Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002385.1 Hibiscus syriacus cultivar Beakdansim tig00004881_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: 90343
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3207 original size:46 final size:46
Alignment explanation
Indices: 3133--3530 Score: 383
Period size: 46 Copynumber: 8.6 Consensus size: 46
3123 TTTCAGTTAC
* *
3133 TTTTCAGCTACTTTTTAAGAGGTCATTTATTACAAAAATAATGT-ACCA
1 TTTT-AGCTAC-TTTTCAGAGGTCATTTATTACAACAATAAT-TCACCA
* **
3181 TTTTAGCTACCTTTT-AGAGGCCATTTATTACAGTAATAATTCACC-
1 TTTTAGCTA-CTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* ** * ** **
3226 GTTTAATTACTTTTCAGAGGTCATTTATTATAGTAATAATTCACTG
1 TTTTAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* * ***
3272 TTTCAGCTATTTTTCAGAGGTCATTTATTACAACAATAATTCATTG
1 TTTTAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* * * * *
3318 TTTCAGATACTTTTCAGAGGCCATTTATTACAGCAATAATTCACCG
1 TTTTAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* * * *
3364 TTATAGTTATTTTTCAGAGGTCATTTATTACATCAATAATTCACCA
1 TTTTAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* * *
3410 TTTCAACTACTTTTCAGAGGCCATTTATTACAACAATAATTCA--A
1 TTTTAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* * *
3454 TGTTTCAGCTACTTTTCAGAGGACATTTATTAAAACAATAATGCACCA
1 T-TTT-AGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
* * *
3502 TTTTAACTACTTTTCAAAGGTTATTTATT
1 TTTTAGCTACTTTTCAGAGGTCATTTATT
3531 GTATTAATAA
Statistics
Matches: 295, Mismatches: 47, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
44 7 0.02
45 36 0.12
46 233 0.79
47 12 0.04
48 7 0.02
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (46 bp):
TTTTAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCA
Found at i:3540 original size:138 final size:137
Alignment explanation
Indices: 3134--3541 Score: 507
Period size: 138 Copynumber: 3.0 Consensus size: 137
3124 TTCAGTTACT
* * *
3134 TTTCAGCTACTTTTTAAGAGGTCATTTATTACAAAAATAATGTACCAT-TTT-AGCTACCTTTT-
1 TTTCAGCTAC-TTTTCAGAGGTCATTTATTACAACAATAAT-T-CAATGTTTCAGCTA-CTTTTC
* * *
3196 AGAGGCCATTTATTACAGTAATAATTCACCGTTTAATTACTTTTCAGAGGTCATTTATTATAGTA
62 AGAGGCCATTTATTACAGCAATAATTCACCTTTTAATTACTTTTCAGAGGTCATTTATTATATTA
**
3261 ATAATTCACTG
127 ATAATTCACCA
* * *
3272 TTTCAGCTATTTTTCAGAGGTCATTTATTACAACAATAATTCATTGTTTCAGATACTTTTCAGAG
1 TTTCAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCAATGTTTCAGCTACTTTTCAGAG
* * * * *
3337 GCCATTTATTACAGCAATAATTCACCGTTATAGTTATTTTTCAGAGGTCATTTATTACATCAATA
66 GCCATTTATTACAGCAATAATTCACC-TTTTAATTACTTTTCAGAGGTCATTTATTATATTAATA
3402 ATTCACCA
130 ATTCACCA
* *
3410 TTTCAACTACTTTTCAGAGGCCATTTATTACAACAATAATTCAATGTTTCAGCTACTTTTCAGAG
1 TTTCAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCAATGTTTCAGCTACTTTTCAGAG
* * * * * * * *
3475 GACATTTATTAAAACAATAATGCACCATTTTAACTACTTTTCAAAGGTTATTTATTGTATTAATA
66 GCCATTTATTACAGCAATAATTCACC-TTTTAATTACTTTTCAGAGGTCATTTATTATATTAATA
3540 AT
130 AT
3542 GCTCATGTTG
Statistics
Matches: 231, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
135 2 0.01
136 9 0.04
137 61 0.26
138 159 0.69
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (137 bp):
TTTCAGCTACTTTTCAGAGGTCATTTATTACAACAATAATTCAATGTTTCAGCTACTTTTCAGAG
GCCATTTATTACAGCAATAATTCACCTTTTAATTACTTTTCAGAGGTCATTTATTATATTAATAA
TTCACCA
Found at i:11255 original size:26 final size:23
Alignment explanation
Indices: 11226--11289 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 23
11216 AGCAAGAAAC
11226 TAAAAACATAATGAAAATAAATAATA
1 TAAAAA-ATAAT-AAAATAAA-AATA
11252 TAAATAAATAATAAAATAAAAATA
1 TAAA-AAATAATAAAATAAAAATA
*
11276 T-ATAAAT-ATAAAAT
1 TAAAAAATAATAAAAT
11290 GTATGTATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 7 0.19
22 4 0.11
23 1 0.03
24 5 0.14
25 8 0.22
26 9 0.25
27 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAAATAATAAAATAAAAATA
Found at i:11256 original size:13 final size:13
Alignment explanation
Indices: 11240--11283 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
11230 AACATAATGA
11240 AAATAAATAATAT
1 AAATAAATAATAT
11253 AAATAAATAATA-
1 AAATAAATAATAT
*
11265 AAATAAAAATATAT
1 AAATAAATA-ATAT
11279 AAATA
1 AAATA
11284 TAAAATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 8 0.29
13 15 0.54
14 5 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:11472 original size:2 final size:2
Alignment explanation
Indices: 11467--11500 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11457 TAGATAAAAA
11467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11501 GGAAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11574 original size:2 final size:2
Alignment explanation
Indices: 11567--11597 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11557 AAATAATAAA
*
11567 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11598 AATAATAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12649 original size:83 final size:82
Alignment explanation
Indices: 12507--12884 Score: 329
Period size: 83 Copynumber: 4.6 Consensus size: 82
12497 ATGTGTCATC
* * * * * * * *
12507 GAGCTGAATGGAATCGAACTCGACA-AT-TTTGATGGCATATAACCCTTCTCGTCTTGAGTTATG
1 GAGCTGAACGTAATCGAACTCGA-AGGTCTTTGATGACAGAT-ACCCTTCTAGCCTTGAGCTATG
** * *
12570 CTGTAAATTTTTTTCCTCT-
64 CTGTAAATGATGTGCCT-TG
* * * *
12589 GAGTTGAATGTAATCAAACTCGAAGGTCTTTGATGACAGATCACCCTTCTAGCCTTGAGTTATGC
1 GAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGACAGAT-ACCCTTCTAGCCTTGAGCTATGC
* * *
12654 TG-CAATGATATGCCTTA
65 TGTAAATGATGTGCCTTG
* * * * * *
12671 GAG-T-TACGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATG
1 GAGCTGAACGTAATCGAACTCGAAGGTC-TTTGATGACAGATA-CCCTTCTAGCCTTGAGCTATG
* *
12734 TTGCAAATGATGTGCCTTG
64 CTGTAAATGATGTGCCTTG
* * *
12753 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTGACAGATAGCCCTTCTAGCCTTGAGCTATGC
1 GAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGACAGATA-CCCTTCTAGCCTTGAGCTATGC
*
12818 TGTAAATGATGCGCCTTG
65 TGTAAATGATGTGCCTTG
** *
12836 GAGCTGAGTGTAATC-AACTCGAAGGTCTTTGTTGACAGATACTCCTTCT
1 GAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGACAGATAC-CCTTCT
12885 TTGAGTTGGA
Statistics
Matches: 248, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
80 19 0.08
81 35 0.14
82 78 0.31
83 96 0.39
84 20 0.08
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (82 bp):
GAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGACAGATACCCTTCTAGCCTTGAGCTATGCT
GTAAATGATGTGCCTTG
Found at i:13522 original size:103 final size:106
Alignment explanation
Indices: 13060--13795 Score: 1107
Period size: 103 Copynumber: 7.0 Consensus size: 106
13050 TGTACTGTTC
* * * * * * *
13060 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAATTTGTTTG-TGATA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
13124 ACCAGCCGTCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
13165 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
13230 ACCAG-TGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
13270 TGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTG-TTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
13333 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
13374 C-AGTCCAATATCCTTCGCTGTGAAGTTGAAACTGACTCTGAAATTGGGAAATT-ATTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
13437 ACCAGCCGTCCCTTCGTT-TGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
13477 CGAGTCCAATAT-CTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * **
13541 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
13582 GGAGTCCAATATCCTTCG--ATGAAGTTG-AATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
13644 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
13685 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
13750 ACCAGCCGTCCCTTCGTTGTAAAGTTAAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
13791 CGAGT
1 CGAGT
13796 GGCACGATAT
Statistics
Matches: 571, Mismatches: 49, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
103 175 0.31
104 165 0.29
105 141 0.25
106 90 0.16
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:13749 original size:209 final size:210
Alignment explanation
Indices: 13061--13795 Score: 1092
Period size: 209 Copynumber: 3.5 Consensus size: 210
13051 GTACTGTTCC
* * * * * * *
13061 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAATTTGTTTG-TGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
13125 CCAGCCGTCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-GAGTCCAATATCCTTCGC-GTGAA
* * *
13190 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG-TGTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
13254 TGAACTTGTGTTGTCTT
194 TGAACTTGTGTTGTCTT
* *
13271 GAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
13334 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCAGTCCAATATCCTTCGCTGTGAAG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAGTCCAATATCCTTCGC-GTGAAG
* * *
13399 TTGAAACTGACTCTGAAATTGGGAAATT-ATTGTTGACAACCAGCCGTCCCTTCGTT-TGAAGTT
130 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
*
13462 GAACTTGTGTTGTCTC
195 GAACTTGTGTTGTCTT
* *
13478 GAGTCCAATAT-CTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * ** *
13542 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG-ATGAAG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-GAGTCCAATATCCTTCGCGTGAAG
*
13606 TTG-AATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTT
130 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
13670 GAACTTGTGTTGTCTT
195 GAACTTGTGTTGTCTT
13686 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
13751 CCAGCCGTCCCTTCGTTGTAAAGTTAAACTTGTGTTGTCTCGAGT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-GAGT
13796 GGCACGATAT
Statistics
Matches: 473, Mismatches: 44, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
206 27 0.06
207 114 0.24
208 139 0.29
209 177 0.37
210 16 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (210 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAGTCCAATATCCTTCGCGTGAAGT
TGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
AACTTGTGTTGTCTT
Found at i:14336 original size:18 final size:19
Alignment explanation
Indices: 14303--14339 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
14293 TGTTGAATCC
*
14303 CCAAATAATGCCCCAATAT
1 CCAAATAATACCCCAATAT
14322 CCAAA-AATACCCCAATAT
1 CCAAATAATACCCCAATAT
14340 TGATATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.19
Consensus pattern (19 bp):
CCAAATAATACCCCAATAT
Found at i:14766 original size:22 final size:22
Alignment explanation
Indices: 14734--14778 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
14724 AGGTTATTGT
14734 GTTTGGCATTTGATGCTCAAAG
1 GTTTGGCATTTGATGCTCAAAG
*
14756 GTTTGGTATTTGATGCTCAAAG
1 GTTTGGCATTTGATGCTCAAAG
14778 G
1 G
14779 ATTGATGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (22 bp):
GTTTGGCATTTGATGCTCAAAG
Found at i:15458 original size:172 final size:172
Alignment explanation
Indices: 15172--15516 Score: 663
Period size: 172 Copynumber: 2.0 Consensus size: 172
15162 ATAAATAGGC
15172 TCAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTCAATCCTGCTCA
1 TCAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTCAATCCTGCTCA
*
15237 AAATGTTTCTCTCTCTTGATTCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAGAATGAT
66 AAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAGAATGAT
15302 TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATT
131 TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATT
*
15344 TCAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGTCTTCAATCCTGCTCA
1 TCAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTCAATCCTGCTCA
*
15409 AAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGAT
66 AAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAGAATGAT
15474 TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATT
131 TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATT
15516 T
1 T
15517 GTCTTTAGGG
Statistics
Matches: 170, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 170 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (172 bp):
TCAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTCAATCCTGCTCA
AAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAGAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATT
Found at i:15580 original size:7 final size:7
Alignment explanation
Indices: 15552--15613 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
15542 TTTTTGTCCC
15552 TTTTTCTT
1 TTTTTC-T
15560 TTTATTCT
1 TTT-TTCT
15568 TGTTTTCT
1 T-TTTTCT
15576 TTTTTCT
1 TTTTTCT
15583 TTTTTC-
1 TTTTTCT
*
15589 -TTTGCT
1 TTTTTCT
*
15595 TTTTGCT
1 TTTTTCT
*
15602 TCTTTCT
1 TTTTTCT
15609 TTTTT
1 TTTTT
15614 GTTCTTGATT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
5 4 0.09
7 27 0.59
8 10 0.22
9 5 0.11
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:15596 original size:19 final size:19
Alignment explanation
Indices: 15574--15610 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15564 TTCTTGTTTT
* *
15574 CTTTTTTCTTTTTTCTTTG
1 CTTTTTGCTTCTTTCTTTG
15593 CTTTTTGCTTCTTTCTTT
1 CTTTTTGCTTCTTTCTTT
15611 TTTGTTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (19 bp):
CTTTTTGCTTCTTTCTTTG
Found at i:20225 original size:13 final size:13
Alignment explanation
Indices: 20207--20262 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
20197 AGAAATGAAA
*
20207 ATAAATAAATAGT
1 ATAAATAAATAAT
20220 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
20234 A-AAATAAAAAAT
1 ATAAATAAATAAT
*
20246 ATATATAAA-AAT
1 ATAAATAAATAAT
20258 ATAAA
1 ATAAA
20263 AATGTATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 14 0.38
13 16 0.43
14 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:20240 original size:26 final size:26
Alignment explanation
Indices: 20209--20287 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
20199 AAATGAAAAT
*
20209 AAATAAATAGTATAAATAAAATAATA
1 AAATAAATAGTATATATAAAATAATA
* *
20235 AAATAAAAAATATATAT-AAA-AATA
1 AAATAAATAGTATATATAAAATAATA
* * *
20259 TAA-AAAT-GTATGTATAATATAATA
1 AAATAAATAGTATATATAAAATAATA
20283 AAATA
1 AAATA
20288 CTAAATAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
22 6 0.15
23 5 0.12
24 12 0.29
25 4 0.10
26 14 0.34
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (26 bp):
AAATAAATAGTATATATAAAATAATA
Found at i:20253 original size:21 final size:22
Alignment explanation
Indices: 20229--20339 Score: 69
Period size: 21 Copynumber: 5.3 Consensus size: 22
20219 TATAAATAAA
20229 ATAATAAAATAAAAA-ATATAT
1 ATAATAAAATAAAAATATATAT
* *
20250 ATAA-AAATATAAAAATGTATGT
1 ATAATAAA-ATAAAAATATATAT
*
20272 ATAATATAAT-AAAATACTA-A-
1 ATAATAAAATAAAAATA-TATAT
*
20292 ATAATAACAATAATAATA-A-AT
1 ATAATAA-AATAAAAATATATAT
* *
20313 A-AATGAAAA-ATAAATATACAT
1 ATAAT-AAAATAAAAATATATAT
20334 ATAATA
1 ATAATA
20340 TTAACTAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
19 5 0.07
20 17 0.24
21 26 0.37
22 20 0.29
23 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (22 bp):
ATAATAAAATAAAAATATATAT
Found at i:20313 original size:16 final size:16
Alignment explanation
Indices: 20272--20315 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
20262 AAATGTATGT
20272 ATAATATAATAAAATA
1 ATAATATAATAAAATA
*
20288 CTAA-ATAATAACAATA
1 ATAATATAATAA-AATA
20304 ATAATA-AATAAA
1 ATAATATAATAAA
20316 TGAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAATATAATAAAATA
Found at i:20466 original size:2 final size:2
Alignment explanation
Indices: 20459--20483 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20449 GATAAAAATA
20459 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20484 ATAGGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20524 original size:4 final size:4
Alignment explanation
Indices: 20515--20582 Score: 50
Period size: 4 Copynumber: 16.5 Consensus size: 4
20505 ACGCAAAGAA
* *
20515 AAAT AAAT AAA- AAATT ATAAT AAAT AAAT AAAT AAA- ATAT AATT AAAT
1 AAAT AAAT AAAT AAA-T A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
20563 ATAT ATAT ACATAT AAAT AA
1 AAAT AAAT A-A-AT AAAT AA
20583 TAAGGGTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
3 5 0.10
4 38 0.73
5 4 0.08
6 5 0.10
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:20529 original size:11 final size:11
Alignment explanation
Indices: 20513--20561 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
20503 TAACGCAAAG
20513 AAAAATAAATA
1 AAAAATAAATA
20524 AAAAATTATAATA
1 AAAAA-TA-AATA
20537 AATAAATAAATA
1 AA-AAATAAATA
* *
20549 AAATATAATTA
1 AAAAATAAATA
20560 AA
1 AA
20562 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 14 0.42
12 8 0.24
13 8 0.24
14 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:23405 original size:21 final size:22
Alignment explanation
Indices: 23379--23460 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 22
23369 TTATATTATA
*
23379 ATATATATATAATTTTTGAAAAC
1 ATATATATAT-AGTTTTGAAAAC
23402 ATAT-TATATAGTTTTGAAAAC
1 ATATATATATAGTTTTGAAAAC
*
23423 ATATATATATGGTAGTTTTTGAAAAT
1 ATATATATA---TAG-TTTTGAAAAC
23449 ATAATATATATA
1 AT-ATATATATA
23461 TATAAATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
21 15 0.29
22 9 0.18
23 4 0.08
24 2 0.04
25 3 0.06
26 11 0.22
27 7 0.14
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (22 bp):
ATATATATATAGTTTTGAAAAC
Found at i:23460 original size:29 final size:28
Alignment explanation
Indices: 23402--23540 Score: 122
Period size: 26 Copynumber: 5.4 Consensus size: 28
23392 TTTTGAAAAC
*
23402 ATAT-TATATAG-TTTTGAAAACAT-AT
1 ATATATATATAGTTTTTGAAAATATAAT
**
23427 ATATAT-GGTAGTTTTTGAAAATATAAT
1 ATATATATATAGTTTTTGAAAATATAAT
** *
23454 ATATATATATAAATTTTGAAAA-A-CAT
1 ATATATATATAGTTTTTGAAAATATAAT
23480 AT-TATAT-TA--TTTTGAAAATATAAT
1 ATATATATATAGTTTTTGAAAATATAAT
23504 ATATATTATATAGTTTTT-AAAATAT-AT
1 ATATA-TATATAGTTTTTGAAAATATAAT
*
23531 ATATACATAT
1 ATATATATAT
23541 TATTATTATT
Statistics
Matches: 93, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
22 9 0.10
23 1 0.01
24 6 0.06
25 14 0.15
26 23 0.25
27 18 0.19
28 18 0.19
29 4 0.04
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (28 bp):
ATATATATATAGTTTTTGAAAATATAAT
Found at i:23471 original size:75 final size:77
Alignment explanation
Indices: 23375--23540 Score: 218
Period size: 76 Copynumber: 2.2 Consensus size: 77
23365 TATATTATAT
*
23375 TATA-ATATATATATAATTTTTG-AAAACATATTATA-TAGTTTTGAAAACAT-ATATATA-T-G
1 TATATATATATATATAAATTTTGAAAAACATATTATATTA-TTTTGAAAACATAATATATATTAG
*
23434 GTAGTTTTTGAAAA
65 ATAGTTTTT-AAAA
* *
23448 TATAATATATATATATAAATTTTGAAAAACATATTATATTATTTTGAAAATATAATATATATTAT
1 TAT-ATATATATATATAAATTTTGAAAAACATATTATATTATTTTGAAAACATAATATATATTAG
23513 ATAGTTTTTAAAA
65 ATAGTTTTTAAAA
*
23526 TATATATATACATAT
1 TATATATATATATAT
23541 TATTATTATT
Statistics
Matches: 81, Mismatches: 5, Indels: 10
0.84 0.05 0.10
Matches are distributed among these distances:
73 3 0.04
74 1 0.01
75 17 0.21
76 24 0.30
77 20 0.25
78 8 0.10
79 8 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (77 bp):
TATATATATATATATAAATTTTGAAAAACATATTATATTATTTTGAAAACATAATATATATTAGA
TAGTTTTTAAAA
Found at i:23502 original size:50 final size:53
Alignment explanation
Indices: 23402--23535 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 53
23392 TTTTGAAAAC
*
23402 ATATTATAT-AGTTTTGAAAACATATATATATGGTAGTTTTTGAAAATATAATAT
1 ATATTATATAAATTTTGAAAACATATATATAT-GTAG-TTTTGAAAATATAATAT
23456 ATA-TATATAAATTTTGAAAAACATAT-TATAT-TA-TTTTGAAAATATAATAT
1 ATATTATATAAATTTTG-AAAACATATATATATGTAGTTTTGAAAATATAATAT
* * *
23506 ATATTATAT-AGTTTTTAAAATATATATATA
1 ATATTATATAAATTTTGAAAACATATATATA
23536 CATATTATTA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
49 8 0.11
50 29 0.40
51 5 0.07
52 2 0.03
53 5 0.07
54 14 0.19
55 9 0.12
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (53 bp):
ATATTATATAAATTTTGAAAACATATATATATGTAGTTTTGAAAATATAATAT
Found at i:23506 original size:21 final size:23
Alignment explanation
Indices: 23378--23508 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 23
23368 ATTATATTAT
*
23378 AATAT-ATATATAATTTTTGAAA
1 AATATAATATATAAATTTTGAAA
*
23400 ACATAT--TATAT-AGTTTTGAAA
1 A-ATATAATATATAAATTTTGAAA
* **
23421 ACATATATATATGGTAGTTTTTGAAAATA
1 A-ATATA-ATAT-ATAAATTTTG--AA-A
23450 TAATATATATATATAAATTTTGAAA
1 -AATATA-ATATATAAATTTTGAAA
* * *
23475 AACATATTATAT-TATTTTG-AA
1 AATATAATATATAAATTTTGAAA
23496 AATATAATATATA
1 AATATAATATATA
23509 TTATATAGTT
Statistics
Matches: 86, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
21 27 0.31
22 12 0.14
23 9 0.10
24 8 0.09
25 2 0.02
26 7 0.08
28 9 0.10
29 11 0.13
30 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (23 bp):
AATATAATATATAAATTTTGAAA
Found at i:25702 original size:23 final size:23
Alignment explanation
Indices: 25675--25718 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
25665 GATTAGAAAC
*
25675 CATGTCTAGGTAGGAAAAAAAAA
1 CATGTCCAGGTAGGAAAAAAAAA
* *
25698 CATGTCCGGGTAGGAACAAAA
1 CATGTCCAGGTAGGAAAAAAA
25719 GCATGTTCGG
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:0.45, C:0.14, G:0.25, T:0.16
Consensus pattern (23 bp):
CATGTCCAGGTAGGAAAAAAAAA
Found at i:25723 original size:22 final size:23
Alignment explanation
Indices: 25683--25732 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
25673 ACCATGTCTA
25683 GGTAGGAAAAAAAAACATGTCCG
1 GGTAGGAAAAAAAAACATGTCCG
* * *
25706 GGTAGG-AACAAAAGCATGTTCG
1 GGTAGGAAAAAAAAACATGTCCG
25728 GGTAG
1 GGTAG
25733 ATATCATACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.40, C:0.12, G:0.32, T:0.16
Consensus pattern (23 bp):
GGTAGGAAAAAAAAACATGTCCG
Found at i:33887 original size:14 final size:14
Alignment explanation
Indices: 33870--33909 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
33860 TAATGTTTTG
*
33870 TCTTCTTCCTCTAT
1 TCTTCTTCATCTAT
33884 TCTTCTTCATCTAT
1 TCTTCTTCATCTAT
33898 TCTTCTTCATCT
1 TCTTCTTCATCT
33910 TTTTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTTCTTCATCTAT
Found at i:34653 original size:20 final size:21
Alignment explanation
Indices: 34628--34678 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
34618 CTTCAAGGAG
34628 TTTCGATACTC-G-GGGTCTAA
1 TTTCGATACTCAGAGGGT-TAA
*
34648 TTTCGATACTCAGAGGGTTGA
1 TTTCGATACTCAGAGGGTTAA
34669 TTTCGATACT
1 TTTCGATACT
34679 AGGGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.39
21 13 0.46
22 4 0.14
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (21 bp):
TTTCGATACTCAGAGGGTTAA
Found at i:41087 original size:4 final size:4
Alignment explanation
Indices: 41030--41077 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
41020 TGGTAAAAAC
41030 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
41078 GCAAATAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:45035 original size:25 final size:26
Alignment explanation
Indices: 45007--45061 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
44997 CAGTGGAGAG
45007 AGAAAAGTAAAAA-TAAAAAAT-AAAA
1 AGAAAAG-AAAAAGTAAAAAATCAAAA
*
45032 AGAAAAGAAAAAGTAACAAATCAAAA
1 AGAAAAGAAAAAGTAAAAAATCAAAA
45058 AGAA
1 AGAA
45062 TCTTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 14 0.52
26 8 0.30
ACGTcount: A:0.76, C:0.04, G:0.11, T:0.09
Consensus pattern (26 bp):
AGAAAAGAAAAAGTAAAAAATCAAAA
Found at i:45602 original size:38 final size:38
Alignment explanation
Indices: 45551--45627 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
45541 CAAGACAAGC
45551 GTTGGTTTAAATATAATGCAAACAACCTCACATATTTA
1 GTTGGTTTAAATATAATGCAAACAACCTCACATATTTA
45589 GTTGGTTTAAATATAATGCAAACAACCTCACATATTTA
1 GTTGGTTTAAATATAATGCAAACAACCTCACATATTTA
45627 G
1 G
45628 ACTTATCACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (38 bp):
GTTGGTTTAAATATAATGCAAACAACCTCACATATTTA
Found at i:48345 original size:9 final size:8
Alignment explanation
Indices: 48322--48360 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
48312 GTATGCTTCC
48322 CCCTTTTT
1 CCCTTTTT
*
48330 CTCTTTTT
1 CCCTTTTT
48338 CCCTTTTT
1 CCCTTTTT
48346 CCCTTTTT
1 CCCTTTTT
*
48354 CTCTTTT
1 CCCTTTT
48361 CATCAGTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
CCCTTTTT
Found at i:52213 original size:2 final size:2
Alignment explanation
Indices: 52206--52355 Score: 112
Period size: 2 Copynumber: 75.0 Consensus size: 2
52196 ATGGATTACT
52206 TA TA TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* ** * * * * *
52249 TA TA TA TA T- TA GA GG CA T- TA AA TG TGA TT TA GTT TGA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA T-A TA TA
* * * *
52289 TT TG TCA -A TC TA CA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52330 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
52356 ATTTACGACA
Statistics
Matches: 119, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
1 5 0.04
2 109 0.92
3 5 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:52549 original size:13 final size:13
Alignment explanation
Indices: 52512--52554 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
52502 AATGACGCTC
52512 AATGTGCGTCATA
1 AATGTGCGTCATA
* *
52525 AATGAGCATCATA
1 AATGTGCGTCATA
*
52538 AATGTGTGTCATA
1 AATGTGCGTCATA
52551 AATG
1 AATG
52555 CGTGTCATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:52559 original size:13 final size:13
Alignment explanation
Indices: 52519--52563 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
52509 CTCAATGTGC
*
52519 GTCATAAATGAGC
1 GTCATAAATGAGT
* *
52532 ATCATAAATGTGT
1 GTCATAAATGAGT
*
52545 GTCATAAATGCGT
1 GTCATAAATGAGT
52558 GTCATA
1 GTCATA
52564 GATTTATGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (13 bp):
GTCATAAATGAGT
Found at i:58343 original size:21 final size:20
Alignment explanation
Indices: 58318--58356 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
58308 CATCAAGGTC
*
58318 TTTGTGGAGGCCATGAAATCT
1 TTTGTAGAGGCCAT-AAATCT
*
58339 TTTGTAGATGCCATAAAT
1 TTTGTAGAGGCCATAAAT
58357 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTGTAGAGGCCATAAATCT
Found at i:65499 original size:24 final size:24
Alignment explanation
Indices: 65427--65504 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 24
65417 ATATCACTTG
*
65427 GCAAACATCCTTACTGATGTTCTT
1 GCAAACGTCCTTACTGATGTTCTT
* * *
65451 GC-AATGTCGTAACAATCTGATGTTCTT
1 GCAAACGTCCT---TA-CTGATGTTCTT
65478 GCAAACGTCCTTACTGATGTTCTT
1 GCAAACGTCCTTACTGATGTTCTT
65502 GCA
1 GCA
65505 GCATTATCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
23 5 0.12
24 16 0.38
25 1 0.02
26 1 0.02
27 13 0.31
28 6 0.14
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (24 bp):
GCAAACGTCCTTACTGATGTTCTT
Found at i:67039 original size:19 final size:19
Alignment explanation
Indices: 66997--67039 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
66987 ACAATCACTC
*
66997 AAGTAATAAAGTGATGAGT
1 AAGTAATAAAGTGATGACT
*
67016 AAGTAATAAAGTGGTGACT
1 AAGTAATAAAGTGATGACT
*
67035 GAGTA
1 AAGTA
67040 TCGTCTCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.28, T:0.26
Consensus pattern (19 bp):
AAGTAATAAAGTGATGACT
Found at i:68903 original size:22 final size:22
Alignment explanation
Indices: 68878--69021 Score: 155
Period size: 22 Copynumber: 6.3 Consensus size: 22
68868 TATATATTAT
*
68878 AATATATAAAATAGTTTTTGAA
1 AATATATAATATAGTTTTTGAA
68900 AATATATAATATAGTTTTTGAA
1 AATATATAATATAGTTTTTGAA
* *
68922 AACATATTATATAG-TTTTGAAA
1 AATATATAATATAGTTTTTG-AA
68944 ACATATAATATATATAGTTTTTGAA
1 A-ATAT-ATA-ATATAGTTTTTGAA
*
68969 AATATATATATATATATATTTTGAA
1 AATATATA-ATATA-GT-TTTTGAA
* * *
68994 AACATATTATATTGTTTTTGAA
1 AATATATAATATAGTTTTTGAA
69016 AATATA
1 AATATA
69022 ATATATATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
21 5 0.05
22 48 0.46
23 13 0.12
24 11 0.11
25 22 0.21
26 5 0.05
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (22 bp):
AATATATAATATAGTTTTTGAA
Found at i:69005 original size:47 final size:46
Alignment explanation
Indices: 68893--69029 Score: 156
Period size: 47 Copynumber: 3.0 Consensus size: 46
68883 ATAAAATAGT
* * * *
68893 TTTTGAAAATATATAATATAGTTTTTG-AAA-ACATAT-TATATAG
1 TTTTGAAAACATATTATATAGTTTTTGAAAATATATATATATATAA
68936 TTTTGAAAACATATAATATATATAGTTTTTGAAAATATATATATATATATA
1 TTTTGAAAAC--AT-AT-TATATAGTTTTTGAAAATATATATATATATA-A
*
68987 TTTTGAAAACATATTATATTGTTTTTGAAAATATA-ATATATAT
1 TTTTGAAAACATATTATATAGTTTTTGAAAATATATATATATAT
69030 TACATAGCTT
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
43 9 0.11
45 2 0.02
46 10 0.12
47 32 0.40
48 5 0.06
49 7 0.09
50 6 0.07
51 10 0.12
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (46 bp):
TTTTGAAAACATATTATATAGTTTTTGAAAATATATATATATATAA
Found at i:69052 original size:47 final size:45
Alignment explanation
Indices: 68950--69053 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 45
68940 GAAAACATAT
* * *
68950 AATATATATAGTTTTTGAAAATATATATATATATATATTTTGAAA
1 AATATATATTGTTTTTGAAAATATATATATATACATACTTTGAAA
*
68995 ACATATTATATTGTTTTTGAAAATATAATATATATTACATAGCTTT-CAA
1 A-ATA-TATATTGTTTTTGAAAATAT-ATATATA-TACATA-CTTTGAAA
69044 AATATATATT
1 AATATATATT
69054 ATACACATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
45 1 0.02
46 3 0.06
47 25 0.50
48 10 0.20
49 8 0.16
50 3 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (45 bp):
AATATATATTGTTTTTGAAAATATATATATATACATACTTTGAAA
Found at i:69111 original size:7 final size:7
Alignment explanation
Indices: 69101--69134 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
69091 CTCTTTTCCT
69101 TTTTTTA
1 TTTTTTA
69108 TTTTTTA
1 TTTTTTA
*
69115 TTTATTA
1 TTTTTTA
69122 TTATTTTA
1 TT-TTTTA
69130 TTTTT
1 TTTTT
69135 AGTTTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTA
Found at i:70623 original size:18 final size:18
Alignment explanation
Indices: 70600--70636 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
70590 TGACACATTT
70600 ATGGTAAAACACAGATCC
1 ATGGTAAAACACAGATCC
70618 ATGGTAAAACACAGATCC
1 ATGGTAAAACACAGATCC
70636 A
1 A
70637 GTAAATGGGA
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:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (18 bp):
ATGGTAAAACACAGATCC
Found at i:74773 original size:22 final size:21
Alignment explanation
Indices: 74736--74776 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
74726 CCATCTCCAT
74736 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
74757 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
74777 ATTCTGTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:74824 original size:21 final size:21
Alignment explanation
Indices: 74799--74838 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
74789 TCTCTATCAT
74799 TTATTTATT-TCATTTCATTCC
1 TTATTT-TTATCATTTCATTCC
74820 TTATTTTTATCATTTCATT
1 TTATTTTTATCATTTCATT
74839 AATCTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTTTTATCATTTCATTCC
Found at i:75144 original size:32 final size:30
Alignment explanation
Indices: 75108--75168 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
75098 AGAAAAAGAT
75108 AAAAAGAATAAA-AAATTCAGAAAAGAAGAAAA
1 AAAAAGAA-AAAGAAATTCA-AAAAG-AGAAAA
75140 AAAAAGAAAAAGAAATTCAAAAAGAGAAA
1 AAAAAGAAAAAGAAATTCAAAAAGAGAAA
75169 GCAAGACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.18
31 8 0.29
32 15 0.54
ACGTcount: A:0.75, C:0.03, G:0.13, T:0.08
Consensus pattern (30 bp):
AAAAAGAAAAAGAAATTCAAAAAGAGAAAA
Found at i:75147 original size:18 final size:17
Alignment explanation
Indices: 75090--75154 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 17
75080 ATTAGAGTGC
*
75090 AAAAAGAAAGAAAAAGA
1 AAAAAGAAAAAAAAAGA
75107 TAAAAAGAATAAAAAATTCAGA
1 -AAAAAGAA-AAAAAA---AGA
75129 AAAGAAGAAAAAAAAAG-
1 AAA-AAGAAAAAAAAAGA
75146 AAAAAGAAA
1 AAAAAGAAA
75155 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
16 6 0.15
17 3 0.07
18 10 0.24
19 5 0.12
21 9 0.22
22 8 0.20
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAGA
Found at i:75150 original size:19 final size:19
Alignment explanation
Indices: 75093--75153 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
75083 AGAGTGCAAA
* *
75093 AAGAAAGAAAAAGATAAA-
1 AAGAAAAAAAAAGAAAAAG
75111 AAGAATAAAAAATTCAG-AAAAG
1 AAGAA-AAAAAA---AGAAAAAG
75133 AAGAAAAAAAAAGAAAAAG
1 AAGAAAAAAAAAGAAAAAG
75152 AA
1 AA
75154 ATTCAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
21 9 0.26
22 7 0.20
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (19 bp):
AAGAAAAAAAAAGAAAAAG
Found at i:79224 original size:10 final size:9
Alignment explanation
Indices: 79209--79271 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 9
79199 ATTAGAGTGC
79209 AAAAAGAAAG
1 AAAAAG-AAG
79219 AAAAAGAA-
1 AAAAAGAAG
79227 AAAAAGAAG
1 AAAAAGAAG
79236 AAAAA-ATTCAG
1 AAAAAGA---AG
79247 AAAAA-AAG
1 AAAAAGAAG
*
79255 AAAAGAAAAG
1 AAAA-AGAAG
79265 AAAAAGA
1 AAAAAGA
79272 CATTCAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
8 15 0.33
9 10 0.22
10 13 0.28
11 8 0.17
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:79236 original size:11 final size:11
Alignment explanation
Indices: 79212--79266 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
79202 AGAGTGCAAA
*
79212 AAGAAAGAAA-
1 AAGAAAAAAAG
79222 AAGAAAAAAAG
1 AAGAAAAAAAG
**
79233 AAGAAAAAATT
1 AAGAAAAAAAG
*
79244 CAGAAAAAAAG
1 AAGAAAAAAAG
*
79255 AA-AAGAAAAG
1 AAGAAAAAAAG
79265 AA
1 AA
79267 AAAGACATTC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
10 18 0.50
11 18 0.50
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:82997 original size:23 final size:24
Alignment explanation
Indices: 82967--83016 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
82957 GATACAACAA
82967 CAACACCATCTCAATTTCAT-CAT
1 CAACACCATCTCAATTTCATCCAT
82990 CAACACCATCTCAATTTCATCCAT
1 CAACACCATCTCAATTTCATCCAT
83014 CAA
1 CAA
83017 GACTATCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (24 bp):
CAACACCATCTCAATTTCATCCAT
Found at i:83099 original size:22 final size:21
Alignment explanation
Indices: 83056--83099 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
83046 TTTATTTATT
*
83056 TCATTTCATTCATTACCTTTA
1 TCATTTCATTAATTACCTTTA
*
83077 TCATTTCATTAATCTTCCTTTA
1 TCATTTCATTAAT-TACCTTTA
83099 T
1 T
83100 TAATCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (21 bp):
TCATTTCATTAATTACCTTTA
Found at i:87135 original size:22 final size:21
Alignment explanation
Indices: 87098--87138 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
87088 ACATCTCTAT
87098 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
87119 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
87139 ATTCCACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:87974 original size:173 final size:172
Alignment explanation
Indices: 87656--87978 Score: 558
Period size: 172 Copynumber: 1.9 Consensus size: 172
87646 TTCCTAGTCT
*
87656 TTAAGAGATAGCCGTTTATAGGAGTTGATACCTAATATCGAGAGAGTTAGGTTAGATCTACGTGA
1 TTAAGAGATAGCAGTTTATAGGAGTTGATACCTAATATC-AGAGAGTTAGGTTAGATCTACGTGA
*
87721 ATAAGGGAACTAATTCAGGATTGTGAGGTTCTAACATGCCTAGAGATAAGGAGAGGGTTTTAAGC
65 ATAAGGGAACTAATCCAGGATTGTGAGGTTCTAACATGCCTAGAGATAAGGAGAGGGTTTTAAGC
87786 GACTAAAAAGGATAATACTTCTTCGATATCACACCATGAGTTG
130 GACTAAAAAGGATAATACTTCTTCGATATCACACCATGAGTTG
*
87829 TTAAGAGATAGTCATTTTATAGGAGTTGATACCTAATATC-GAGAGTTAGGTTAGATCTACGTGA
1 TTAAGAGATAG-CAGTTTATAGGAGTTGATACCTAATATCAGAGAGTTAGGTTAGATCTACGTGA
* *
87893 ATAAGGGAACTAATCCAGGATTGTGAGGTTCTAACCTGTCTTAGAGATAAGGAGAGGGTTTTAAG
65 ATAAGGGAACTAATCCAGGATTGTGAGGTTCTAACATG-CCTAGAGATAAGGAGAGGGTTTTAAG
*
87958 CGACTAAAAGGGATAATACTT
129 CGACTAAAAAGGATAATACTT
87979 AATTGATAGG
Statistics
Matches: 142, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
172 60 0.42
173 56 0.39
174 26 0.18
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (172 bp):
TTAAGAGATAGCAGTTTATAGGAGTTGATACCTAATATCAGAGAGTTAGGTTAGATCTACGTGAA
TAAGGGAACTAATCCAGGATTGTGAGGTTCTAACATGCCTAGAGATAAGGAGAGGGTTTTAAGCG
ACTAAAAAGGATAATACTTCTTCGATATCACACCATGAGTTG
Found at i:89920 original size:21 final size:20
Alignment explanation
Indices: 89872--89913 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
89862 GTTTCTCTAT
*
89872 AAGA-ATTTATGGCTTCGAC
1 AAGAGATTTATGGCTTCAAC
89891 AAGAGATTTCATGGCTTCAAC
1 AAGAGATTT-ATGGCTTCAAC
89912 AA
1 AA
89914 ATGATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
AAGAGATTTATGGCTTCAAC
Done.