Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003137.1 Hibiscus syriacus cultivar Beakdansim tig00006582_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: 96347
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2760 original size:18 final size:18
Alignment explanation
Indices: 2737--2806 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
2727 CCGTAGAATT
2737 TGTCCCGTAA-GACCACTA
1 TGTCCCG-AAGGACCACTA
2755 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2773 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2791 TATCCCAAAGGACCAC
1 TGTCCCGAAGGACCAC
2807 ATAGACCCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
17 2 0.04
18 47 0.96
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:7644 original size:17 final size:17
Alignment explanation
Indices: 7594--7645 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
7584 TTTATATCTG
*
7594 TAAAAAAATTAATTAAA-
1 TAAAATAATTAA-TAAAT
7611 TAAAAT-ATTAA-ACAAT
1 TAAAATAATTAATA-AAT
7627 TAAAATAATTAATAAAT
1 TAAAATAATTAATAAAT
7644 TA
1 TA
7646 CTAAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 2 0.07
16 11 0.37
17 15 0.50
18 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATAATTAATAAAT
Found at i:12177 original size:3 final size:3
Alignment explanation
Indices: 12171--12212 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12161 AAAGTACTTA
12171 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12213 GAGAATGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13576 original size:2 final size:2
Alignment explanation
Indices: 13569--13636 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
13559 ATGAAATGAG
13569 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
13611 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
13637 GTTTGGCTAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14200 original size:20 final size:19
Alignment explanation
Indices: 14172--14210 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
14162 ATATGATCTT
*
14172 TTGACCAATGTTTTTCGTTA
1 TTGACCAATGATTTT-GTTA
*
14192 TTGATCAATGATTTTGTTA
1 TTGACCAATGATTTTGTTA
14211 ATTCCTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (19 bp):
TTGACCAATGATTTTGTTA
Found at i:16048 original size:20 final size:20
Alignment explanation
Indices: 15996--16057 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
15986 AAATCAGAGA
* *
15996 AAAATATGTCACTAAGACAGAG
1 AAAACATGTCACAAAGAC--AG
*
16018 ATAAACGTGTCACAAAGACAG
1 A-AAACATGTCACAAAGACAG
16039 AAAACATGTCACAAAGACA
1 AAAACATGTCACAAAGACA
16058 TAATTATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 17 0.49
21 3 0.09
22 1 0.03
23 14 0.40
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAACATGTCACAAAGACAG
Found at i:16982 original size:14 final size:14
Alignment explanation
Indices: 16963--17000 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
16953 CTGTCTACAT
16963 GCAGAGATTT-TTAC
1 GCAGAGATTTATT-C
*
16977 GCAGAGATTTATTT
1 GCAGAGATTTATTC
16991 GCAGAGATTT
1 GCAGAGATTT
17001 CTTCCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (14 bp):
GCAGAGATTTATTC
Found at i:22213 original size:6 final size:6
Alignment explanation
Indices: 22202--22226 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22192 AAATCTACTG
22202 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
22227 CATGTTAGAG
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:29346 original size:12 final size:13
Alignment explanation
Indices: 29331--29364 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
29321 TTTTATTAAT
29331 ATTTT-TTATAAA
1 ATTTTATTATAAA
29343 ATTTTATT-TAAA
1 ATTTTATTATAAA
29355 ATTTTATTAT
1 ATTTTATTAT
29365 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTATTATAAA
Found at i:29512 original size:31 final size:31
Alignment explanation
Indices: 29471--29566 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 31
29461 TATTAGACAA
29471 TTTAA-CAAAAATATTAAAAAATATTAATAT
1 TTTAATCAAAAATATTAAAAAATATTAATAT
* * *
29501 TTTAAGT-AAAAATA--ATAACATTTTAAATAAT
1 TTTAA-TCAAAAATATTAAAAAATATT-AAT-AT
* *
29532 TTTTATCAAAAATATTAAAATAATAATAATAT
1 TTTAATCAAAAATATTAAAA-AATATTAATAT
29564 TTT
1 TTT
29567 TAATTACACA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
29 7 0.14
30 9 0.18
31 20 0.40
32 5 0.10
33 6 0.12
34 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
TTTAATCAAAAATATTAAAAAATATTAATAT
Found at i:29513 original size:21 final size:21
Alignment explanation
Indices: 29487--29526 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29477 AAAAATATTA
* *
29487 AAAAATATTAATATTTTAAGT
1 AAAAATAATAACATTTTAAGT
29508 AAAAATAATAACATTTTAA
1 AAAAATAATAACATTTTAA
29527 ATAATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAATAATAACATTTTAAGT
Found at i:31470 original size:13 final size:13
Alignment explanation
Indices: 31452--31479 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31442 GTTATATTGA
31452 TTTTTCCCTCAAT
1 TTTTTCCCTCAAT
31465 TTTTTCCCTCAAT
1 TTTTTCCCTCAAT
31478 TT
1 TT
31480 AAGGGTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTCCCTCAAT
Found at i:31708 original size:13 final size:13
Alignment explanation
Indices: 31690--31716 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31680 TTTATTGTTA
31690 TAACTTTTTTTAT
1 TAACTTTTTTTAT
31703 TAACTTTTTTTAT
1 TAACTTTTTTTAT
31716 T
1 T
31717 TTATATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (13 bp):
TAACTTTTTTTAT
Found at i:33791 original size:17 final size:17
Alignment explanation
Indices: 33769--33802 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
33759 TTAAATAATC
33769 CACGTAATATAGATTTT
1 CACGTAATATAGATTTT
33786 CACGTAATATAGATTTT
1 CACGTAATATAGATTTT
33803 AAACATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
CACGTAATATAGATTTT
Found at i:45499 original size:25 final size:25
Alignment explanation
Indices: 45447--45499 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
45437 GATCATTCAG
*
45447 TTTTTAAATTTAAATATTTAATATA
1 TTTTTAAATTTAAATATTAAATATA
* *
45472 TTTTTAAATTTTTATTATTAAATA-A
1 TTTTTAAA-TTTAAATATTAAATATA
45497 TTT
1 TTT
45500 AAACATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTTAAATTTAAATATTAAATATA
Found at i:48129 original size:28 final size:28
Alignment explanation
Indices: 48093--48146 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
48083 ATCACTATTA
48093 TTTTTATTTAATTAAGATATGATCACTT
1 TTTTTATTTAATTAAGATATGATCACTT
*
48121 TTTTTATTTAATTAAGATGTGATCAC
1 TTTTTATTTAATTAAGATATGATCAC
48147 CACGAGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (28 bp):
TTTTTATTTAATTAAGATATGATCACTT
Found at i:49294 original size:45 final size:45
Alignment explanation
Indices: 49223--49346 Score: 153
Period size: 45 Copynumber: 2.7 Consensus size: 45
49213 TATCGAATCT
* * *
49223 GTTGGTTTCGGTT-TGGGTCAAGCTTTAGATTTTCGGATCAATTC-G
1 GTTGGTTTCGGTTCT-GATCAACCTTTAGATTTTAGG-TCAATTCGG
*
49268 GTTGGTTTCGGTTCTGATCAACCTTTAAAATTTTAGGTCAATTCGG
1 GTTGGTTTCGGTTCTGATCAACCTTT-AGATTTTAGGTCAATTCGG
* *
49314 GTTGGTTTAGGTTCAGATCAACCTTTAGATTTT
1 GTTGGTTTCGGTTCTGATCAACCTTTAGATTTT
49347 GAAGTTAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 35 0.51
46 34 0.49
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (45 bp):
GTTGGTTTCGGTTCTGATCAACCTTTAGATTTTAGGTCAATTCGG
Found at i:49320 original size:46 final size:46
Alignment explanation
Indices: 49223--49340 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
49213 TATCGAATCT
* * * *
49223 GTTGGTTTCGGTT-TGGGTCAAGCTTT-AGATTTTCGGATCAATTCG
1 GTTGGTTTCGGTTCT-GATCAACCTTTAAAATTTTAGGATCAATTCG
49268 GTTGGTTTCGGTTCTGATCAACCTTTAAAATTTTAGG-TCAATTCGG
1 GTTGGTTTCGGTTCTGATCAACCTTTAAAATTTTAGGATCAATTC-G
* *
49314 GTTGGTTTAGGTTCAGATCAACCTTTA
1 GTTGGTTTCGGTTCTGATCAACCTTTA
49341 GATTTTGAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 29 0.45
46 35 0.55
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (46 bp):
GTTGGTTTCGGTTCTGATCAACCTTTAAAATTTTAGGATCAATTCG
Found at i:49357 original size:46 final size:45
Alignment explanation
Indices: 49240--49357 Score: 132
Period size: 46 Copynumber: 2.6 Consensus size: 45
49230 TCGGTTTGGG
* * * *
49240 TCAAGCTTTAGATTTTCGGA-TCAATTCGGTTGGTTTCGGTTCTGA
1 TCAACCTTTAGATTTT-GAAGTCAATTCGGTTGGTTTAGGTTCAGA
* *
49285 TCAACCTTTAAAATTTT-AGGTCAATTCGGGTTGGTTTAGGTTCAGA
1 TCAACCTTT-AGATTTTGAAGTCAATTC-GGTTGGTTTAGGTTCAGA
*
49331 TCAACCTTTAGATTTTGAAGTTAATTC
1 TCAACCTTTAGATTTTGAAGTCAATTC
49358 AGATTTTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
45 21 0.35
46 39 0.65
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (45 bp):
TCAACCTTTAGATTTTGAAGTCAATTCGGTTGGTTTAGGTTCAGA
Found at i:52775 original size:2 final size:2
Alignment explanation
Indices: 52768--52795 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52758 TTTCTTTTTA
52768 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
52796 GTAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59638 original size:23 final size:23
Alignment explanation
Indices: 59612--59656 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
59602 TCCCTCGTCA
59612 TTTATCTTTCATGATTATATTAG
1 TTTATCTTTCATGATTATATTAG
59635 TTTATCTTTCATGATTATATTA
1 TTTATCTTTCATGATTATATTA
59657 ATGTCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTATCTTTCATGATTATATTAG
Found at i:61389 original size:22 final size:22
Alignment explanation
Indices: 61364--61412 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
61354 CCAAATAACA
*
61364 AAAAAATGTCA-AAAAACATAAT
1 AAAAAATGCCATAAAAACAT-AT
* *
61386 AAAATATGCCATAAAAGCATAT
1 AAAAAATGCCATAAAAACATAT
61408 AAAAA
1 AAAAA
61413 CGTGTCATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAAATGCCATAAAAACATAT
Found at i:67013 original size:15 final size:14
Alignment explanation
Indices: 66980--67013 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
66970 TTATGATTAA
*
66980 TTTTATTTAAATTT
1 TTTTATTTAAATCT
66994 TTTTATTTAAATACT
1 TTTTATTTAAAT-CT
67009 TTTTA
1 TTTTA
67014 GATCTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATTTAAATCT
Found at i:67467 original size:7 final size:7
Alignment explanation
Indices: 67434--67474 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
67424 CTGATTTTCA
67434 ATAATAT
1 ATAATAT
67441 AT-ATAT
1 ATAATAT
67447 ATATATAT
1 ATA-ATAT
67455 ATAATAT
1 ATAATAT
*
67462 AAAATAT
1 ATAATAT
67469 ATAATA
1 ATAATA
67475 ATTTAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:67910 original size:24 final size:24
Alignment explanation
Indices: 67882--67927 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
67872 TTGTAACGAT
*
67882 TTTTCTTTACTCTTGTGGCACGCG
1 TTTTCTCTACTCTTGTGGCACGCG
* *
67906 TTTTCTCTGCTCTTGTTGCACG
1 TTTTCTCTACTCTTGTGGCACG
67928 ATCCTCACGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.07, C:0.26, G:0.20, T:0.48
Consensus pattern (24 bp):
TTTTCTCTACTCTTGTGGCACGCG
Found at i:71376 original size:23 final size:24
Alignment explanation
Indices: 71328--71378 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
71318 TTGTTTGATT
*
71328 TGATTAAAAAAAGGAATTCAATTAA
1 TGATTAAAAAAA-GAATTCAACTAA
71353 TGATTAAAGAAAA-AA-TCAACTAA
1 TGATTAAA-AAAAGAATTCAACTAA
71376 TGA
1 TGA
71379 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.42
24 2 0.08
25 8 0.33
26 4 0.17
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (24 bp):
TGATTAAAAAAAGAATTCAACTAA
Found at i:72017 original size:32 final size:32
Alignment explanation
Indices: 71976--72037 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
71966 AACAGGGTTG
* * *
71976 GTCGCCATCCCTTCTATGTGATACCAAAGGAA
1 GTCGCCATCCCTTCCATGCGACACCAAAGGAA
72008 GTCGCCATCCCTTCCATGCGACACCAAAGG
1 GTCGCCATCCCTTCCATGCGACACCAAAGG
72038 GTATTTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (32 bp):
GTCGCCATCCCTTCCATGCGACACCAAAGGAA
Found at i:85402 original size:105 final size:105
Alignment explanation
Indices: 85220--85432 Score: 408
Period size: 105 Copynumber: 2.0 Consensus size: 105
85210 ATCCAATAAG
*
85220 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAATGG
1 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAACGG
85285 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
66 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
*
85325 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGAGGAAATTTTTGTACAACGG
1 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAACGG
85390 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
66 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
85430 CAT
1 CAT
85433 TGAATCAAAG
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (105 bp):
CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAACGG
AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
Found at i:85750 original size:27 final size:28
Alignment explanation
Indices: 85702--85754 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
85692 ACACCATAAA
85702 ATCCTAAGAACACAACTTTAATCAATGC
1 ATCCTAAGAACACAACTTTAATCAATGC
*
85730 ATCCTAAG-ACATAACTTTAATCAAT
1 ATCCTAAGAACACAACTTTAATCAAT
85755 TACTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (28 bp):
ATCCTAAGAACACAACTTTAATCAATGC
Found at i:89311 original size:30 final size:30
Alignment explanation
Indices: 89264--89428 Score: 188
Period size: 30 Copynumber: 5.5 Consensus size: 30
89254 GAAAGGGATA
* * *
89264 TAATTCCATGCAAATGTCAAAATGGGGAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
* *
89294 TAA-CTCTATGCAGATGTCAAAGCGGGGAAT
1 TAATC-CCATGCAGATGTCAAAACGGGGAAT
*
89324 TAATCCCATGCAGATGTCAAAACGGGAAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
* *
89354 CAATCCCATGCAGATGTCAGAACGGGGAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
* * * * *
89384 TAATCTCATGCAGACGTCAGAACAGAGAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
*
89414 TAATCCCATACAGAT
1 TAATCCCATGCAGAT
89429 CGAAAATACA
Statistics
Matches: 114, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
30 113 0.99
31 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (30 bp):
TAATCCCATGCAGATGTCAAAACGGGGAAT
Found at i:95338 original size:3 final size:3
Alignment explanation
Indices: 95324--95401 Score: 61
Period size: 3 Copynumber: 26.3 Consensus size: 3
95314 ACGACAAACA
* * * * *
95324 AAG AAA AAG AAG AAG AAG AAG AAG AGG AAG AGG AAG AGG AAG AGGG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG
* * *
95370 AAG AGG AAG AGG AAG -AG AAG -AG AAG AGG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
95402 GTGTTGTATA
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
2 4 0.07
3 50 0.89
4 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:95347 original size:6 final size:6
Alignment explanation
Indices: 95332--95402 Score: 101
Period size: 6 Copynumber: 12.0 Consensus size: 6
95322 CAAAGAAAAA
* *
95332 GAAGAA GAAGAA GAAGAG GAAGAG GAAGAG GAAGAGG GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA-G GAAGAG GAAGAG
95381 GAAGA- GAAGA- GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG
95403 TGTTGTATAT
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
5 10 0.16
6 46 0.74
7 6 0.10
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:95378 original size:25 final size:22
Alignment explanation
Indices: 95332--95402 Score: 97
Period size: 25 Copynumber: 3.0 Consensus size: 22
95322 CAAAGAAAAA
95332 GAAGAAGAAGAAGAAGAGGAAGAG
1 GAAG-AGAAG-AGAAGAGGAAGAG
95356 GAAGAGGAAGAGGGAAGAGGAAGAG
1 GAAGA-GAAGA--GAAGAGGAAGAG
95381 GAAGAGAAGAGAAGAGGAAGAG
1 GAAGAGAAGAGAAGAGGAAGAG
95403 TGTTGTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.27
23 2 0.05
24 13 0.30
25 17 0.39
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (22 bp):
GAAGAGAAGAGAAGAGGAAGAG
Done.