Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 56 of 349
Found at i:16305759 original size:5 final size:5
Alignment explanation
Indices: 16305749--16305781 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
16305739 TTGTGTGTTC
16305749 TTTAT TTTAT TTT-T TTTATT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
16305782 TCACATGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTAT
Found at i:16313152 original size:10 final size:10
Alignment explanation
Indices: 16313139--16313194 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
16313129 TATTTTAGAT
16313139 AATTTTTTTA
1 AATTTTTTTA
16313149 AATTTTTTTA
1 AATTTTTTTA
***
16313159 TAATTTAAAT-
1 -AATTTTTTTA
*
16313169 AATATTTTTA
1 AATTTTTTTA
16313179 AATTTTTTTA
1 AATTTTTTTA
16313189 TAATTT
1 -AATTT
16313195 AACACTTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 5 0.14
10 19 0.54
11 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:16313161 original size:21 final size:21
Alignment explanation
Indices: 16313137--16313194 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
16313127 ATTATTTTAG
16313137 ATAATTTTTTTAAATTTTTTT
1 ATAATTTTTTTAAATTTTTTT
*** *
16313158 ATAATTTAAAT-AATATTTTT
1 ATAATTTTTTTAAATTTTTTT
16313178 A-AATTTTTTTATAATTT
1 ATAATTTTTTTA-AATTT
16313195 AACACTTATA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 6 0.22
20 9 0.33
21 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATAATTTTTTTAAATTTTTTT
Found at i:16313171 original size:30 final size:30
Alignment explanation
Indices: 16313132--16313196 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
16313122 AAATTATTAT
* *
16313132 TTTAGATAATTTTTTTAAATTTTTTTATAA
1 TTTAAATAATATTTTTAAATTTTTTTATAA
16313162 TTTAAATAATATTTTTAAATTTTTTTATAA
1 TTTAAATAATATTTTTAAATTTTTTTATAA
16313192 TTTAA
1 TTTAA
16313197 CACTTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTAAATAATATTTTTAAATTTTTTTATAA
Found at i:16313214 original size:29 final size:27
Alignment explanation
Indices: 16313180--16313246 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
16313170 ATATTTTTAA
16313180 ATTTTTTTATAATTTAACACTTATATAT
1 ATTTTTTTATAATTTAACA-TTATATAT
* * * *
16313208 ATATTTTTTAAAATTTCACATTATGTTT
1 AT-TTTTTTATAATTTAACATTATATAT
16313236 ATTTTTTTATA
1 ATTTTTTTATA
16313247 TTTTTTTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 8 0.24
28 10 0.30
29 15 0.45
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTTTTTTATAATTTAACATTATATAT
Found at i:16316498 original size:36 final size:36
Alignment explanation
Indices: 16316455--16316526 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
16316445 CCAAATACGC
16316455 CACCTACCTCCACTACACCTATCCCATCACATTCAA
1 CACCTACCTCCACTACACCTATCCCATCACATTCAA
* *
16316491 CACCTACCTCCACTACACCTTTTCCATCACATTCAA
1 CACCTACCTCCACTACACCTATCCCATCACATTCAA
16316527 TGTCTCACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.25
Consensus pattern (36 bp):
CACCTACCTCCACTACACCTATCCCATCACATTCAA
Found at i:16319222 original size:1 final size:1
Alignment explanation
Indices: 16319216--16319240 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16319206 CTGCAGAGAC
16319216 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
16319241 GGGAGCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16328005 original size:118 final size:117
Alignment explanation
Indices: 16327780--16328014 Score: 443
Period size: 117 Copynumber: 2.0 Consensus size: 117
16327770 ATTGTGCACA
*
16327780 ATAATTTATTCCTGACTAAAAAAGGCTCGCACGAATACACATGCATGTGGTTCGAACTGTTGACA
1 ATAATTTATTCCTGACTAAAAAAGGCTCACACGAATACACATGCATGTGGTTCGAACTGTTGACA
16327845 TAGTAAATGGTCATGTTTCCAAACAGTTGTAAACCTATTTCCCAATTCTAAC
66 TAGTAAATGGTCATGTTTCCAAACAGTTGTAAACCTATTTCCCAATTCTAAC
*
16327897 ATAATTTATTCCTGACTAAAAAAGGCTCACACGAATACACATGCATGTGGTTTGAACTGTATGAC
1 ATAATTTATTCCTGACTAAAAAAGGCTCACACGAATACACATGCATGTGGTTCGAACTGT-TGAC
16327962 ATAGTAAATGGTCATGTTTCCAAACAGTTGTAAACCTATTTCCCAATTCTAAC
65 ATAGTAAATGGTCATGTTTCCAAACAGTTGTAAACCTATTTCCCAATTCTAAC
16328015 CAGGGTTACA
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
117 58 0.50
118 57 0.50
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (117 bp):
ATAATTTATTCCTGACTAAAAAAGGCTCACACGAATACACATGCATGTGGTTCGAACTGTTGACA
TAGTAAATGGTCATGTTTCCAAACAGTTGTAAACCTATTTCCCAATTCTAAC
Found at i:16329211 original size:35 final size:36
Alignment explanation
Indices: 16329162--16329230 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
16329152 CTTAGAAAAA
* *
16329162 GCTTTTACTAATATTTCTAACGATTTACCAATATTG
1 GCTTTTACCAATATTTCTAACGATTCACCAATATTG
*
16329198 GCTTTT-CCAATATTTCTAAGGATTCACCAATAT
1 GCTTTTACCAATATTTCTAACGATTCACCAATAT
16329231 CGTTAGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 24 0.80
36 6 0.20
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (36 bp):
GCTTTTACCAATATTTCTAACGATTCACCAATATTG
Found at i:16335676 original size:149 final size:150
Alignment explanation
Indices: 16335494--16335799 Score: 596
Period size: 149 Copynumber: 2.0 Consensus size: 150
16335484 TTAAGAAAAA
16335494 TAAAATTATGAGTAATACTGTATTAGAATTAGAGTTGCATATGGGTCGGACCCTAAAAAAATTCT
1 TAAAATTATGAGTAATACTGTATTAGAATTAGAGTTGCATATGGGTCGGACCCTAAAAAAATTCT
16335559 AGGCTCAATTGATAGGCCCGACCTAACTCAGCCTGAAAAATGGATTTAAATTTTTGCCCAAATTC
66 AGGCTCAATTGATAGGCCCGACCTAACTCAGCCTGAAAAATGGATTTAAATTTTTGCCCAAATTC
*
16335624 GATCTGAAT-AAAAAAATGC
131 GACCTGAATAAAAAAAATGC
16335643 TAAAATTATGAGTAATACTGTATTAGAATTAGAGTTGCATATGGGTCGGACCCTAAAAAAATTCT
1 TAAAATTATGAGTAATACTGTATTAGAATTAGAGTTGCATATGGGTCGGACCCTAAAAAAATTCT
16335708 AGGCTCAATTGATAGGCCCGACCTAACTCAGCCTGAAAAATGGATTTAAATTTTTGCCCAAATTC
66 AGGCTCAATTGATAGGCCCGACCTAACTCAGCCTGAAAAATGGATTTAAATTTTTGCCCAAATTC
16335773 GACCTGAATAAAAAAAATGC
131 GACCTGAATAAAAAAAATGC
16335793 TAAAATT
1 TAAAATT
16335800 GGAGTCTGAT
Statistics
Matches: 155, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
149 138 0.89
150 17 0.11
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (150 bp):
TAAAATTATGAGTAATACTGTATTAGAATTAGAGTTGCATATGGGTCGGACCCTAAAAAAATTCT
AGGCTCAATTGATAGGCCCGACCTAACTCAGCCTGAAAAATGGATTTAAATTTTTGCCCAAATTC
GACCTGAATAAAAAAAATGC
Found at i:16336018 original size:18 final size:18
Alignment explanation
Indices: 16335997--16336051 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
16335987 AAATAATAGC
16335997 AAAATTAACAATAAAATA
1 AAAATTAACAATAAAATA
**
16336015 AAAATTATACAAT-ATCTA
1 AAAATTA-ACAATAAAATA
*
16336033 AAAAATAACAATAAAATA
1 AAAATTAACAATAAAATA
16336051 A
1 A
16336052 TAGCAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.17
18 20 0.67
19 5 0.17
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTAACAATAAAATA
Found at i:16336062 original size:22 final size:22
Alignment explanation
Indices: 16336037--16336079 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16336027 TATCTAAAAA
16336037 ATAACAATAAAATAATAGCAAT
1 ATAACAATAAAATAATAGCAAT
* * *
16336059 ATAATAATGAAATGATAGCAA
1 ATAACAATAAAATAATAGCAA
16336080 AACAGTGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAT
Found at i:16338111 original size:22 final size:21
Alignment explanation
Indices: 16338068--16338106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16338058 TTATCCCAAA
*
16338068 CTCTCAAACCTTTTTACTTTT
1 CTCTCAAAACTTTTTACTTTT
16338089 CTCTCAAAAC-TTTTACTT
1 CTCTCAAAACTTTTTACTT
16338107 CTTTCCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (21 bp):
CTCTCAAAACTTTTTACTTTT
Found at i:16338291 original size:30 final size:30
Alignment explanation
Indices: 16338247--16338305 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16338237 AACTTTTTAT
*
16338247 TTTTTCCCAAAACTTTTACT-CCTTCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCAC
16338276 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
1 TTTTCCCC-AAAACTTTTACTCCCTTCCCA
16338306 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 12 0.44
31 8 0.30
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:16338545 original size:17 final size:17
Alignment explanation
Indices: 16338515--16338610 Score: 65
Period size: 17 Copynumber: 5.5 Consensus size: 17
16338505 TAGTAATAAT
*
16338515 TTTAT-TTATATAAACTA
1 TTTATATTAT-TAAATTA
16338532 TTTATATTATTAAATTAAA
1 TTTATATTATTAAATT--A
* *
16338551 TTTCACATT-TTATATTA
1 TTT-ATATTATTAAATTA
*
16338568 TTTATATTATTAAATTG
1 TTTATATTATTAAATTA
*
16338585 TTTAGTCA-TATTGAA-TA
1 TTTA-T-ATTATTAAATTA
16338602 TTTATATTA
1 TTTATATTA
16338611 AAATTAAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
15 1 0.02
16 7 0.11
17 29 0.46
18 11 0.17
19 11 0.17
20 4 0.06
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTATATTATTAAATTA
Found at i:16356261 original size:17 final size:17
Alignment explanation
Indices: 16356239--16356326 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 17
16356229 GCCCTACTAA
*
16356239 ATCACCTCACTAACTCC
1 ATCACCCCACTAACTCC
16356256 ATCACCCCACTAA----
1 ATCACCCCACTAACTCC
16356269 ATCACCCCACTAACTCC
1 ATCACCCCACTAACTCC
* * *
16356286 ATCACCCAATTAA-ACC
1 ATCACCCCACTAACTCC
16356302 AT---CCCACTAACTCC
1 ATCACCCCACTAACTCC
16356316 ATCACCCCACT
1 ATCACCCCACT
16356327 TGCCACTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 19 0.34
14 4 0.07
16 4 0.07
17 29 0.52
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (17 bp):
ATCACCCCACTAACTCC
Found at i:16356268 original size:30 final size:29
Alignment explanation
Indices: 16356234--16356350 Score: 136
Period size: 30 Copynumber: 4.1 Consensus size: 29
16356224 CCCACGCCCT
16356234 ACTAAATCACCTCACTAACTCCATCACCCC
1 ACTAAATCACC-CACTAACTCCATCACCCC
*
16356264 ACTAAATCACCCCACTAACTCCATCACCCA
1 ACTAAATCA-CCCACTAACTCCATCACCCC
* *
16356294 ATTAAACCATCCCACTAACTCCATCACCCC
1 ACTAAATCA-CCCACTAACTCCATCACCCC
*
16356324 ACT---T--GCCACTAACTCCATCACCCC
1 ACTAAATCACCCACTAACTCCATCACCCC
16356348 ACT
1 ACT
16356351 TGCCTACAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
24 22 0.28
30 54 0.69
31 2 0.03
ACGTcount: A:0.32, C:0.47, G:0.01, T:0.20
Consensus pattern (29 bp):
ACTAAATCACCCACTAACTCCATCACCCC
Found at i:16356274 original size:13 final size:13
Alignment explanation
Indices: 16356256--16356281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16356246 CACTAACTCC
16356256 ATCACCCCACTAA
1 ATCACCCCACTAA
16356269 ATCACCCCACTAA
1 ATCACCCCACTAA
16356282 CTCCATCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:16356337 original size:24 final size:24
Alignment explanation
Indices: 16356305--16356354 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
16356295 TTAAACCATC
16356305 CCACTAACTCCATCACCCCACTTG
1 CCACTAACTCCATCACCCCACTTG
16356329 CCACTAACTCCATCACCCCACTTG
1 CCACTAACTCCATCACCCCACTTG
16356353 CC
1 CC
16356355 TACAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.52, G:0.04, T:0.20
Consensus pattern (24 bp):
CCACTAACTCCATCACCCCACTTG
Found at i:16356735 original size:3 final size:3
Alignment explanation
Indices: 16356712--16356876 Score: 83
Period size: 3 Copynumber: 55.7 Consensus size: 3
16356702 AGGGAGAGTG
* * *
16356712 TTA TTT TTA ATA TTG TTA TTA TTA TATA TTA TTA TTA -TA TTTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA
* * * *
16356757 TTA TTA CTG TTA CTA TTA TT- TTA -TA TATA TTTA TTA TCA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TT-A
* * ** ** * * *
16356803 TTT TTT TTA TTA GAA ACA -TA TTG TTA TTT TTA TTA TTT TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
16356849 TTA TTA TTA TTA TTA ATA -TA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16356877 GTCTTCTATT
Statistics
Matches: 122, Mismatches: 28, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
2 13 0.11
3 96 0.79
4 12 0.10
5 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:16356743 original size:10 final size:11
Alignment explanation
Indices: 16356728--16356876 Score: 75
Period size: 11 Copynumber: 13.9 Consensus size: 11
16356718 TTAATATTGT
16356728 TATTATTA-TA
1 TATTATTATTA
16356738 TATTATTATTA
1 TATTATTATTA
*
16356749 TA-T-TTATTT
1 TATTATTATTA
* *
16356758 TATTACTGTTA
1 TATTATTATTA
16356769 CTATTATT-TTA
1 -TATTATTATTA
16356780 TATATATTTATTA
1 TAT-TA-TTATTA
16356793 TCATTATTA--A
1 T-ATTATTATTA
16356803 T-TT-TT-TT-
1 TATTATTATTA
** **
16356810 TATTAGAAACA
1 TATTATTATTA
* *
16356821 TATTGTTATTTT
1 TATTATTA-TTA
*
16356833 TATTATTTTTA
1 TATTATTATTA
16356844 TATTATTATTA
1 TATTATTATTA
*
16356855 TTATTATTAATA
1 -TATTATTATTA
16356867 TATTATTATT
1 TATTATTATT
16356877 GTCTTCTATT
Statistics
Matches: 102, Mismatches: 21, Indels: 31
0.66 0.14 0.20
Matches are distributed among these distances:
7 3 0.03
8 4 0.04
9 7 0.07
10 15 0.15
11 38 0.37
12 27 0.26
13 6 0.06
14 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:16356846 original size:23 final size:23
Alignment explanation
Indices: 16356820--16356876 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
16356810 TATTAGAAAC
* * **
16356820 ATATTGTTATTTTTATTATTTTT
1 ATATTATTATTATTATTATTAAT
16356843 ATATTATTATTATTATTATTAAT
1 ATATTATTATTATTATTATTAAT
16356866 ATATTATTATT
1 ATATTATTATT
16356877 GTCTTCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATATTATTATTATTATTATTAAT
Found at i:16359252 original size:24 final size:24
Alignment explanation
Indices: 16359174--16359253 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
16359164 TAAACTCCTT
16359174 TGAGCTGATGAACAGTAAGCTC-TA
1 TGAGCTG-TGAACAGTAAGCTCTTA
* * *
16359198 TCGAGCTAG-AAACAGTAAACTCTGA
1 T-GAGCT-GTGAACAGTAAGCTCTTA
**
16359223 CAAGCTGTGAACAGTAAGCTCTTA
1 TGAGCTGTGAACAGTAAGCTCTTA
16359247 TGAGCTG
1 TGAGCTG
16359254 ATATATCGGT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
23 1 0.02
24 34 0.81
25 6 0.14
26 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (24 bp):
TGAGCTGTGAACAGTAAGCTCTTA
Found at i:16366147 original size:9 final size:9
Alignment explanation
Indices: 16366128--16366160 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
16366118 TATAAAGTAC
16366128 AATATTATTA
1 AATA-TATTA
16366138 AATATATTA
1 AATATATTA
16366147 AATATATTA
1 AATATATTA
16366156 AATAT
1 AATAT
16366161 GATTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATATATTA
Found at i:16366199 original size:16 final size:15
Alignment explanation
Indices: 16366173--16366214 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
16366163 TTTATTATTT
*
16366173 TAATAAATTTTTTGA
1 TAATAAATTTTTTAA
*
16366188 TATTATAATTTTTTAA
1 TAATA-AATTTTTTAA
16366204 TAATAAATTTT
1 TAATAAATTTT
16366215 AACAATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TAATAAATTTTTTAA
Found at i:16371858 original size:15 final size:15
Alignment explanation
Indices: 16371838--16371869 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16371828 CCTTTTGCTC
16371838 TTCGATTTCACTACT
1 TTCGATTTCACTACT
16371853 TTCGATTTCACTACT
1 TTCGATTTCACTACT
16371868 TT
1 TT
16371870 TGTTTGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCGATTTCACTACT
Found at i:16379584 original size:23 final size:23
Alignment explanation
Indices: 16379541--16379584 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16379531 ATACATAAAC
* *
16379541 TAAAACATATAAACAAGGAAATA
1 TAAAACAAATAAACAAAGAAATA
*
16379564 TAAAACAAATAAATAAAGAAA
1 TAAAACAAATAAACAAAGAAA
16379585 ACAAAAAAAA
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:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (23 bp):
TAAAACAAATAAACAAAGAAATA
Found at i:16380575 original size:21 final size:21
Alignment explanation
Indices: 16380535--16380575 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16380525 ATTATTGTAC
* **
16380535 GTATATTTCTAATATTATATT
1 GTATATTTCTAACACAATATT
16380556 GTATATTTCTAACACAATAT
1 GTATATTTCTAACACAATAT
16380576 ATATATATAT
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:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (21 bp):
GTATATTTCTAACACAATATT
Found at i:16385198 original size:23 final size:23
Alignment explanation
Indices: 16385172--16385216 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16385162 TGGGTATGTG
*
16385172 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
16385195 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
16385217 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:16398359 original size:37 final size:37
Alignment explanation
Indices: 16398313--16398434 Score: 147
Period size: 37 Copynumber: 3.3 Consensus size: 37
16398303 TCCATTTGAA
* *
16398313 AACATGCCAAGTGCTCATAAGAGCTTATCCACCCGAT
1 AACATGCCAAATGCTCATAAGAGCTTATCCACCAGAT
* * ** * *
16398350 AACACGCCAATTGCTCCGAAGAGC-TAGTCCAACAGAA
1 AACATGCCAAATGCTCATAAGAGCTTA-TCCACCAGAT
*
16398387 AACATGCCAAATGCTCATAAGAGCTAATCCACCAGAT
1 AACATGCCAAATGCTCATAAGAGCTTATCCACCAGAT
16398424 AACATGCCAAA
1 AACATGCCAAA
16398435 ACAGGGAGTA
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
36 2 0.03
37 66 0.96
38 1 0.01
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.17
Consensus pattern (37 bp):
AACATGCCAAATGCTCATAAGAGCTTATCCACCAGAT
Found at i:16398660 original size:10 final size:10
Alignment explanation
Indices: 16398637--16398665 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16398627 CAATAAAACA
16398637 ATTATATC-T
1 ATTATATCAT
16398646 ATTATATCAT
1 ATTATATCAT
16398656 ATTATATCAT
1 ATTATATCAT
16398666 CTAACATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTATATCAT
Found at i:16400434 original size:19 final size:20
Alignment explanation
Indices: 16400410--16400450 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16400400 ATAAATTGTA
*
16400410 AAAAATTGAAAACT-TAAAT
1 AAAAATTAAAAACTCTAAAT
*
16400429 AAAAATTAAAAATTCTAAAT
1 AAAAATTAAAAACTCTAAAT
16400449 AA
1 AA
16400451 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATTAAAAACTCTAAAT
Found at i:16400469 original size:26 final size:25
Alignment explanation
Indices: 16400410--16400475 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
16400400 ATAAATTGTA
* *
16400410 AAAAATTGAAAACTTAA-ATAAAAATT
1 AAAAATTCAAAA--TAATATAAAAAAT
*
16400436 AAAAATTCTAAATAATATAAAAAAT
1 AAAAATTCAAAATAATATAAAAAAT
*
16400461 AAATTATTCAAAATA
1 AAA-AATTCAAAATA
16400476 TTGGAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 3 0.09
25 11 0.33
26 19 0.58
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAATTCAAAATAATATAAAAAAT
Found at i:16403336 original size:49 final size:49
Alignment explanation
Indices: 16403268--16403555 Score: 295
Period size: 49 Copynumber: 6.0 Consensus size: 49
16403258 CAAATTGTGA
* *
16403268 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
16403317 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
** * **
16403367 AATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGT-CTCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATAATT
* **
16403416 AGGTCAC--GTGT-G---T-AGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * **
16403459 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTATACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
16403509 GGTCACATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATAA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
16403556 CTTTGGCTAC
Statistics
Matches: 198, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
43 35 0.18
44 1 0.01
45 4 0.02
46 1 0.01
47 1 0.01
48 4 0.02
49 86 0.43
50 66 0.33
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:16403447 original size:43 final size:43
Alignment explanation
Indices: 16403386--16403474 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
16403376 TGTAGTACTA
*
16403386 AGTGCAGGCTACTACGTGTCTCAGATGGTTAGGTCACGTGTGT
1 AGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGT
16403429 AGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGT
1 AGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGT
16403472 AGT
1 AGT
16403475 ACTAAGTGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (43 bp):
AGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGT
Found at i:16403483 original size:93 final size:97
Alignment explanation
Indices: 16403267--16403558 Score: 310
Period size: 99 Copynumber: 3.0 Consensus size: 97
16403257 ACAAATTGTG
* *
16403267 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTC-CACGTGTAG-
* *
16403332 ACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
64 A-TAAGTGCAGGCTACTACGCGTACCAGATAACTT
* **
16403367 A-ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGT-CTCAGATGGTTAGGT-CACGTGT-G
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATAATT-GGTCCACGTGTAG
* * **
16403428 -T-AGTGCAGGCTACTACGTGTATCAGAT-GGTT
64 ATAAGTGCAGGCTACTACGCGTACCAGATAACTT
* ** *
16403459 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTATACTGGATAATTGGTCACATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTC-CACGTGTAG-
* *
16403524 ACTAAGTGCAGGCTATTATGCGTACCAGATAACTT
64 A-TAAGTGCAGGCTACTACGCGTACCAGATAACTT
16403559 TGGCTACAAG
Statistics
Matches: 156, Mismatches: 24, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
92 6 0.04
93 62 0.40
94 8 0.05
95 1 0.01
97 1 0.01
98 8 0.05
99 64 0.41
100 6 0.04
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (97 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCCACGTGTAGAT
AAGTGCAGGCTACTACGCGTACCAGATAACTT
Found at i:16408730 original size:38 final size:38
Alignment explanation
Indices: 16408676--16408764 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 38
16408666 GATATGTTTT
*
16408676 ACATATATTCAATTCAAAAAT-GCCAGTAGACATGCTTA
1 ACATGTATTCAATTCAAAAATAG-CAGTAGACATGCTTA
* * *
16408714 ACATGTATTCAGTTCAACATTAGCAGTAGACATGCTTA
1 ACATGTATTCAATTCAAAAATAGCAGTAGACATGCTTA
*
16408752 ACATGTACTCAAT
1 ACATGTATTCAAT
16408765 AGGGTGGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
38 43 0.98
39 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (38 bp):
ACATGTATTCAATTCAAAAATAGCAGTAGACATGCTTA
Found at i:16409627 original size:45 final size:45
Alignment explanation
Indices: 16409578--16409668 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
16409568 TATTTCATTC
16409578 ACACATAAATTTGTTAATTTTTTTTACATTGAATCCAAATCCGGA
1 ACACATAAATTTGTTAATTTTTTTTACATTGAATCCAAATCCGGA
16409623 ACACATAAATTTGTTAATTTTTTTTACATTGAATCCAAATCCGGA
1 ACACATAAATTTGTTAATTTTTTTTACATTGAATCCAAATCCGGA
16409668 A
1 A
16409669 TCATGAATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (45 bp):
ACACATAAATTTGTTAATTTTTTTTACATTGAATCCAAATCCGGA
Found at i:16415397 original size:13 final size:13
Alignment explanation
Indices: 16415379--16415409 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16415369 AACAAGAGAA
16415379 AATCGAAGAAAAC
1 AATCGAAGAAAAC
*
16415392 AATCGAAGAACAC
1 AATCGAAGAAAAC
16415405 AATCG
1 AATCG
16415410 GAGCCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (13 bp):
AATCGAAGAAAAC
Found at i:16421498 original size:22 final size:23
Alignment explanation
Indices: 16421470--16421517 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
16421460 TTCTCTTAAC
*
16421470 AAAAAATTTAAAA-AATTTCTAA
1 AAAAAATTCAAAATAATTTCTAA
*
16421492 AAAAAATTCAAAATAATTTTTAA
1 AAAAAATTCAAAATAATTTCTAA
16421515 AAA
1 AAA
16421518 TTCAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATTCAAAATAATTTCTAA
Found at i:16421533 original size:18 final size:18
Alignment explanation
Indices: 16421493--16421549 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
16421483 AATTTCTAAA
*
16421493 AAAAATTCAAAATAATTTTT
1 AAAAATTC-AAAT-ATTTAT
16421513 AAAAATTCAAATATTTAT
1 AAAAATTCAAATATTTAT
16421531 AAAAATTCCAAAT-TTTAT
1 AAAAATT-CAAATATTTAT
16421549 A
1 A
16421550 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 18 0.51
19 9 0.26
20 8 0.23
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTCAAATATTTAT
Found at i:16421580 original size:19 final size:16
Alignment explanation
Indices: 16421557--16421608 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 16
16421547 ATATATTTTT
*
16421557 TAAAATATTATAAAAAA
1 TAAAAAATT-TAAAAAA
16421574 TAAAAAATTTAAAAAA
1 TAAAAAATTTAAAAAA
16421590 TAAATAAAAATTTAAAAAA
1 T--A-AAAAATTTAAAAAA
16421609 CTCTAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 8 0.26
17 8 0.26
18 1 0.03
19 14 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATTTAAAAAA
Found at i:16421596 original size:20 final size:19
Alignment explanation
Indices: 16421571--16421608 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
16421561 ATATTATAAA
16421571 AAATAAAAAATTTAAAAAAT
1 AAAT-AAAAATTTAAAAAAT
16421591 AAATAAAAATTTAAAAAA
1 AAATAAAAATTTAAAAAA
16421609 CTCTAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAAATTTAAAAAAT
Found at i:16422027 original size:16 final size:16
Alignment explanation
Indices: 16421994--16422027 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16421984 TGGGGGTGTT
* *
16421994 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16422010 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16422026 AA
1 AA
16422028 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16424856 original size:21 final size:21
Alignment explanation
Indices: 16424830--16424870 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16424820 AGACGAGCAA
* *
16424830 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16424851 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16424871 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16426807 original size:16 final size:16
Alignment explanation
Indices: 16426774--16426807 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16426764 GGAGATTGTT
* *
16426774 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16426790 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16426806 AA
1 AA
16426808 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16428557 original size:21 final size:19
Alignment explanation
Indices: 16428532--16428581 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
16428522 AGAAGTTAGA
16428532 AATTTTAAAATATTATATTAT-
1 AATTTTAAAA-A-TA-ATTATG
16428553 AATTTTAACAAATAATTATG
1 AATTTTAA-AAATAATTATG
16428573 AATTTTAAA
1 AATTTTAAA
16428582 CCTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.22
20 10 0.37
21 9 0.33
22 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
AATTTTAAAAATAATTATG
Found at i:16429257 original size:14 final size:14
Alignment explanation
Indices: 16429238--16429279 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
16429228 GTTTGCAAGT
16429238 AAAATGATTTCTGG
1 AAAATGATTTCTGG
16429252 AAAATGATTTACT-G
1 AAAATGATTT-CTGG
16429266 AAAAT-ATTTTCTGG
1 AAAATGA-TTTCTGG
16429280 TATTTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 20 0.80
15 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:16429387 original size:20 final size:20
Alignment explanation
Indices: 16429362--16429400 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16429352 GCTTTTACAT
16429362 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
16429382 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
16429401 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:16432735 original size:52 final size:48
Alignment explanation
Indices: 16432552--16432758 Score: 168
Period size: 47 Copynumber: 4.2 Consensus size: 48
16432542 TGCACATAGT
* * ** * *
16432552 CACATATCACATACCGAGGCCATAACCCAGCCATGGTCTTACACGG-AT
1 CACATATCACAT-CCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
* * * * * * *
16432600 CACATATCACA-CTGATGTCATATCCCAAATATGGTCTTATACAGTAG
1 CACATATCACATCCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
16432647 CACATATCACA-CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACATCCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
16432694 CACATATCACATTTGTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAAAT
1 CACATATCACA----TCCGAAGCCATAGCCCAGATATGGTCTTATACGG-AAG
*
16432747 CACATTTCACAT
1 CACATATCACAT
16432759 GCTGTCATGG
Statistics
Matches: 130, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
46 24 0.18
47 53 0.41
48 11 0.08
49 1 0.01
52 29 0.22
53 12 0.09
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (48 bp):
CACATATCACATCCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:16436406 original size:50 final size:50
Alignment explanation
Indices: 16436324--16436423 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
16436314 GAGATGAATT
*
16436324 GCTAGGAGTGATGGCGGTAATTATGAATTTTTTTAAAGAATATTGAAGTA
1 GCTAGGAGTGATGGCGGTAATTATGAAGTTTTTTAAAGAATATTGAAGTA
*
16436374 GCTATGAGTGATGGCGGTAATTATGAAGTTTTTTAAAGAATATTGAAGTA
1 GCTAGGAGTGATGGCGGTAATTATGAAGTTTTTTAAAGAATATTGAAGTA
16436424 ATCTTTGCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (50 bp):
GCTAGGAGTGATGGCGGTAATTATGAAGTTTTTTAAAGAATATTGAAGTA
Found at i:16443186 original size:47 final size:46
Alignment explanation
Indices: 16443090--16443267 Score: 198
Period size: 47 Copynumber: 3.8 Consensus size: 46
16443080 GGAAATTGAG
* * *
16443090 ATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATGA-GAATTATG-AGGC
1 ATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATG---GATGCAAGC
*
16443137 ATCCGAACTCGTTGAGTTGCGTTTAGAGTTCACTTATGGATGCAAGC
1 ATCCGAACTCGTTGAGTTGCGTTTCGAGTTCA-TTATGGATGCAAGC
* * * * * *
16443184 ATCCAAACTCGTTGAGCTGTGTTCCGAGTTTATTATGGATGCAAAC
1 ATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATGGATGCAAGC
* *
16443230 ACCCGAGCTCGTTGAGTTGCGTTTCGAGTTCATTATGG
1 ATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATGG
16443268 GTGAGATTAT
Statistics
Matches: 110, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
46 47 0.43
47 60 0.55
48 2 0.02
49 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATGGATGCAAGC
Found at i:16443241 original size:46 final size:46
Alignment explanation
Indices: 16443142--16443267 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 46
16443132 GAGGCATCCG
* ** * *
16443142 AACTCGTTGAGTTGCGTTTAGAGTTCACTTATGGATGCAAGCATCCA
1 AACTCGTTGAGCTGCGTTCCGAGTTCA-TTATGGATGCAAACACCCA
* * *
16443189 AACTCGTTGAGCTGTGTTCCGAGTTTATTATGGATGCAAACACCCG
1 AACTCGTTGAGCTGCGTTCCGAGTTCATTATGGATGCAAACACCCA
* * *
16443235 AGCTCGTTGAGTTGCGTTTCGAGTTCATTATGG
1 AACTCGTTGAGCTGCGTTCCGAGTTCATTATGG
16443268 GTGAGATTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
46 44 0.67
47 22 0.33
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (46 bp):
AACTCGTTGAGCTGCGTTCCGAGTTCATTATGGATGCAAACACCCA
Found at i:16446444 original size:9 final size:9
Alignment explanation
Indices: 16446432--16446461 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16446422 ATTATAATAT
16446432 TTATATTTA
1 TTATATTTA
16446441 TTATATTTA
1 TTATATTTA
*
16446450 TTGTATTTA
1 TTATATTTA
16446459 TTA
1 TTA
16446462 CATGTCTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATATTTA
Found at i:16446542 original size:19 final size:19
Alignment explanation
Indices: 16446518--16446609 Score: 77
Period size: 19 Copynumber: 4.9 Consensus size: 19
16446508 ACTTATGTAT
16446518 TATATTATATATATTTTAA
1 TATATTATATATATTTTAA
*
16446537 TATATTATATGTATTTTAA
1 TATATTATATATATTTTAA
*
16446556 TATTATGT-TATATATATT-A
1 TA-TAT-TATATATATTTTAA
* *
16446575 TATA-CATATAT-TTTCAA
1 TATATTATATATATTTTAA
16446592 TATTATTA-ATTATATTTT
1 TA-TATTATA-TATATTTT
16446610 CTTATAATCT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.04
17 8 0.14
18 5 0.09
19 27 0.47
20 14 0.25
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATTATATATATTTTAA
Found at i:16446682 original size:22 final size:22
Alignment explanation
Indices: 16446657--16446700 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16446647 TATGTTCCTA
*
16446657 AATACTATGTTA-TATATATTTT
1 AATACCATGTTAGTAT-TATTTT
16446679 AATACCATGTTAGTATTATTTT
1 AATACCATGTTAGTATTATTTT
16446701 TGTACTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (22 bp):
AATACCATGTTAGTATTATTTT
Found at i:16459573 original size:91 final size:91
Alignment explanation
Indices: 16459407--16459575 Score: 214
Period size: 91 Copynumber: 1.9 Consensus size: 91
16459397 TTCTGTTTTT
* * * * *
16459407 AAAATTCAACTCATATTTCGAGAAATGAGTTAAGCCTCAAGACACGTTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
*
16459472 GTTCTTTCAAAAAAAAATAAAAAAGA
66 GTTCTGTCAAAAAAAAATAAAAAAGA
* ** * * *
16459498 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
16459563 TGTT-TGTCAAAAA
66 -GTTCTGTCAAAAA
16459576 TCAACTCATA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
91 62 0.95
92 3 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (91 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
GTTCTGTCAAAAAAAAATAAAAAAGA
Found at i:16459650 original size:90 final size:88
Alignment explanation
Indices: 16459553--16459816 Score: 290
Period size: 90 Copynumber: 3.0 Consensus size: 88
16459543 GCTGAGGTAA
16459553 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
1 TTTCAATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
*
16459618 GCTGAGGAGTTTTCAATTTCTGTTT
65 GCTGAGGA-TTTTAAATTTCTGTTT
* * * *
16459643 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACAT
1 TTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
* * *
16459708 GCTGAGCTATTTTTAATTTC-G-AT
65 GCTGAG-GATTTTAAATTTCTGTTT
* * * **
16459731 TTT-AATGTCTGTTTT-AAAGAGTCAATTCATATTAAGAGAGGTGAGTTGAGCCTCAGG---ACA
1 TTTCAATTTCTGTTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACA
*
16459791 CGCTGAGGTATTTTAAATTTCTGTTT
64 TGCTGAGG-ATTTTAAATTTCTGTTT
16459817 GTCAAAAATC
Statistics
Matches: 147, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
84 20 0.14
85 4 0.03
86 34 0.23
87 7 0.05
88 4 0.03
89 1 0.01
90 73 0.50
91 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (88 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
CTGAGGATTTTAAATTTCTGTTT
Found at i:16459836 original size:73 final size:73
Alignment explanation
Indices: 16459752--16460015 Score: 260
Period size: 73 Copynumber: 3.4 Consensus size: 73
16459742 TTTTAAAGAG
* * *
16459752 TCAATTCATATTAAGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCTGTTT
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCTGTTT
16459817 GTCAAAAA
66 GTCAAAAA
* * * * * * * *
16459825 TCAACTCATATTGCGAGAAGTGAGTTGAGCAT-TGGCTCATGTGCTGAGCTATTTTTAATTCCTG
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGG-ACA--CGCTGAGGTATTTTAAATTTCTG
*
16459889 TTTTAATGTCTGTTTTAAAGAG
63 --TT--TGTC------AAA-AA
* *
16459911 TCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCTGTTT
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCTGTTT
16459976 GTCAAAAA
66 GTCAAAAA
*
16459984 TCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCT
16460016 TGGCTCACGT
Statistics
Matches: 150, Mismatches: 26, Indels: 30
0.73 0.13 0.15
Matches are distributed among these distances:
72 2 0.01
73 59 0.39
74 3 0.02
75 19 0.13
77 2 0.01
79 4 0.03
80 4 0.03
82 2 0.01
84 19 0.13
85 3 0.02
86 31 0.21
87 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.34
Consensus pattern (73 bp):
TCAACTCATATTACGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAAATTTCTGTTT
GTCAAAAA
Found at i:16459891 original size:75 final size:74
Alignment explanation
Indices: 16459792--16460050 Score: 252
Period size: 75 Copynumber: 3.3 Consensus size: 74
16459782 CTCAGGACAC
* *
16459792 GCTGAGGTATTTTAAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCAT
1 GCTGAGCTATTTTAAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
16459857 TGGCTCATGT
66 TGGCTCA-GT
* * * * * *
16459867 GCTGAGCTATTTTTAATTCCTGTTTTAATGTCTGTTTTAAAGAGTCAATTCATATTACGAGAGGT
1 GCTGAGCTATTTTAAATTTCTG--TT--TGTC------AAA-AATCAACTCATATTGCGAGAAGT
* * *
16459932 GAGTTGAGCCTCAGG-ACA-C
55 GAGTTGAGCCT-TGGCTCAGT
*
16459951 GCTGAGGTATTTTAAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 GCTGAGCTATTTTAAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
16460016 TGGCTCACGT
66 TGGCTCA-GT
* *
16460026 GCTGAGCTATTTTTAATTTTTGTTT
1 GCTGAGCTATTTTAAATTTCTGTTT
16460051 TAATGTCTAT
Statistics
Matches: 145, Mismatches: 24, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
72 2 0.01
73 32 0.22
74 3 0.02
75 41 0.28
77 2 0.01
79 4 0.03
80 4 0.03
82 2 0.01
84 19 0.13
85 3 0.02
86 31 0.21
87 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (74 bp):
GCTGAGCTATTTTAAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
TGGCTCAGT
Found at i:16459934 original size:86 final size:84
Alignment explanation
Indices: 16459825--16460099 Score: 277
Period size: 86 Copynumber: 3.4 Consensus size: 84
16459815 TTGTCAAAAA
* * *
16459825 TCAACTCATATTGCGAGAAGTGAGTTGAGCATTGGCTCATGTGCTGAGCTATTTTTAATTCCTGT
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCTTGGCTCA-GTGCTGAGCTATTTTTAATTTCTGT
16459890 TTTAATGTCTGTTTTAAAGAG
65 TTTAATGTCT-TTTTAAAGAG
* * * * * * *
16459911 TCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGG-ACA-CGCTGAGGTATTTTAAATTTCTG-
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCT-TGGCTCAGTGCTGAGCTATTTTTAATTTCTGT
*
16459973 -TT--TGTC-----AAA-AA
65 TTTAATGTCTTTTTAAAGAG
* *
16459984 TCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTTAATTTTTGT
1 TCAACTCATATTACGAGAAGTGAGTTGAGCCTTGGCTCA-GTGCTGAGCTATTTTTAATTTCTGT
16460049 TTTAATGTCTATTTTAAAGAG
65 TTTAATGTCT-TTTTAAAGAG
* * *
16460070 TCAATTCATATTACAAGAAATGAGTTGAGC
1 TCAACTCATATTACGAGAAGTGAGTTGAGC
16460100 TCAGGATCAC
Statistics
Matches: 149, Mismatches: 25, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
72 2 0.01
73 32 0.21
74 3 0.02
75 19 0.13
77 2 0.01
79 4 0.03
80 4 0.03
82 2 0.01
84 19 0.13
85 3 0.02
86 57 0.38
87 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
TCAACTCATATTACGAGAAGTGAGTTGAGCCTTGGCTCAGTGCTGAGCTATTTTTAATTTCTGTT
TTAATGTCTTTTTAAAGAG
Found at i:16459936 original size:159 final size:159
Alignment explanation
Indices: 16459659--16460105 Score: 781
Period size: 159 Copynumber: 2.8 Consensus size: 159
16459649 TTTATATTTT
*
16459659 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACATGCTGAGCTATTTTTAA
1 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTTAA
*
16459724 TTTC-GATTTTAATGTCTGTTTTAAAGAGTCAATTCATATTAAGAGAGGTGAGTTGAGCCTCAGG
66 TTTCTG-TTTTAATGTCTGTTTTAAAGAGTCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGG
16459788 ACACGCTGAGGTATTTTAAATTTCTGTTTG
130 ACACGCTGAGGTATTTTAAATTTCTGTTTG
* *
16459818 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCATTGGCTCATGTGCTGAGCTATTTTTAA
1 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTTAA
*
16459883 TTCCTGTTTTAATGTCTGTTTTAAAGAGTCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
66 TTTCTGTTTTAATGTCTGTTTTAAAGAGTCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
16459948 CACGCTGAGGTATTTTAAATTTCTGTTTG
131 CACGCTGAGGTATTTTAAATTTCTGTTTG
16459977 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTTAA
1 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTTAA
* * * **
16460042 TTTTTGTTTTAATGTCTATTTTAAAGAGTCAATTCATATTACAAGAAATGAGTTGAG-CTCAGGA
66 TTTCTGTTTTAATGTCTGTTTTAAAGAGTCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
16460106 TCACATGCCA
Statistics
Matches: 274, Mismatches: 13, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
158 7 0.03
159 266 0.97
160 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (159 bp):
TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTTAA
TTTCTGTTTTAATGTCTGTTTTAAAGAGTCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
CACGCTGAGGTATTTTAAATTTCTGTTTG
Found at i:16461920 original size:9 final size:9
Alignment explanation
Indices: 16461908--16461937 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16461898 ATTATAATAT
16461908 TTATATTTA
1 TTATATTTA
16461917 TTATATTTA
1 TTATATTTA
*
16461926 TTGTATTTA
1 TTATATTTA
16461935 TTA
1 TTA
16461938 CATGTCGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATATTTA
Found at i:16462018 original size:19 final size:19
Alignment explanation
Indices: 16461994--16462054 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
16461984 ACTTATGTAT
16461994 TATATTATATATATATTAA
1 TATATTATATATATATTAA
* *
16462013 TATATTATATGTATTTTAA
1 TATATTATATATATATTAA
16462032 TATTATGT-TATATATATT-A
1 TA-TAT-TATATATATATTAA
16462051 TATA
1 TATA
16462055 CATATATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.06
19 22 0.61
20 11 0.31
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATATTATATATATATTAA
Found at i:16462160 original size:24 final size:24
Alignment explanation
Indices: 16462133--16462179 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16462123 TATGTTCCTA
*
16462133 AATACTATGTTA-TATATATTTTTT
1 AATACCATGTTAGTAT-TATTTTTT
16462157 AATACCATGTTAGTATTATTTTT
1 AATACCATGTTAGTATTATTTTT
16462180 GTACTATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
AATACCATGTTAGTATTATTTTTT
Found at i:16462858 original size:26 final size:26
Alignment explanation
Indices: 16462829--16462884 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
16462819 TGATACAAAT
*
16462829 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16462855 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16462881 TGAT
1 TGAT
16462885 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16464401 original size:26 final size:25
Alignment explanation
Indices: 16464372--16464423 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
16464362 TTTACAGTTT
16464372 TACCCCTAGTAGATAAATTACCGAAA
1 TACCCCTAG-AGATAAATTACCGAAA
* * *
16464398 TACCCCTAGGGTTAAATTACCTAAA
1 TACCCCTAGAGATAAATTACCGAAA
16464423 T
1 T
16464424 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (25 bp):
TACCCCTAGAGATAAATTACCGAAA
Found at i:16468599 original size:21 final size:21
Alignment explanation
Indices: 16468544--16468589 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
16468534 TGTAGCATAG
*
16468544 AAGTGCATAT-AGGGGCACGA
1 AAGTGCAAATCAGGGGCACGA
*
16468564 GAGTGCAAATCAGGGGCACGA
1 AAGTGCAAATCAGGGGCACGA
16468585 AAGTG
1 AAGTG
16468590 TAATCAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.35, C:0.15, G:0.37, T:0.13
Consensus pattern (21 bp):
AAGTGCAAATCAGGGGCACGA
Found at i:16468600 original size:20 final size:21
Alignment explanation
Indices: 16468556--16468601 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16468546 GTGCATATAG
* *
16468556 GGGCACGAGAGTGCAAATCAG
1 GGGCACGAAAGTGCAAATCAA
*
16468577 GGGCACGAAAGTG-TAATCAA
1 GGGCACGAAAGTGCAAATCAA
16468597 GGGCA
1 GGGCA
16468602 TTGGAGGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.35, C:0.17, G:0.37, T:0.11
Consensus pattern (21 bp):
GGGCACGAAAGTGCAAATCAA
Found at i:16473556 original size:15 final size:15
Alignment explanation
Indices: 16473538--16473572 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
16473528 ATAATAGTAG
*
16473538 TAATAGTAATAAAAA
1 TAATAGTAACAAAAA
16473553 TAATAGTAACAAAAA
1 TAATAGTAACAAAAA
16473568 TAATA
1 TAATA
16473573 CCAAGGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (15 bp):
TAATAGTAACAAAAA
Found at i:16473734 original size:17 final size:18
Alignment explanation
Indices: 16473714--16473751 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16473704 CAAAAATGAT
16473714 AATGATAATA-AAATAAA
1 AATGATAATAGAAATAAA
* *
16473731 AATGATACTAGCAATAAA
1 AATGATAATAGAAATAAA
16473749 AAT
1 AAT
16473752 AGTAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (18 bp):
AATGATAATAGAAATAAA
Found at i:16474077 original size:3 final size:3
Alignment explanation
Indices: 16473685--16474065 Score: 189
Period size: 3 Copynumber: 125.0 Consensus size: 3
16473675 AAATAAAGAT
* * * * * * *
16473685 ATA ATA GTA ATA ATA ATT ACA AAA ATG ATA ATG ATA ATA A-A ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** * * * *
16473732 ATG ATA CTA GCA ATA AAA ATA GTA ATA ATA GTA ATA AGA ACGTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA ATA
* * *
16473779 AAA AGA A-A AGA GATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
* * * * * * *
16473825 AT- ATA TTG ATA ATGA ACA ATA ATA A-A AGGA ATA AAA ATA ACA GTA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* * * * * *
16473870 ATA ATA AGA TTA TTA ATA ATA TTA ATA ATA GTA ATA ATA ACA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
16473917 ATAA ATA ATA ATA TATA CATGA AAA ATA AAA ATA ATA ATG ATA ATA GTA
1 AT-A ATA ATA ATA -ATA -AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
16473966 ATA AAA ATA AAA ACA GTA ACA ATG ATA ATA ATA ATA TTG ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
16474012 ATA ATA ATA GTA ATA ATA ATA CTA ATA ATA ATA A-A GTGA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
16474057 ATA ATA ATA
1 ATA ATA ATA
16474066 GATTCATAAT
Statistics
Matches: 275, Mismatches: 86, Indels: 34
0.70 0.22 0.09
Matches are distributed among these distances:
2 11 0.04
3 239 0.87
4 22 0.08
5 3 0.01
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:16475862 original size:16 final size:15
Alignment explanation
Indices: 16475825--16475867 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
16475815 AAAATTTGAT
*
16475825 TTTAAAATAATTTTAA
1 TTTAAAATGA-TTTAA
*
16475841 TATAAAATGATTTAA
1 TTTAAAATGATTTAA
16475856 GTTTAAAATGAT
1 -TTTAAAATGAT
16475868 AAGAAACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (15 bp):
TTTAAAATGATTTAA
Found at i:16477485 original size:13 final size:13
Alignment explanation
Indices: 16477464--16477529 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
16477454 AGTTTGGCAA
16477464 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
16477477 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
16477490 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
* *
16477503 TGATTTTGAGAAG
1 TGCTTTTGAAAAG
16477516 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
16477529 T
1 T
16477530 TTGGTTTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:16488147 original size:166 final size:166
Alignment explanation
Indices: 16487873--16488189 Score: 571
Period size: 166 Copynumber: 1.9 Consensus size: 166
16487863 TCATGGAAAA
16487873 TTTGAGAAATAATGATTTGTATGAATTGATATACGTCCCTAGAGAAATTGGCTAGCTTGACAAAA
1 TTTGAGAAATAATGATTTGTATGAATTGATATACGTCCCTAGAGAAATTGGCTAGCTTGACAAAA
16487938 GGATAAAAATGCTTAGATTTCAAGTTATGAACTTAAGGACTAAATTGTGAAAAGTTCAAATGTTA
66 GGATAAAAATGCTTAGATTTCAAGTTATGAACTTAAGGACTAAATTGTGAAAAGTTCAAATGTTA
*
16488003 GGGGAAAAATAGTAATTTTGCCCCTAACATTTGAAC
131 GAGGAAAAATAGTAATTTTGCCCCTAACATTTGAAC
* * * *
16488039 TTTGAGAAATAATGGTTTGTATGGATTGATATAGGTCCCTAGAGAAATTGGCTAGCTTGAGAAAA
1 TTTGAGAAATAATGATTTGTATGAATTGATATACGTCCCTAGAGAAATTGGCTAGCTTGACAAAA
*
16488104 GGATAAAAATGGTTAGATTTCAAGTTATGAACTTAAGGACTAAATTGTGAAAAGTTCAAATGTTA
66 GGATAAAAATGCTTAGATTTCAAGTTATGAACTTAAGGACTAAATTGTGAAAAGTTCAAATGTTA
*
16488169 GAGGCAAAATAGTAATTTTGC
131 GAGGAAAAATAGTAATTTTGC
16488190 AAATTATGGA
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 144 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (166 bp):
TTTGAGAAATAATGATTTGTATGAATTGATATACGTCCCTAGAGAAATTGGCTAGCTTGACAAAA
GGATAAAAATGCTTAGATTTCAAGTTATGAACTTAAGGACTAAATTGTGAAAAGTTCAAATGTTA
GAGGAAAAATAGTAATTTTGCCCCTAACATTTGAAC
Found at i:16490827 original size:40 final size:40
Alignment explanation
Indices: 16490771--16490848 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
16490761 TATTTTTGTA
** **
16490771 TTGGTTATTGTTTGTCATTGTCTAGGTTATATGAAAGTTT
1 TTGGTTATTGCCTGTCATTACCTAGGTTATATGAAAGTTT
* *
16490811 TTGGTTATTGCCTGTCATTACCTAGGTTGTATTAAAGT
1 TTGGTTATTGCCTGTCATTACCTAGGTTATATGAAAGT
16490849 GTTCGATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.49
Consensus pattern (40 bp):
TTGGTTATTGCCTGTCATTACCTAGGTTATATGAAAGTTT
Found at i:16490859 original size:40 final size:40
Alignment explanation
Indices: 16490783--16490859 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
16490773 GGTTATTGTT
** * * *
16490783 TGTCATTGTCTAGGTTATATGAAAGTTTTTGGTTATTGCC
1 TGTCATTACCTAGGTTATATGAAAGTGTTCGATTATTGCC
* *
16490823 TGTCATTACCTAGGTTGTATTAAAGTGTTCGATTATT
1 TGTCATTACCTAGGTTATATGAAAGTGTTCGATTATT
16490860 ATTTTCCATG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (40 bp):
TGTCATTACCTAGGTTATATGAAAGTGTTCGATTATTGCC
Found at i:16493422 original size:21 final size:21
Alignment explanation
Indices: 16493370--16493443 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
16493360 ATAACCAAAT
*
16493370 AGTTGCCCCAACTCAACAAGA
1 AGTTGCCCCAACTTAACAAGA
* * *
16493391 AGCTACCCCAACTTACCAAGA
1 AGTTGCCCCAACTTAACAAGA
* ** *
16493412 AGTTGCGCCAACTTGTCAACA
1 AGTTGCCCCAACTTAACAAGA
*
16493433 AGCTGCCCCAA
1 AGTTGCCCCAA
16493444 GAGAAAAGCT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.35, G:0.15, T:0.16
Consensus pattern (21 bp):
AGTTGCCCCAACTTAACAAGA
Found at i:16494486 original size:3 final size:3
Alignment explanation
Indices: 16494478--16494514 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16494468 ACATCTCCAT
16494478 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
16494515 ACCTAAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16504022 original size:9 final size:9
Alignment explanation
Indices: 16504008--16504033 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16503998 TTTTTTGTTG
16504008 TTTGCTCCT
1 TTTGCTCCT
16504017 TTTGCTCCT
1 TTTGCTCCT
16504026 TTTGCTCC
1 TTTGCTCC
16504034 CCAAATGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.12, T:0.54
Consensus pattern (9 bp):
TTTGCTCCT
Found at i:16516312 original size:11 final size:11
Alignment explanation
Indices: 16516298--16516338 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
16516288 TGTTTTCTCT
16516298 CTATTTTGCTA
1 CTATTTTGCTA
*
16516309 CTATTTTACTA
1 CTATTTTGCTA
* *
16516320 TTATGTTGCTA
1 CTATTTTGCTA
16516331 CTATTTTG
1 CTATTTTG
16516339 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:16516582 original size:12 final size:12
Alignment explanation
Indices: 16516561--16516594 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16516551 TATATATTTT
*
16516561 AAAATTATATAA
1 AAAATAATATAA
16516573 AAAATAATATAA
1 AAAATAATATAA
*
16516585 AAATTAATAT
1 AAAATAATAT
16516595 GGGTTGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:16516774 original size:25 final size:21
Alignment explanation
Indices: 16516720--16516764 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
16516710 TTTAGTTGGC
*
16516720 CCCGAAACTGACTCCACCCAG
1 CCCGAACCTGACTCCACCCAG
*
16516741 CCCGAACCTGACTCCACCCGG
1 CCCGAACCTGACTCCACCCAG
16516762 CCC
1 CCC
16516765 ATGAACACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.53, G:0.16, T:0.09
Consensus pattern (21 bp):
CCCGAACCTGACTCCACCCAG
Found at i:16519305 original size:29 final size:28
Alignment explanation
Indices: 16519215--16519298 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
16519205 ATGACATGTG
**
16519215 ACAAAAAATGATAAAAA-A-TAAAAATTA
1 ACAAAAAAT-ATAAAAATATTAAATTTTA
* ** *
16519242 ATAAAAGTTATAAAAATATTATATTTTA
1 ACAAAAAATATAAAAATATTAAATTTTA
16519270 ACAAAAAATATAAAAATATTTAAATTTTA
1 ACAAAAAATATAAAAATA-TTAAATTTTA
16519299 TTTAAAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
26 7 0.16
27 7 0.16
28 21 0.48
29 9 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
ACAAAAAATATAAAAATATTAAATTTTA
Found at i:16519344 original size:19 final size:19
Alignment explanation
Indices: 16519312--16519363 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
16519302 AAAATTAGAA
* *
16519312 AAAAAATTACAAAAATTGT
1 AAAAAATTATAAAAATCGT
**
16519331 AAAATTTTATAAAAATCGT
1 AAAAAATTATAAAAATCGT
16519350 AAAAAATTATAAAA
1 AAAAAATTATAAAA
16519364 TTTTATAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:16519344 original size:29 final size:29
Alignment explanation
Indices: 16519312--16519372 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
16519302 AAAATTAGAA
*
16519312 AAAAAAT-TACAAAAATTGTAAAATTTTAT
1 AAAAAATCTA-AAAAATTATAAAATTTTAT
16519341 -AAAAATCGTAAAAAATTATAAAATTTTAT
1 AAAAAATC-TAAAAAATTATAAAATTTTAT
16519370 AAA
1 AAA
16519373 TTCATAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 6 0.21
29 18 0.64
30 4 0.14
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAAATCTAAAAAATTATAAAATTTTAT
Found at i:16519363 original size:9 final size:9
Alignment explanation
Indices: 16519313--16519435 Score: 58
Period size: 9 Copynumber: 13.0 Consensus size: 9
16519303 AAATTAGAAA
*
16519313 AAAAATTAC
1 AAAAATTAT
*
16519322 AAAAATTGT
1 AAAAATTAT
*
16519331 AAAATTTTAT
1 AAAA-ATTAT
16519341 AAAAATCGTA-
1 AAAAAT--TAT
16519351 AAAAATTAT
1 AAAAATTAT
*
16519360 -AAAATTTT
1 AAAAATTAT
*
16519368 ATAAATTCAT
1 AAAAATT-AT
*
16519378 AAGAAAATTAA
1 -A-AAAATTAT
16519389 AAAAATGTA-
1 AAAAAT-TAT
16519398 AAGAAA-TAT
1 AA-AAATTAT
16519407 -AAAATTCAT
1 AAAAATT-AT
16519416 AAAAAGTATAT
1 AAAAA-T-TAT
16519427 AAAAATTAT
1 AAAAATTAT
16519436 TGTACTAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 32
0.68 0.08 0.25
Matches are distributed among these distances:
7 3 0.03
8 13 0.15
9 29 0.33
10 25 0.28
11 12 0.14
12 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:16519384 original size:29 final size:29
Alignment explanation
Indices: 16519322--16519392 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
16519312 AAAAAATTAC
* *
16519322 AAAAATTGTAAAATTTTATAAAAATCGTA
1 AAAAATTATAAAATTTTATAAAAATCATA
*
16519351 AAAAATTATAAAATTTTAT-AAATTCATA
1 AAAAATTATAAAATTTTATAAAAATCATA
*
16519379 AGAAAATTAAAAAA
1 A-AAAATTATAAAA
16519393 ATGTAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 8 0.22
29 29 0.78
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAATTATAAAATTTTATAAAAATCATA
Found at i:16519625 original size:19 final size:19
Alignment explanation
Indices: 16519601--16519637 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16519591 TTAAATGACA
16519601 TTTTTATGCA-TTTTATAAT
1 TTTTTATG-ATTTTTATAAT
16519620 TTTTTATGATTTTTATAA
1 TTTTTATGATTTTTATAA
16519638 AAATTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTATGATTTTTATAAT
Found at i:16519678 original size:29 final size:28
Alignment explanation
Indices: 16519612--16519717 Score: 74
Period size: 29 Copynumber: 3.8 Consensus size: 28
16519602 TTTTATGCAT
* * *
16519612 TTTATAATTTTTTATGATTTTTATAAAAA
1 TTTATAATTTTTTATAATTTTT-TTATAA
* *
16519641 TTTACAATTTTTTCTAATTTTTTTATAA
1 TTTATAATTTTTTATAATTTTTTTATAA
* * *
16519669 TTTAATAA-TTGTTATAGCTTTTATTAT--
1 TTT-ATAATTTTTTATA-ATTTTTTTATAA
* *
16519696 TTTTTTATTTTTTATAATTTTT
1 TTTATAATTTTTTATAATTTTT
16519718 CCCACATGTC
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
26 6 0.10
27 10 0.17
28 13 0.22
29 30 0.51
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTATAATTTTTTATAATTTTTTTATAA
Found at i:16519715 original size:10 final size:10
Alignment explanation
Indices: 16519611--16519717 Score: 57
Period size: 10 Copynumber: 11.3 Consensus size: 10
16519601 TTTTTATGCA
16519611 TTTTATAATT
1 TTTTATAATT
*
16519621 TTTTATGA-T
1 TTTTATAATT
**
16519630 TTTTATAAAA
1 TTTTATAATT
* *
16519640 ATTTACAATT
1 TTTTATAATT
*
16519650 TTTTCTAATTT
1 TTTTATAA-TT
16519661 TTTTATAA--
1 TTTTATAATT
*
16519669 TTTAATAA-T
1 TTTTATAATT
* **
16519678 TGTTAT-AGC
1 TTTTATAATT
*
16519687 TTTTATTATT
1 TTTTATAATT
16519697 TTTT-T-ATT
1 TTTTATAATT
16519705 TTTTATAATT
1 TTTTATAATT
16519715 TTT
1 TTT
16519718 CCCACATGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 14
0.69 0.17 0.13
Matches are distributed among these distances:
8 15 0.21
9 19 0.26
10 29 0.40
11 9 0.12
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:16546134 original size:26 final size:26
Alignment explanation
Indices: 16546105--16546214 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
16546095 TGATACAAAT
16546105 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
16546131 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
16546157 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
16546183 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
16546209 TGATAA
1 TGATAA
16546215 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:16547881 original size:27 final size:27
Alignment explanation
Indices: 16547840--16547955 Score: 169
Period size: 27 Copynumber: 4.3 Consensus size: 27
16547830 GAGGAAGCGT
*
16547840 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
16547867 TTTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
16547894 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
16547921 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
16547949 TCTGGTG
1 TCTGGTG
16547956 AATCTGTCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 72 0.91
28 7 0.09
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:16547972 original size:54 final size:54
Alignment explanation
Indices: 16547851--16547979 Score: 154
Period size: 54 Copynumber: 2.4 Consensus size: 54
16547841 CTGGTGGCTA
* **
16547851 TGCCACAAATATCTGATT-TGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTC
1 TGCCACATATATCTG-TTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGAATC
* *
16547905 TGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGAATC
1 TGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTG-ATCTGGTGAATC
* **
16547960 TGTCTTAT-TATCTGTTCTGG
1 TGCCACATATATCTGTTCTGG
16547980 CAGCCATGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
53 2 0.03
54 48 0.74
55 15 0.23
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (54 bp):
TGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGAATC
Found at i:16549052 original size:46 final size:46
Alignment explanation
Indices: 16548999--16549171 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
16548989 TTGGGCATCC
* *
16548999 GAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
* * * *
16549045 GAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG--TCT
* *
16549092 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
16549138 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16549172 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 7 0.07
45 2 0.02
46 58 0.55
47 26 0.25
48 2 0.02
50 8 0.08
51 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
Found at i:16549151 original size:93 final size:93
Alignment explanation
Indices: 16548992--16549162 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
16548982 AGGATATTTG
* * *
16548992 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCTGAACTCGTTGAG
16549057 TTGAGTCCGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTTGAGAGATGTAACTA
*
16549085 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCTGAACTCGTTGAG
16549150 TTGAGTCCGAGTT
66 TTGAGTCCGAGTT
16549163 CACTTATGGG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCTGAACTCGTTGAG
TTGAGTCCGAGTTTGAGAGATGTAACTA
Found at i:16556050 original size:46 final size:46
Alignment explanation
Indices: 16555997--16556166 Score: 139
Period size: 46 Copynumber: 3.7 Consensus size: 46
16555987 GGCATCTGAA
16555997 CTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAG
1 CTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAG
* * * **** * * *
16556043 CTCATTGAGTTAAGTCCAACTTCGGGAGATGTAACT-AGGCAT-T-CGAA
1 CTCATTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGA-GAATGTCCGAG
* * * * *
16556090 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAG
1 CTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAG
*
16556136 CTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 CTCATTGAGTTGAGTCCGAGTTCACTTATGG
16556167 GCGGGTTATA
Statistics
Matches: 90, Mismatches: 27, Indels: 14
0.69 0.21 0.11
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 54 0.60
47 25 0.28
48 3 0.03
49 4 0.04
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
CTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAG
Found at i:16562835 original size:33 final size:33
Alignment explanation
Indices: 16562798--16562863 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
16562788 ATTACATATC
16562798 ATTATATAAAATTATGAGTCCAAAACTTTACTA
1 ATTATATAAAATTATGAGTCCAAAACTTTACTA
16562831 ATTATATAAAATTATGAGTCCAAAACTTTACTA
1 ATTATATAAAATTATGAGTCCAAAACTTTACTA
16562864 TCTTATCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (33 bp):
ATTATATAAAATTATGAGTCCAAAACTTTACTA
Found at i:16567732 original size:6 final size:7
Alignment explanation
Indices: 16567717--16567742 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16567707 CGCTTTGAAA
16567717 TTTTATT
1 TTTTATT
16567724 TTTTATT
1 TTTTATT
16567731 TTTTATT
1 TTTTATT
16567738 TTTTA
1 TTTTA
16567743 AAAGGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:16567842 original size:19 final size:19
Alignment explanation
Indices: 16567818--16567855 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16567808 GAAATGAATA
16567818 ATTTCAGGAAAATAGGTTG
1 ATTTCAGGAAAATAGGTTG
*
16567837 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGAAAATAGGTTG
16567856 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (19 bp):
ATTTCAGGAAAATAGGTTG
Found at i:16568779 original size:19 final size:20
Alignment explanation
Indices: 16568746--16568785 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
16568736 ATATATGTAT
16568746 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
16568765 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
16568785 A
1 A
16568786 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:16569080 original size:13 final size:13
Alignment explanation
Indices: 16569048--16569073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16569038 CTTTTTCTTC
16569048 ATTTTTTTATTTT
1 ATTTTTTTATTTT
16569061 ATTTTTTTATTTT
1 ATTTTTTTATTTT
16569074 TTATTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:16572209 original size:24 final size:21
Alignment explanation
Indices: 16572162--16572213 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
16572152 TCACGGAGTT
16572162 GAAGAAGCTACTTGGAAACTA
1 GAAGAAGCTACTTGGAAACTA
* *
16572183 GAAGAAGCTACTTGGGAACTG
1 GAAGAAGCTACTTGGAAACTA
16572204 GAAGAAGCTA
1 GAAGAAGCTA
16572214 TAAAAGGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.17
Consensus pattern (21 bp):
GAAGAAGCTACTTGGAAACTA
Found at i:16576041 original size:27 final size:27
Alignment explanation
Indices: 16576011--16576460 Score: 281
Period size: 27 Copynumber: 16.7 Consensus size: 27
16576001 TATAGGGTAG
* *
16576011 AATTACTAAAATACCCTTGGTTTACAA
1 AATTACTAAAATACCCTTGATTTATAA
* * *
16576038 AATTACT-GAATACCCTTGGTTTACAA
1 AATTACTAAAATACCCTTGATTTATAA
* * *
16576064 AATTACCAAAATACCC-TCAATTAGTAA
1 AATTACTAAAATACCCTTGATTTA-TAA
* * *
16576091 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACTAAAATACCCTTGA-TTTATAA
* * * *
16576118 AATTACCAAAATACCCTCGACTTGTAA
1 AATTACTAAAATACCCTTGATTTATAA
* * * *
16576145 AATTACCAAAATACCCTCGACTTGTAA
1 AATTACTAAAATACCCTTGATTTATAA
* * *
16576172 AATTACCAAAATACCCTTGACTTGTAA
1 AATTACTAAAATACCCTTGATTTATAA
* * * *
16576199 AATTACCAAAATACCCTCGACTTGTAA
1 AATTACTAAAATACCCTTGATTTATAA
** * *
16576226 AATTA-TCAAAATACCCTCAACTTGTAA
1 AATTACT-AAAATACCCTTGATTTATAA
* ** *
16576253 AATTACTCAAATACCCTCAATTT-TTA
1 AATTACTAAAATACCCTTGATTTATAA
* * *
16576279 AATTACCAAAATA-CCTCTAATTTAGAA
1 AATTACTAAAATACCCT-TGATTTATAA
* * *
16576306 AATTATTGAAATACCCTTGATTTAGAA
1 AATTACTAAAATACCCTTGATTTATAA
* *
16576333 AATTA-TAGAAATACCCCTGATTTACAA
1 AATTACTA-AAATACCCTTGATTTATAA
*
16576360 AATTACAAAAATACCCTTGACTTTCA-AA
1 AATTACTAAAATACCCTTGA-TTT-ATAA
* *
16576388 AATTA-TAGAAATACCATTGGTTTGA-AA
1 AATTACTA-AAATACCCTTGATTT-ATAA
* * * *
16576415 AATTACTGAAATACCCTTGGTTTGTAG
1 AATTACTAAAATACCCTTGATTTATAA
* * *
16576442 ATTTACCAAAACACCCTTG
1 AATTACTAAAATACCCTTG
16576461 TAGGGTGAAA
Statistics
Matches: 361, Mismatches: 45, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
25 3 0.01
26 47 0.13
27 280 0.78
28 30 0.08
29 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGATTTATAA
Found at i:16576159 original size:81 final size:79
Alignment explanation
Indices: 16576062--16576293 Score: 333
Period size: 81 Copynumber: 2.9 Consensus size: 79
16576052 CTTGGTTTAC
16576062 AAAATTACCAAAATACCCTCAATTAGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCTCAATT-GTAAAATTACCAAAATA-CCCTAGTTTGTAAAATTACCAA
16576127 AATACCCTCGACTTGT
64 AATACCCTCGACTTGT
* * *
16576143 AAAATTACCAAAATACCCTCGACTTGTAAAATTACCAAAATACCCTTGACTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCTC-AATTGTAAAATTACCAAAATACCCTAG-TTTGTAAAATTACCAA
16576208 AATACCCTCGACTTGT
64 AATACCCTCGACTTGT
* * *
16576224 AAAATTATCAAAATACCCTCAACTTGTAAAATTACTC-AAATACCCTCAATTT-TTAAATTACCA
1 AAAATTACCAAAATACCCTCAA-TTGTAAAATTAC-CAAAATACCCT-AGTTTGTAAAATTACCA
16576287 AAATACC
63 AAATACC
16576294 TCTAATTTAG
Statistics
Matches: 137, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
80 23 0.17
81 110 0.80
82 4 0.03
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.28
Consensus pattern (79 bp):
AAAATTACCAAAATACCCTCAATTGTAAAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAA
TACCCTCGACTTGT
Found at i:16576417 original size:55 final size:54
Alignment explanation
Indices: 16576287--16576433 Score: 154
Period size: 55 Copynumber: 2.7 Consensus size: 54
16576277 TAAATTACCA
* * * ***
16576287 AAATACCTCTAATTTAGAAAATTATTGAAATACCCTTGATTTAGAAAATTATAG
1 AAATACCACTGATTTACAAAATTACAAAAATACCCTTGATTTAGAAAATTATAG
*
16576341 AAATACCCCTGATTTACAAAATTACAAAAATACCCTTGACTTTCA-AAAATTATAG
1 AAATACCACTGATTTACAAAATTACAAAAATACCCTTGA-TTT-AGAAAATTATAG
* * **
16576396 AAATACCATTGGTTTGA-AAAATTACTGAAATACCCTTG
1 AAATACCACTGATTT-ACAAAATTACAAAAATACCCTTG
16576434 GTTTGTAGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
54 33 0.42
55 44 0.56
56 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (54 bp):
AAATACCACTGATTTACAAAATTACAAAAATACCCTTGATTTAGAAAATTATAG
Found at i:16577209 original size:22 final size:22
Alignment explanation
Indices: 16577184--16577237 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
16577174 ATTGCTGTGA
16577184 TGTTTACGGCTATGTGTTGTCC
1 TGTTTACGGCTATGTGTTGTCC
*
16577206 TGTTTACGGTTATGTGTTGTCC
1 TGTTTACGGCTATGTGTTGTCC
* *
16577228 TATCTACGGC
1 TGTTTACGGC
16577238 GTTGAGCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
TGTTTACGGCTATGTGTTGTCC
Found at i:16580500 original size:46 final size:45
Alignment explanation
Indices: 16580447--16580622 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
16580437 TATTTGGGCA
16580447 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
16580493 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
16580540 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
16580586 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16580623 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:16580602 original size:93 final size:93
Alignment explanation
Indices: 16580443--16580614 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
16580433 AGGATATTTG
* *
16580443 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
16580508 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
16580536 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
16580601 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
16580615 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:16583913 original size:15 final size:15
Alignment explanation
Indices: 16583893--16583961 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
16583883 ATATCTTGGG
16583893 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
16583908 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
16583923 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
16583938 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
16583953 TTTCTTTAT
1 TTTCTTTAT
16583962 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:16583962 original size:30 final size:30
Alignment explanation
Indices: 16583884--16583971 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
16583874 CATAGTATCA
* * * *
16583884 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
16583914 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
16583944 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
16583972 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:16586407 original size:46 final size:45
Alignment explanation
Indices: 16586354--16586526 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 45
16586344 TTGGGCATCT
*
16586354 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
* *** * *
16586400 GAACTCGTTGAGTTGAGTTCGAGTTCGAGAGATGTAATTAG-GCA-TCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCC
* *
16586447 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
*
16586493 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16586527 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.62
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCC
Found at i:16586506 original size:93 final size:93
Alignment explanation
Indices: 16586347--16586518 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
16586337 AGGATATTTG
* * **
16586347 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
16586412 TTGAGTTCGAGTTCGAGAGATGTAATTA
66 TTGAGTCCGAGTTCGAGAGATGTAATTA
* *
16586440 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
16586505 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
16586519 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAATTA
Found at i:16593052 original size:17 final size:18
Alignment explanation
Indices: 16593030--16593063 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16593020 TCCTCCTGCT
*
16593030 CTCTTTT-TTTTTTTCTC
1 CTCTTTTCTTTCTTTCTC
16593047 CTCTTTTCTTTCTTTCT
1 CTCTTTTCTTTCTTTCT
16593064 TTGTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
CTCTTTTCTTTCTTTCTC
Found at i:16597429 original size:27 final size:28
Alignment explanation
Indices: 16597385--16597437 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
16597375 TTTTTGATCC
* * *
16597385 TTTTAAAATTTAATTATTTAA-TTTATT
1 TTTTAAAAATAAAATATTTAACTTTATT
16597412 TTTTAAAAATAAAATATTTAACTTTA
1 TTTTAAAAATAAAATATTTAACTTTA
16597438 ACCCTATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTTAAAAATAAAATATTTAACTTTATT
Found at i:16608217 original size:3 final size:3
Alignment explanation
Indices: 16608209--16608349 Score: 110
Period size: 3 Copynumber: 46.3 Consensus size: 3
16608199 TGATAAAAGG
*
16608209 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA CCTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * *
16608257 CGATA CTA ATA ATA GTA ATA ATA AGA A-A ATTA ATA TTA ATA TTA ATA
1 --ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
** * *
16608304 ATA ATGGA A-A ATA ATA ATA GCA ATG ATA AT- ATA GTA ATA ATA ATA
1 ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16608349 A
1 A
16608350 AAGTGAAATT
Statistics
Matches: 109, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
2 8 0.07
3 93 0.85
4 4 0.04
5 4 0.04
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16608448 original size:22 final size:23
Alignment explanation
Indices: 16608423--16608467 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
16608413 GATAGGAAAT
*
16608423 AATAATATGGTAA-AAAAATAAC
1 AATAATATGATAATAAAAATAAC
16608445 AATAATATGATAATAAAAATAAC
1 AATAATATGATAATAAAAATAAC
16608468 GGTGGTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (23 bp):
AATAATATGATAATAAAAATAAC
Found at i:16608765 original size:12 final size:12
Alignment explanation
Indices: 16608750--16608793 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
16608740 TAGAATATAA
16608750 TAATAATAATAG
1 TAATAATAATAG
16608762 TAATAATAATAG
1 TAATAATAATAG
**
16608774 -ATATAGCAATAG
1 TA-ATAATAATAG
16608786 TAATAATA
1 TAATAATA
16608794 GTAATGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 24 0.92
13 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:16608879 original size:27 final size:25
Alignment explanation
Indices: 16608811--16608880 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 25
16608801 TAATAGCATG
16608811 ATAATATTAGAAAT-AT-ACAATAT
1 ATAATATTAGAAATAATAACAATAT
* *
16608834 ATAGTATTAGAAGTAAATACACAATAT
1 ATAATATTAGAAAT-AATA-ACAATAT
16608861 ATACATATTAGAAATAATAA
1 ATA-ATATTAGAAATAATAA
16608881 TAATGTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 12 0.32
25 2 0.05
26 1 0.03
27 14 0.37
28 9 0.24
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (25 bp):
ATAATATTAGAAATAATAACAATAT
Found at i:16608942 original size:21 final size:20
Alignment explanation
Indices: 16608913--16608966 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
16608903 TAATACTTCA
*
16608913 TAAATATATACATATATATAT
1 TAAACATATACATATATA-AT
*
16608934 TAAAGATATATACATATATAAT
1 T-AA-ACATATACATATATAAT
*
16608956 AAAACATATAC
1 TAAACATATAC
16608967 TAATATTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 4 0.14
23 15 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAACATATACATATATAAT
Done.