Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008318.1 Hibiscus syriacus cultivar Beakdansim tig00111016_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: 501449
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:427339 original size:20 final size:20
Alignment explanation
Indices: 427309--427384 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
427299 TCGCATTGCG
*
427309 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
427329 AATTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
427349 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
427369 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
427385 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:427401 original size:34 final size:34
Alignment explanation
Indices: 427296--427404 Score: 110
Period size: 34 Copynumber: 3.0 Consensus size: 34
427286 TGCGATTTTC
* * *
427296 ATTTCGCATTGCGATTTTCTCGTTGCGATAGCCA
1 ATTTCGCGTTGCGATTTTCCCGTTGCGATAGTCA
*
427330 ATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCA
1 ATTTCGCGTTGC----G--ATTTTCCCGTTGCGATAGTCA
* *
427370 TTTTCGCGTTGCGATTTCCCCGTTGCGATAGTCA
1 ATTTCGCGTTGCGATTTTCCCGTTGCGATAGTCA
427404 A
1 A
427405 ATGAATGTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
34 30 0.48
36 1 0.02
38 1 0.02
40 30 0.48
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (34 bp):
ATTTCGCGTTGCGATTTTCCCGTTGCGATAGTCA
Found at i:427623 original size:20 final size:20
Alignment explanation
Indices: 427607--427683 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
427597 ATTGCGATTT
*
427607 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
427627 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
427647 TCAGTATCGCGTTGCAAAAG
1 TCAGAATCGCGTTGCGAAAG
*
427667 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
427684 TTTTGTATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:427710 original size:41 final size:42
Alignment explanation
Indices: 427598--427728 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 42
427588 TTGAAGATGA
* * *
427598 TTGCGA-TTT-TCAGAATCTCGTTGCGAAAGTCAGAATCGCG
1 TTGCGATTTTGTCAGTATCGCGTTGCGAAAGTCAGTATCGCG
** *
427638 TTGCGA--AAGTCAGTATCGCGTTGCAAAAGTCAGTATCGCG
1 TTGCGATTTTGTCAGTATCGCGTTGCGAAAGTCAGTATCGCG
* * *
427678 TTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGTATCGCA
1 TTGCGATTTTGTCAGTATCGCGTTGCGAAAGTCAGTATCGCG
427719 TTGCGATTTT
1 TTGCGATTTT
427729 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
40 39 0.51
41 35 0.46
42 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (42 bp):
TTGCGATTTTGTCAGTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:427725 original size:20 final size:20
Alignment explanation
Indices: 427616--427724 Score: 130
Period size: 20 Copynumber: 5.4 Consensus size: 20
427606 TTCAGAATCT
*
427616 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
427636 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
427656 CGTTGCAAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** *
427676 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
*
427697 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
427717 CATTGCGA
1 CGTTGCGA
427725 TTTTCCAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:427740 original size:21 final size:20
Alignment explanation
Indices: 427714--427765 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
427704 ATAGTCAGTA
*
427714 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
427735 TCGCATTACGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
427755 TCGCATTGCGA
1 TCGCATTGCGA
427766 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:427785 original size:21 final size:20
Alignment explanation
Indices: 427755--427807 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
427745 ATTTACTTAT
427755 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
* *
427776 TCGCAATGCGAAATTGTAAAA
1 TCGCATTGCG-AATTGGAAAA
427797 TCGCATTGCGA
1 TCGCATTGCGA
427808 TAGTCATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:427865 original size:20 final size:20
Alignment explanation
Indices: 427842--427887 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
427832 GGAAACTGAT
*
427842 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
427862 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
427881 TTGCGAT
1 TTGCGAT
427888 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:428196 original size:9 final size:9
Alignment explanation
Indices: 428182--428215 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
428172 GATTTTCATA
428182 ATATTTATT
1 ATATTTATT
428191 ATATTTATT
1 ATATTTATT
*
428200 ATATTTTTT
1 ATATTTATT
*
428209 ATTTTTA
1 ATATTTA
428216 CTTTATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATATTTATT
Found at i:428222 original size:18 final size:18
Alignment explanation
Indices: 428182--428224 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
428172 GATTTTCATA
*
428182 ATATTTATTATATTTATT
1 ATATTTTTTATATTTATT
*
428200 ATATTTTTTATTTTTACTT
1 ATATTTTTTATATTTA-TT
428219 -TATTTT
1 ATATTTT
428225 CAGATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
ATATTTTTTATATTTATT
Found at i:429741 original size:8 final size:7
Alignment explanation
Indices: 429717--429758 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
429707 TTTTCATACA
429717 TGCA-TT
1 TGCATTT
429723 TGCATTT
1 TGCATTT
429730 TGCATCTT
1 TGCAT-TT
429738 TGCATTT
1 TGCATTT
* *
429745 TTCATTG
1 TGCATTT
429752 TGCATTT
1 TGCATTT
429759 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:429741 original size:15 final size:14
Alignment explanation
Indices: 429717--429758 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
429707 TTTTCATACA
429717 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
429730 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
429745 TTCATTGTGCATTT
1 TGCATTTTGCATTT
429759 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:436627 original size:113 final size:113
Alignment explanation
Indices: 436425--436985 Score: 759
Period size: 113 Copynumber: 5.0 Consensus size: 113
436415 CAAAGATTTG
* * * * * *
436425 AATCCATTACTCAATGGATCAAC-ATGCCAG-GTAGAGTTCATAATGAGAATAACTCATCTGAAG
1 AATCCATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
*
436488 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
*
436537 AATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
436602 AGGAATAAGAAGATCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCA
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
*
436650 AATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
436715 AGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTGTTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
* * * * * * *
436763 AATTCATCATTTGATGGATCAACATTGCCAG-GTATAGTTCATAATGAGAAGAACTCGTCTGAAG
1 AATCCATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * **
436827 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
* * *
436876 AATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAGGAACTCGTCTGAAGA
1 AATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
436941 AGGAAGAAGAAGTTCATAATAAGAACAACTTGTTCGACCTTTTGC
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
436986 ATGACTCTAT
Statistics
Matches: 399, Mismatches: 46, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
112 21 0.05
113 376 0.94
114 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
Found at i:437340 original size:3 final size:3
Alignment explanation
Indices: 437332--437381 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
437322 TTTTTATTGA
* *
437332 TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
437377 TAT TA
1 TAT TA
437382 CAAACAGGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:438653 original size:31 final size:31
Alignment explanation
Indices: 438605--438712 Score: 78
Period size: 32 Copynumber: 3.4 Consensus size: 31
438595 TTTAACTACA
*
438605 AGTTTTATTACTT-TTTATATTTTAACATTAT
1 AGTTTTATT-TTTATTTATATTTTAACATTAT
*
438636 AGTTTTATTTTTA-TT-TATTTTAGTCATTATTT
1 AGTTTTATTTTTATTTATATTTTA-ACATTA--T
* * * * *
438668 AGTTATATTTTAATTTAAATATTAATTATTAT
1 AGTTTTATTTTTATTTATATTTTAA-CATTAT
*
438700 TGTTTTATTTTTA
1 AGTTTTATTTTTA
438713 ATATAAATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
29 7 0.12
30 9 0.15
31 9 0.15
32 23 0.39
33 2 0.03
34 9 0.15
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (31 bp):
AGTTTTATTTTTATTTATATTTTAACATTAT
Found at i:438983 original size:17 final size:17
Alignment explanation
Indices: 438963--439001 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
438953 ATATTTTTTT
438963 ATATATTATATATATAA
1 ATATATTATATATATAA
* *
438980 ATATATTTTTTATATAA
1 ATATATTATATATATAA
*
438997 TTATA
1 ATATA
439002 AATTTGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATTATATATATAA
Found at i:439688 original size:21 final size:21
Alignment explanation
Indices: 439662--439737 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
439652 GTGGCAGGTG
439662 CATGGATGCACTTCAGGGGTA
1 CATGGATGCACTTCAGGGGTA
439683 CATGGATGCACTTCAGGGGTA
1 CATGGATGCACTTCAGGGGTA
* * * *
439704 CATGAATGCACTGCAGGAGTG
1 CATGGATGCACTTCAGGGGTA
439725 CATGGATGCACTT
1 CATGGATGCACTT
439738 TGACACCCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (21 bp):
CATGGATGCACTTCAGGGGTA
Found at i:441523 original size:12 final size:12
Alignment explanation
Indices: 441503--441572 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
441493 GATACATGAC
*
441503 CTGAATTCTGTT
1 CTGATTTCTGTT
*
441515 CTGATTTCTGGT
1 CTGATTTCTGTT
441527 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
441539 CTGATATCTGTT
1 CTGATTTCTGTT
441551 CTGAATTT-TGTT
1 CTG-ATTTCTGTT
*
441563 TTGATTTCTG
1 CTGATTTCTG
441573 ATATCTCCGT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.12
12 37 0.77
13 5 0.10
ACGTcount: A:0.13, C:0.14, G:0.20, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:441534 original size:24 final size:24
Alignment explanation
Indices: 441503--441572 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
441493 GATACATGAC
441503 CTGAATTCTGTTCTGATTTCTGGT
1 CTGAATTCTGTTCTGATTTCTGGT
* * *
441527 CTGGATTCTGTTCTGATATCTGTT
1 CTGAATTCTGTTCTGATTTCTGGT
* *
441551 CTGAATTTTGTTTTGATTTCTG
1 CTGAATTCTGTTCTGATTTCTG
441573 ATATCTCCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.13, C:0.14, G:0.20, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGGT
Found at i:446223 original size:12 final size:12
Alignment explanation
Indices: 446185--446266 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
446175 ATTTCCGACT
446185 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
446197 TG-ATACATGACC
1 TGAATTC-TGTTC
446209 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
446221 TGATTTCTGATC
1 TGAATTCTGTTC
*
446233 TGGATTCTGTTC
1 TGAATTCTGTTC
446245 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
446257 TGAATTCTGT
1 TGAATTCTGT
446267 GTTGATTTCT
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
11 5 0.09
12 45 0.82
13 5 0.09
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.46
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:446272 original size:24 final size:24
Alignment explanation
Indices: 446171--446279 Score: 116
Period size: 24 Copynumber: 4.5 Consensus size: 24
446161 AAATATTTTA
*
446171 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
446195 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
446219 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
446243 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
446267 GT-TGATTTCTGAT
1 -TCTGATTTCTGAT
446280 ATCTCGTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.03
24 65 0.92
25 4 0.06
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:446276 original size:48 final size:48
Alignment explanation
Indices: 446171--446279 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
446161 AAATATTTTA
* *
446171 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATACATGACCTGAATTCTGT
**
446219 TCTGATTTCTGATCTGGATTCTGTTCTGATATC-TGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATA-CATGACCTGAATTCTGT
446267 GT-TGATTTCTGAT
1 -TCTGATTTCTGAT
446280 ATCTCGTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
48 51 0.94
49 3 0.06
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.47
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATACATGACCTGAATTCTGT
Found at i:450994 original size:23 final size:23
Alignment explanation
Indices: 450936--450986 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
450926 TCGTATAAAC
* *
450936 GCACCGAAGTACCACGTAGAATT
1 GCACCGAAGTGCCCCGTAGAATT
*
450959 GTACCGAAGTGCCCCGTAGAATT
1 GCACCGAAGTGCCCCGTAGAATT
450982 GCACC
1 GCACC
450987 TTAGTGCCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (23 bp):
GCACCGAAGTGCCCCGTAGAATT
Found at i:451717 original size:63 final size:64
Alignment explanation
Indices: 451641--451777 Score: 152
Period size: 63 Copynumber: 2.2 Consensus size: 64
451631 GCACCATACC
** *
451641 ATGCATCGATGCATAAAT-CCTATTCGATGTTTATATTT-AAGGGGGTGCATCGATGCACTCCTT
1 ATGCATCGATGCATAAATGCC-ATTCGATGTTTATATTTAAAAAGAGTGCATCGATGCACTCCTT
* ** * * * *
451704 ATGCATTGATGCATCGATGGCATTCGATGTTTGTATTTAAAAAGAGTGCATCGATGCACTTCAT
1 ATGCATCGATGCATAAATGCCATTCGATGTTTATATTTAAAAAGAGTGCATCGATGCACTCCTT
*
451768 GTGCATCGAT
1 ATGCATCGAT
451778 TCACCTTGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
63 31 0.52
64 29 0.48
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCATAAATGCCATTCGATGTTTATATTTAAAAAGAGTGCATCGATGCACTCCTT
Found at i:457911 original size:23 final size:23
Alignment explanation
Indices: 457880--457939 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
457870 TCATATAAAC
* * *
457880 GCACTGAAGTGCTACGTAGAATT
1 GCACCGAAGTGCCACATAGAATT
*
457903 GCACCGAAGTGCCGCATAGAATT
1 GCACCGAAGTGCCACATAGAATT
* *
457926 GTACCGTAGTGCCA
1 GCACCGAAGTGCCA
457940 TATAAGATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (23 bp):
GCACCGAAGTGCCACATAGAATT
Found at i:458205 original size:31 final size:30
Alignment explanation
Indices: 458161--458219 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
458151 TATTGTATAG
*
458161 ACATATAATTTCCAT-ATCTTTATCACATAA
1 ACATATAATTTCCATCA-CCTTATCACATAA
*
458191 ACATATCATGTTCCATCACCTTATCACAT
1 ACATATAAT-TTCCATCACCTTATCACAT
458220 GGCTTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.32
31 16 0.64
32 1 0.04
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACCTTATCACATAA
Found at i:458291 original size:25 final size:25
Alignment explanation
Indices: 458263--458324 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
458253 CTTAATGCAT
*
458263 ATAATATGAATTGATATCATGTATC
1 ATAATATGAATTGAGATCATGTATC
* *
458288 ATAATATGAAATGCGATCATGTATC
1 ATAATATGAATTGAGATCATGTATC
*
458313 AAAATATTGAAT
1 ATAATA-TGAAT
458325 CTAGACTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (25 bp):
ATAATATGAATTGAGATCATGTATC
Found at i:458661 original size:55 final size:56
Alignment explanation
Indices: 458601--458708 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
458591 CATAAATCCT
** * *
458601 ATTCGATGTTTATATTTAAGGA-AGTGTATCGATGCACTCCTTATGCATCGATGGC
1 ATTCGATGTTTATATTTAAAAAGAGTGCATCGATGCACTCCATATGCATCGATGGC
* * *
458656 ATTCGATGTTTGTATTTAAAAAGAGTGCATCGATGCACTTCATGTGCATCGAT
1 ATTCGATGTTTATATTTAAAAAGAGTGCATCGATGCACTCCATATGCATCGAT
458709 ACACCTTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
55 19 0.42
56 26 0.58
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (56 bp):
ATTCGATGTTTATATTTAAAAAGAGTGCATCGATGCACTCCATATGCATCGATGGC
Found at i:459231 original size:3 final size:3
Alignment explanation
Indices: 459223--459252 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
459213 GTCTCACGGG
459223 GAA GAA GAAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GAA GA
459253 GAAATTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:463512 original size:14 final size:14
Alignment explanation
Indices: 463493--463520 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
463483 CGCTGGGCAT
463493 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
463507 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
463521 AAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:463686 original size:33 final size:33
Alignment explanation
Indices: 463644--463728 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
463634 GCGACCTACC
* *
463644 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAT
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
463677 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
463710 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
463729 TCGGATAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.08, C:0.38, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:463818 original size:29 final size:29
Alignment explanation
Indices: 463785--463842 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
463775 GTAATCTCTT
*
463785 GTAGGTCGCCGGGAAG-ACATGGCGACCTA
1 GTAGGTCGCCCGG-AGTACATGGCGACCTA
*
463814 GTAGGTCGCCCGGAGTGCATGGCGACCTA
1 GTAGGTCGCCCGGAGTACATGGCGACCTA
463843 CGGCTAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.16
Consensus pattern (29 bp):
GTAGGTCGCCCGGAGTACATGGCGACCTA
Found at i:467124 original size:27 final size:28
Alignment explanation
Indices: 467099--467153 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
467089 ACTAATTATT
467099 CATTATTGTGAA-ATATAATTTTTTATATA
1 CATT-TTGTGAATATAT-ATTTTTTATATA
*
467128 CATTTTGTGTATATATA-TTTTTATAT
1 CATTTTGTGAATATATATTTTTTATAT
467154 GTATGTGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (28 bp):
CATTTTGTGAATATATATTTTTTATATA
Found at i:477229 original size:17 final size:17
Alignment explanation
Indices: 477195--477246 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
477185 ACCGGACAAA
* *
477195 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
477212 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
477229 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
477244 TTT
1 TTT
477247 CTACTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:478892 original size:22 final size:22
Alignment explanation
Indices: 478860--478915 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
478850 AAAGTTAACG
*
478860 GTCAACTGTCAAACCGATCAAA
1 GTCAACGGTCAAACCGATCAAA
* *
478882 GTCAACGGTCAGACCGGTCAAA
1 GTCAACGGTCAAACCGATCAAA
478904 GTCAACGAGTCA
1 GTCAACG-GTCA
478916 GGTAAAAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (22 bp):
GTCAACGGTCAAACCGATCAAA
Found at i:483035 original size:24 final size:26
Alignment explanation
Indices: 482998--483046 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
482988 TATTGAATTA
*
482998 AAATAGATCTGTATATAAAATATTGC
1 AAATAGATCTGTATATAAAAAATTGC
*
483024 AAATA-AT-TGTATGTAAAAAATTG
1 AAATAGATCTGTATATAAAAAATTG
483047 TTTCTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 2 0.10
26 5 0.24
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (26 bp):
AAATAGATCTGTATATAAAAAATTGC
Found at i:483494 original size:2 final size:2
Alignment explanation
Indices: 483487--483518 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
483477 ACTTTATAAA
*
483487 AT AT AT AT AT AT AC 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
483519 TTGATATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:487381 original size:20 final size:20
Alignment explanation
Indices: 487333--487428 Score: 128
Period size: 18 Copynumber: 5.0 Consensus size: 20
487323 CACTGAATAT
487333 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
487352 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
487371 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
487390 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
487409 TTGTCCCGTAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
487429 AAATCCCTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
18 32 0.48
19 2 0.03
20 32 0.48
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:487381 original size:38 final size:38
Alignment explanation
Indices: 487333--487426 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
487323 CACTGAATAT
487333 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
* * *
487371 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
*
487409 TTGTCCCGTAGGACCACT
1 TTGTCCCGAAGGACCACT
487427 GAAAATCCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
Found at i:494108 original size:21 final size:21
Alignment explanation
Indices: 494064--494109 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
494054 GATTTCTGGG
* * *
494064 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
494085 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
494106 CAAG
1 CAAG
494110 CGAACCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:494182 original size:24 final size:22
Alignment explanation
Indices: 494133--494174 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
494123 ACAGAATGTC
494133 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
494154 TAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
494175 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.33, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:495243 original size:31 final size:31
Alignment explanation
Indices: 495125--495248 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 31
495115 GTCGAGGGTT
495125 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTACGGAACATATGGACAGT-A
* *
495156 TTACCTATG-TCTTTC-GAGACATATGGATAGTA
1 -TACCTATGTTC-TACGGA-ACATATGGACAGTA
*
495188 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
495219 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
495249 TGCCGAGGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
31 51 0.66
32 25 0.32
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:495290 original size:30 final size:30
Alignment explanation
Indices: 495235--495337 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
495225 GGTTCTTCGG
* * * *
495235 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGATGATCTTTAT
495265 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGATGATCTTTAT
495295 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGATGATCTTTAT
495325 GACCTCTGGATAG
1 GACCTCTGGATAG
495338 GTCCTTCGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGATGATCTTTAT
Found at i:497023 original size:31 final size:30
Alignment explanation
Indices: 496968--497026 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
496958 TTAGGTCCAT
496968 AAGGAATTACCAGTCGATGATGAACCTATAC
1 AAGGAATTACCAGTCGAT-ATGAACCTATAC
496999 AAGGAATTACCAGTAGCGAT-TGAACCTA
1 AAGGAATTACCAGT--CGATATGAACCTA
497027 CCAGAGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 22 0.85
33 4 0.15
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (30 bp):
AAGGAATTACCAGTCGATATGAACCTATAC
Found at i:499024 original size:14 final size:15
Alignment explanation
Indices: 499005--499035 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
498995 ATTAATTAAA
499005 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
499019 TATTTTATGTTAATT
1 TATTTTATGTTAATT
499034 TA
1 TA
499036 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Done.