 110 0.55
37 64 0.32
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:3802506 original size:73 final size:74
Alignment explanation
Indices: 3802414--3802694 Score: 284
Period size: 73 Copynumber: 4.0 Consensus size: 74
3802404 CAAAGATTGG
* * * *
3802414 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAATGTCTTAAGAGA
1 TGTTTCAAGAGAAACTTGTCTCAAGAGAGACAAAACTTTGTTCCAAGAGAAACTGTCTCAAGAGA
3802478 GACAAAATT
66 GACAAAATT
* * *
3802487 TGTTTCAAGAGAAA-TTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TGTTTCAAGAGAAACTTGTCTCAAGAGAGACAAAACTTTGTTCCAAGAGAAACTGTCTCAAGAGA
*
3802551 GACGAAATT
66 GACAAAATT
* * * * * *
3802560 TGTTTCAAG-GAAAACATAT-TC---AGAG-----ATTTTGTTCCAAGGGAAACTGTCTTAAGAT
1 TGTTTCAAGAG-AAACTTGTCTCAAGAGAGACAAAACTTTGTTCCAAGAGAAACTGTCTCAAGAG
*
3802615 AGGCAAAATT
65 AGACAAAATT
* * * *
3802625 TGTTTCAAGGGAAACTT-CCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGACA
1 TGTTTCAAGAGAAACTTGTCTCAAGAGAGACAAAACTTTGTTCCAAGAGAAACTGTCTCAAGAGA
3802688 GACAAAA
66 GACAAAA
3802695 CCTTGTTTTG
Statistics
Matches: 169, Mismatches: 26, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
65 47 0.28
66 1 0.01
68 4 0.02
70 4 0.02
72 32 0.19
73 79 0.47
74 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (74 bp):
TGTTTCAAGAGAAACTTGTCTCAAGAGAGACAAAACTTTGTTCCAAGAGAAACTGTCTCAAGAGA
GACAAAATT
Found at i:3802630 original size:174 final size:177
Alignment explanation
Indices: 3802356--3802695 Score: 492
Period size: 174 Copynumber: 1.9 Consensus size: 177
3802346 GTGTTTCGAG
* ** *
3802356 AGAAACTGTCTCCAGGGAGGTAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
1 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTCCA
*
3802421 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAATGT-CTTAAGAGAGACAAAA
66 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAAT-TCCTCAAGAGAGACAAAA
* *
3802485 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
130 TTTGTTTCAAGAGAAACTGTCTCAAGACAGACAAAACTTAGTTCCAAA
* * *
3802533 AGAAACTGTCTCAAGGGAGACGAAA-TTTGTTTCAAG-GAAAACATATTCAGAGATT-TTGTTCC
1 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAG-AAACATATTCAAAGATTGGTGTTCC
* * * * *
3802595 AAGGGAAACTGTCTTAAGATAGGCAAAA-TTTGTTTCAAGGGAAACTTCCTCAAGAGAGACAAAA
65 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAATTCCTCAAGAGAGACAAAA
3802659 TTTGTTTCAAGAGAAACTGTCTCAAGACAGACAAAAC
130 TTTGTTTCAAGAGAAACTGTCTCAAGACAGACAAAAC
3802696 CTTGTTTTGA
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
173 1 0.01
174 67 0.46
175 30 0.21
176 27 0.18
177 21 0.14
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (177 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTCCA
AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAATTCCTCAAGAGAGACAAAAT
TTGTTTCAAGAGAAACTGTCTCAAGACAGACAAAACTTAGTTCCAAA
Found at i:3802701 original size:138 final size:138
Alignment explanation
Indices: 3802449--3802702 Score: 359
Period size: 138 Copynumber: 1.8 Consensus size: 138
3802439 GAGACAAAAC
* *
3802449 TTTGTTTCAAGGGAAAATGTCTTAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGA
1 TTTGTTCCAAGGGAAAATGTCTTAAGAGAGACAAAATTTGTTTCAAGAGAAATTGCCTCAAGAGA
** * *
3802514 GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACATAT
66 GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGACAGACAAAACTTGTTTCAAGGAAAACATAT
3802579 TCAGAGAT
131 TCAGAGAT
* * * *
3802587 TTTGTTCCAAGGGAAACTGTCTTAAGATAGGCAAAATTTGTTTCAAGGGAAACTT-CCTCAAGAG
1 TTTGTTCCAAGGGAAAATGTCTTAAGAGAGACAAAATTTGTTTCAAGAGAAA-TTGCCTCAAGAG
* * *
3802651 AGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGACAGACAAAACCTTGTTT
65 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGACAGACAAAA-CTTGTTT
3802703 TGAGTAAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 30 0.30
138 69 0.68
139 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (138 bp):
TTTGTTCCAAGGGAAAATGTCTTAAGAGAGACAAAATTTGTTTCAAGAGAAATTGCCTCAAGAGA
GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGACAGACAAAACTTGTTTCAAGGAAAACATAT
TCAGAGAT
Found at i:3804204 original size:95 final size:93
Alignment explanation
Indices: 3804014--3804269 Score: 309
Period size: 95 Copynumber: 2.7 Consensus size: 93
3804004 GGCTAGCAGG
* * * * *
3804014 ATCCATAAAGCTGGGGCTTTTTAACCAATTGCTCTAGAGGGACAACTTAA-ATCATTGTATA-GA
1 ATCCATAAAGC-GGGGC-GTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTATTGTATATTA
*
3804077 TAATCACCTTTATCAGGCAAGCTGAATATT
64 TAATCACCTTTATCAAGCAAGCTGAATATT
* *
3804107 ATCCATAAAGTCGGGGCGTTTAACTAATTGCTCTAGAGGAACAACTCAAGTTTTATTGTATATTA
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTATATTA
* * *
3804172 TAATCACTTTTATCAAGCTAGTTGAATATT
64 TAATCACCTTTATCAAGCAAGCTGAATATT
* * *
3804202 ATCCATAAAGCCGAGGTGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTATAT-T
3804267 ATA
63 ATA
3804270 TATATAATTA
Statistics
Matches: 140, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
92 28 0.20
93 15 0.11
94 10 0.07
95 83 0.59
96 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (93 bp):
ATCCATAAAGCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTATTGTATATTATA
ATCACCTTTATCAAGCAAGCTGAATATT
Found at i:3806300 original size:21 final size:21
Alignment explanation
Indices: 3806275--3806317 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3806265 CCCCTTTGAC
3806275 CATCTTCATATGGTCTTCCAT
1 CATCTTCATATGGTCTTCCAT
* **
3806296 CATCTTGATATTTTCTTCCAT
1 CATCTTCATATGGTCTTCCAT
3806317 C
1 C
3806318 TTTTTCGCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.47
Consensus pattern (21 bp):
CATCTTCATATGGTCTTCCAT
Found at i:3811702 original size:10 final size:10
Alignment explanation
Indices: 3811689--3811754 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
3811679 TTTTTTGAAA
3811689 TTTTGGCTTT
1 TTTTGGCTTT
3811699 TTTTGGCTCTT
1 TTTTGGCT-TT
*
3811710 TTTTTG-TTT
1 TTTTGGCTTT
*
3811719 TTTTGCCATTT
1 TTTTGGC-TTT
* *
3811730 TTTTTGCCTT
1 TTTTGGCTTT
**
3811740 TTTTGTTTTT
1 TTTTGGCTTT
3811750 TTTTG
1 TTTTG
3811755 TTTTTTGAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 6 0.14
10 22 0.51
11 15 0.35
ACGTcount: A:0.02, C:0.11, G:0.14, T:0.74
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:3811719 original size:19 final size:19
Alignment explanation
Indices: 3811697--3811761 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
3811687 AATTTTGGCT
3811697 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGCTCTTTTTTTG
*
3811716 TTTTTTTGC-CATTTTTTTTG
1 TTTTTTGGCTC--TTTTTTTG
*
3811736 CCTTTTTT-G-TTTTTTTTTG
1 --TTTTTTGGCTCTTTTTTTG
3811755 TTTTTTG
1 TTTTTTG
3811762 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
17 6 0.16
18 1 0.03
19 16 0.42
20 8 0.21
21 1 0.03
22 6 0.16
ACGTcount: A:0.02, C:0.09, G:0.12, T:0.77
Consensus pattern (19 bp):
TTTTTTGGCTCTTTTTTTG
Found at i:3811719 original size:20 final size:19
Alignment explanation
Indices: 3811696--3811760 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
3811686 AAATTTTGGC
3811696 TTTTTTTGGCTCTTTTTTTG
1 TTTTTTTGGCT-TTTTTTTG
*
3811716 TTTTTTTGCCATTTTTTTTG
1 TTTTTTTGGC-TTTTTTTTG
* *
3811736 CCTTTTTT-GTTTTTTTTTG
1 -TTTTTTTGGCTTTTTTTTG
3811755 TTTTTT
1 TTTTTT
3811761 GAAAAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 5 0.13
19 9 0.24
20 17 0.45
21 7 0.18
ACGTcount: A:0.02, C:0.09, G:0.11, T:0.78
Consensus pattern (19 bp):
TTTTTTTGGCTTTTTTTTG
Found at i:3814831 original size:13 final size:13
Alignment explanation
Indices: 3814813--3814837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3814803 TTAATTGCGA
3814813 AAATTGAAAATTT
1 AAATTGAAAATTT
3814826 AAATTGAAAATT
1 AAATTGAAAATT
3814838 AAAAATTCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATTGAAAATTT
Found at i:3815012 original size:23 final size:23
Alignment explanation
Indices: 3814986--3815030 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3814976 AAGAAACAAA
3814986 AAAT-AGAAAAAAAATAAATAAAT
1 AAATGAGAAAAAAAA-AAATAAAT
* *
3815009 AAATGAGATAAAACAAAATAAA
1 AAATGAGAAAAAAAAAAATAAA
3815031 AACAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
AAATGAGAAAAAAAAAAATAAAT
Found at i:3815034 original size:11 final size:11
Alignment explanation
Indices: 3815018--3815043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3815008 TAAATGAGAT
3815018 AAAACAAAATA
1 AAAACAAAATA
3815029 AAAACAAAATA
1 AAAACAAAATA
3815040 AAAA
1 AAAA
3815044 GTAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAACAAAATA
Found at i:3819532 original size:40 final size:40
Alignment explanation
Indices: 3819488--3819569 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
3819478 ATTAATCACC
3819488 CAAAACACAATATCAA-TCATATATTGAACAAACAAGACAT
1 CAAAACACAATATCAAGT-ATATATTGAACAAACAAGACAT
* * *
3819528 CAAAATACAATATCAAGTATATATTGAACAAATAAGGCAT
1 CAAAACACAATATCAAGTATATATTGAACAAACAAGACAT
3819568 CA
1 CA
3819570 CACTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (40 bp):
CAAAACACAATATCAAGTATATATTGAACAAACAAGACAT
Found at i:3819979 original size:18 final size:19
Alignment explanation
Indices: 3819940--3819980 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
3819930 TAAAAATTAA
*
3819940 AAAAATATTAATTTTATTT
1 AAAAATATTAATTTTATCT
3819959 AAAAA-ATTATATTTT-TCT
1 AAAAATATTA-ATTTTATCT
3819977 AAAA
1 AAAA
3819981 GTACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAATATTAATTTTATCT
Found at i:3827496 original size:30 final size:30
Alignment explanation
Indices: 3827394--3827484 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
3827384 CACGAAGGAC
3827394 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3827424 CTATCCAGAGGTCAAAAAGGTCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3827454 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3827484 C
1 C
3827485 AGTCCATAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3827513 original size:60 final size:60
Alignment explanation
Indices: 3827394--3827513 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
3827384 CACGAAGGAC
* ** *
3827394 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCAAAAAGGTCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCAAAAAGAACCTAGGTAA
* ***
3827454 CTATCCAGAGGTCATAAAGATCCTCAGTAAC-AGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAACTA-TCCAGAGGTCAAAAAGAACCTAGGTAA
3827514 ACTGTCTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 50 0.98
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (60 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGGTCAAAAAGAACCTAGGTAA
Found at i:3828315 original size:20 final size:19
Alignment explanation
Indices: 3828248--3828322 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
3828238 AATGAAGGTA
3828248 TGCATCGATGCACTATACAG
1 TGCATCGATGCACT-TACAG
* *
3828268 TGTATCGATGCATCCTTAACGG
1 TGCATCGATGCA--CTT-ACAG
* *
3828290 TACATCGATGCACTTACTTG
1 TGCATCGATGCACTTAC-AG
*
3828310 TGCATCGGTGCAC
1 TGCATCGATGCAC
3828323 AAAATACATT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 26 0.59
21 1 0.02
22 15 0.34
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTTACAG
Found at i:3832999 original size:30 final size:30
Alignment explanation
Indices: 3832965--3833067 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
3832955 CCCGAAGGAC
3832965 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3832995 CTATCCAGAGGTCAAAAAGGTCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3833025 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3833055 CTGTCCATAGGTC
1 CTATCCAGAGGTC
3833068 CCGAAGAACC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Done.