Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007861.1 Hibiscus syriacus cultivar Beakdansim tig00110226_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: 673920
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:613661 original size:19 final size:19
Alignment explanation
Indices: 613637--613675 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
613627 TCGAATGCAT
613637 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
613656 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
613675 T
1 T
613676 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:615701 original size:22 final size:21
Alignment explanation
Indices: 615677--615716 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
615667 GAGAAATTAT
615677 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
615698 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
615717 AAAAAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:619577 original size:24 final size:23
Alignment explanation
Indices: 619549--619628 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
619539 CACTTAACAA
619549 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCC-TTGAATG
*
619573 TGCATCGATGCATCCACATG-A--
1 TGCATCGATGCATCC-CTTGAATG
* *
619594 TGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCATCCCTTGAATG
619617 TGCATCGATGCA
1 TGCATCGATGCA
619629 CAAGACCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.06
21 14 0.30
23 12 0.26
24 17 0.36
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCATCCCTTGAATG
Found at i:622196 original size:21 final size:21
Alignment explanation
Indices: 622172--622211 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
622162 TTTTCAAAGG
622172 CATGCA-CTGATGCATCAATAC
1 CATGCATC-GATGCATCAATAC
622193 CATGCATCGATGCATCAAT
1 CATGCATCGATGCATCAAT
622212 GAATAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCATCGATGCATCAATAC
Found at i:622261 original size:19 final size:19
Alignment explanation
Indices: 622237--622275 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
622227 TCGAATGCAT
622237 TCCATGCACCGATACACTC
1 TCCATGCACCGATACACTC
* *
622256 TCCATGCATCGATGCACTC
1 TCCATGCACCGATACACTC
622275 T
1 T
622276 GATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATACACTC
Found at i:622354 original size:64 final size:63
Alignment explanation
Indices: 622172--622381 Score: 192
Period size: 64 Copynumber: 3.2 Consensus size: 63
622162 TTTTCAAAGG
** ** *
622172 CATGCA-CTGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCA
1 CATGCATC-GATGCA-CAAT-CCATGCATCGATGCA-CGCTG-ATTTATTAAAACATCGAATGCA
*
622236 TTC
61 TTT
* * ** *
622239 CATGCACCGATACACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTAAAACATCGAATGCATTT
* * *
622303 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TTCAAACATCGAATGCACT
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATTAAAACATCGAATGCATT
622366 T
63 T
622367 CATGCATCGATGCAC
1 CATGCATCGATGCAC
622382 TCTTGTGCAC
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
63 2 0.02
64 82 0.68
65 16 0.13
66 6 0.05
67 13 0.11
68 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTATTAAAACATCGAATGCATTT
Found at i:623179 original size:39 final size:39
Alignment explanation
Indices: 623133--623207 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
623123 ACTAAACCAA
* * *
623133 CCATCCCACCAGAAATAAGTTTCACATAGGGTAAACTAG
1 CCATCCCACCAGAAACAAGCTCCACATAGGGTAAACTAG
* * *
623172 CCATCCCACTAGCAACAAGCTCCACGTAGGGTAAAC
1 CCATCCCACCAGAAACAAGCTCCACATAGGGTAAAC
623208 CAGTCTTCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.17
Consensus pattern (39 bp):
CCATCCCACCAGAAACAAGCTCCACATAGGGTAAACTAG
Found at i:623504 original size:21 final size:20
Alignment explanation
Indices: 623490--623528 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
623480 GTTTATTGGA
623490 TATCTTATTTTGTTTATAATG
1 TATCTTATTTTGTTTAT-ATG
623511 TATCTTATTTTGTTTATA
1 TATCTTATTTTGTTTATA
623529 GTGGCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (20 bp):
TATCTTATTTTGTTTATATG
Found at i:623827 original size:52 final size:52
Alignment explanation
Indices: 623760--623886 Score: 220
Period size: 52 Copynumber: 2.4 Consensus size: 52
623750 ACTGAAGTTG
623760 TACAAAATTCTACCATTACAACAATTGATTTAAAGTTGATATGAAG-TTCAAT
1 TACAAAATTCTACCATTACAACAATTGATTTAAAGTTGATATGAAGTTTC-AT
*
623812 TACATAATTCTACCATTACAACAATTGATTTAAAGTTGATATGAAGTTTCAT
1 TACAAAATTCTACCATTACAACAATTGATTTAAAGTTGATATGAAGTTTCAT
*
623864 TACACAATTCTACCATTACAACA
1 TACAAAATTCTACCATTACAACA
623887 TAACACCCTA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 69 0.96
53 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (52 bp):
TACAAAATTCTACCATTACAACAATTGATTTAAAGTTGATATGAAGTTTCAT
Found at i:627429 original size:2 final size:2
Alignment explanation
Indices: 627422--627495 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
627412 TAATTTACCC
*
627422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
627464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
627496 ATTCAATCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:635395 original size:18 final size:18
Alignment explanation
Indices: 635372--635406 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
635362 AAATTACACA
635372 AATAATTATTAATATTTG
1 AATAATTATTAATATTTG
* *
635390 AATAATTTTTTATATTT
1 AATAATTATTAATATTT
635407 TACTTAAATT
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AATAATTATTAATATTTG
Found at i:638266 original size:55 final size:54
Alignment explanation
Indices: 638173--638330 Score: 178
Period size: 55 Copynumber: 2.9 Consensus size: 54
638163 ATATTCGGAA
* * *
638173 AACGGGTTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCACTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
*
638226 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCACTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* ** * * *
638282 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
638331 ATCAATTGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
53 18 0.20
54 24 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (54 bp):
AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:638385 original size:55 final size:55
Alignment explanation
Indices: 638324--638835 Score: 680
Period size: 55 Copynumber: 9.3 Consensus size: 55
638314 GAACTTGAAG
* * *
638324 AATCTTCATCAATTGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * * * *
638379 AATCTTCAACAAATCTTGTCTGCTCCCTA-TTCCTTCAGAGAATATAAAACTTGAAC
1 AATCTTCATC-AATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
*
638435 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * *
638490 AATCTTCAACAGTCGTGTCTGCTCCCTATTT-ATGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * *
638545 ATTTTTCATCAATCGTGTCTGCTCCCCA-TTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
638600 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* *
638655 AATCTTCAACAATCGTGTCTGCTCCCCA-TTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
*
638710 AATCTTCATCAATCGTGTCTGCTCCCCA-TTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
* * * * *
638765 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGATC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
638820 AATCTTCAAT-AATCGT
1 AATCTTC-ATCAATCGT
638836 TGGGAAATCT
Statistics
Matches: 407, Mismatches: 38, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
54 6 0.01
55 349 0.86
56 52 0.13
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (55 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
Found at i:638611 original size:165 final size:164
Alignment explanation
Indices: 638324--638835 Score: 781
Period size: 165 Copynumber: 3.1 Consensus size: 164
638314 GAACTTGAAG
* * * * *
638324 AATCTTCATCAATTGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTT-CTCAGAGAGTATAAGACTCGAACAATCTTCATC
* * * * *
638389 AAATCTTGTCTGCTCCCTATTCCTTCAGAGAATATAAAACTTGAACAATCTTCATCAATCGTGTC
65 -AATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTC
*
638454 TGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAAC
129 TGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
* * * *
638490 AATCTTCAACAGTCGTGTCTGCTCCCTATTTATGCAGAGAGTATAAGACTCGAACATTTTTCATC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCT-CAGAGAGTATAAGACTCGAACAATCTTCATC
638555 AATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
65 AATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
638620 GCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
130 GCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
* *
638655 AATCTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTC-TCAGAGAGTATAAGACTCGAACAATCTTCATC
* *
638720 AATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
65 AATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCT
* * *
638785 GCCCCCTATTTCTTCAGAGAGTATAAGACTCGATC
130 GCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
*
638820 AATCTTCAATAATCGT
1 AATCTTCAACAATCGT
638836 TGGGAAATCT
Statistics
Matches: 317, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
165 262 0.83
166 55 0.17
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (164 bp):
AATCTTCAACAATCGTGTCTGCTCCCTATTTCTCAGAGAGTATAAGACTCGAACAATCTTCATCA
ATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
CTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
Found at i:639805 original size:34 final size:35
Alignment explanation
Indices: 639757--639837 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 35
639747 TGAACCCTTC
*
639757 TTTTTTTCCATTTTTTCATTTT-TCATTTTTTTCT
1 TTTTTTTTCATTTTTTCATTTTCTCATTTTTTTCT
*
639791 TTTTTTTTCTTTTTTTCATTTTCACTCATTTTTTTCT
1 TTTTTTTTCATTTTTTCATTTT--CTCATTTTTTTCT
639828 TCTTCTTTTT
1 T-TT-TTTTT
639838 TCTTCAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 20 0.50
37 13 0.32
38 2 0.05
39 5 0.12
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (35 bp):
TTTTTTTTCATTTTTTCATTTTCTCATTTTTTTCT
Found at i:639834 original size:43 final size:42
Alignment explanation
Indices: 639754--639838 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 42
639744 TCTTGAACCC
* *
639754 TTCTTTTTTTCCATTTTTTCATTTTTCATTTTTTTCTTTTTTT
1 TTCTTTTTTTCCATTTTCTCATTTTT-ATTTTCTTCTTTTTTT
639797 TTCTTTTTTT-CATTTTCACTCATTTTT-TTCTTCTTCTTTTTT
1 TTCTTTTTTTCCATTTT--CTCATTTTTATT-TTCTTCTTTTTT
639839 CTTCAAGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 8 0.22
43 21 0.57
44 8 0.22
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (42 bp):
TTCTTTTTTTCCATTTTCTCATTTTTATTTTCTTCTTTTTTT
Found at i:643336 original size:8 final size:8
Alignment explanation
Indices: 643323--643350 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
643313 AAAAGAAGAT
643323 ATATATAC
1 ATATATAC
643331 ATATATAC
1 ATATATAC
643339 ATATATAC
1 ATATATAC
643347 ATAT
1 ATAT
643351 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:659153 original size:21 final size:21
Alignment explanation
Indices: 659129--659170 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
659119 AGTGGTCTTT
659129 GACTATTTTTTGGATTTTGTA
1 GACTATTTTTTGGATTTTGTA
659150 GACTATTTTTTGGATTTTGTA
1 GACTATTTTTTGGATTTTGTA
659171 TGAACTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (21 bp):
GACTATTTTTTGGATTTTGTA
Found at i:660677 original size:11 final size:11
Alignment explanation
Indices: 660661--660685 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
660651 AATCTTATTC
660661 TTTCTCTCTAT
1 TTTCTCTCTAT
660672 TTTCTCTCTAT
1 TTTCTCTCTAT
660683 TTT
1 TTT
660686 ATAGTTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCTCTCTAT
Found at i:661939 original size:3 final size:3
Alignment explanation
Indices: 661931--661956 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
661921 TGTGCATTAC
661931 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
661957 GTTTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:663511 original size:14 final size:14
Alignment explanation
Indices: 663492--663518 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
663482 TAGTAGCACA
663492 TGAAATTCAATAAT
1 TGAAATTCAATAAT
663506 TGAAATTCAATAA
1 TGAAATTCAATAA
663519 ATCCAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
TGAAATTCAATAAT
Found at i:669617 original size:31 final size:32
Alignment explanation
Indices: 669566--669710 Score: 170
Period size: 32 Copynumber: 4.6 Consensus size: 32
669556 CTAGTCAAGG
* *
669566 TGCATTC-TA-AATACACATTATGGTTAGGTG
1 TGCATTCATATAATGCACATTATGGTTAGGTT
669596 TGCATTC-TATAATGCACATTATGGTTAGGTT
1 TGCATTCATATAATGCACATTATGGTTAGGTT
* * *
669627 TGCATTCATATAATGCATAGTATGGCTAGGTT
1 TGCATTCATATAATGCACATTATGGTTAGGTT
* * * *
669659 TGCATTCAAATAATGCATAGTATGGTCAGGTT
1 TGCATTCATATAATGCACATTATGGTTAGGTT
* *
669691 TACATTCAGATAATGCACAT
1 TGCATTCATATAATGCACAT
669711 GAGTATCAGT
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 9 0.09
31 26 0.26
32 66 0.65
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (32 bp):
TGCATTCATATAATGCACATTATGGTTAGGTT
Found at i:671838 original size:21 final size:21
Alignment explanation
Indices: 671812--671969 Score: 225
Period size: 21 Copynumber: 7.6 Consensus size: 21
671802 TTTGACTGGA
671812 AGTATCGATACTGCCAAAGGT
1 AGTATCGATACTGCCAAAGGT
671833 AGTATCGATACTGCC-AAGAGT
1 AGTATCGATACTGCCAAAG-GT
*
671854 AGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAAGGT
671875 AGTA-CGATACTGCC-AAGAGT
1 AGTATCGATACTGCCAAAG-GT
*
671895 AGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAAGGT
671916 AGTATCGATACTGCC-AAGAGT
1 AGTATCGATACTGCCAAAG-GT
*
671937 AGTATCGATACTGCCAAGGGT
1 AGTATCGATACTGCCAAAGGT
*
671958 AGTATTGATACT
1 AGTATCGATACT
671970 ACCCCTGCAG
Statistics
Matches: 124, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
19 2 0.02
20 21 0.17
21 95 0.77
22 6 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (21 bp):
AGTATCGATACTGCCAAAGGT
Found at i:671876 original size:42 final size:42
Alignment explanation
Indices: 671812--671969 Score: 291
Period size: 42 Copynumber: 3.8 Consensus size: 42
671802 TTTGACTGGA
*
671812 AGTATCGATACTGCCAAAGGTAGTATCGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
671854 AGTATCGATACTGCCAAGGGTAGTA-CGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
671895 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
*
671937 AGTATCGATACTGCCAAGGGTAGTATTGATACT
1 AGTATCGATACTGCCAAGGGTAGTATCGATACT
671970 ACCCCTGCAG
Statistics
Matches: 113, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
41 41 0.36
42 72 0.64
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (42 bp):
AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGT
Found at i:671982 original size:83 final size:83
Alignment explanation
Indices: 671812--671989 Score: 277
Period size: 83 Copynumber: 2.1 Consensus size: 83
671802 TTTGACTGGA
671812 AGTATCGATACTGCCAAAGGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGTAG
1 AGTATCGATACTGCCAAAGGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGTAG
* * *
671877 TACGATACTGCCAAGAGT
66 TACGATACTACCAACAGC
*
671895 AGTATCGATACTGCCAAGGGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGTAG
1 AGTATCGATACTGCCAAAGGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGTAG
* * *
671960 TATTGATACTACC-CCTGC
66 TA-CGATACTACCAACAGC
671978 AGTATCGATACT
1 AGTATCGATACT
671990 CAATGTGTCA
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 79 0.91
84 8 0.09
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (83 bp):
AGTATCGATACTGCCAAAGGTAGTATCGATACTGCCAAGAGTAGTATCGATACTGCCAAGGGTAG
TACGATACTACCAACAGC
Done.