Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007416.1 Hibiscus syriacus cultivar Beakdansim tig00020047_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: 87986
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:9115 original size:4 final size:4
Alignment explanation
Indices: 9108--9134 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9098 CCATGCATGT
9108 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
9135 GTTGAACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:9205 original size:14 final size:14
Alignment explanation
Indices: 9186--9225 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9176 AATGTGAAGT
9186 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
9200 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
9214 AATCTCTGCATA
1 AATCCCTGCATA
9226 TAGACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:15085 original size:23 final size:23
Alignment explanation
Indices: 15051--15112 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
15041 ACTCCCCCTT
15051 GGGTATCGATACTTCATCTTCTA
1 GGGTATCGATACTTCATCTTCTA
*
15074 GGGTATCAATACTTCATCTTCTA
1 GGGTATCGATACTTCATCTTCTA
15097 GGGTATCGATACTTCA
1 GGGTATCGATACTTCA
15113 ATGAGTATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (23 bp):
GGGTATCGATACTTCATCTTCTA
Found at i:15588 original size:14 final size:16
Alignment explanation
Indices: 15559--15593 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
15549 ATAATAAATA
15559 TAAAAGAAGATTTTTT
1 TAAAAGAAGATTTTTT
15575 TAAAA-AAG-TTTTTT
1 TAAAAGAAGATTTTTT
15589 TAAAA
1 TAAAA
15594 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 3 0.16
16 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
TAAAAGAAGATTTTTT
Found at i:15610 original size:19 final size:18
Alignment explanation
Indices: 15591--15639 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
15581 AGTTTTTTTA
15591 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
15609 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
15628 AAATAAACAAAT
1 AAATAAA-AAAT
15640 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:16406 original size:72 final size:64
Alignment explanation
Indices: 16240--16418 Score: 209
Period size: 64 Copynumber: 2.7 Consensus size: 64
16230 TAAAACATCT
* **
16240 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATAATAATC
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAAAATAAAATAATAAAA
*
16304 TAAATCCTAATTAAAACACTAAAACCTATTTCAACTAAAATACCTAAAACAAAGATAAAAT-ATA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCT--AA-AAA-ATAAAATAATA
16368 AAA
62 AAA
*
16371 TAATATCCTAAAACTTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 TAA-ATCCT--AA-TTAAAACACT-AAAACCTATTTAAACTAAAATAC
16419 AAAGATAAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
63 5 0.05
64 38 0.38
66 2 0.02
67 10 0.10
68 11 0.11
70 2 0.02
71 9 0.09
72 22 0.22
ACGTcount: A:0.56, C:0.16, G:0.01, T:0.27
Consensus pattern (64 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAATAAAATAATAAAA
Found at i:18122 original size:27 final size:27
Alignment explanation
Indices: 18069--18143 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
18059 CTGTTCAGAG
** *
18069 AAAAATAAAATAAAATTGAGTATATGA
1 AAAAATAAAATAAAATAAAGGATATGA
*
18096 TAAAATAAAATAAAATAAATGGA-ATGA
1 AAAAATAAAATAAAATAAA-GGATATGA
*
18123 AATAAATACAATGAAAATAAA
1 AA-AAATAAAAT-AAAATAAA
18144 ACGAAATGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 21 0.54
28 10 0.26
29 8 0.21
ACGTcount: A:0.67, C:0.01, G:0.09, T:0.23
Consensus pattern (27 bp):
AAAAATAAAATAAAATAAAGGATATGA
Found at i:18125 original size:14 final size:15
Alignment explanation
Indices: 18098--18143 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
18088 GTATATGATA
*
18098 AAATAAAAT-AAAAT
1 AAATACAATGAAAAT
**
18112 AAATGGAATG-AAAT
1 AAATACAATGAAAAT
18126 AAATACAATGAAAAT
1 AAATACAATGAAAAT
18141 AAA
1 AAA
18144 ACGAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (15 bp):
AAATACAATGAAAAT
Found at i:21823 original size:64 final size:61
Alignment explanation
Indices: 21680--21823 Score: 132
Period size: 64 Copynumber: 2.2 Consensus size: 61
21670 CTTAAATCCT
* **
21680 AATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTCTAAATCCA
1 AATT-AAA-ACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATAAAATATTAAAAAT-CA
* *
21744 AATTAAAACACTAAAACCTATTTTAACTAAAATACCTAAAACAA-AGATAAAATA-TAAAAAT-A
1 AATTAAAAC-TTAAAA-CTATTTAAACTAAAATACCTAAAA-AATA-ATAAAATATTAAAAATCA
21806 ATATCCTAAAACTTAAAA
1 A-AT--TAAAACTTAAAA
21824 TACTAAAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
62 4 0.06
63 10 0.15
64 38 0.57
65 15 0.22
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (61 bp):
AATTAAAACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATAAAATATTAAAAATCA
Found at i:22265 original size:83 final size:83
Alignment explanation
Indices: 22122--22283 Score: 270
Period size: 83 Copynumber: 2.0 Consensus size: 83
22112 TACCCTAAGC
* * *
22122 CCAAAAATCTTTGTTTCTCTCATCTAAAACCTTCTAAATCACTCTTAAAGTGCCCCAAGACCCCT
1 CCAAAAATCTTTGTTTCTCTCATCTAAAACCTTCCAAATAACTCTTAAAGTACCCCAAGACCCCT
22187 AAATGGTGTTTAAACCTT
66 AAATGGTGTTTAAACCTT
** *
22205 CCAAAAATCTTTGTTTCTCTTGTCTAAAACCTTCCAAATAACTCTTAAAGTACCCGAAGACCCCT
1 CCAAAAATCTTTGTTTCTCTCATCTAAAACCTTCCAAATAACTCTTAAAGTACCCCAAGACCCCT
22270 AAATGGTGTTTAAA
66 AAATGGTGTTTAAA
22284 GCTTATTTAG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (83 bp):
CCAAAAATCTTTGTTTCTCTCATCTAAAACCTTCCAAATAACTCTTAAAGTACCCCAAGACCCCT
AAATGGTGTTTAAACCTT
Found at i:30345 original size:20 final size:19
Alignment explanation
Indices: 30320--30358 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
30310 TGCTTTCTTT
30320 TCAAATAACTAAAGAAATAA
1 TCAAATAAC-AAAGAAATAA
*
30340 TCAAATAACAAATAAATAA
1 TCAAATAACAAAGAAATAA
30359 ACCTGCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (19 bp):
TCAAATAACAAAGAAATAA
Found at i:30746 original size:6 final size:6
Alignment explanation
Indices: 30735--30759 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30725 CGGCCACCAT
30735 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
30760 CCTCTCCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:30885 original size:10 final size:10
Alignment explanation
Indices: 30870--30894 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30860 CGATAGACGA
30870 ATATTAAATG
1 ATATTAAATG
30880 ATATTAAATG
1 ATATTAAATG
30890 ATATT
1 ATATT
30895 CTCCCAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATATTAAATG
Found at i:31628 original size:2 final size:2
Alignment explanation
Indices: 31621--31651 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31611 TATATGGCTC
31621 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 T
31652 GGAAAACTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37391 original size:25 final size:25
Alignment explanation
Indices: 37357--37409 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
37347 CTCACTACAA
37357 ATGGTCATCGAGTATGAGATGTATG
1 ATGGTCATCGAGTATGAGATGTATG
37382 ATGGTCATCGAGTATGAGATGTATG
1 ATGGTCATCGAGTATGAGATGTATG
37407 ATG
1 ATG
37410 AGTTTGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (25 bp):
ATGGTCATCGAGTATGAGATGTATG
Found at i:39632 original size:18 final size:18
Alignment explanation
Indices: 39609--39650 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
39599 GAGTGTGGTC
39609 ACCTTGGCTCTGTTTAAA
1 ACCTTGGCTCTGTTTAAA
39627 ACCTTGGCTCTGTTTAAA
1 ACCTTGGCTCTGTTTAAA
39645 ACCTTG
1 ACCTTG
39651 ACTCAGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (18 bp):
ACCTTGGCTCTGTTTAAA
Found at i:46046 original size:22 final size:22
Alignment explanation
Indices: 45974--46044 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
45964 AGTTAAGTTA
45974 TTTTTAAAAATATACATTTAAC
1 TTTTTAAAAATATACATTTAAC
45996 TTTTTAAAAATATACATTTAAC
1 TTTTTAAAAATATACATTTAAC
* *
46018 TTTTTAAAAATATTATATTCAAC
1 TTTTTAAAAATA-TACATTTAAC
46041 TTTT
1 TTTT
46045 AACCAAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 34 0.74
23 12 0.26
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTTAAAAATATACATTTAAC
Found at i:47811 original size:2 final size:2
Alignment explanation
Indices: 47804--47846 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
47794 AGTTGGACTG
47804 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
47846 T
1 T
47847 GAACTCTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49152 original size:9 final size:9
Alignment explanation
Indices: 49138--49165 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49128 TGGAACTGTT
49138 CACGCGCCG
1 CACGCGCCG
49147 CACGCGCCG
1 CACGCGCCG
49156 CACGCGCCG
1 CACGCGCCG
49165 C
1 C
49166 CGCAGGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.57, G:0.32, T:0.00
Consensus pattern (9 bp):
CACGCGCCG
Found at i:49219 original size:10 final size:10
Alignment explanation
Indices: 49190--49277 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
49180 GCTGCTGGAA
49190 AACCGGTTTG
1 AACCGGTTTG
*
49200 -ACCAGTTTTG
1 AACC-GGTTTG
49210 AACCGGTTTG
1 AACCGGTTTG
*
49220 -ACCGGTTCG
1 AACCGGTTTG
*
49229 AACCAGTTTG
1 AACCGGTTTG
*
49239 -ACCGGTCTG
1 AACCGGTTTG
49248 AACCGGTTTG
1 AACCGGTTTG
*
49258 -ACCGGTCTG
1 AACCGGTTTG
*
49267 AACCGGGTTG
1 AACCGGTTTG
49277 A
1 A
49278 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 33 0.53
11 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:49237 original size:19 final size:19
Alignment explanation
Indices: 49190--49279 Score: 103
Period size: 19 Copynumber: 4.7 Consensus size: 19
49180 GCTGCTGGAA
* *
49190 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
49210 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
*
49229 AACCAGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
49248 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
49267 AACCGGGTTGACC
1 AACCGGTTTGACC
49280 CGACCCGACT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
18 2 0.03
19 49 0.77
20 13 0.20
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:49270 original size:38 final size:39
Alignment explanation
Indices: 49190--49279 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
49180 GCTGCTGGAA
* *
49190 AACCGGTTTGACCAGTTTTGAACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTTCG
*
49229 AACCAGTTTGACC-GGTCTGAACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTTC-G
*
49267 AACCGGGTTGACC
1 AACCGGTTTGACC
49280 CGACCCGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 2 0.04
38 31 0.69
39 12 0.27
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (39 bp):
AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTTCG
Found at i:49295 original size:17 final size:17
Alignment explanation
Indices: 49273--49330 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
49263 TCTGAACCGG
*
49273 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
49290 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
49307 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
49324 GTTGACC
1 GTTGACC
49331 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:49330 original size:7 final size:7
Alignment explanation
Indices: 49320--49355 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
49310 GACCCGACCC
49320 GACCGTT
1 GACCGTT
49327 GACCG-T
1 GACCGTT
49333 GACCGTT
1 GACCGTT
49340 GACCG-T
1 GACCGTT
49346 GACCGTT
1 GACCGTT
49353 GAC
1 GAC
49356 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:49338 original size:13 final size:13
Alignment explanation
Indices: 49320--49355 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
49310 GACCCGACCC
49320 GACCGTTGACCGT
1 GACCGTTGACCGT
49333 GACCGTTGACCGT
1 GACCGTTGACCGT
49346 GACCGTTGAC
1 GACCGTTGAC
49356 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:50294 original size:63 final size:63
Alignment explanation
Indices: 50226--50349 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
50216 CTAATGTGAC
* ** * *
50226 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
50289 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
50350 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:56593 original size:9 final size:9
Alignment explanation
Indices: 56561--56649 Score: 79
Period size: 10 Copynumber: 9.3 Consensus size: 9
56551 CTGCTGGAAA
*
56561 ACCGGTTTT
1 ACCGGTTTG
*
56570 ACCAGTTTTG
1 ACC-GGTTTG
56580 AACCGGTTTG
1 -ACCGGTTTG
*
56590 ACCGGTTCG
1 ACCGGTTTG
56599 AACCGGTTTG
1 -ACCGGTTTG
*
56609 ACCGGTCTG
1 ACCGGTTTG
56618 AACCGGTTTG
1 -ACCGGTTTG
*
56628 ACCGGTCTG
1 ACCGGTTTG
*
56637 AACCGGGTTG
1 -ACCGGTTTG
56647 ACC
1 ACC
56650 CGACCCGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.46
10 32 0.49
11 3 0.05
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:56603 original size:19 final size:19
Alignment explanation
Indices: 56578--56649 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
56568 TTACCAGTTT
56578 TGAACCGGTTTGACCGGT-
1 TGAACCGGTTTGACCGGTC
56596 TCGAACCGGTTTGACCGGTC
1 T-GAACCGGTTTGACCGGTC
56616 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
56635 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
56650 CGACCCGACT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
18 1 0.02
19 49 0.96
20 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:56624 original size:38 final size:39
Alignment explanation
Indices: 56560--56649 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
56550 GCTGCTGGAA
* * *
56560 AACCGGTTTTACCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCT-G
56599 AACCGGTTTGACC-GGTCTGAACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
*
56637 AACCGGGTTGACC
1 AACCGGTTTGACC
56650 CGACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 33 0.72
39 13 0.28
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.28
Consensus pattern (39 bp):
AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
Found at i:56665 original size:17 final size:17
Alignment explanation
Indices: 56643--56700 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
56633 TCTGAACCGG
*
56643 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
56660 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
56677 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
56694 GTTGACC
1 GTTGACC
56701 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:56700 original size:7 final size:7
Alignment explanation
Indices: 56690--56725 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
56680 GACCCGACCC
56690 GACCGTT
1 GACCGTT
56697 GACCG-T
1 GACCGTT
56703 GACCGTT
1 GACCGTT
56710 GACCG-T
1 GACCGTT
56716 GACCGTT
1 GACCGTT
56723 GAC
1 GAC
56726 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:56708 original size:13 final size:13
Alignment explanation
Indices: 56690--56725 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
56680 GACCCGACCC
56690 GACCGTTGACCGT
1 GACCGTTGACCGT
56703 GACCGTTGACCGT
1 GACCGTTGACCGT
56716 GACCGTTGAC
1 GACCGTTGAC
56726 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:57678 original size:63 final size:63
Alignment explanation
Indices: 57595--57718 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
57585 CTAATGTGAC
* ** * *
57595 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAAGCCCTGCA-GCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAAGCCCT-CAGGCCCTAAGATGTGT
* * *
57658 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAAGCCCTCAGGCCCTAAGATGT
57719 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 48 0.94
64 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAAGCCCTCAGGCCCTAAGATGTGT
Found at i:63719 original size:3 final size:3
Alignment explanation
Indices: 63713--63830 Score: 140
Period size: 3 Copynumber: 39.3 Consensus size: 3
63703 TTTTTTTAAT
63713 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63760 TTA TTA TTA TTA TTA TGT- TTA TGT- TTA TGT- TTA TGT- TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA T-TA TTA T-TA TTA T-TA TTA TTA TTA
63805 TTA TGT- TTA TTA TTA TTA TTAA TTA T
1 TTA T-TA TTA TTA TTA TTA TT-A TTA T
63831 GTTACATATA
Statistics
Matches: 103, Mismatches: 0, Indels: 24
0.81 0.00 0.19
Matches are distributed among these distances:
2 7 0.07
3 88 0.85
4 8 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:71504 original size:21 final size:21
Alignment explanation
Indices: 71475--71520 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
71465 TCCAAGTGAG
* *
71475 GATGCAGGCGAAAGCATGGGT
1 GATGAAGGCGAAAGCATCGGT
71496 GATGAAGGCGAAAGCATCGGT
1 GATGAAGGCGAAAGCATCGGT
71517 GATG
1 GATG
71521 CACCTGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.41, T:0.15
Consensus pattern (21 bp):
GATGAAGGCGAAAGCATCGGT
Found at i:76718 original size:45 final size:44
Alignment explanation
Indices: 76629--76719 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
76619 TATTGTGTCA
* * *
76629 TTTATTTTATATTACTAAATATAAGTTCGTCTTTAAAACCATTT
1 TTTATTTTATATTACTAAATATAAGTTCATCATTAAAAACATTT
* *
76673 TTTATTTTATATTATTAACATATAAGTTCATCATTAAAAATATTT
1 TTTATTTTATATTACTAA-ATATAAGTTCATCATTAAAAACATTT
76718 TT
1 TT
76720 AGATCCGTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 17 0.41
45 24 0.59
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (44 bp):
TTTATTTTATATTACTAAATATAAGTTCATCATTAAAAACATTT
Found at i:76719 original size:44 final size:43
Alignment explanation
Indices: 76629--76720 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 43
76619 TATTGTGTCA
* *
76629 TTTATTTTATATTACTAAATATAAGTTCGTCTTTAAAACCATTT
1 TTTATTTTATATTACTAAATATAAGTTCATCATTAAAA-CATTT
*
76673 TTTATTTTATATTATTAACATATAAGTTCATCATTAAAA-ATATT
1 TTTATTTTATATTACTAA-ATATAAGTTCATCATTAAAACAT-TT
76717 TTTA
1 TTTA
76721 GATCCGTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 23 0.53
45 18 0.42
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (43 bp):
TTTATTTTATATTACTAAATATAAGTTCATCATTAAAACATTT
Found at i:86121 original size:86 final size:86
Alignment explanation
Indices: 85976--86141 Score: 235
Period size: 86 Copynumber: 1.9 Consensus size: 86
85966 TAATTAGCAC
* * * *
85976 CTATCATTCAAGTTGCGGCTATAATTCGTCGTTATTGGTGTTATTCCACTTCACACCGTTATTTT
1 CTATCATTCAAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTCCACTTCACACCGTTATTTT
* *
86041 TTGTAATAATGGTTTTAGGCT
66 CTATAATAATGGTTTTAGGCT
* *
86062 CTATCCATT-AAGTTGAGACTACAATTTGTCGTTATTGGTGTGATTTCACTTCACACCGTTATTT
1 CTAT-CATTCAAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTCCACTTCACACCGTTATTT
*
86126 TCTATAATAGTGGTTT
65 TCTATAATAATGGTTT
86142 CGGACACTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
86 66 0.94
87 4 0.06
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (86 bp):
CTATCATTCAAGTTGAGACTACAATTCGTCGTTATTGGTGTGATTCCACTTCACACCGTTATTTT
CTATAATAATGGTTTTAGGCT
Done.