Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000770.1 Hibiscus syriacus cultivar Beakdansim tig00001495_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: 64651
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:1249 original size:13 final size:13
Alignment explanation
Indices: 1231--1256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1221 TTTTGAAAAA
1231 TCAAAATCATTTT
1 TCAAAATCATTTT
1244 TCAAAATCATTTT
1 TCAAAATCATTTT
1257 GTTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
TCAAAATCATTTT
Found at i:9088 original size:24 final size:24
Alignment explanation
Indices: 9061--9155 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
9051 AAACGGAGAT
9061 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
9085 ATCAGATATCAGAACAAAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
9109 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
9133 GTCATG-TATCAAAATAGAATTCA
1 ATCA-GAAATCAAAACAGAATTCA
9156 AGCCAGAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:9090 original size:12 final size:12
Alignment explanation
Indices: 9063--9132 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
9053 ACGGAGATAT
* *
9063 CAGAAATCAAAA
1 CAGAATTCAGAA
*
9075 CAGAATTCAGAT
1 CAGAATTCAGAA
9087 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
9099 CAAAATCCAGAT
1 CAGAATTCAGAA
*
9111 CAGAAATCAGAA
1 CAGAATTCAGAA
*
9123 CATAATTCAG
1 CAGAATTCAG
9133 GTCATGTATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:12972 original size:22 final size:22
Alignment explanation
Indices: 12924--12974 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
12914 TTAAATTTAT
*
12924 TTTATTACATAATATTTTTACA
1 TTTATTACATAATATTTTAACA
12946 TTTATTACAT-ATATTTCTAAACA
1 TTTATTACATAATATTT-T-AACA
12969 -TTATTA
1 TTTATTA
12975 TATTTTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.23
22 17 0.65
23 3 0.12
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATTACATAATATTTTAACA
Found at i:25447 original size:13 final size:13
Alignment explanation
Indices: 25429--25469 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
25419 CAACCTGTTG
25429 ACTTTGACCGTTA
1 ACTTTGACCGTTA
* *
25442 ACTTTGACAGTTG
1 ACTTTGACCGTTA
*
25455 ACTTTGGCCGTTA
1 ACTTTGACCGTTA
25468 AC
1 AC
25470 CCGAAAAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (13 bp):
ACTTTGACCGTTA
Found at i:29392 original size:29 final size:29
Alignment explanation
Indices: 29368--29424 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29358 ACAATATTTT
*
29368 TTAATTTTTATTAAT-GAAAGAAATAATTC
1 TTAATTTTTAGTAATAGAAA-AAATAATTC
29397 TTAATTTTTAGTAATAGAAAAAATAATT
1 TTAATTTTTAGTAATAGAAAAAATAATT
29425 TGAATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (29 bp):
TTAATTTTTAGTAATAGAAAAAATAATTC
Found at i:32446 original size:20 final size:20
Alignment explanation
Indices: 32421--32472 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
32411 ACTTTTGAAC
32421 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACTATCTCAAG
32441 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACTATCTCAAG
*
32461 AGTTTCTAAACT
1 AGTTTCGAAACT
32473 TTACCTAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
AGTTTCGAAACTATCTCAAG
Found at i:33795 original size:22 final size:23
Alignment explanation
Indices: 33770--33819 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
33760 ATATTATTAA
33770 TAAAAATTATA-A-AAATATATTT
1 TAAAAATTATAGAGAAATA-ATTT
*
33792 TAAAATTTATAGATGAAATAATTT
1 TAAAAATTATAGA-GAAATAATTT
33816 TAAA
1 TAAA
33820 TATATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
24 8 0.33
25 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAAAATTATAGAGAAATAATTT
Found at i:33865 original size:17 final size:16
Alignment explanation
Indices: 33807--33858 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
33797 TTTATAGATG
* *
33807 AAATAATTTTAAATAT
1 AAATAATTTAAAATTT
*
33823 -ATTAATTATAAAATTT
1 AAATAATT-TAAAATTT
33839 AAATAATTTAAATATTT
1 AAATAATTTAAA-ATTT
33856 AAA
1 AAA
33859 ACATTTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.21
16 10 0.34
17 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATAATTTAAAATTT
Found at i:34289 original size:25 final size:25
Alignment explanation
Indices: 34255--34312 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
34245 TTCAGATTTC
*
34255 AGTCGGATTTTGTCAGGTTATGTCA
1 AGTCGGATTTTGTCAGGTTAGGTCA
34280 AGTCGGATTTTGTCAGGTTAGGTCA
1 AGTCGGATTTTGTCAGGTTAGGTCA
*
34305 AATCGGAT
1 AGTCGGAT
34313 ATAAGTTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.36
Consensus pattern (25 bp):
AGTCGGATTTTGTCAGGTTAGGTCA
Found at i:35347 original size:4 final size:4
Alignment explanation
Indices: 35340--35457 Score: 62
Period size: 4 Copynumber: 29.2 Consensus size: 4
35330 ATGATGCATG
* * * * *
35340 TATA TATA AATA TATA TAAA TA-A GTATT TATA TATA TA-A GTATA CATG
1 TATA TATA TATA TATA TATA TATA -TATA TATA TATA TATA -TATA TATA
* * * * * * * *
35388 CATA CATA -AGTA TATA TGTA TGATG TATG TATG TATA TATG TATG TATA
1 TATA TATA TA-TA TATA TATA T-ATA TATA TATA TATA TATA TATA TATA
35437 TATA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA T
35458 GATAATTTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
3 3 0.03
4 86 0.92
5 4 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:35408 original size:8 final size:8
Alignment explanation
Indices: 35310--35457 Score: 77
Period size: 8 Copynumber: 18.6 Consensus size: 8
35300 ACTTATAATA
35310 TATATATG
1 TATATATG
35318 TATA-ATG
1 TATATATG
*
35325 TATGTATG
1 TATATATG
**
35333 -ATGCATG
1 TATATATG
*
35340 TATATATA
1 TATATATG
* *
35348 AATATATA
1 TATATATG
* *
35356 TAAATAAG
1 TATATATG
* *
35364 TATTTATA
1 TATATATG
*
35372 TATATAAG
1 TATATATG
*
35380 TATACATG
1 TATATATG
* *
35388 CATACATAAG
1 --TATATATG
35398 TATATATG
1 TATATATG
*
35406 TAT-GATG
1 TATATATG
*
35413 TATGTATG
1 TATATATG
35421 TATATATG
1 TATATATG
* *
35429 TATGTATA
1 TATATATG
*
35437 TATATATA
1 TATATATG
*
35445 TATATATA
1 TATATATG
35453 TATAT
1 TATAT
35458 GATAATTTAA
Statistics
Matches: 105, Mismatches: 30, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
7 18 0.17
8 82 0.78
10 5 0.05
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (8 bp):
TATATATG
Found at i:35430 original size:12 final size:12
Alignment explanation
Indices: 35397--35451 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
35387 GCATACATAA
35397 GTATATATGTAT
1 GTATATATGTAT
*
35409 G-ATGTATGTAT
1 GTATATATGTAT
35420 GTATATATGTAT
1 GTATATATGTAT
*
35432 GTATATATATAT
1 GTATATATGTAT
*
35444 ATATATAT
1 GTATATAT
35452 ATATATGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.26
12 28 0.74
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (12 bp):
GTATATATGTAT
Found at i:35494 original size:16 final size:16
Alignment explanation
Indices: 35475--35519 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
35465 TAATTTAAAA
35475 ATAAAAAATAAAAATT
1 ATAAAAAATAAAAATT
* * *
35491 ATAAAAATTATAATTT
1 ATAAAAAATAAAAATT
*
35507 ATATAAAATAAAA
1 ATAAAAAATAAAA
35520 CATCTATGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAAAATAAAAATT
Found at i:36386 original size:37 final size:38
Alignment explanation
Indices: 36225--36401 Score: 154
Period size: 38 Copynumber: 4.8 Consensus size: 38
36215 TCAAGGGAAA
* *
36225 AAATT-AATGATTTATTTTCTTTTACAAAATAGGAAAAT
1 AAATTCAACGATTTATTTTCTTTTACAAAACA-GAAAAT
* * *
36263 AAATCCAACGATTTA-ATCCTTTTACAAAACAGAAAAAT
1 AAATTCAACGATTTATTTTCTTTTACAAAACAG-AAAAT
* * *
36301 TAATCCAAC----TATTTT-TTTTATAAAACAGGAAAAT
1 AAATTCAACGATTTATTTTCTTTTACAAAACA-GAAAAT
** *
36335 AAATTCAAATATTTATTTTCTTTTACAAAACATAAAAT
1 AAATTCAACGATTTATTTTCTTTTACAAAACAGAAAAT
* *
36373 -AATTCATCGATTTATTTTCTTTTAAAAAA
1 AAATTCAACGATTTATTTTCTTTTACAAAA
36402 TATAATCATT
Statistics
Matches: 112, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
34 24 0.21
35 2 0.02
37 26 0.23
38 41 0.37
39 19 0.17
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (38 bp):
AAATTCAACGATTTATTTTCTTTTACAAAACAGAAAAT
Found at i:36435 original size:58 final size:59
Alignment explanation
Indices: 36368--36505 Score: 142
Period size: 58 Copynumber: 2.4 Consensus size: 59
36358 TACAAAACAT
* **
36368 AAAAT-AATTCATCGATTTATTTTC-TTTTAAAAAATATAATCATTTAAGATTCTCAAG
1 AAAATAAATTCATCGATTTATTTTCTTTTTAAAAAATAGAATCATCCAAGATTCTCAAG
* * * * *
36425 AAAATAAATTCAAT-AATTT-GTTTCTTTTTAAAAGATAGAATTATCCATGATTCTCAAG
1 AAAATAAATTC-ATCGATTTATTTTCTTTTTAAAAAATAGAATCATCCAAGATTCTCAAG
* *
36483 AAAATAAATTAAACGA-TTATTTT
1 AAAATAAATTCATCGATTTATTTT
36506 TCTTACAAAG
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
57 12 0.19
58 50 0.78
59 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (59 bp):
AAAATAAATTCATCGATTTATTTTCTTTTTAAAAAATAGAATCATCCAAGATTCTCAAG
Found at i:36535 original size:58 final size:58
Alignment explanation
Indices: 36382--36536 Score: 136
Period size: 58 Copynumber: 2.7 Consensus size: 58
36372 TAATTCATCG
* * *** * *
36382 ATTTATTTTCTT-TTAAAAAATATAATCATTTAAGATTCTCAAGAAAATAAATTCAATA
1 ATTTA-TTTCTTCTTAAAAGATAGAATCAACCAAGATTCTCAAGAAAATAAATTAAACA
* * * * * *
36440 ATTTGTTTCTTTTTAAAAGATAGAATTATCCATGATTCTCAAGAAAATAAATTAAACG
1 ATTTATTTCTTCTTAAAAGATAGAATCAACCAAGATTCTCAAGAAAATAAATTAAACA
*
36498 A-TTATTT-TTCTTACAAAGTTAGAATCAACACAAGATTCT
1 ATTTATTTCTTCTTA-AAAGATAGAATCAAC-CAAGATTCT
36537 ATTGATTAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
56 5 0.06
57 23 0.29
58 50 0.64
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (58 bp):
ATTTATTTCTTCTTAAAAGATAGAATCAACCAAGATTCTCAAGAAAATAAATTAAACA
Found at i:41050 original size:46 final size:44
Alignment explanation
Indices: 40998--41100 Score: 118
Period size: 46 Copynumber: 2.3 Consensus size: 44
40988 TCATTAAAAA
* *
40998 TATTAATTTACTAATAGATAATAAAAAAGATGA-TAAATTACTAAT
1 TATTAATTTACTAATAAACAATAAAAAA-AT-ACTAAATTACTAAT
* *
41043 CTATTAATTTTCTAATAAACAATAAAAAAATACTAAATTATTAAT
1 -TATTAATTTACTAATAAACAATAAAAAAATACTAAATTACTAAT
* *
41088 TAGTATTTTACTA
1 TATTAATTTACTA
41101 CACTCAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
44 11 0.22
45 13 0.27
46 25 0.51
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (44 bp):
TATTAATTTACTAATAAACAATAAAAAAATACTAAATTACTAAT
Found at i:44845 original size:23 final size:22
Alignment explanation
Indices: 44794--44845 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
44784 AATATTCTCA
* *
44794 AACTT-AGCTCATTTGAAGCTC
1 AACTTGAGCTCAATTCAAGCTC
*
44815 AAGTTTGAGCTCAATTCAAGCTC
1 AA-CTTGAGCTCAATTCAAGCTC
44838 GAACTTGA
1 -AACTTGA
44846 ACCTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 18 0.75
24 2 0.08
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (22 bp):
AACTTGAGCTCAATTCAAGCTC
Found at i:47074 original size:2 final size:2
Alignment explanation
Indices: 47063--47097 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
47053 AAATTTAAAT
*
47063 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47098 GTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48939 original size:14 final size:13
Alignment explanation
Indices: 48901--48953 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
48891 TTTCACTTAA
48901 AATATTATAT-AT
1 AATATTATATAAT
*
48913 AATATTTTAATAAT
1 AATATTAT-ATAAT
48927 AATATTGATATAAAT
1 AATATT-ATAT-AAT
*
48942 AATATTAAATAA
1 AATATTATATAA
48954 ATTAATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.21
13 4 0.12
14 13 0.38
15 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AATATTATATAAT
Found at i:48954 original size:14 final size:14
Alignment explanation
Indices: 48911--48961 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
48901 AATATTATAT
*
48911 ATAATATTTTAAT-A
1 ATAATA-TTAAATAA
*
48925 ATAATATTGATATAA
1 ATAATATT-AAATAA
48940 ATAATATTAAATAA
1 ATAATATTAAATAA
48954 ATTAATAT
1 A-TAATAT
48962 AATATTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 2 0.06
14 14 0.45
15 15 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATAATATTAAATAA
Found at i:52278 original size:21 final size:20
Alignment explanation
Indices: 52250--52288 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
52240 TGATCAAATG
52250 ATATTATTTTAGT-ATTTTAT
1 ATATTATTTT-GTGATTTTAT
52270 ATATATATTTTGTGATTTT
1 ATAT-TATTTTGTGATTTT
52289 TAGGTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
ATATTATTTTGTGATTTTAT
Found at i:54493 original size:2 final size:2
Alignment explanation
Indices: 54486--54536 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
54476 AAAAGATGTA
54486 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
54528 AT AT AT AT A
1 AT AT AT AT A
54537 AATTGCTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56878 original size:5 final size:5
Alignment explanation
Indices: 56868--56893 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56858 ATTTATTTAT
56868 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
56894 AAATAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:56940 original size:16 final size:17
Alignment explanation
Indices: 56921--56957 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
56911 TAAAATATTA
56921 TTTT-AAATAATTAC-AT
1 TTTTAAAATAA-TACAAT
56937 TTTTAAAATAATACAAT
1 TTTTAAAATAATACAAT
56954 TTTT
1 TTTT
56958 TATCCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAAAATAATACAAT
Found at i:58009 original size:2 final size:2
Alignment explanation
Indices: 58002--58043 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
57992 CTTTTATTCT
58002 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
58044 ATTGGGTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63735 original size:23 final size:23
Alignment explanation
Indices: 63692--63737 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
63682 GTGTTCATTT
*
63692 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
63715 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
63737 T
1 T
63738 TCTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Done.