Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002567.1 Hibiscus syriacus cultivar Beakdansim tig00005210_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: 322000
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:255542 original size:33 final size:33
Alignment explanation
Indices: 255500--255567 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
255490 ATTGAGATTG
*
255500 ATGTGTGTGTATACTTATATGTATTTATATGAT
1 ATGTGTGTGTATACTTATATGTATGTATATGAT
*
255533 ATGTGTGTGTATACTTATATGTGTGTATATGAT
1 ATGTGTGTGTATACTTATATGTATGTATATGAT
255566 AT
1 AT
255568 ATATACTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (33 bp):
ATGTGTGTGTATACTTATATGTATGTATATGAT
Found at i:255554 original size:18 final size:18
Alignment explanation
Indices: 255500--255558 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
255490 ATTGAGATTG
255500 ATGTGTGTGTATACTTAT
1 ATGTGTGTGTATACTTAT
* *
255518 ATGTAT-T-TATA-TGAT
1 ATGTGTGTGTATACTTAT
255533 ATGTGTGTGTATACTTAT
1 ATGTGTGTGTATACTTAT
255551 ATGTGTGT
1 ATGTGTGT
255559 ATATGATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 8 0.24
16 5 0.15
17 5 0.15
18 16 0.47
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (18 bp):
ATGTGTGTGTATACTTAT
Found at i:255557 original size:16 final size:16
Alignment explanation
Indices: 255503--255561 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
255493 GAGATTGATG
255503 TGTGTGTATACTTATA
1 TGTGTGTATACTTATA
* * *
255519 TGTATTTATA-TGATATG
1 TGTGTGTATACT--TATA
255536 TGTGTGTATACTTATA
1 TGTGTGTATACTTATA
255552 TGTGTGTATA
1 TGTGTGTATA
255562 TGATATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.03
16 21 0.62
17 11 0.32
18 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.20, T:0.51
Consensus pattern (16 bp):
TGTGTGTATACTTATA
Found at i:261457 original size:17 final size:16
Alignment explanation
Indices: 261435--261503 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
261425 CCGTGTCCCG
*
261435 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
* *
261452 ACCCGG-TAATCGAGT
1 ACCCGGATATTCGGGT
*
261467 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
261484 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
261499 ACCCG
1 ACCCG
261504 ATACCCGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:261470 original size:15 final size:15
Alignment explanation
Indices: 261447--261503 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
261437 CCGGATGTTA
261447 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
261462 CGAGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
261478 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
261494 CGGGTACCCG
1 CGGGTACCCG
261504 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:261471 original size:32 final size:32
Alignment explanation
Indices: 261435--261503 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
261425 CCGTGTCCCG
261435 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
* * *
261467 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
261499 ACCCG
1 ACCCG
261504 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGAGT
Found at i:262827 original size:21 final size:21
Alignment explanation
Indices: 262789--262852 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
262779 TTTGTAATAG
*
262789 GGGAACCGATTCCCCTGCTACA
1 GGGAATCGATT-CCCTGCTACA
262811 GGGAATCGATTCCCTGCTACA
1 GGGAATCGATTCCCTGCTACA
*
262832 GGGAATCGATACCCTGCTACA
1 GGGAATCGATTCCCTGCTACA
262853 ATACTGCTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 30 0.75
22 10 0.25
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.20
Consensus pattern (21 bp):
GGGAATCGATTCCCTGCTACA
Found at i:264825 original size:18 final size:18
Alignment explanation
Indices: 264802--264837 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
264792 CACTCAAAAA
264802 CTCTAAATCTTTAATCTT
1 CTCTAAATCTTTAATCTT
* *
264820 CTCTAACTCTTTTATCTT
1 CTCTAAATCTTTAATCTT
264838 TTGATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (18 bp):
CTCTAAATCTTTAATCTT
Found at i:267228 original size:2 final size:2
Alignment explanation
Indices: 267221--267271 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
267211 TCAAACTATC
267221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
267263 TA TA TA TA T
1 TA TA TA TA T
267272 TCTTTCTAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:268961 original size:19 final size:20
Alignment explanation
Indices: 268937--268989 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
268927 ATATATGTTT
268937 TATGAACAGTAA-AATAC-G
1 TATGAACAGTAATAATACTG
268955 ATATGAACAGTGAATAATACTG
1 -TATGAACAGT-AATAATACTG
*
268977 TTTGAACAGTAAT
1 TATGAACAGTAAT
268990 GAACAATACC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 5 0.17
21 14 0.47
22 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (20 bp):
TATGAACAGTAATAATACTG
Found at i:269095 original size:21 final size:22
Alignment explanation
Indices: 269053--269097 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
269043 GTTTGTAATA
*
269053 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTACCCTGCTAC
*
269075 AGGGAATCGA-TACCTTGCTAC
1 AGGGAATCGATTACCCTGCTAC
269096 AG
1 AG
269098 TACTGCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (22 bp):
AGGGAATCGATTACCCTGCTAC
Found at i:270790 original size:21 final size:20
Alignment explanation
Indices: 270760--270799 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
270750 TTTTTCCTTT
270760 AGGGGGAATC-GATACCCCCC
1 AGGGGGAATCTG-TACCCCCC
270780 AGGGGGAAATCTGTACCCCC
1 AGGGGG-AATCTGTACCCCC
270800 TGCACAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 11 0.61
22 1 0.06
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.12
Consensus pattern (20 bp):
AGGGGGAATCTGTACCCCCC
Found at i:273467 original size:10 final size:10
Alignment explanation
Indices: 273440--273469 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
273430 CGTTATTTTA
*
273440 AAATTAAATT
1 AAATTAATTT
273450 AAATTAATTT
1 AAATTAATTT
273460 AAATTAATTT
1 AAATTAATTT
273470 TTTCTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTAATTT
Found at i:275337 original size:16 final size:18
Alignment explanation
Indices: 275305--275339 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
275295 ATATAAAAAC
275305 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
275323 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
275339 A
1 A
275340 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:275466 original size:2 final size:2
Alignment explanation
Indices: 275453--275491 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
275443 AAAATAAGAA
*
275453 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
275492 ATAACACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:275537 original size:34 final size:34
Alignment explanation
Indices: 275477--275571 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 34
275467 ATATATATAT
* * *
275477 ATATATATATATATAATAACACTAATAAAAAAAC
1 ATATATACATATATAATAAAAATAATAAAAAAAC
* * **
275511 ATATATACATATATAATAAAATTAAT-AGAAAGT
1 ATATATACATATATAATAAAAATAATAAAAAAAC
* *
275544 A-ATATGCATATATAACAAAAATAATAAA
1 ATATATACATATATAATAAAAATAATAAA
275572 GTAGGAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
32 21 0.42
33 6 0.12
34 23 0.46
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (34 bp):
ATATATACATATATAATAAAAATAATAAAAAAAC
Found at i:275985 original size:35 final size:36
Alignment explanation
Indices: 275915--276014 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 36
275905 GTGCTTGTGG
* * *
275915 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
275952 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
* *
275987 ATCATATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
276015 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.47
36 11 0.20
37 18 0.33
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:277257 original size:204 final size:205
Alignment explanation
Indices: 276478--277837 Score: 1423
Period size: 210 Copynumber: 6.5 Consensus size: 205
276468 ATTGTTCCGA
* * * * **
276478 GTCCAATATCC-TCTGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAGT
1 GTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
* * * * * *
276542 CAGTCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAG
65 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
* * * * * * *
276607 ATGAAATTGACTCTGAACGAA-ATCTTGTTGACAATCAGTCGTCTCTTCGTTGTGAAGTTGAACT
130 TTGAAATTGGCTCTGAA-GAAGTTGTTGTTGACAGTCAGCCGTCCCTTCG-TGTGAAGTTGAACT
* * *
276671 TGTGTTATCTCGA
193 TGTGTTGTCTTGG
** * * *
276684 GTCCAATATCCTTCGCTACGAAGTTGAAATTGGCTCTGAAATTTGAAAAATATTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACC
* *
276749 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCC-TC-CATCGT
66 AGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTTCGC-T-GT
* * * ** *
276812 GGAGTTGAAATCGCGGATGAAACTGAA-AAGTTGTTCGTTGACAACCAGTCGTCCCTTCGTTGTG
126 GAAGTTGAAAT--TGGCT----CTGAAGAAGTTGTT-GTTGACAGTCAGCCGTCCCTTCG-TGTG
*
276876 AAGTTGAACTTGTGTTGTCTCGG
183 AAGTTGAACTTGTGTTGTCTTGG
* * * * * *
276899 GTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGAC
1 GT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
276963 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTG
62 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTG
* * * *
277028 AAGTTGAGATTGGCTCCG-A-AA-TTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGA
127 AAGTTGAAATTGGCTCTGAAGAAGTTG-TTGTTGACAGTCAGCCGTCCCTTCG-TGTGAAGTTGA
* *
277090 GCTTGTGCTGTCTTGG
190 ACTTGTGTTGTCTTGG
* *
277106 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACC
*
277171 AGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
* * * * *
277236 TGAGATTGGCTC-CAA-AA-TTGCTTGTCGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAGA-T
131 TGAAATTGGCTCTGAAGAAGTTG-TTGTTGACAGTCAGCCGTCCCTTCG-TGTGAAGTTGA-ACT
*
277297 TGTGCTGTCTTGG
193 TGTGTTGTCTTGG
*
277310 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CTTGAAACTGGGAAATTA-TTGTTGACAAC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC-TGAAATTGGGAAATTATTTGTTGACAAC
* * *
277373 CAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAG
65 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
*
277438 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG-CAGCGGTCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGA-A----GAAGTTGTTGTTGAC-AGTCAGCCGTCCCTTCGT-GTGAAGTT
**
277502 GAACTTGCATTGTC-TGG
188 GAACTTGTGTTGTCTTGG
* * * * *
277519 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT-GTTGTTGACAAG
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
* * * *
277583 CAACGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGA
65 CAGCCGTCCCTTCGCT-GTGAAGTTGAACTTGTGTTGTCTCG-AGTCCAATATCCTTCGCTGTGA
*
277646 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG-CAGCGGTCCCTTCGTCGTGAAG
128 AGTTGAAATTGGCTCTG--A---AGAAGTTGTTGTTGAC-AGTCAGCCGTCCCTTCGT-GTGAAG
*
277710 TTGAACTTGCGTTGTC-TGG
186 TTGAACTTGTGTTGTCTTGG
* * * * *
277729 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
* * *
277794 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTCTCGAGT
65 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT
277838 GCCACAATAT
Statistics
Matches: 1005, Mismatches: 101, Indels: 91
0.84 0.08 0.08
Matches are distributed among these distances:
203 85 0.08
204 236 0.23
205 3 0.00
206 88 0.09
207 50 0.05
208 9 0.01
209 26 0.03
210 270 0.27
211 55 0.05
212 3 0.00
213 5 0.00
214 5 0.00
215 72 0.07
216 4 0.00
217 3 0.00
218 91 0.09
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (205 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACC
AGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
TGAAATTGGCTCTGAAGAAGTTGTTGTTGACAGTCAGCCGTCCCTTCGTGTGAAGTTGAACTTGT
GTTGTCTTGG
Found at i:277424 original size:105 final size:105
Alignment explanation
Indices: 276475--277837 Score: 1189
Period size: 105 Copynumber: 13.0 Consensus size: 105
276465 AATATTGTTC
* * * * *
276475 CGAGTCCAATATCC-TCTGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTC-GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGAC
* * * * *
276539 -AGTCAGTC-GCCCCTTTG-CTGTGAAGTTGAGCTTGTGCTGTCT
64 AAG-CAG-CGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* * * * * * *
276581 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AA---CGAA-ATCTTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAA
* * * * *
276641 TCAGTC-GTCTCTTCGTTGTGAAGTTGAACTTGTGTTATCT
66 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** ** *
276681 CGAGTCCAATATCCTTCGCTACGAAGTTGAAATTGGCTCTGAAATTTGAAAAATAT-TTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAGT-TGTTGTTGAC
* * * *
276745 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 AAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * * ** * **
276787 CGAGTGGCACGATATCCTCCATCGTGGAGTTGAAA-TCGCGGATGAAACTGAAAAGTTGTTCGTT
1 CGAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTGGC-TCTGAAATTGGGAAGTTGTT-GTT
* * *
276851 GACAACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
61 GACAAGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * * * *
276896 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTG
1 CGAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTG
* * *
276961 ACAACCAGCCGTCCCTTCG-CTGTGAAGTTGAACTTGTGTTGTCT
62 ACAAGCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* * * * *
277005 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATT-----G--CTTGTCGAC-A
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAA
* * * * *
277062 GTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCT
66 G-CAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* * * * * * *
277103 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-GTTGTTGACA
* * * *
277168 ACCAGCCGTCCCTTCG-CTGTGAAGTTGAACTTGTGTTATCT
65 AGCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* * * *
277209 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTC--CAA-----AA-TTGCTTGTCGAC-
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACA
* * * *
277265 AGTCAGCTGCCCCTTCG-CTGTGAAGTTGAGA-TTGTGCTGTCT
65 AG-CAGCGGTCCCTTCGTC-GTGAAGTTGA-ACTTGCGTTGTCT
* * * * * *
277307 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CTTGAAACTGGGAAATTATTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGGGAAGTTGTTGTTGACA
* * ** *
277371 ACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCT
65 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
277412 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAA
*
277477 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
277517 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAA
*
277582 GCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
277622 -GAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACA
1 CG-AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACA
277686 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
277727 GGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACA
* * * *
277792 ACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTCT
65 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
277833 CGAGT
1 CGAGT
277838 GCCACAATAT
Statistics
Matches: 1072, Mismatches: 134, Indels: 102
0.82 0.10 0.08
Matches are distributed among these distances:
97 3 0.00
98 159 0.15
99 3 0.00
100 77 0.07
101 4 0.00
102 3 0.00
104 4 0.00
105 387 0.36
106 247 0.23
107 6 0.01
108 14 0.01
109 160 0.15
110 5 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAA
GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:278586 original size:36 final size:36
Alignment explanation
Indices: 278541--278923 Score: 312
Period size: 36 Copynumber: 10.9 Consensus size: 36
278531 GAAGATTTTG
* *
278541 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
278577 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
278614 AGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *** * *
278650 TGTTTCAA-AGAAA--ATAT--ATTTA-A-ATATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
278679 TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
278715 TATTTCAAGGGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
278751 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
278788 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* * * * *
278825 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
278853 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
278890 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
278924 CTCTTCTAGT
Statistics
Matches: 279, Mismatches: 47, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.01
29 26 0.09
30 8 0.03
31 1 0.00
32 3 0.01
33 2 0.01
34 3 0.01
35 7 0.03
36 145 0.52
37 78 0.28
38 4 0.01
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:278636 original size:37 final size:36
Alignment explanation
Indices: 278553--278637 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
278543 TTTCAAGAGT
** * * *
278553 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGA
1 AACTGTCTCAAGAAAGACAAAATTAGTTCCAAAAGA
278589 AACTGTCTCAAGAAAGACAAAACTTAGTTCCAAAAGA
1 AACTGTCTCAAGAAAGACAAAA-TTAGTTCCAAAAGA
278626 AACTGTCTCAAG
1 AACTGTCTCAAG
278638 GGGGACGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 20 0.47
37 23 0.53
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (36 bp):
AACTGTCTCAAGAAAGACAAAATTAGTTCCAAAAGA
Found at i:278700 original size:102 final size:101
Alignment explanation
Indices: 278575--278758 Score: 251
Period size: 102 Copynumber: 1.8 Consensus size: 101
278565 GGAGACAAAA
* * *
278575 TTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTTA-TTCCAAAAGAAAATGTCTCAAGAG
* * *
278640 GGACGAAATTTGTTTCAAAGAAAATATATTTAAATAT
65 AGACAAAATTTATTTCAAAGAAAATATATTTAAATAT
* * * * **
278677 TTTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTTATTCCAAAAGAAAATGTCTCAAGAGA
278742 GACAAAATTTATTTCAA
66 GACAAAATTTATTTCAA
278759 GGGAAACTGT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
101 34 0.49
102 36 0.51
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTTATTCCAAAAGAAAATGTCTCAAGAGA
GACAAAATTTATTTCAAAGAAAATATATTTAAATAT
Found at i:278709 original size:138 final size:138
Alignment explanation
Indices: 278482--278795 Score: 364
Period size: 138 Copynumber: 2.3 Consensus size: 138
278472 TTGTTTCATG
* * * * * * *
278482 AGAAACGGTCTCAAGGGAAACAAAATTATGTCTT-AAGGGAAATAAATTTGAAGAT-TTTGTGTT
1 AGAAACTGTCTCAAGAGAGACAAAATTTTGT-TTCAAAGAAAATATATTT-AA-ATATTT-TGTT
* * * * *
278545 TCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGACAAA
62 TCAAGAGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAAAGACAAA
278610 ACTTAGTTCCAAA
127 ACTTA-TTCCAAA
* * *
278623 AGAAACTGTCTCAAGGGGGACGAAA-TTTGTTTCAAAGAAAATATATTTAAATATTTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAAGAAAATATATTTAAATATTTTGTTTCAA
* * * *
278687 GGGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTT
66 GAGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTT
* *
278752 ATTTCAAG
131 ATTCCAAA
*
278760 GGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
278796 GGGAAATTAT
Statistics
Matches: 147, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
137 26 0.18
138 77 0.52
139 7 0.05
140 16 0.11
141 21 0.14
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (138 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAAGAAAATATATTTAAATATTTTGTTTCAA
GAGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAAAGACAAAACTT
ATTCCAAA
Found at i:278918 original size:175 final size:174
Alignment explanation
Indices: 278541--278923 Score: 507
Period size: 174 Copynumber: 2.2 Consensus size: 174
278531 GAAGATTTTG
* * * *
278541 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGA
* * * *
278606 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATTTGTTTCAAAGAAAATATATTT
66 CAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTATTTCAAAGAAAATATATTT
*
278671 AAATATTTTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATT
131 AAATATTTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATT
* * * *
278715 TATTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGA
* * * ** * * * *
278780 CAAAATTTTGTTTCAAGGGAAATTATCTCAAGAGAGACGAAAATTTATTTCAAGGGAAATGT-TT
66 CAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACG-AAATTTATTTCAAAGAAAATATATT
* * * *
278844 TCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
130 TAAATATTT-TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATT
278890 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
278924 CTCTTCTAGT
Statistics
Matches: 179, Mismatches: 28, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
174 96 0.54
175 83 0.46
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (174 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGA
CAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTATTTCAAAGAAAATATATTT
AAATATTTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATT
Found at i:278973 original size:35 final size:35
Alignment explanation
Indices: 278541--278973 Score: 144
Period size: 36 Copynumber: 12.4 Consensus size: 35
278531 GAAGATTTTG
* *
278541 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAAT-T
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* *
278577 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAACT
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGACAAATCT
* * * *
278613 TAGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAAT-T
1 T-GTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* *** * *
278650 TGTTTCAAAGAAAA---TAT--ATTTA-A-ATATTT
1 TGTTTC-AAGAAAACTGTCTCAAGAGAGACAAATCT
278679 TGTTTCAAGGGAAAA-TGTCTCAAGAGAGACAAAAT-T
1 TGTTTCAA--GAAAACTGTCTCAAGAGAGAC-AAATCT
*
278715 TATTTCAAGGGAAAA-TGTCTCAAGAGAGACAAAAT-T
1 TGTTTCAA--GAAAACTGTCTCAAGAGAGAC-AAATCT
* * *
278751 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATCT
* * *
278788 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAAAT-T
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGAC--AAATCT
* * * * *
278825 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAA-GAAAACTG-TCTCAAGAGAGACAAATCT
*
278853 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT-T
1 -TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* *
278890 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATCT
* * * *
278925 T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATCT
*
278961 TGTTTTAAGAAAA
1 TGTTTCAAGAAAA
278974 ACAATCATGA
Statistics
Matches: 311, Mismatches: 49, Indels: 75
0.71 0.11 0.17
Matches are distributed among these distances:
27 1 0.00
28 7 0.02
29 20 0.06
30 9 0.03
31 1 0.00
32 3 0.01
33 2 0.01
34 6 0.02
35 42 0.14
36 130 0.42
37 81 0.26
38 9 0.03
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAAAACTGTCTCAAGAGAGACAAATCT
Found at i:279432 original size:18 final size:18
Alignment explanation
Indices: 279405--279440 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
279395 TGTTGAATCC
*
279405 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
279423 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
279441 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:279882 original size:22 final size:22
Alignment explanation
Indices: 279856--279904 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
279846 TTGTGTTTGG
* *
279856 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
279878 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
279900 TCAAA
1 TCAAA
279905 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:279911 original size:22 final size:22
Alignment explanation
Indices: 279868--279911 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
279858 AAAGGTTTGG
* * *
279868 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
279890 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
279912 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:280556 original size:23 final size:22
Alignment explanation
Indices: 280530--280597 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
280520 TTGCATGTGC
*
280530 TTTTTGTCCCTTTTTCTTTTTG
1 TTTTTGTCTCTTTTTCTTTTTG
*
280552 ATTTTTG-CTCTTTTTACCTTTTG
1 -TTTTTGTCTCTTTTT-CTTTTTG
*
280575 TTCTTGTTTCTCTTTTTCTTTTT
1 TT-TT-TGTCTCTTTTTCTTTTT
280598 TCTTTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.24
23 14 0.38
24 6 0.16
25 8 0.22
ACGTcount: A:0.03, C:0.18, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTGTCTCTTTTTCTTTTTG
Found at i:280585 original size:7 final size:7
Alignment explanation
Indices: 280569--280630 Score: 61
Period size: 8 Copynumber: 8.0 Consensus size: 7
280559 CTCTTTTTAC
280569 CTTTTGTT
1 CTTTT-TT
*
280577 CTTGTTT
1 CTTTTTT
280584 CTCTTTTT
1 CT-TTTTT
280592 CTTTTTT
1 CTTTTTT
280599 CTTTTTTT
1 C-TTTTTT
280607 GCTTTTTT
1 -CTTTTTT
280615 GCTTCTTTT
1 -CTT-TTTT
280624 CTTTTTT
1 CTTTTTT
280631 GTTCTTGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
7 14 0.29
8 29 0.60
9 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (7 bp):
CTTTTTT
Found at i:280599 original size:15 final size:14
Alignment explanation
Indices: 280540--280630 Score: 65
Period size: 16 Copynumber: 5.9 Consensus size: 14
280530 TTTTTGTCCC
**
280540 TTTTTCTTTTTGAT
1 TTTTTCTTTTTTCT
*
280554 TTTTGCTCTTTTTACCT
1 TTTT--TCTTTTT-TCT
*
280571 TTTGTTCTTGTTTCT
1 TTT-TTCTTTTTTCT
280586 CTTTTTCTTTTTTCTT
1 -TTTTTCTTTTTTC-T
280602 TTTTTGCTTTTTTGCT
1 TTTTT-CTTTTTT-CT
280618 TCTTTTCTTTTTT
1 T-TTTTCTTTTTT
280631 GTTCTTGATT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.06
15 16 0.25
16 33 0.52
17 9 0.14
18 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTCTTTTTTCT
Found at i:280611 original size:16 final size:16
Alignment explanation
Indices: 280540--280630 Score: 64
Period size: 15 Copynumber: 5.8 Consensus size: 16
280530 TTTTTGTCCC
*
280540 TTTTTCTTTTTGA--T
1 TTTTTCTTTTTTACTT
*
280554 TTTTGCTCTTTTTACCTT
1 TTTTTCT-TTTTTA-CTT
* * *
280572 TTGTTCTTGTTT-CTC
1 TTTTTCTTTTTTACTT
280587 TTTTTCTTTTTT-CTT
1 TTTTTCTTTTTTACTT
*
280602 TTTTTGCTTTTTTGCTT
1 TTTTT-CTTTTTTACTT
*
280619 CTTTTCTTTTTT
1 TTTTTCTTTTTT
280631 GTTCTTGATT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
14 6 0.10
15 24 0.39
16 14 0.23
17 11 0.18
18 6 0.10
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTTTTACTT
Found at i:280631 original size:16 final size:16
Alignment explanation
Indices: 280588--280636 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
280578 TTGTTTCTCT
*
280588 TTTTCTTTTTT-CTTT
1 TTTTCTTTTTTGCTTC
280603 TTTTGCTTTTTTGCTTC
1 TTTT-CTTTTTTGCTTC
280620 TTTTCTTTTTTG-TTC
1 TTTTCTTTTTTGCTTC
280635 TT
1 TT
280637 GATTGGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 9 0.29
16 15 0.48
17 7 0.23
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTTGCTTC
Found at i:281841 original size:8 final size:8
Alignment explanation
Indices: 281825--281863 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
281815 AATGTATATG
281825 AAAATGCA
1 AAAATGCA
*
281833 AAAAGGCA
1 AAAATGCA
281841 AAAATGC-
1 AAAATGCA
281848 AAAATGCA
1 AAAATGCA
*
281856 AGAATGCA
1 AAAATGCA
281864 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:281851 original size:15 final size:15
Alignment explanation
Indices: 281825--281863 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
281815 AATGTATATG
281825 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
281841 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
281856 AGAATGCA
1 AAAATGCA
281864 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:282406 original size:18 final size:18
Alignment explanation
Indices: 282383--282422 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
282373 ATTAGTCTTT
282383 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
282401 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
282419 CAGA
1 CAGA
282423 CTTGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:284561 original size:16 final size:18
Alignment explanation
Indices: 284529--284563 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
284519 ATATAAAAAC
284529 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
284547 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
284563 A
1 A
284564 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:284598 original size:2 final size:2
Alignment explanation
Indices: 284593--284667 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
284583 AAGTAAAAGC
284593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
284635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
284668 AGTAAAATAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:284807 original size:32 final size:31
Alignment explanation
Indices: 284740--284830 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 31
284730 GGAAATATAT
* *
284740 AAATATATATATAT-ATATAACTAATAAAAA
1 AAATATACATATATAATAAAACTAATAAAAA
* *
284770 AAATATACATATATAATAAAATTAATAGAAAG
1 AAATATACATATATAATAAAACTAATA-AAAA
* * *
284802 TAATATGCATATATAACAAGAA-TAATAAA
1 AAATATACATATATAATAA-AACTAATAAA
284831 GTAGGAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
30 13 0.25
31 12 0.24
32 24 0.47
33 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (31 bp):
AAATATACATATATAATAAAACTAATAAAAA
Found at i:285247 original size:35 final size:37
Alignment explanation
Indices: 285185--285276 Score: 118
Period size: 35 Copynumber: 2.6 Consensus size: 37
285175 GGATCATATC
* * *
285185 TTTAG-GAGTTTAAAACATAGCAAAATTCTATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
*
285221 TTTAG-GAG-TTGAATCCTAGCAGAATTCTATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
*
285256 TTTTGAGAGTTTGAATCCTAG
1 TTTAGAGAGTTTGAATCCTAG
285277 TAGGACGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
35 27 0.55
36 11 0.22
37 11 0.22
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (37 bp):
TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
Found at i:297292 original size:19 final size:19
Alignment explanation
Indices: 297268--297357 Score: 171
Period size: 19 Copynumber: 4.7 Consensus size: 19
297258 AATGCATTTT
297268 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
297287 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
297306 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
297325 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
*
297344 ATGCATCAATGCAC
1 ATGCATCGATGCAC
297358 TTAGGCTTAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACACACC
Found at i:297418 original size:121 final size:121
Alignment explanation
Indices: 297204--297421 Score: 321
Period size: 121 Copynumber: 1.8 Consensus size: 121
297194 AATGCAGTTT
* * * * * *
297204 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTAATGAAAACATCGAATGCATTTTA
1 ATGCATCGATGCACACACCATGCATCAATGCACTCAGGCTTAATCAAAACATCAAATGCATTTTA
*
297269 TGCATCGATGCACACACCATGCATCGATGCACACACCATGCATCGATGCACACACC
66 TGCATCGATGCACACACCATGCACCGATGCACACACCATGCATCGATGCACACACC
* *
297325 ATGCATCGATGCACACACCATGCATCAATGCACTTAGGCTTATTCAAAACATCAAATGCATTTTA
1 ATGCATCGATGCACACACCATGCATCAATGCACTCAGGCTTAATCAAAACATCAAATGCATTTTA
**
297390 TGCATCGATGCACAC-TTAGTGCACCGATGCAC
66 TGCATCGATGCACACACCA-TGCACCGATGCAC
297422 TAAGTGTTCC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
120 1 0.01
121 84 0.99
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (121 bp):
ATGCATCGATGCACACACCATGCATCAATGCACTCAGGCTTAATCAAAACATCAAATGCATTTTA
TGCATCGATGCACACACCATGCACCGATGCACACACCATGCATCGATGCACACACC
Found at i:299554 original size:15 final size:15
Alignment explanation
Indices: 299536--299566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
299526 ATCTTAAAGC
299536 TTCTTTTGATAAATT
1 TTCTTTTGATAAATT
*
299551 TTCTTTTGTTAAATT
1 TTCTTTTGATAAATT
299566 T
1 T
299567 GAATCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (15 bp):
TTCTTTTGATAAATT
Found at i:300440 original size:44 final size:44
Alignment explanation
Indices: 300390--300486 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
300380 TTGTGCTTAA
* *
300390 TGCATCGATACA-C-TTAATAGTGCATCGATGCATCCCTTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCA-CCCTTTGAATG
* * *
300434 TGCATCGATACACCATGAAGGTGCACCGATGCACTCTTTTAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACCCTTTGAATG
300478 TGCATCGAT
1 TGCATCGAT
300487 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 30 0.65
45 13 0.28
46 3 0.07
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACCCTTTGAATG
Found at i:302042 original size:64 final size:64
Alignment explanation
Indices: 301971--302131 Score: 241
Period size: 64 Copynumber: 2.5 Consensus size: 64
301961 GAATAAATTG
* * * * * *
301971 AACATCGAATGTAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAA
* * *
302035 AATATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGGCTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAA
302099 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
302132 TTAGTGCACC
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 87 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAA
Found at i:302145 original size:64 final size:63
Alignment explanation
Indices: 301971--302149 Score: 232
Period size: 64 Copynumber: 2.8 Consensus size: 63
301961 GAATAAATTG
* * * * *
301971 AACATCGAATGTAGTTTATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGCTTAATCAA
* * * *
302035 AATATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGGCTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGCTTAATCAA
* *
302099 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
302150 AAGTGTTCCA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
63 1 0.01
64 99 0.99
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGCTTAATCAA
Found at i:304088 original size:30 final size:30
Alignment explanation
Indices: 304052--304119 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
304042 GTCCCCATCT
304052 CCGTTTAACATAAATAG-TTTTTC-CTCGTCC
1 CCGTTTAACATAAA-AGATTTTTCTC-CGTCC
* *
304082 CCGTTTAGCATAAACGATTTTTCTCCGTCC
1 CCGTTTAACATAAAAGATTTTTCTCCGTCC
304112 CCGTTTAA
1 CCGTTTAA
304120 TTCGATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 31 0.94
31 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (30 bp):
CCGTTTAACATAAAAGATTTTTCTCCGTCC
Found at i:308384 original size:2 final size:2
Alignment explanation
Indices: 308377--308405 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
308367 AACTTTTGGA
308377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
308406 GGAAAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:312284 original size:16 final size:16
Alignment explanation
Indices: 312263--312299 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
312253 GGGTTATACA
312263 TAGCTAGAAGTTAGCT
1 TAGCTAGAAGTTAGCT
312279 TAGCTAGAAGTTAGCT
1 TAGCTAGAAGTTAGCT
312295 TAGCT
1 TAGCT
312300 GCCTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (16 bp):
TAGCTAGAAGTTAGCT
Found at i:314749 original size:5 final size:5
Alignment explanation
Indices: 314739--314773 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
314729 CGATATTACT
*
314739 TGTCA TGTCA TGTCA TGTCA TGTCA GGTCA TGTCA
1 TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA
314774 GGGTGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (5 bp):
TGTCA
Found at i:320590 original size:24 final size:24
Alignment explanation
Indices: 320538--320608 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
320528 AAAATTTGAA
* *
320538 TCATT-AAAATAAATTTAGATATT
1 TCATTAAAAATAAATTCAAATATT
*
320561 TAATTAAAAATAAATTCAAATCA-T
1 TCATTAAAAATAAATTCAAAT-ATT
* * *
320585 TCATTAACACTAAATTCAAGTATT
1 TCATTAAAAATAAATTCAAATATT
320609 GAAATAGACT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 5 0.13
24 32 0.84
25 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (24 bp):
TCATTAAAAATAAATTCAAATATT
Done.