Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009091.1 Hibiscus syriacus cultivar Beakdansim tig00112538_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: 76838
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:993 original size:3 final size:3
Alignment explanation
Indices: 987--1023 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
977 CCCATCATCC
* *
987 CTT CTT CTT CTT CTT CTT CTT CTT CAT CAT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1024 ATCTGACAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.05, C:0.35, G:0.00, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:1025 original size:9 final size:9
Alignment explanation
Indices: 989--1027 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
979 CATCATCCCT
*
989 TCTTCTTCT
1 TCTTCTTCA
*
998 TCTTCTTCT
1 TCTTCTTCA
*
1007 TCTTCATCA
1 TCTTCTTCA
1016 TCTTCTTCA
1 TCTTCTTCA
1025 TCT
1 TCT
1028 GACAGCCCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:7268 original size:31 final size:32
Alignment explanation
Indices: 7183--7272 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
7173 TAAAAGTTAT
* *
7183 AAAATGATCACT-AAACTTTACCAAACTATTAC
1 AAAATGATCATTAAAAC-TTATCAAACTATTAC
*
7215 AAAATGGTCATTAAAACTTATCAAACTATTAC
1 AAAATGATCATTAAAACTTATCAAACTATTAC
* *
7247 AAAATGATCCTT-ATACTTATCAAACT
1 AAAATGATCATTAAAACTTATCAAACT
7273 TTATTATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 13 0.25
32 34 0.67
33 4 0.08
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (32 bp):
AAAATGATCATTAAAACTTATCAAACTATTAC
Found at i:8205 original size:18 final size:19
Alignment explanation
Indices: 8184--8222 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
8174 TTTTTTATAA
*
8184 ATTTTTTAT-TAAAAATTT
1 ATTTTATATCTAAAAATTT
*
8202 ATTTTATATCTAAAATTTT
1 ATTTTATATCTAAAAATTT
8221 AT
1 AT
8223 AAATCGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTATATCTAAAAATTT
Found at i:20036 original size:23 final size:23
Alignment explanation
Indices: 20009--20056 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
19999 TCGATAGAAA
20009 AAAAAATTAACGGTCTATCACTAG
1 AAAAAA-TAACGGTCTATCACTAG
* * *
20033 AAAAAATATCTGTTTATCACTAG
1 AAAAAATAACGGTCTATCACTAG
20056 A
1 A
20057 TTTCCCCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (23 bp):
AAAAAATAACGGTCTATCACTAG
Found at i:32440 original size:32 final size:31
Alignment explanation
Indices: 32404--32479 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
32394 CGGGGCCGTG
*
32404 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
32436 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
32467 GAGCCTACCTAAG
1 GGGCCTACCTAAG
32480 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:32463 original size:63 final size:63
Alignment explanation
Indices: 32357--32479 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
32347 ACCTAAGGGA
* * ** *
32357 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
32420 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
32480 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:35320 original size:7 final size:7
Alignment explanation
Indices: 35308--35346 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
35298 GGTCAACGTG
35308 GGTCAAC
1 GGTCAAC
35315 GGTCAAC
1 GGTCAAC
35322 GGGTCAAC
1 -GGTCAAC
35330 GGTCAAC
1 GGTCAAC
35337 GGGTCAAC
1 -GGTCAAC
35345 GG
1 GG
35347 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:35327 original size:15 final size:15
Alignment explanation
Indices: 35307--35346 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
35297 TGGTCAACGT
35307 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
35322 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
35337 GGGTCAACGG
1 GGGTCAACGG
35347 GTCGGGTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:35328 original size:8 final size:8
Alignment explanation
Indices: 35307--35349 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
35297 TGGTCAACGT
35307 GGGTCAAC
1 GGGTCAAC
35315 -GGTCAAC
1 GGGTCAAC
35322 GGGTCAAC
1 GGGTCAAC
35330 -GGTCAAC
1 GGGTCAAC
35337 GGGTCAAC
1 GGGTCAAC
35345 GGGTC
1 GGGTC
35350 GGGTCGGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:35354 original size:13 final size:13
Alignment explanation
Indices: 35349--35384 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
35339 GTCAACGGGT
35349 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
35362 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
35375 CGGGTCGGGT
1 CGGGTCGGGT
35385 CGGGTCGGGT
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:0.17, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:35363 original size:18 final size:18
Alignment explanation
Indices: 35336--35389 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
35326 CAACGGTCAA
*
35336 CGGGTCAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
35354 CGGGTAAA-----CGGGT
1 CGGGTAAACGGGTCGGGT
35367 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
35385 CGGGT
1 CGGGT
35390 CGGGTTATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 13 0.43
18 17 0.57
ACGTcount: A:0.15, C:0.19, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:37525 original size:32 final size:31
Alignment explanation
Indices: 37489--37563 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
37479 CGGGGCCGTG
*
37489 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
* **
37521 GGGCCTACC-GAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
37551 GAGCCTACCTAAG
1 GGGCCTACCTAAG
37564 TGTCACATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 21 0.58
31 6 0.17
32 9 0.25
ACGTcount: A:0.27, C:0.31, G:0.28, T:0.15
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:40410 original size:15 final size:15
Alignment explanation
Indices: 40390--40421 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40380 GGTCAACGTG
40390 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
40405 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
40420 GG
1 GG
40422 GTCGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:40429 original size:13 final size:13
Alignment explanation
Indices: 40424--40460 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40414 GTCAACGGGT
40424 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
40437 CTGGTCGGGTAAA
1 CGGGTCGGGTCAA
40450 CGGGTCGGGTC
1 CGGGTCGGGTC
40461 GGGTTATGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:40434 original size:18 final size:18
Alignment explanation
Indices: 40411--40464 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
40401 CAACGGTCAA
40411 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
40429 CGGGTCAAC---T--GGT
1 CGGGTCAACGGGTCGGGT
*
40442 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
40460 CGGGT
1 CGGGT
40465 TATGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 11 0.37
15 1 0.03
16 1 0.03
18 17 0.57
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:40442 original size:8 final size:8
Alignment explanation
Indices: 40389--40424 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
40379 TGGTCAACGT
40389 GGGTCAAC
1 GGGTCAAC
40397 GGGTCAAC
1 GGGTCAAC
40405 -GGTCAAC
1 GGGTCAAC
40412 GGGTCAAC
1 GGGTCAAC
40420 GGGTC
1 GGGTC
40425 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.22, C:0.25, G:0.39, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:42682 original size:73 final size:74
Alignment explanation
Indices: 42513--42685 Score: 197
Period size: 75 Copynumber: 2.3 Consensus size: 74
42503 GGCGATTGGC
* * *
42513 ATTCTAATTTTTTGTTCCTGGTACCAGACCGACCCACATTCATGATAAAATTTGTTCATACAAAT
1 ATTCTAATTTTTCGTTCCTAGTACCAGACCGACCCACATTCATGATAAAA-TTGTGCATACAAAT
* *
42578 AGTGATTTAT
65 AATAATTTAT
* * * * * * *
42588 ATTCTAATTTTTCATTTCTAGTACC-GAATCGATCCACATTCATGGTAAAA-TGTGCATACGAGT
1 ATTCTAATTTTTCGTTCCTAGTACCAG-ACCGACCCACATTCATGATAAAATTGTGCATACAAAT
*
42651 AATAATTTGT
65 AATAATTTAT
42661 ATTCTAATTTTTCGTTCCTAGTACC
1 ATTCTAATTTTTCGTTCCTAGTACC
42686 TATCCACATT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
73 40 0.49
74 1 0.01
75 41 0.50
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (74 bp):
ATTCTAATTTTTCGTTCCTAGTACCAGACCGACCCACATTCATGATAAAATTGTGCATACAAATA
ATAATTTAT
Found at i:46773 original size:25 final size:25
Alignment explanation
Indices: 46743--46792 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
46733 ATCTCCTTTG
46743 TATTTCTTGTTCCCTCATCTTAATC
1 TATTTCTTGTTCCCTCATCTTAATC
46768 TATTTCTTGTTCCCTCATCTTAATC
1 TATTTCTTGTTCCCTCATCTTAATC
46793 ATCATCATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.04, T:0.52
Consensus pattern (25 bp):
TATTTCTTGTTCCCTCATCTTAATC
Found at i:46998 original size:111 final size:111
Alignment explanation
Indices: 46804--47025 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
46794 TCATCATCGT
46804 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
1 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
46869 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
66 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
46915 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
1 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
46980 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
66 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
47026 GGAAGAAAGC
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (111 bp):
TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
Found at i:49475 original size:2 final size:2
Alignment explanation
Indices: 49468--49494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49458 CAACATCAAT
49468 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 T
49495 TACACACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49573 original size:6 final size:6
Alignment explanation
Indices: 49562--49630 Score: 120
Period size: 6 Copynumber: 11.3 Consensus size: 6
49552 TGGTAGCTGG
49562 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
*
49610 TCTTTCG TCTTCC TCTTCC TC
1 TC-TTCC TCTTCC TCTTCC TC
49631 GTGGCTGAAG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
6 55 0.92
7 5 0.08
ACGTcount: A:0.00, C:0.48, G:0.01, T:0.51
Consensus pattern (6 bp):
TCTTCC
Found at i:55012 original size:60 final size:60
Alignment explanation
Indices: 54875--55012 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
54865 CTGGTTATTA
* * *
54875 ATAGTCGAATGACTATTTTGTAACTTTTAATAGTCGAGTGACTCAATAAAGCAACATCTT
1 ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGTGACTCAACAAAGCAACATCTT
* * * * *
54935 ATAGTCGAAGGATCATTTTATAACTTTTAATAGTCGA-TGGACTCAACAAAGTAATATTTT
1 ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGT-GACTCAACAAAGCAACATCTT
*
54995 ATAGTCGGATGACCATTT
1 ATAGTCGAATGACCATTT
55013 ATGTACTTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 65 0.98
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (60 bp):
ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGTGACTCAACAAAGCAACATCTT
Found at i:63069 original size:12 final size:12
Alignment explanation
Indices: 63052--63076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63042 GCTAAACGGC
63052 AGGTTAATGCAA
1 AGGTTAATGCAA
63064 AGGTTAATGCAA
1 AGGTTAATGCAA
63076 A
1 A
63077 TGGAAACGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
AGGTTAATGCAA
Found at i:63180 original size:21 final size:21
Alignment explanation
Indices: 63154--63194 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
63144 CGACATGCAA
63154 ATGCTTGGATCTCTCGGCGTC
1 ATGCTTGGATCTCTCGGCGTC
*
63175 ATGCTTGGATCTCTTGGCGT
1 ATGCTTGGATCTCTCGGCGT
63195 TATTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.24, G:0.29, T:0.37
Consensus pattern (21 bp):
ATGCTTGGATCTCTCGGCGTC
Found at i:66352 original size:23 final size:24
Alignment explanation
Indices: 66309--66366 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 24
66299 TTGCATGATA
66309 CAGACGTGCAGGCCCCCCCACATG
1 CAGACGTGCAGGCCCCCCCACATG
66333 CAGACGTGCAGG-CCCCCCACATG
1 CAGACGTGCAGGCCCCCCCACATG
66356 CAGACGTGCAG
1 CAGACGTGCAG
66367 CCTGCTCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.22, C:0.41, G:0.28, T:0.09
Consensus pattern (24 bp):
CAGACGTGCAGGCCCCCCCACATG
Found at i:66599 original size:30 final size:30
Alignment explanation
Indices: 66563--66625 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
66553 AAATTGTGTT
66563 AAAGACGCCGAGAGATCCAACCTTCCATGC
1 AAAGACGCCGAGAGATCCAACCTTCCATGC
* *
66593 AAAGACGCCGAGAGCTCCAAGCTTCCATGC
1 AAAGACGCCGAGAGATCCAACCTTCCATGC
66623 AAA
1 AAA
66626 TCTGCTGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.21, T:0.13
Consensus pattern (30 bp):
AAAGACGCCGAGAGATCCAACCTTCCATGC
Found at i:70253 original size:12 final size:12
Alignment explanation
Indices: 70236--70284 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
70226 ATAATTCAAG
70236 TATTATATTAGA
1 TATTATATTAGA
*
70248 TATTATTTTA-A
1 TATTATATTAGA
*
70259 TA-TATA-TATA
1 TATTATATTAGA
*
70269 TATTACATTAGA
1 TATTATATTAGA
70281 TATT
1 TATT
70285 TTCAAAGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 2 0.07
10 6 0.20
11 6 0.20
12 16 0.53
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (12 bp):
TATTATATTAGA
Done.