Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004343.1 Hibiscus syriacus cultivar Beakdansim tig00009516_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: 87892
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:637 original size:2 final size:2
Alignment explanation
Indices: 630--663 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
620 TGGACACTAA
630 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
664 GCATATTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8390 original size:17 final size:16
Alignment explanation
Indices: 8368--8401 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8358 AGAATTATAT
* *
8368 TTAAAAAATCGAAAAC
1 TTAAAAAAACCAAAAC
8384 TTAAAAAAACCAAAAC
1 TTAAAAAAACCAAAAC
8400 TT
1 TT
8402 TGAAAACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.21
Consensus pattern (16 bp):
TTAAAAAAACCAAAAC
Found at i:8661 original size:15 final size:16
Alignment explanation
Indices: 8637--8669 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8627 TAGTTTAGGA
8637 TTAGGAATTT-AGATT
1 TTAGGAATTTGAGATT
*
8652 TTAGGGATTTGAGATT
1 TTAGGAATTTGAGATT
8668 TT
1 TT
8670 TTTTGTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (16 bp):
TTAGGAATTTGAGATT
Found at i:10582 original size:18 final size:19
Alignment explanation
Indices: 10559--10602 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
10549 AACATTCTCA
10559 GTAATCCT-ATTCTCACTG
1 GTAATCCTAATTCTCACTG
* *
10577 GTAATCTTACATTCTTACTG
1 GTAATCCTA-ATTCTCACTG
10597 GTAATC
1 GTAATC
10603 TTACATTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (19 bp):
GTAATCCTAATTCTCACTG
Found at i:10596 original size:20 final size:20
Alignment explanation
Indices: 10567--10610 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
10557 CAGTAATCCT
10567 ATTCTCACTGGTAATCTTAC
1 ATTCTCACTGGTAATCTTAC
*
10587 ATTCTTACTGGTAATCTTAC
1 ATTCTCACTGGTAATCTTAC
10607 ATTC
1 ATTC
10611 CGTGAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (20 bp):
ATTCTCACTGGTAATCTTAC
Found at i:23687 original size:21 final size:21
Alignment explanation
Indices: 23663--23707 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23653 CCGTAGCCAT
*
23663 CACCTCCACCGCCC-CCTCCAC
1 CACCACCACC-CCCACCTCCAC
*
23684 CACCACCACCCCCACTTCCAC
1 CACCACCACCCCCACCTCCAC
23705 CAC
1 CAC
23708 AACAACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.20, C:0.69, G:0.02, T:0.09
Consensus pattern (21 bp):
CACCACCACCCCCACCTCCAC
Found at i:23794 original size:24 final size:24
Alignment explanation
Indices: 23758--23819 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
23748 TGAACCTTCT
* *
23758 CCTCCTCCTCCACCACCACCACCG
1 CCTCCACCGCCACCACCACCACCG
* * * *
23782 CCTCCACTGCCACCTCCTCCTCCG
1 CCTCCACCGCCACCACCACCACCG
23806 CCTCCACCGCCACC
1 CCTCCACCGCCACC
23820 TCCAGACCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.66, G:0.06, T:0.15
Consensus pattern (24 bp):
CCTCCACCGCCACCACCACCACCG
Found at i:23803 original size:18 final size:18
Alignment explanation
Indices: 23758--23823 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
23748 TGAACCTTCT
23758 CCTCCTCCTCCACCACCA
1 CCTCCTCCTCCACCACCA
* * **
23776 CCACCGCCTCCACTGCCA
1 CCTCCTCCTCCACCACCA
* *
23794 CCTCCTCCTCCGCCTCCA
1 CCTCCTCCTCCACCACCA
* *
23812 CCGCCACCTCCA
1 CCTCCTCCTCCA
23824 GACCCTACAC
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.14, C:0.65, G:0.06, T:0.15
Consensus pattern (18 bp):
CCTCCTCCTCCACCACCA
Found at i:25762 original size:2 final size:2
Alignment explanation
Indices: 25755--25782 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25745 AATCAATCAA
25755 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
25783 TAGGTCAGGT
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:35555 original size:13 final size:13
Alignment explanation
Indices: 35537--35561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35527 ATTTTCTTCC
35537 AATGGAAAACTCA
1 AATGGAAAACTCA
35550 AATGGAAAACTC
1 AATGGAAAACTC
35562 GCAAATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
AATGGAAAACTCA
Found at i:37283 original size:12 final size:12
Alignment explanation
Indices: 37266--37305 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
37256 TGAGATCGAG
37266 GAGGAGGAGGAA
1 GAGGAGGAGGAA
37278 GAGGAGGAGGAA
1 GAGGAGGAGGAA
* *
37290 AAGGAGGAAGAA
1 GAGGAGGAGGAA
37302 GAGG
1 GAGG
37306 CTTGGCTACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (12 bp):
GAGGAGGAGGAA
Found at i:59131 original size:60 final size:59
Alignment explanation
Indices: 59049--59232 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 59
59039 CGCATGTGGT
* *
59049 GGGCTTGGGAAAACACTAGGTGGGTTTGGAACTATTTGTGGTGGATTTGGAGTTCCGGGC
1 GGGCTTGGAAAAATACTAGGTGGGTTTGGAACTATTTG-GGTGGATTTGGAGTTCCGGGC
* ** * * * * *
59109 GGGTTTGGAAAGGTACTAGGTGGGCTTGGAACTA-TTGCAGGTGGATTTAGAGCTCCAGGT
1 GGGCTTGGAAAAATACTAGGTGGGTTTGGAACTATTTG--GGTGGATTTGGAGTTCCGGGC
* * * * *
59169 GGGCTTGGAAAAATGCTAGGTGGGTTTGGAACTGTCTCGGGTGGATTCGGAGTTCCGGGT
1 GGGCTTGGAAAAATACTAGGTGGGTTTGGAACTAT-TTGGGTGGATTTGGAGTTCCGGGC
59229 GGGC
1 GGGC
59233 CTGGTGGGGG
Statistics
Matches: 99, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
59 3 0.03
60 94 0.95
62 2 0.02
ACGTcount: A:0.18, C:0.12, G:0.41, T:0.28
Consensus pattern (59 bp):
GGGCTTGGAAAAATACTAGGTGGGTTTGGAACTATTTGGGTGGATTTGGAGTTCCGGGC
Found at i:64436 original size:17 final size:17
Alignment explanation
Indices: 64411--64459 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
64401 AAATTATAAA
*
64411 AAAACCTCAAAATCCCT
1 AAAATCTCAAAATCCCT
64428 AAAATCTCAAAATCCCT
1 AAAATCTCAAAATCCCT
64445 AAAATCTCAAAATCC
1 AAAATCTCAAAATCC
64460 TAACACTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATCTCAAAATCCCT
Found at i:64439 original size:8 final size:8
Alignment explanation
Indices: 64411--64458 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
64401 AAATTATAAA
*
64411 AAAACCTC
1 AAAATCTC
*
64419 AAAATCCC
1 AAAATCTC
64427 TAAAATCTC
1 -AAAATCTC
*
64436 AAAATCCC
1 AAAATCTC
64444 TAAAATCTC
1 -AAAATCTC
64453 AAAATC
1 AAAATC
64459 CTAACACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAATCTC
Found at i:66887 original size:21 final size:20
Alignment explanation
Indices: 66820--66871 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
66810 AACTTCGACT
66820 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
66840 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
66860 ATCGCAATGCGA
1 ATCGCAATGCGA
66872 TAGTCCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:67440 original size:5 final size:5
Alignment explanation
Indices: 67430--67470 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
67420 GCCGTCCGTC
67430 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
67471 TCGTCGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:67459 original size:6 final size:6
Alignment explanation
Indices: 67433--67492 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
67423 GTCCGTCTCG
*
67433 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT CGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
67478 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
67493 AATACGTGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 15 0.29
6 37 0.71
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:67630 original size:21 final size:19
Alignment explanation
Indices: 67578--67632 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
67568 CGTTGCTATT
67578 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
67597 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
67620 TTGGACTATCGCA
1 TTGGACTATCGCA
67633 TTGCGATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 6 0.20
21 13 0.43
23 11 0.37
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:67638 original size:21 final size:19
Alignment explanation
Indices: 67578--67632 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 19
67568 CGTTGCTATT
*
67578 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAGCGAAC
*
67597 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGC-A-GCGAAC
67620 TTGGACTATCGCA
1 TTGGACTATCGCA
67633 TTGCGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 1 0.03
21 10 0.34
22 1 0.03
23 11 0.38
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAGCGAAC
Found at i:67668 original size:41 final size:41
Alignment explanation
Indices: 67623--67926 Score: 520
Period size: 41 Copynumber: 7.4 Consensus size: 41
67613 CGCGAACTTG
67623 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
*
67664 GACTATCGCATTGCGATTTACATATTCGGATTGCGATAGCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
*
67705 GACTATCGTATTGCGATTTACATATTCGCATTGCGATAGCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
*
67746 AACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
* *
67787 GACTATCGTATTGCGATTTACATATTCGCATTGCGATAGCG
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
*
67828 GACTATCGCATTGCGATTTACATATTCGTATTGCGATAGCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
67869 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAG-CC
* *
67911 AAGT-TCGCATTGCGAT
1 GACTATCGCATTGCGAT
67927 AGTCGAAGTT
Statistics
Matches: 248, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 244 0.98
42 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
Found at i:67929 original size:21 final size:20
Alignment explanation
Indices: 67628--67946 Score: 124
Period size: 21 Copynumber: 15.6 Consensus size: 20
67618 ACTTGGACTA
* *
67628 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCA-AT
*
67648 TCGCATTGCGATAG-CCGACT
1 TCGCATTGCGATAGTCC-AAT
* *
67668 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
* *
67689 TCGGATTGCGATAG-CCGACT
1 TCGCATTGCGATAGTCC-AAT
* * *
67709 ATCGTATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
67730 TCGCATTGCGATAG-CCAACT
1 TCGCATTGCGATAGTCCAA-T
* *
67750 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
*
67771 TCGCATTGCGATAG-CCGACT
1 TCGCATTGCGATAGTCC-AAT
* * *
67791 ATCGTATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
* *
67812 TCGCATTGCGATAG-CGGACT
1 TCGCATTGCGATAGTC-CAAT
* *
67832 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
* *
67853 TCGTATTGCGATAG-CCGACT
1 TCGCATTGCGATAGTCC-AAT
* *
67873 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
67894 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
*
67915 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAA-T
*
67936 TCGCGTTGCGA
1 TCGCATTGCGA
67947 ATCTGAAAAT
Statistics
Matches: 220, Mismatches: 47, Indels: 63
0.67 0.14 0.19
Matches are distributed among these distances:
19 1 0.00
20 98 0.45
21 120 0.55
22 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCCAAT
Found at i:68462 original size:43 final size:43
Alignment explanation
Indices: 68412--68721 Score: 267
Period size: 43 Copynumber: 7.2 Consensus size: 43
68402 TGAGAACAAA
* * *
68412 AAACGCCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATACCTA-TAGCGGCGTTTTTGGAAC
* *
68455 AAACGCCGCAAAAGGTCGATACCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAATACCTATAGCGGCGTTTTTGGAAC
* * * *
68498 AAACACTGCAAAAAGTTATGATA--TATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCA--ATACCTATAGCGGCGTTTTTGGA-AC
* * * *
68542 AAACGCCGCAAAAGAT-AAGACTTATA-CTGGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTCAATACCTATAGC-GGCGTTTTTGGAAC
* * * * *
68584 AAACGTCGTAAAAGGTC-AGACCTATAGTGGCGTTTTTGTACAC
1 AAACGCCGCAAAAGGTCAATACCTATAGCGGCGTTTTTGGA-AC
* * * *
68627 AAACGCCGCAAAATGTC-AGACCTATAACGGCGTTTTTGAACAC
1 AAACGCCGCAAAAGGTCAATACCTATAGCGGCGTTTTTGGA-AC
* * *
68670 AAACGCCGTAAAAAGTC-AGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATACCTATAGCGGCGTTTTTGGA-AC
68713 AAACGCCGC
1 AAACGCCGC
68722 TAATTACCTT
Statistics
Matches: 221, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.01
42 36 0.16
43 167 0.76
44 13 0.06
45 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATACCTATAGCGGCGTTTTTGGAAC
Found at i:68616 original size:85 final size:86
Alignment explanation
Indices: 68440--68721 Score: 297
Period size: 86 Copynumber: 3.3 Consensus size: 86
68430 ATATCTATTA
* * * * * * * *
68440 CGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTCGATACCTATAGCGGCGTTTTTGGA-ATAAACA
1 CGGCGTTTTTGGATACAAACGCCGCAAAATGT-AAGACCTATAACGGCGTTTTTGAACACAAACG
* * * **
68503 CTGCAAAAAGTTATGATATATAG
65 CCGTAAAAAGTCA-GACCTATAG
*
68526 CGGCGTTTTTGGATACAAACGCCGCAAAA-GATAAGACTTAT-ACTGGCGTTTTT-AGA-ACAAA
1 CGGCGTTTTTGGATACAAACGCCGCAAAATG-TAAGACCTATAAC-GGCGTTTTTGA-ACACAAA
* *
68587 CGTCGTAAAAGGTCAGACCTATAG
63 CGCCGTAAAAAGTCAGACCTATAG
* * * *
68611 TGGCGTTTTTGTACACAAACGCCGCAAAATGTCAGACCTATAACGGCGTTTTTGAACACAAACGC
1 CGGCGTTTTTGGATACAAACGCCGCAAAATGTAAGACCTATAACGGCGTTTTTGAACACAAACGC
68676 CGTAAAAAGTCAGACCTATAG
66 CGTAAAAAGTCAGACCTATAG
68697 CGGCGTTTTTGGATACAAACGCCGC
1 CGGCGTTTTTGGATACAAACGCCGC
68722 TAATTACCTT
Statistics
Matches: 163, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
85 52 0.32
86 95 0.58
87 16 0.10
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (86 bp):
CGGCGTTTTTGGATACAAACGCCGCAAAATGTAAGACCTATAACGGCGTTTTTGAACACAAACGC
CGTAAAAAGTCAGACCTATAG
Found at i:68662 original size:128 final size:129
Alignment explanation
Indices: 68440--68721 Score: 320
Period size: 128 Copynumber: 2.2 Consensus size: 129
68430 ATATCTATTA
* * * *
68440 CGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGATACCTATAGCGGCGTTTTTGGAATAAACACT
1 CGGCGTTTTTAGAACAAACGCCGCAAAAGGTCGAGACCTATAGCGGCGTTTTTGGAACAAACACC
* * * * * *
68505 GCAAAAAGTTATGATATATAGCGGCGTTTTTGGATACAAACGCCGC-AAAAGATAAGACTTATA-
66 GCAAAAAGTCATGACATATAACGGCGTTTTTGAACACAAACGCCGCAAAAAG-TAAGACCTATAG
* * * * *
68568 CTGGCGTTTTTAGAACAAACGTCGTAAAAGGTC-AGACCTATAGTGGCGTTTTTGTACACAAACG
1 C-GGCGTTTTTAGAACAAACGCCGCAAAAGGTCGAGACCTATAGCGGCGTTTTTGGA-ACAAACA
* * * *
68632 CCGCAAAATGTCA-GACCTATAACGGCGTTTTTGAACACAAACGCCGTAAAAAGTCAGACCTATA
64 CCGCAAAAAGTCATGACATATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTAAGACCTATA
68696 G
129 G
*
68697 CGGCGTTTTTGGATACAAACGCCGC
1 CGGCGTTTTTAGA-ACAAACGCCGC
68722 TAATTACCTT
Statistics
Matches: 127, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
128 69 0.54
129 58 0.46
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (129 bp):
CGGCGTTTTTAGAACAAACGCCGCAAAAGGTCGAGACCTATAGCGGCGTTTTTGGAACAAACACC
GCAAAAAGTCATGACATATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTAAGACCTATAG
Found at i:72384 original size:21 final size:20
Alignment explanation
Indices: 72346--72389 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
72336 AGCATAAAAA
*
72346 TGGTAGTGAAATATATGGGTT
1 TGGTAGTGAAATAGAT-GGTT
72367 TGGTAGTGAAGA-AGATGGTT
1 TGGTAGTGAA-ATAGATGGTT
72387 TGG
1 TGG
72390 GTAAACGGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.34
Consensus pattern (20 bp):
TGGTAGTGAAATAGATGGTT
Found at i:72593 original size:41 final size:41
Alignment explanation
Indices: 72491--72913 Score: 404
Period size: 41 Copynumber: 10.3 Consensus size: 41
72481 TTGTAAACAC
* * * * * *
72491 AAACGCCACTATAGTACAAGTGTATAGCAGCGTTTGAAT-A
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*
72531 AAACACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
72572 AAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
72613 AAATGCCACTAAATTACGAGTCTTTAGCGACGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * * * * * *
72655 CAAATGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
72697 AAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
72738 AAACGCCACTAAAGTATGAGTC-TTAGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * * ** *
72779 CAAACGCCACTATAGTAC-ATGTGTATAATGACGTTTGTATAA
1 -AAACGCCACTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAA
* * * *
72821 AAACGCCACTAAAGTACAATTCTATAGCGGCATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
72862 AAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT-AA
*
72903 AACCGCCACTA
1 AAACGCCACTA
72914 TCGATGAACC
Statistics
Matches: 315, Mismatches: 59, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
40 48 0.15
41 203 0.64
42 21 0.07
43 43 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:72697 original size:125 final size:125
Alignment explanation
Indices: 72491--72898 Score: 491
Period size: 124 Copynumber: 3.3 Consensus size: 125
72481 TTGTAAACAC
* * * * * * * * * *
72491 AAACGCCACTATAGTACAAGTGTATAGCAGCGTTTG--AATA-AAACACCACTAAAGTACGAGTC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTG
* * * *
72553 TTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
66 TATAACGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
72613 AAATGCCACTAAATTACGAGTCTTTAGCGACGTTTGTAAACACAAATGCCACTATAGTACAAGTG
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTG
* * *
72678 TATAACGGCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAA
66 TATAACGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
72738 AAACGCCACTAAAGTATGAGTC-TTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTG
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTG
* * * * * * *
72802 TATAATGACGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCATTTGTATAA
66 TATAACGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
72862 AAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT
72899 TGAAAACCGC
Statistics
Matches: 241, Mismatches: 41, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
122 28 0.12
124 111 0.46
125 102 0.42
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (125 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTG
TATAACGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:72766 original size:165 final size:167
Alignment explanation
Indices: 72481--72913 Score: 515
Period size: 165 Copynumber: 2.6 Consensus size: 167
72471 ACTTGCGGCG
*
72481 TTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCAGCGTTTGAATAAAACA-CCACTAAAG
1 TTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAA-AGCCACTAAAG
* * * *
72545 TACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTA
65 TACGCGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTA
* * * * *
72610 TA-A-AAATGCCACTAAATTACGA-GTCTTTAGCGACGT
130 AACACAAACGCCACTAAAGTAC-ATGTCTATAACGACGT
* *
72646 TTGTAAACACAAATGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTAAAG
1 TTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAA-GCCACTAAAG
* *
72711 TACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTC-TTAGCGGCGTTTGTA
65 TACGCGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTA
* * *
72775 AACACAAACGCCACTATAGTACATGTGTATAATGACGT
130 AACACAAACGCCACTAAAGTACATGTCTATAACGACGT
* * * * * *
72813 TTGTATA-A-AAACGCCACTAAAGTACAATTCTATAGCGGCATTTGTATAAAAACGCCACTAAAG
1 TTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAA-GCCACTAAAG
* * *
72876 TACTAC-TCTTTTGCGGCGTTTGT-TGAAAACCGCCACTA
65 TAC-GCGTCTTTAGCGGCGTTTGTAT-AAAAACGCCACTA
72914 TCGATGAACC
Statistics
Matches: 231, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
164 2 0.01
165 143 0.62
166 56 0.24
167 30 0.13
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (167 bp):
TTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAAGCCACTAAAGT
ACGCGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAA
ACACAAACGCCACTAAAGTACATGTCTATAACGACGT
Found at i:74412 original size:37 final size:36
Alignment explanation
Indices: 74353--74472 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
74343 ATCCTATTAT
* *
74353 CATTTTTC-AACAAACATATACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
74389 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
74425 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
74460 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
74473 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:74428 original size:21 final size:21
Alignment explanation
Indices: 74404--74464 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
74394 TTCAAAGAAA
74404 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
74425 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
74439 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
74460 CATTT
1 CATTT
74465 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:74481 original size:35 final size:36
Alignment explanation
Indices: 74355--74499 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
74345 CCTATTATCA
*
74355 TTTTTCAACA-AACA-TATACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
74390 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
74427 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
74463 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
74497 TTT
1 TTT
74500 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:79021 original size:21 final size:21
Alignment explanation
Indices: 78996--79056 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
78986 TTCAATGAAA
78996 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
79017 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
79031 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
79052 CATTT
1 CATTT
79057 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:79023 original size:35 final size:35
Alignment explanation
Indices: 78957--79057 Score: 166
Period size: 35 Copynumber: 2.9 Consensus size: 35
78947 ATTTTTTAAC
* * *
78957 AAACATCTACCAAACTTTGAAAAACTATTTTCAATG
1 AAACATTTACCAAACTTTG-AAAACCATTTTCAAAG
78993 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
79028 AAACATTTACCAAACTTTGAAAACCATTTT
1 AAACATTTACCAAACTTTGAAAACCATTTT
79058 TTCAAAGTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 44 0.71
36 18 0.29
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.31
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:79073 original size:35 final size:36
Alignment explanation
Indices: 78964--79091 Score: 131
Period size: 35 Copynumber: 3.6 Consensus size: 36
78954 AACAAACATC
* * * *
78964 TACCAAACTTTGAAAAAC-TATTTTCAATGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
*
79000 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
***
79035 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
79070 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
79092 AATAATTTCA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
34 14 0.17
35 43 0.52
36 17 0.20
37 9 0.11
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
Done.