Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003422.1 Hibiscus syriacus cultivar Beakdansim tig00007205_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: 51530
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:5501 original size:20 final size:20
Alignment explanation
Indices: 5476--5522 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 20
5466 CATTTGCTTG
5476 AATTAAGTAATAAA-TAAAT
1 AATTAAGTAATAAAGTAAAT
5495 AAATTAAGTAATAAAGGTAAAT
1 -AATTAAGTAATAAA-GTAAAT
5517 AATTAA
1 AATTAA
5523 AAAATTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.56
21 6 0.24
22 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (20 bp):
AATTAAGTAATAAAGTAAAT
Found at i:5680 original size:3 final size:3
Alignment explanation
Indices: 5672--5719 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
5662 CTCTTCACTG
* * *
5672 TCA TCA TCA TCG CCA TCA TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5720 GGAGTAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.31, C:0.38, G:0.02, T:0.29
Consensus pattern (3 bp):
TCA
Found at i:5695 original size:18 final size:18
Alignment explanation
Indices: 5672--5719 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
5662 CTCTTCACTG
*
5672 TCATCATCATCGCCATCA
1 TCATCATCATCACCATCA
5690 TCATCATCATCACCATCA
1 TCATCATCATCACCATCA
5708 TCATCATCATCA
1 TCATCATCATCA
5720 GGAGTAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.31, C:0.38, G:0.02, T:0.29
Consensus pattern (18 bp):
TCATCATCATCACCATCA
Found at i:7592 original size:19 final size:17
Alignment explanation
Indices: 7570--7625 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
7560 TATAGAAATT
*
7570 AATATTTAACTAATACTAA
1 AATATTTAAATAA-A-TAA
7589 AATA-TTAAATAAATAA
1 AATATTTAAATAAATAA
* *
7605 AATATTAACAATAATTAA
1 AATATTTA-AATAAATAA
7623 AAT
1 AAT
7626 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 18 0.56
19 4 0.12
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATTTAAATAAATAA
Found at i:7623 original size:18 final size:16
Alignment explanation
Indices: 7586--7634 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
7576 TAACTAATAC
7586 TAAAATATTAAATAAA
1 TAAAATATTAAATAAA
*
7602 TAAAATATTAACAATAAT
1 TAAAATATT-A-AATAAA
*
7620 TAAAAT-TAAAATAAA
1 TAAAATATTAAATAAA
7635 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 2 0.07
18 11 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATATTAAATAAA
Found at i:10857 original size:36 final size:36
Alignment explanation
Indices: 10817--10945 Score: 122
Period size: 35 Copynumber: 3.6 Consensus size: 36
10807 GTTCAGTTTT
*
10817 GATCAAGCTGGTAATTCCTTATATAGGTTTAACACC
1 GATCAAGCTGGTAATTCCTTATATAGGTTCAACACC
* ** *
10853 GATC-AGTTGGTAATTCCTTAT-TGCAGGTTCATTTA-T
1 GATCAAGCTGGTAATTCCTTATAT--AGGTTCA-ACACC
* *
10889 GATCAAGCTGATAATTCCTTATATATGTTCAACACC
1 GATCAAGCTGGTAATTCCTTATATAGGTTCAACACC
* *
10925 GATCAA-TTGGTAATTTCTTAT
1 GATCAAGCTGGTAATTCCTTAT
10946 GGACCTAAGG
Statistics
Matches: 73, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
34 1 0.01
35 29 0.40
36 26 0.36
37 16 0.22
38 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (36 bp):
GATCAAGCTGGTAATTCCTTATATAGGTTCAACACC
Found at i:10905 original size:72 final size:72
Alignment explanation
Indices: 10804--10945 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 72
10794 GAAGTCTCTA
* * *
10804 CAGGTTCAGTTTTGATCAAGCTGGTAATTCCTTATATAGGTTTAACACCGATCAGTTGGTAATTC
1 CAGGTTCAGTTTTGATCAAGCTGATAATTCCTTATATAGGTTCAACACCGATCAATTGGTAATTC
10869 CTTATTG
66 CTTATTG
*
10876 CAGGTTCA-TTTATGATCAAGCTGATAATTCCTTATATATGTTCAACACCGATCAATTGGTAATT
1 CAGGTTCAGTTT-TGATCAAGCTGATAATTCCTTATATAGGTTCAACACCGATCAATTGGTAATT
*
10940 TCTTAT
65 CCTTAT
10946 GGACCTAAGG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 3 0.05
72 61 0.95
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (72 bp):
CAGGTTCAGTTTTGATCAAGCTGATAATTCCTTATATAGGTTCAACACCGATCAATTGGTAATTC
CTTATTG
Found at i:26170 original size:25 final size:26
Alignment explanation
Indices: 26141--26189 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
26131 AATAATGACG
26141 ATAAATATTT-TATA-ATTTAAAAATT
1 ATAAAT-TTTATATATATTTAAAAATT
*
26166 ATAAATTTTATATATTTTTAAAAA
1 ATAAATTTTATATATATTTAAAAA
26190 ATTTATTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 10 0.48
26 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAAATTTTATATATATTTAAAAATT
Found at i:26333 original size:20 final size:22
Alignment explanation
Indices: 26283--26333 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
26273 TTATTATTCA
26283 TTAATTATTAAAATATCACTTCT
1 TTAA-TATTAAAATATCACTTCT
*
26306 TT-AT-TTAAAATAT-TCTT-T
1 TTAATATTAAAATATCACTTCT
26324 TTAATATTAA
1 TTAATATTAA
26334 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.12
19 5 0.20
20 13 0.52
21 1 0.04
22 1 0.04
23 2 0.08
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATATTAAAATATCACTTCT
Found at i:27618 original size:21 final size:21
Alignment explanation
Indices: 27594--27635 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27584 ATTATAATCA
*
27594 CTTATT-TTTAAATTTTTAAAT
1 CTTATTATTT-AATTTTAAAAT
27615 CTTATTATTTAATTTTAAAAT
1 CTTATTATTTAATTTTAAAAT
27636 TATTCATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
CTTATTATTTAATTTTAAAAT
Found at i:28983 original size:38 final size:38
Alignment explanation
Indices: 28922--29008 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
28912 TTTATTTTGT
* *
28922 TCGGGTCGAG-TTTTTTAAGTGTGATATTCGGGT-TGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAG-G
*
28959 TCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCAGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGG
28997 TCGGGTCGGGTT
1 TCGGGTCGGGTT
29009 CGGGTTTAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 9 0.20
38 35 0.78
39 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.38, T:0.40
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGG
Found at i:29024 original size:243 final size:246
Alignment explanation
Indices: 28496--29058 Score: 795
Period size: 243 Copynumber: 2.2 Consensus size: 246
28486 AGTGTGATAT
* *
28496 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCAGACCGACCCGAAAATATATATAATTTGGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTTGGGT
28561 CGAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTCG
66 CGAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTA-TT---GT---GTCGGGTCG
28626 GATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTAAGGT
124 GATTTCTAATTCATATATT---GTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC-GG-AAGGT
*
28691 TTTCTAAGTGTGATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATATTCGGTTCGGA
184 TTTCTAAGTGTGATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGA
* *
28754 TCGGGTCGGGGTCGGGTTTAGGGTGAAAAAAACCGGACCGACTCGAAAATATATATAATTCGGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATT----T
*
28819 CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATA-TTTTTTATTA-T-T-TCGGGTCGGA
62 -GGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTGTGTCGGGTCGGA
*
28880 TTTCTAATTCATATA-T-TCGGGTCGGATGAAACTTTATTTTGTTCGGGTC-G-A-GTTTTTTAA
126 TTTCTAATTCATATATTGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGAAGGTTTTCTAA
* *
28940 GTGTGATATTCGGGTTGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCAGG-
191 GTGTGATATTCGGGTCGAGTC-GGTCGGGTTTTTTTAAGTGTGATATTCGGGTC-GGA
28997 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAATATATATAATTT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCG-AAAATATATATAATTT
29059 TACTTTATAT
Statistics
Matches: 286, Mismatches: 11, Indels: 34
0.86 0.03 0.10
Matches are distributed among these distances:
240 1 0.00
242 28 0.10
243 74 0.26
244 17 0.06
245 1 0.00
247 33 0.12
251 1 0.00
252 25 0.09
256 1 0.00
258 56 0.20
260 1 0.00
262 11 0.04
263 37 0.13
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (246 bp):
TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTTGGGT
CGAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTGTGTCGGGTCGGATTTCT
AATTCATATATTGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGAAGGTTTTCTAAGTGTG
ATATTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGA
Found at i:30894 original size:11 final size:14
Alignment explanation
Indices: 30860--30892 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
30850 ATTATATCAC
30860 ATAATAATTTAATT
1 ATAATAATTTAATT
30874 ATAATAATTTAATT
1 ATAATAATTTAATT
30888 ATAAT
1 ATAAT
30893 TTTTGTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAATAATTTAATT
Found at i:31973 original size:66 final size:66
Alignment explanation
Indices: 31891--32017 Score: 245
Period size: 66 Copynumber: 1.9 Consensus size: 66
31881 AATATGAAGG
31891 TTTGCAGTAGGTATGTGTTCAATGTGGTGTTTATGGTCATACAAAGAATTATTGTAAGGAATGTA
1 TTTGCAGTAGGTATGTGTTCAATGTGGTGTTTATGGTCATACAAAGAATTATTGTAAGGAATGTA
31956 A
66 A
*
31957 TTTGCAGTAGGTATGTGTTCACTGTGGTGTTTATGGTCATACAAAGAATTATTGTAAGGAA
1 TTTGCAGTAGGTATGTGTTCAATGTGGTGTTTATGGTCATACAAAGAATTATTGTAAGGAA
32018 GGTCAGGATC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.38
Consensus pattern (66 bp):
TTTGCAGTAGGTATGTGTTCAATGTGGTGTTTATGGTCATACAAAGAATTATTGTAAGGAATGTA
A
Found at i:40406 original size:22 final size:22
Alignment explanation
Indices: 40378--40540 Score: 135
Period size: 22 Copynumber: 7.8 Consensus size: 22
40368 GAAGGTTTAT
*
40378 AGTGATCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* * *
40400 AGTGATCCTTCGGGACGTATCT
1 AGTGGTCCTTCGGGACATATCC
* * * *
40422 AGAGGTCCTTCAGGACGTATCT
1 AGTGGTCCTTCGGGACATATCC
40444 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
** *
40466 AGTGGTCCTTCAAGAC--GT--
1 AGTGGTCCTTCGGGACATATCC
* *
40484 AGTGGTCCTTCGGGATATATCT
1 AGTGGTCCTTCGGGACATATCC
* *
40506 AGTGGTCCTTAGGGACGTA---
1 AGTGGTCCTTCGGGACATATCC
40525 A-TGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
40541 AATATTCACT
Statistics
Matches: 116, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
18 26 0.22
19 1 0.01
20 2 0.02
22 87 0.75
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:40454 original size:44 final size:42
Alignment explanation
Indices: 40377--40540 Score: 167
Period size: 44 Copynumber: 3.9 Consensus size: 42
40367 CGAAGGTTTA
* * * * *
40377 TAGTGATCCTTCGGGACATATCCAGTGATCCTTCGGGACGTATC
1 TAGTGGTCCTTCAGGACGTAT--AGTGGTCCTTCGGGACATATC
*
40421 TAGAGGTCCTTCAGGACGTATCTAGTGGTCCTTCGGGACATATC
1 TAGTGGTCCTTCAGGACGTA--TAGTGGTCCTTCGGGACATATC
* * *
40465 CAGTGGTCCTTCAAGACG--TAGTGGTCCTTCGGGATATATC
1 TAGTGGTCCTTCAGGACGTATAGTGGTCCTTCGGGACATATC
40505 TAGTGGTCCTT-AGGGACGTA-A-TGGTCCTTCGGGACA
1 TAGTGGTCCTTCA-GGACGTATAGTGGTCCTTCGGGACA
40541 AATATTCACT
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
39 1 0.01
40 49 0.48
41 1 0.01
44 50 0.49
46 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (42 bp):
TAGTGGTCCTTCAGGACGTATAGTGGTCCTTCGGGACATATC
Found at i:40483 original size:66 final size:62
Alignment explanation
Indices: 40377--40521 Score: 173
Period size: 66 Copynumber: 2.3 Consensus size: 62
40367 CGAAGGTTTA
* ** *
40377 TAGTGATCCTTCGGGACATATCCAGTGATCCTTCGGGACGTATCTAGAGGTCCTTCAGGACGTAT
1 TAGTGGTCCTTCGGGACATATCCAGTGATCCTTCAAGACG----TAGAGGTCCTTCAGGACATAT
40442 C
62 C
* * * *
40443 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCAAGACGTAGTGGTCCTTCGGGATATATC
1 TAGTGGTCCTTCGGGACATATCCAGTGATCCTTCAAGACGTAGAGGTCCTTCAGGACATATC
*
40505 TAGTGGTCCTTAGGGAC
1 TAGTGGTCCTTCGGGAC
40522 GTAATGGTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
62 34 0.49
66 36 0.51
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.30
Consensus pattern (62 bp):
TAGTGGTCCTTCGGGACATATCCAGTGATCCTTCAAGACGTAGAGGTCCTTCAGGACATATC
Found at i:40498 original size:40 final size:40
Alignment explanation
Indices: 40400--40540 Score: 167
Period size: 40 Copynumber: 3.4 Consensus size: 40
40390 GGACATATCC
* * *
40400 AGTGATCCTTCGGGACGTATCTAGAGGTCCTTCAGGACGTATCT
1 AGTGGTCCTTCGGGACATATCTAGTGGTCCTTCAGGACG----T
* *
40444 AGTGGTCCTTCGGGACATATCCAGTGGTCCTTCAAGACGT
1 AGTGGTCCTTCGGGACATATCTAGTGGTCCTTCAGGACGT
*
40484 AGTGGTCCTTCGGGATATATCTAGTGGTCCTT-AGGGACGT
1 AGTGGTCCTTCGGGACATATCTAGTGGTCCTTCA-GGACGT
*
40524 AATGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
40541 AATATTCACT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 51 0.59
44 34 0.40
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACATATCTAGTGGTCCTTCAGGACGT
Found at i:47374 original size:22 final size:22
Alignment explanation
Indices: 47346--47507 Score: 160
Period size: 22 Copynumber: 7.7 Consensus size: 22
47336 GAGGGTTTAT
47346 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
** *
47368 AGTGGTCCTTCAAGACGTATCC
1 AGTGGTCCTTCGGGACATATCC
* *
47390 AGTGGTCCTTCGAGACGTATCC
1 AGTGGTCCTTCGGGACATATCC
* **
47412 AGTGGTCATTCGGGACATATTT
1 AGTGGTCCTTCGGGACATATCC
* *
47434 AGTGGTCCTTTGGG--ATGT--
1 AGTGGTCCTTCGGGACATATCC
*
47452 AGTGGTCCTTCGGG--ATGT--
1 AGTGGTCCTTCGGGACATATCC
47470 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
*
47492 AGTGGTCCTTAGGGAC
1 AGTGGTCCTTCGGGAC
47508 GTACTAGTCC
Statistics
Matches: 121, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
18 31 0.26
20 6 0.05
22 84 0.69
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:47456 original size:18 final size:18
Alignment explanation
Indices: 47433--47484 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
47423 GGGACATATT
*
47433 TAGTGGTCCTTTGGGATG
1 TAGTGGTCCTTCGGGATG
47451 TAGTGGTCCTTCGGGATG
1 TAGTGGTCCTTCGGGATG
47469 TAGTGGTCCTTCGGGA
1 TAGTGGTCCTTCGGGA
47485 CATATCCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.12, C:0.15, G:0.38, T:0.35
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGATG
Found at i:47484 original size:58 final size:58
Alignment explanation
Indices: 47345--47524 Score: 164
Period size: 58 Copynumber: 3.0 Consensus size: 58
47335 TGAGGGTTTA
* * *
47345 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCA-AGACGTATCCAGTGGTCCTTCGAGACGTA
1 TAGTGGTCATTCGGGACATATCCAGTGGTCCTT-AGGGACGTA--C--TAGTCCTTCG-G--G-A
*
47409 TC
57 TG
* ** * * * *
47411 CAGTGGTCATTCGGGACATATTTAGTGGTCCTTTGGGATGTAGTGGTCCTTCGGGATG
1 TAGTGGTCATTCGGGACATATCCAGTGGTCCTTAGGGACGTACTAGTCCTTCGGGATG
*
47469 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTAGGGACGTACTAGTCCTTCGGGA
1 TAGTGGTCATTCGGGACATATCCAGTGGTCCTTAGGGACGTACTAGTCCTTCGGGA
47525 CAAATATTCA
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
58 50 0.52
59 1 0.01
61 1 0.01
62 10 0.10
66 34 0.35
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.31
Consensus pattern (58 bp):
TAGTGGTCATTCGGGACATATCCAGTGGTCCTTAGGGACGTACTAGTCCTTCGGGATG
Found at i:47496 original size:40 final size:40
Alignment explanation
Indices: 47345--47526 Score: 147
Period size: 40 Copynumber: 4.5 Consensus size: 40
47335 TGAGGGTTTA
* *
47345 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCAAGACGTATC
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTC--G--GGATG
* * * * *
47389 CAGTGGTCCTTCGAGACGTATCCAGTGGTCATTCGGGACATATT
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGG----ATG
* *
47433 TAGTGGTCCTTTGGG--ATGT--AGTGGTCCTTCGGGATG
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATG
* *
47469 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTAGGGACG
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATG
* *
47509 TACTAGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
47527 AATATTCACT
Statistics
Matches: 111, Mismatches: 19, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
36 16 0.14
38 3 0.03
40 45 0.41
42 3 0.03
44 44 0.40
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (40 bp):
TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGATG
Done.