Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009073.1 Hibiscus syriacus cultivar Beakdansim tig00112505_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: 329414
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:175740 original size:23 final size:23
Alignment explanation
Indices: 175684--175731 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
175674 GATCCCTCAC
175684 ACACACACACACATTAGCATATT
1 ACACACACACACATTAGCATATT
175707 ACACACACACACATTAGCATATT
1 ACACACACACACATTAGCATATT
175730 AC
1 AC
175732 TCTTCCACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.31, G:0.04, T:0.21
Consensus pattern (23 bp):
ACACACACACACATTAGCATATT
Found at i:175821 original size:101 final size:104
Alignment explanation
Indices: 175713--175920 Score: 332
Period size: 101 Copynumber: 2.0 Consensus size: 104
175703 TATTACACAC
* *
175713 ACACACATTAGCATATTACTCTTCCACAAGTGTAATAATAGCTTGTGGTTTATTTTCAAGGG-TA
1 ACACACATTAGCATATTACTCTTCCACAAGTGTAATAATAACTTGTGGTTTATTTTCAAGGGAAA
175777 A-A-ATTTGGGTTTCTCCACCTACATCTAAAACTCTAGG
66 ATATATTTGGGTTTCTCCACCTACATCTAAAACTCTAGG
* *
175814 ACACACATTAGCATATTACTCTTTCACAAGTGTAATAATAACTTGTGGTTTATTTTCACGGGAAA
1 ACACACATTAGCATATTACTCTTCCACAAGTGTAATAATAACTTGTGGTTTATTTTCAAGGGAAA
* *
175879 ATATTATTTGGGTTTCTCCTCCTATATCTAAAACTCTAGG
66 ATA-TATTTGGGTTTCTCCACCTACATCTAAAACTCTAGG
175919 AC
1 AC
175921 TCAAGTTAAG
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
101 59 0.61
102 2 0.02
103 1 0.01
105 35 0.36
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (104 bp):
ACACACATTAGCATATTACTCTTCCACAAGTGTAATAATAACTTGTGGTTTATTTTCAAGGGAAA
ATATATTTGGGTTTCTCCACCTACATCTAAAACTCTAGG
Found at i:176862 original size:18 final size:18
Alignment explanation
Indices: 176841--176875 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
176831 GTCTTTTTCA
176841 ACGAAAAAATCTTTCGAC
1 ACGAAAAAATCTTTCGAC
* *
176859 ACGAAAATATTTTTCGA
1 ACGAAAAAATCTTTCGA
176876 GATATACTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
ACGAAAAAATCTTTCGAC
Found at i:181733 original size:21 final size:23
Alignment explanation
Indices: 181690--181758 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
181680 GTTTATTTCT
181690 AAATAATTAAAATATATTATTAA
1 AAATAATTAAAATATATTATTAA
* *
181713 AAATAA-TAAATTAT-TTTTTAA
1 AAATAATTAAAATATATTATTAA
* * *
181734 AGAT-ATTAACATTAAATTATTAA
1 AAATAATTAA-AATATATTATTAA
181757 AA
1 AA
181759 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 11 0.30
23 13 0.35
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
AAATAATTAAAATATATTATTAA
Found at i:183393 original size:39 final size:39
Alignment explanation
Indices: 183350--183424 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
183340 GGGCCGTGGT
*
183350 TAGGTTGTTGGGGCCATGTGTAAATTCTTATAAAGGGAC
1 TAGGTTGTCGGGGCCATGTGTAAATTCTTATAAAGGGAC
*
183389 TAGGTTGTCGGGGCCGTGTGTAAATTCTTATAAAGG
1 TAGGTTGTCGGGGCCATGTGTAAATTCTTATAAAGG
183425 TGCCCCTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (39 bp):
TAGGTTGTCGGGGCCATGTGTAAATTCTTATAAAGGGAC
Found at i:183465 original size:31 final size:31
Alignment explanation
Indices: 183423--183498 Score: 134
Period size: 31 Copynumber: 2.4 Consensus size: 31
183413 TTCTTATAAA
183423 GGTGCCCCTATTTTCTAGATATATTCAATTTT
1 GGTG-CCCTATTTTCTAGATATATTCAATTTT
183455 GGTGCCCTATTTTCTAGATATATTCAATTTT
1 GGTGCCCTATTTTCTAGATATATTCAATTTT
*
183486 GGGGCCCTATTTT
1 GGTGCCCTATTTT
183499 TATGTTTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 39 0.91
32 4 0.09
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (31 bp):
GGTGCCCTATTTTCTAGATATATTCAATTTT
Found at i:183654 original size:2 final size:2
Alignment explanation
Indices: 183647--183709 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
183637 ACACCCCTGC
183647 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
183689 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
183710 CGACATATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:193850 original size:20 final size:20
Alignment explanation
Indices: 193821--193862 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
193811 CTTAAGGCAT
* *
193821 ATGTAGGTTCGTATAGGTGC
1 ATGTACGTTCATATAGGTGC
*
193841 ATGTACGTTCATATAGTTGC
1 ATGTACGTTCATATAGGTGC
193861 AT
1 AT
193863 TTAGAAGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (20 bp):
ATGTACGTTCATATAGGTGC
Found at i:200628 original size:23 final size:23
Alignment explanation
Indices: 200586--200647 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
200576 TTGGTGCAGA
* *
200586 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
200608 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
200631 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
200648 GTAGAGGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:202271 original size:18 final size:18
Alignment explanation
Indices: 202239--202273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
202229 AACACACGAC
*
202239 GAACAAGCTCCACCAGAG
1 GAACAAGCACCACCAGAG
*
202257 GAACAAGCACGACCAGA
1 GAACAAGCACCACCAGA
202274 AGATCAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.31, G:0.23, T:0.03
Consensus pattern (18 bp):
GAACAAGCACCACCAGAG
Found at i:209545 original size:45 final size:46
Alignment explanation
Indices: 209490--209659 Score: 249
Period size: 46 Copynumber: 3.8 Consensus size: 46
209480 TATAAAATTT
* *
209490 CTTATCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCACGTAAGCTTATTTTACCAATATA
*
209535 CTTACCATTTAATCCCATAAACACGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCACGTAAGCTTATTTTACCAATATA
*
209581 CTTACCATTTAAT-CCATAAGCACGTAAGCTTATTTTACCAATATG
1 CTTACCATTTAATCCCATAAGCACGTAAGCTTATTTTACCAATATA
* * *
209626 CTTGCCA-TT-ATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATCCCATAAGCACGTAAGCTTATTT
209660 GCATACTTAC
Statistics
Matches: 116, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
43 2 0.02
44 23 0.20
45 45 0.39
46 46 0.40
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCACGTAAGCTTATTTTACCAATATA
Found at i:209820 original size:40 final size:40
Alignment explanation
Indices: 209746--209821 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
209736 AGTCAAATGT
* * *
209746 TGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCTAATAA
1 TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTAATAA
* *
209786 TGCACCGTAGTGTTGAGGTCGAGATTTACCCACCTA
1 TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTA
209822 GTACATCGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (40 bp):
TGCACCGAAGTGCTGAGGTCGAGATTTACCCACCTAATAA
Found at i:213909 original size:14 final size:14
Alignment explanation
Indices: 213890--213972 Score: 74
Period size: 13 Copynumber: 6.3 Consensus size: 14
213880 TTTGTCCTGG
*
213890 TTATAAATATTATA
1 TTATAATTATTATA
213904 TTATAATTATTACTA
1 TTATAATTATTA-TA
213919 TTAT-ATTA-T-TA
1 TTATAATTATTATA
213930 TTAT-ATTATTATA
1 TTATAATTATTATA
213943 -TA-ACATTATTATA
1 TTATA-ATTATTATA
213956 --ATAATTATTAGTA
1 TTATAATTATTA-TA
213969 TTAT
1 TTAT
213973 TAATATCAGG
Statistics
Matches: 59, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
11 10 0.17
12 11 0.19
13 15 0.25
14 15 0.25
15 8 0.14
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:213928 original size:3 final size:3
Alignment explanation
Indices: 213897--213974 Score: 63
Period size: 3 Copynumber: 26.7 Consensus size: 3
213887 TGGTTATAAA
* *
213897 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
213942 ATAA CAT TAT TAT AAT AAT TAT TAG TAT TAT TA
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
213975 ATATCAGGTA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:213939 original size:11 final size:11
Alignment explanation
Indices: 213897--213974 Score: 72
Period size: 11 Copynumber: 7.2 Consensus size: 11
213887 TGGTTATAAA
213897 TATTATATTA-
1 TATTATATTAT
* *
213907 TAAT-TATTAC
1 TATTATATTAT
213917 TATTATATTAT
1 TATTATATTAT
213928 TATTATATTAT
1 TATTATATTAT
**
213939 TA-TATAACAT
1 TATTATATTAT
*
213949 TATTATAATAAT
1 TATTAT-ATTAT
213961 TATTAGTATTAT
1 TATTA-TATTAT
213973 TA
1 TA
213975 ATATCAGGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 5 0.09
10 14 0.25
11 21 0.38
12 14 0.25
13 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (11 bp):
TATTATATTAT
Found at i:230426 original size:20 final size:19
Alignment explanation
Indices: 230401--230468 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
230391 TGAAGCTAAA
230401 TATGAATTTGAAATTAAAGT
1 TATGAATTTGAAA-TAAAGT
*
230421 TATGAATTTGAAAATAAAGC
1 TATGAATTTG-AAATAAAGT
230441 TATGAATCTT-AAATAAA-T
1 TATGAAT-TTGAAATAAAGT
230459 TATGAATTTG
1 TATGAATTTG
230469 GAAAGTTCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.05
18 7 0.16
19 7 0.16
20 22 0.51
21 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (19 bp):
TATGAATTTGAAATAAAGT
Found at i:233946 original size:19 final size:19
Alignment explanation
Indices: 233922--233964 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
233912 GCATGCATGC
233922 TTGTTTAATCGCTACTGAT
1 TTGTTTAATCGCTACTGAT
233941 TTGTTTAATCGCTACTGAT
1 TTGTTTAATCGCTACTGAT
233960 TTGTT
1 TTGTT
233965 CATTTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGTTTAATCGCTACTGAT
Found at i:239340 original size:26 final size:26
Alignment explanation
Indices: 239310--239401 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 26
239300 TGTTGAAAAG
239310 GAAGAGGAGAAAGGAGAAGGGACACT
1 GAAGAGGAGAAAGGAGAAGGGACACT
* * * *
239336 GAAGACGGA-AAAAGAGAA-AGAAAAT
1 GAAGA-GGAGAAAGGAGAAGGGACACT
*
239361 GAAGAGG-GTAAAGGATAAGGGACACT
1 GAAGAGGAG-AAAGGAGAAGGGACACT
*
239387 GCAA-AGGAAAAAGGA
1 G-AAGAGGAGAAAGGA
239402 AGAGGAGAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
24 2 0.04
25 16 0.32
26 27 0.54
27 5 0.10
ACGTcount: A:0.52, C:0.07, G:0.36, T:0.05
Consensus pattern (26 bp):
GAAGAGGAGAAAGGAGAAGGGACACT
Found at i:239374 original size:51 final size:50
Alignment explanation
Indices: 239304--239399 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
239294 AGAACTTGTT
239304 GAAAAGGAAGAGGAGAAAGGAGAAGGGACACTG-AAGACGGAAAAAGAGAAA
1 GAAAAGGAAGAGGAGAAAGGAGAAGGGACACTGCAA-A-GGAAAAAGAGAAA
* *
239355 GAAAATGAAGAGG-GTAAAGGATAAGGGACACTGCAAAGGAAAAAG
1 GAAAAGGAAGAGGAG-AAAGGAGAAGGGACACTGCAAAGGAAAAAG
239400 GAAGAGGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
50 9 0.22
51 30 0.73
52 2 0.05
ACGTcount: A:0.53, C:0.06, G:0.35, T:0.05
Consensus pattern (50 bp):
GAAAAGGAAGAGGAGAAAGGAGAAGGGACACTGCAAAGGAAAAAGAGAAA
Found at i:239430 original size:19 final size:19
Alignment explanation
Indices: 239389--239445 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
239379 GGGACACTGC
*
239389 AAAGGAAAAAGGAAGAGGAG
1 AAAGGAAAAA-GAAAAGGAG
* *
239409 AAAGGAAAACGAAAAGGGG
1 AAAGGAAAAAGAAAAGGAG
**
239428 AAAAAAAAAAGAAAAGGA
1 AAAGGAAAAAGAAAAGGA
239446 TGAGGGAACA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (19 bp):
AAAGGAAAAAGAAAAGGAG
Found at i:241797 original size:2 final size:2
Alignment explanation
Indices: 241790--241824 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
241780 CAATCTACAT
241790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
241825 TTACGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:241968 original size:85 final size:85
Alignment explanation
Indices: 241879--242092 Score: 281
Period size: 85 Copynumber: 2.5 Consensus size: 85
241869 AATGATGTGT
241879 GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACCCACAAATGTATGT
1 GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACCCACAAATGTATGT
241944 CA-AGAAGATTTATGACGGGG
66 CATAGAA-ATTTATGACGGGG
* * * * * *
241964 GCTTCAATGACGCGCAATGTAAGTCATACATGCATGTCATAAATTTATGGCGCACAAATGTGTGT
1 GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACCCACAAATGTATGT
***
242029 CATCTTAATTTATGACGGGG
66 CATAGAAATTTATGACGGGG
* *
242049 GCTTCAATGACACTCAATGA-ACGTCATTA-ATGCGTGTCATAAAT
1 GCTTCAATGACACGCAAT-ATAAGTCA-TACATGCGTGTCATAAAT
242093 GTGTGTCATA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
85 109 0.97
86 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (85 bp):
GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACCCACAAATGTATGT
CATAGAAATTTATGACGGGG
Found at i:242087 original size:13 final size:13
Alignment explanation
Indices: 242071--242110 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
242061 CTCAATGAAC
*
242071 GTCATTAATGCGT
1 GTCATAAATGCGT
*
242084 GTCATAAATGTGT
1 GTCATAAATGCGT
242097 GTCATAAATAGCGT
1 GTCATAAAT-GCGT
242111 CATATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:246324 original size:14 final size:14
Alignment explanation
Indices: 246294--246327 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
246284 GTGAAATTCT
246294 AAATTTTTAAATAA
1 AAATTTTTAAATAA
*
246308 AAATTGTTTATATAA
1 AAATT-TTTAAATAA
246323 AAATT
1 AAATT
246328 CTATTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
AAATTTTTAAATAA
Found at i:256406 original size:18 final size:18
Alignment explanation
Indices: 256383--256419 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
256373 GTTAAATTAC
*
256383 ATTAAGTTCATATTTATT
1 ATTAAGTTCATATTAATT
*
256401 ATTAAGTTTATATTAATT
1 ATTAAGTTCATATTAATT
256419 A
1 A
256420 AGATTAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTAAGTTCATATTAATT
Found at i:262837 original size:23 final size:23
Alignment explanation
Indices: 262802--262854 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
262792 CAGGAGGCAT
262802 CGATA-CCCCTTTGAATGGGTAC
1 CGATACCCCCTTTGAATGGGTAC
262824 CGATACCCCCTTTGAATGGGTAC
1 CGATACCCCCTTTGAATGGGTAC
*
262847 AGATACCC
1 CGATACCC
262855 TCCACGAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (23 bp):
CGATACCCCCTTTGAATGGGTAC
Found at i:268296 original size:125 final size:122
Alignment explanation
Indices: 268080--268501 Score: 520
Period size: 117 Copynumber: 3.5 Consensus size: 122
268070 TAGTATAATC
268080 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCG-A-ATATATATTT
* * *
268145 TGGTTTAAAGTAAGCTAAGTTTATTATTTTAGGTAAGAATATATTCAAAATATTTTAAAATAT
64 TGGTTTAAAGTAGGC-AAGTTTATTATTTAAGTTAAG-ATATATT-AAAATA-TTTAAAATAT
268208 TTAAATTCTTAACTAT-AAAATATATA-TTTATTATTTTTTCTTAATTTATCGAATATATATTTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTA-TTTTTCTTAATTTATCGAATATATATTTT
268271 GGTTTAAAGTAGGTCAAGTTTATTATTTAAGTTAAGA-ATA-T---ATATTTAAAATAT
65 GGTTTAAAGTAGG-CAAGTTTATTATTTAAGTTAAGATATATTAAAATATTTAAAATAT
*
268325 TTAAATTATTAACTAT-AAAA-ATATA--TTATTATTTTTCTTAATTTATCGAATATATATTTTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATA--TTT
*
268386 TGGTTTAAAGTAGGCCAAGTTTATT-TTTAAGTTAAGTATATATTTAAAATA-TT----TGT
64 TGGTTTAAAGTAGG-CAAGTTTATTATTTAAGTTAAG-ATATA-TTAAAATATTTAAAATAT
* *
268442 TTAAATTCTTAAC-AGTAAAAATATATATTTTATTTTTTTTTCTTAATTTATTGAATATAT
1 TTAAATTCTTAACTA-TAAAAATATATATTTTA-TTATTTTTCTTAATTTATCGAATATAT
268502 TTTAAAGTAG
Statistics
Matches: 268, Mismatches: 9, Indels: 40
0.85 0.03 0.13
Matches are distributed among these distances:
114 25 0.09
115 17 0.06
116 34 0.13
117 47 0.18
118 7 0.03
119 6 0.02
121 5 0.02
122 29 0.11
123 3 0.01
124 1 0.00
125 42 0.16
126 9 0.03
127 27 0.10
128 16 0.06
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (122 bp):
TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATTTTG
GTTTAAAGTAGGCAAGTTTATTATTTAAGTTAAGATATATTAAAATATTTAAAATAT
Found at i:283345 original size:14 final size:15
Alignment explanation
Indices: 283313--283345 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
283303 TTAACAATTC
283313 AAAGTTCTAAATCTG
1 AAAGTTCTAAATCTG
283328 -AAGTTCTAAATC-G
1 AAAGTTCTAAATCTG
283341 AAAGT
1 AAAGT
283346 AGGCAAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (15 bp):
AAAGTTCTAAATCTG
Found at i:284371 original size:12 final size:12
Alignment explanation
Indices: 284354--284393 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
284344 TGGTTCGAGT
284354 TCAAAAAGTTTA
1 TCAAAAAGTTTA
284366 TCAAAAAG--T-
1 TCAAAAAGTTTA
284375 TCAAAAAGTTTA
1 TCAAAAAGTTTA
284387 TCAAAAA
1 TCAAAAA
284394 CTATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.32
10 1 0.04
11 1 0.04
12 15 0.60
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (12 bp):
TCAAAAAGTTTA
Found at i:284375 original size:21 final size:21
Alignment explanation
Indices: 284351--284393 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
284341 TATTGGTTCG
284351 AGTTCAAAAAGTTTATCAAAA
1 AGTTCAAAAAGTTTATCAAAA
284372 AGTTCAAAAAGTTTATCAAAA
1 AGTTCAAAAAGTTTATCAAAA
284393 A
1 A
284394 CTATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (21 bp):
AGTTCAAAAAGTTTATCAAAA
Found at i:284840 original size:22 final size:23
Alignment explanation
Indices: 284801--284850 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
284791 GAGGGTATCA
284801 GTACCCACTCAAAGGGGGAATCG
1 GTACCCACTCAAAGGGGGAATCG
* *
284824 GTACCCATTC-AAGGGGGTATCG
1 GTACCCACTCAAAGGGGGAATCG
*
284846 ATACC
1 GTACC
284851 TCCTGCACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
GTACCCACTCAAAGGGGGAATCG
Found at i:288665 original size:22 final size:20
Alignment explanation
Indices: 288631--288670 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
288621 AAGACTATTT
288631 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAA-TTTGAAATA
*
288652 TCATTTTTATAATTTGAAA
1 TCATTTTT-CAATTTGAAA
288671 GTAAAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (20 bp):
TCATTTTTCAATTTGAAATA
Found at i:292338 original size:8 final size:8
Alignment explanation
Indices: 292325--292359 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
292315 AGAACCAAAC
292325 ACAGGAAA
1 ACAGGAAA
292333 ACAGGAAA
1 ACAGGAAA
292341 ACAGGAAA
1 ACAGGAAA
292349 ACAGGAAA
1 ACAGGAAA
292357 ACA
1 ACA
292360 TTTTCCGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.63, C:0.14, G:0.23, T:0.00
Consensus pattern (8 bp):
ACAGGAAA
Found at i:305683 original size:20 final size:20
Alignment explanation
Indices: 305658--305695 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
305648 TTTTGGTGCA
*
305658 GAGGGAATCGATACCCCCAT
1 GAGGGAAACGATACCCCCAT
305678 GAGGGAAACGATACCCCC
1 GAGGGAAACGATACCCCC
305696 TGGGTTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.11
Consensus pattern (20 bp):
GAGGGAAACGATACCCCCAT
Found at i:311302 original size:18 final size:18
Alignment explanation
Indices: 311281--311320 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
311271 CTTTTGACTG
311281 TTGGTGCAACTTTGAATA
1 TTGGTGCAACTTTGAATA
*
311299 TTGGTGCAACTTTGAATG
1 TTGGTGCAACTTTGAATA
311317 TTGG
1 TTGG
311321 ATCATGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.40
Consensus pattern (18 bp):
TTGGTGCAACTTTGAATA
Found at i:311661 original size:9 final size:9
Alignment explanation
Indices: 311656--311771 Score: 62
Period size: 9 Copynumber: 12.2 Consensus size: 9
311646 TGCTATACTA
311656 AATATATAT
1 AATATATAT
311665 AATATAAATAT
1 AATAT--ATAT
311676 AATATATACT
1 AATATATA-T
311686 ATATACTATAT
1 A-ATA-TATAT
*
311697 AACGTA-ATAAA
1 AA--TATAT-AT
311708 AATACTATAT
1 AATA-TATAT
311718 AATATATAT
1 AATATATAT
*
311727 ACTATATA-
1 AATATATAT
*
311735 AA-ATCTA-
1 AATATATAT
311742 AATACTATA-
1 AATA-TATAT
311751 AATATATAT
1 AATATATAT
*
311760 TATATAATAT
1 AATAT-ATAT
311770 AA
1 AA
311772 CACCATATGC
Statistics
Matches: 85, Mismatches: 8, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 33 0.39
10 15 0.18
11 19 0.22
12 6 0.07
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:311682 original size:7 final size:7
Alignment explanation
Indices: 311615--311770 Score: 69
Period size: 7 Copynumber: 22.1 Consensus size: 7
311605 GGACCTATAA
311615 ATAATA-
1 ATAATAT
311621 ATAATA-
1 ATAATAT
*
311627 ATAATAA
1 ATAATAT
*
311634 ATACTAT
1 ATAATAT
311641 ATAA-AT
1 ATAATAT
*
311647 GCT-ATACT
1 -ATAATA-T
311655 A-AATAT
1 ATAATAT
311661 AT-ATAAT
1 ATAAT-AT
311668 ATAA-AT
1 ATAATAT
311674 ATAATAT
1 ATAATAT
*
311681 ATACTAT
1 ATAATAT
*
311688 ATACTAT
1 ATAATAT
311695 ATAACGTA-
1 ATAA--TAT
*
311703 ATAA-AA
1 ATAATAT
*
311709 ATACTAT
1 ATAATAT
311716 ATAATAT
1 ATAATAT
311723 ATATACTAT
1 ATA-A-TAT
*
311732 ATAAAAT
1 ATAATAT
*
311739 CTAAATACT
1 AT-AATA-T
311748 ATAAATAT
1 AT-AATAT
*
311756 ATATTAT
1 ATAATAT
311763 ATAATAT
1 ATAATAT
311770 A
1 A
311771 ACACCATATG
Statistics
Matches: 117, Mismatches: 16, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
5 1 0.01
6 28 0.24
7 59 0.50
8 14 0.12
9 15 0.13
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:311717 original size:28 final size:28
Alignment explanation
Indices: 311672--311759 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 28
311662 TATAATATAA
311672 ATATAATATATACTATATACTATATA-ACGT
1 ATATAA-A-ATACTATATACTATATATAC-T
*
311702 A-ATAAAAATACTATATAATATATATACT
1 ATAT-AAAATACTATATACTATATATACT
* *
311730 ATATAAAAT-CTAAATACTATAAATA-T
1 ATATAAAATACTATATACTATATATACT
311756 ATAT
1 ATAT
311760 TATATAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
26 5 0.10
27 13 0.25
28 23 0.45
29 7 0.14
30 3 0.06
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (28 bp):
ATATAAAATACTATATACTATATATACT
Found at i:311755 original size:75 final size:76
Alignment explanation
Indices: 311625--311770 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 76
311615 ATAATAATAA
* *
311625 TAATAATAAATACTATATAAATGCTATACTAAATATATATAATATAAATATAATATATACTATAT
1 TAATAATAAATACTATATAAATGATATACTAAATAAATATAATATAAATATAATATATACTATAT
*
311690 ACTATATAACG
66 AATATATAACG
* * * *
311701 TAATAA-AAATACTATATAATAT-ATATACTATATAAAATCTAA-AT-ACTATAAATATATATTA
1 TAATAATAAATACTATATAA-ATGATATACTAAAT-AAATATAATATAAATAT-AATATATACTA
311762 TATAATATA
63 TATAATATA
311771 ACACCATATG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
74 4 0.07
75 42 0.70
76 14 0.23
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (76 bp):
TAATAATAAATACTATATAAATGATATACTAAATAAATATAATATAAATATAATATATACTATAT
AATATATAACG
Found at i:316413 original size:25 final size:24
Alignment explanation
Indices: 316359--316413 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
316349 GAGATATTTT
*
316359 AATTTTAATTTTTTACATTTTTAAT
1 AATTTTAATTTTTTA-ATTTTTAAA
*
316384 GATTTTATATATTTTT-ATTTTTAAA
1 AATTTTA-AT-TTTTTAATTTTTAAA
316409 AATTT
1 AATTT
316414 ATTGAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 18 0.72
26 2 0.08
27 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
AATTTTAATTTTTTAATTTTTAAA
Found at i:319098 original size:24 final size:24
Alignment explanation
Indices: 319066--319140 Score: 150
Period size: 24 Copynumber: 3.1 Consensus size: 24
319056 CTACGGAAAT
319066 TGCTCTCAACCTGGCGTTGGGGGC
1 TGCTCTCAACCTGGCGTTGGGGGC
319090 TGCTCTCAACCTGGCGTTGGGGGC
1 TGCTCTCAACCTGGCGTTGGGGGC
319114 TGCTCTCAACCTGGCGTTGGGGGC
1 TGCTCTCAACCTGGCGTTGGGGGC
319138 TGC
1 TGC
319141 CTACTACCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.08, C:0.29, G:0.37, T:0.25
Consensus pattern (24 bp):
TGCTCTCAACCTGGCGTTGGGGGC
Found at i:321458 original size:21 final size:20
Alignment explanation
Indices: 321434--321511 Score: 50
Period size: 21 Copynumber: 3.7 Consensus size: 20
321424 CCGCAAGGAT
321434 ATATGCCCATCCCACCAGTTC
1 ATATG-CCATCCCACCAGTTC
* * ** *
321455 ATATGTCATCTCTGCAGGGGT-
1 ATATGCCATCCCACCA--GTTC
*
321476 ATATGCCCAGCCCACCAGTTC
1 ATATG-CCATCCCACCAGTTC
321497 ATATGCCATCTCCAC
1 ATATGCCATC-CCAC
321512 AGGGTTACAT
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
20 13 0.32
21 19 0.47
22 8 0.20
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (20 bp):
ATATGCCATCCCACCAGTTC
Found at i:321515 original size:42 final size:42
Alignment explanation
Indices: 321382--321515 Score: 178
Period size: 42 Copynumber: 3.2 Consensus size: 42
321372 AATTATAACG
* * *
321382 CCACAGGGGTACATGCCCAGCCCACCATTTCAGATGCCATCT
1 CCACAGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCT
* * * * *
321424 CCGCAAGGATATATGCCCATCCCACCAGTTCATATGTCATCT
1 CCACAGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCT
**
321466 CTGCAGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCT
1 CCACAGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCT
321508 CCACAGGG
1 CCACAGGG
321516 TTACATTCCT
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (42 bp):
CCACAGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCT
Found at i:321530 original size:42 final size:42
Alignment explanation
Indices: 321382--321532 Score: 176
Period size: 42 Copynumber: 3.6 Consensus size: 42
321372 AATTATAACG
* *
321382 CCACAGGGGTACATGCCCAGCCCACCATTTCAGATGCCATCT
1 CCACAGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCT
* * * * * *
321424 CCGCAAGGATATATGCCCATCCCACCAGTTCATATGTCATCT
1 CCACAGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCT
** *
321466 CTGCAGGGGTATATGCCCAGCCCACCAGTTCATATGCCATCT
1 CCACAGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCT
* * *
321508 CCACAGGGTTACATTCCTAGCCCAC
1 CCACAGGGGTACATGCCCAGCCCAC
321533 AAGGGTACAT
Statistics
Matches: 90, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCACAGGGGTACATGCCCAGCCCACCAGTTCATATGCCATCT
Found at i:321557 original size:21 final size:22
Alignment explanation
Indices: 321508--321551 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
321498 TATGCCATCT
*
321508 CCAC-AGGGTTACATTCCTAGC
1 CCACAAGGGTTACATACCTAGC
321529 CCACAAGGG-TACATACCTAGC
1 CCACAAGGGTTACATACCTAGC
321550 CC
1 CC
321552 GTAAGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.18
Consensus pattern (22 bp):
CCACAAGGGTTACATACCTAGC
Found at i:321824 original size:3 final size:3
Alignment explanation
Indices: 321816--321842 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
321806 ACAAAATGTC
321816 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
321843 AGTGAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Done.