Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000890.1 Hibiscus syriacus cultivar Beakdansim tig00001740_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: 72972
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:3396 original size:21 final size:22
Alignment explanation
Indices: 3372--3412 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3362 ACATATAATG
*
3372 TAAAAT-AAAATATTTACAACA
1 TAAAATAAAAACATTTACAACA
3393 TAAAATAAAAACATTTACAA
1 TAAAATAAAAACATTTACAA
3413 TATGTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAAAAACATTTACAACA
Found at i:3541 original size:30 final size:29
Alignment explanation
Indices: 3500--3720 Score: 195
Period size: 30 Copynumber: 7.5 Consensus size: 29
3490 TTGAACTTAC
* *
3500 AAGGACCAAAATAGCAAAAATGAAAACTTA
1 AAGGACTAAAATAGCAAAAAT-AAAATTTA
*
3530 AAGGACTAAAATGGCACAAACAT-AAATTTAA
1 AAGGACTAAAATAGCA-AAA-ATAAAATTT-A
*
3561 AAGG-CTAAAATAGCAAAACA-GAAATTTA
1 AAGGACTAAAATAGCAAAA-ATAAAATTTA
* *
3589 AAAGACCAAAATAGCACAAACA-AAAATTTA
1 AAGGACTAAAATAGCA-AAA-ATAAAATTTA
* *
3619 AAGGACTAAAATAGAAAAAATAGAGATTTA
1 AAGGACTAAAATAGCAAAAATA-AAATTTA
* *
3649 AGGGACT-AAATAG-AAACAATAGACATTTA
1 AAGGACTAAAATAGCAAA-AATA-AAATTTA
*
3678 AAGGACTAAAATAGCAAAACAT-AAACTTA
1 AAGGACTAAAATAGCAAAA-ATAAAATTTA
3707 AAGGACTAAAATAG
1 AAGGACTAAAATAG
3721 TATTAACAGA
Statistics
Matches: 163, Mismatches: 16, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
28 8 0.05
29 67 0.41
30 73 0.45
31 13 0.08
32 2 0.01
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (29 bp):
AAGGACTAAAATAGCAAAAATAAAATTTA
Found at i:3737 original size:29 final size:29
Alignment explanation
Indices: 3493--3752 Score: 168
Period size: 30 Copynumber: 8.8 Consensus size: 29
3483 TAAATATTTG
* *
3493 AACTTACAAGGACCAAAATAGCAAAA-ATGAA
1 AACTTA-AAGGACTAAAATAGTAAAACA-G-A
* * *
3524 AACTTAAAGGACTAAAATGGCACAAACATA
1 AACTTAAAGGACTAAAATAGTA-AAACAGA
* *
3554 AATTTAAAAGG-CTAAAATAGCAAAACAGA
1 AACTT-AAAGGACTAAAATAGTAAAACAGA
* * * * *
3583 AATTTAAAAGACCAAAATAGCACAAACAAA
1 AACTTAAAGGACTAAAATAGTA-AAACAGA
* * *
3613 AATTTAAAGGACTAAAATAGAAAAAATAGA
1 AACTTAAAGGACTAAAATAG-TAAAACAGA
* * * * *
3643 GATTTAAGGGACT-AAATAGAAACAATAGA
1 AACTTAAAGGACTAAAATAGTAA-AACAGA
* * * *
3672 CATTTAAAGGACTAAAATAGCAAAACATA
1 AACTTAAAGGACTAAAATAGTAAAACAGA
*
3701 AACTTAAAGGACTAAAATAGTATTAACAGA
1 AACTTAAAGGACTAAAATAGTA-AAACAGA
* *
3731 AACTAAAAGGGCT-AAATAGTAA
1 AACTTAAAGGACTAAAATAGTAA
3753 TTACAAAATA
Statistics
Matches: 191, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.04
29 75 0.39
30 93 0.49
31 15 0.08
32 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (29 bp):
AACTTAAAGGACTAAAATAGTAAAACAGA
Found at i:3740 original size:59 final size:59
Alignment explanation
Indices: 3500--3746 Score: 216
Period size: 59 Copynumber: 4.2 Consensus size: 59
3490 TTGAACTTAC
* * *
3500 AAGGACCAAAATAGCAAAA-ATGAAAACTTAAAGGACTAAAATGGCACAAACATAAATTTAA
1 AAGGACTAAAATAGCAAAACAT--AAACTTAAAGGACTAAAATAGCACAAACAGAAA-TTAA
* * * * * *
3561 AAGG-CTAAAATAGCAAAACAGAAATTTAAAAGACCAAAATAGCACAAACAAAAATTTA
1 AAGGACTAAAATAGCAAAACATAAACTTAAAGGACTAAAATAGCACAAACAGAAATTAA
* * * * * * *
3619 AAGGACTAAAATAG-AAAAAATAGAGATTTAAGGGACT-AAATAG-AAACAATAGACATTTA
1 AAGGACTAAAATAGCAAAACATA-A-ACTTAAAGGACTAAAATAGCACA-AACAGAAATTAA
* ** *
3678 AAGGACTAAAATAGCAAAACATAAACTTAAAGGACTAAAATAGTATTAACAGAAACTAA
1 AAGGACTAAAATAGCAAAACATAAACTTAAAGGACTAAAATAGCACAAACAGAAATTAA
*
3737 AAGGGCTAAA
1 AAGGACTAAA
3747 TAGTAATTAC
Statistics
Matches: 151, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
58 25 0.17
59 91 0.60
60 30 0.20
61 5 0.03
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.17
Consensus pattern (59 bp):
AAGGACTAAAATAGCAAAACATAAACTTAAAGGACTAAAATAGCACAAACAGAAATTAA
Found at i:4785 original size:32 final size:32
Alignment explanation
Indices: 4748--4903 Score: 215
Period size: 32 Copynumber: 4.9 Consensus size: 32
4738 GAAGGACCTA
* * *
4748 TCCATATGTTCCAAAGAACATAGGTAACATTG
1 TCCATATGTCCCAAAGGACATAGGTAACACTG
*
4780 TCCATATGTCCCGAAGGACATAGGTAACACTG
1 TCCATATGTCCCAAAGGACATAGGTAACACTG
*
4812 TCTATATGTCCCAAAGGACATAGGTAACACTG
1 TCCATATGTCCCAAAGGACATAGGTAACACTG
* *
4844 TCTATATGTCCCGAAA-AACATAGGTAACACTG
1 TCCATATGTCCC-AAAGGACATAGGTAACACTG
* *
4876 TCCATATGTCCCGAAGGACATATGTAAC
1 TCCATATGTCCCAAAGGACATAGGTAAC
4904 CCTCGACTCT
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 2 0.02
32 106 0.95
33 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (32 bp):
TCCATATGTCCCAAAGGACATAGGTAACACTG
Found at i:8646 original size:21 final size:21
Alignment explanation
Indices: 8620--8660 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8610 GTTGCTTAGA
* *
8620 ATCTATTAGTATCGGTACTAT
1 ATCTATAAGTATCGATACTAT
8641 ATCTATAAGTATCGATACTA
1 ATCTATAAGTATCGATACTA
8661 CCTGCATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (21 bp):
ATCTATAAGTATCGATACTAT
Found at i:11702 original size:36 final size:36
Alignment explanation
Indices: 11651--11723 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
11641 TACATACTTC
*
11651 ATAACATTAGGAGTTGAGGATTGAGGATCATTTGAG
1 ATAACATTAGAAGTTGAGGATTGAGGATCATTTGAG
* *
11687 ATAACATTAGAAGTTGAGGTTTGAGGGTCATTTGAG
1 ATAACATTAGAAGTTGAGGATTGAGGATCATTTGAG
11723 A
1 A
11724 CAATTTCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (36 bp):
ATAACATTAGAAGTTGAGGATTGAGGATCATTTGAG
Found at i:21461 original size:123 final size:123
Alignment explanation
Indices: 21242--21492 Score: 493
Period size: 123 Copynumber: 2.0 Consensus size: 123
21232 TGAGTTGTTG
21242 GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
1 GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
21307 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTTA
66 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTTA
*
21365 GAAGCTTTGAATTGTGAGTCACTCTCGTATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
1 GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
21430 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTTA
66 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTTA
21488 GAAGC
1 GAAGC
21493 ATCTACTTGT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 127 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (123 bp):
GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTTA
Found at i:21732 original size:60 final size:60
Alignment explanation
Indices: 21632--21768 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
21622 ATTTAAGGGT
* * *
21632 AAAG-TACACAAATGGTCCCTTGACTATAGGTTCATACTTTGTTGAGTCCCCCGACTATTA
1 AAAGTTACA-AAATAGTCCCTTGACTATAGGGTCATACTTTGTTGAGTCCCCCAACTATTA
* ** * * *
21692 AAAGTTACAAAATAGTCCTTTGACTATAGGGTGTTGCTTTGTTGAGTCTCTCAACTATTA
1 AAAGTTACAAAATAGTCCCTTGACTATAGGGTCATACTTTGTTGAGTCCCCCAACTATTA
* *
21752 AAAATTATAAAATAGTC
1 AAAGTTACAAAATAGTC
21769 ACCCGACTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 61 0.94
61 4 0.06
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (60 bp):
AAAGTTACAAAATAGTCCCTTGACTATAGGGTCATACTTTGTTGAGTCCCCCAACTATTA
Found at i:28255 original size:9 final size:9
Alignment explanation
Indices: 28243--28277 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
28233 AAGAAATGAA
28243 AAAGAAAAG
1 AAAGAAAAG
28252 AAAGAAAAG
1 AAAGAAAAG
*
28261 AAAGAAAAT
1 AAAGAAAAG
28270 AAAGAAAA
1 AAAGAAAA
28278 CTATTGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:31890 original size:2 final size:2
Alignment explanation
Indices: 31883--31918 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31873 ACTTAATGTA
31883 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
31919 CTAAAGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35944 original size:3 final size:3
Alignment explanation
Indices: 35938--35970 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
35928 TATGTAACAT
*
35938 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
35971 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:35953 original size:6 final size:6
Alignment explanation
Indices: 35925--35984 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
35915 GTAAAAAAAA
* * * * *
35925 TAATAT GTAACAT TAATAA TAATAT TAATAA TAATAA TAATA- TAATTT
1 TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
35973 TAATA- TAATAT T
1 TAATAT TAATAT T
35985 TATAATCCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAATAT
Found at i:36356 original size:55 final size:54
Alignment explanation
Indices: 36274--36467 Score: 268
Period size: 55 Copynumber: 3.6 Consensus size: 54
36264 CCCTCTTTTT
* *
36274 TTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAACACTCGTGTCTGTTCCCTATTCC
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACA-TCGTGTCTGTTCCCTATTCC
*
36328 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCT-TCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-ATCGTGTCTGT-TCCCTATTCC
* * *
36383 TTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCATGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-ATCGTGTCTGTTCCCTATTCC
36438 TTCAGAGAGTATAAGACTCGAACAATCTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTC
36468 TTCTTATGGG
Statistics
Matches: 126, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
54 18 0.14
55 107 0.85
56 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (54 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACATCGTGTCTGTTCCCTATTCC
Found at i:36485 original size:55 final size:55
Alignment explanation
Indices: 36318--36632 Score: 233
Period size: 55 Copynumber: 5.8 Consensus size: 55
36308 TCGTGTCTGT
* ** * *
36318 TCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAC-AAT-CGTGTCTTC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGT-TC-GC
* **
36373 TCCCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCAT--G-TCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTA--ATGGGTTC-GC
*
36428 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTTATGGGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
* * * * * *
36483 TCCCTCTTTCTTCAGAGAGTAT-AGAACTTGAA-TATCTTCTTCAAACGGGTT-GC
1 TCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCTTCTAATGGGTTCGC
* * * * * * *
36536 TCCCTCTTTC-TCTAGGGAGTATAAAACTCGGAC-ATCTTCTTCAAACGGGTTCGC
1 TCCCTATTCCTTC-AGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
* * *
36590 TCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGAAC-ATCTTCTTCT
1 TCCCTATTCCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCTTCT
36633 GCTTCACTAC
Statistics
Matches: 227, Mismatches: 21, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
52 2 0.01
53 46 0.20
54 58 0.26
55 115 0.51
56 3 0.01
57 1 0.00
58 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
Found at i:36486 original size:110 final size:109
Alignment explanation
Indices: 36251--36628 Score: 306
Period size: 110 Copynumber: 3.5 Consensus size: 109
36241 AGTATTTTGC
* * * *
36251 CAATGGGTTCGTTCCCTCTTTTTTTCAGGGAGTAT-AGAACTCAAACATCTTCAACACTCGTGTC
1 CAATGGGTTCGCTCCCTCTTTCTTT-AGAGAGTATAAGAACTCAAACATCTTCAACACTCATGTC
* *
36315 TGTTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAA
65 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * * * *
36360 CAAT-CGTGTCTTCTCCCTATTCCTTTAGAGAGTATAAG-ACTCGAACAATCTTCAACTA-TCAT
1 CAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAAC-ATCTTCAAC-ACTCAT
**
36422 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTT
62 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * ** * ** ** **
36470 CTTATGGGTTCGCTCCCTCTTTCTTCAGAGAGTAT-AGAACTTGAATATCTTCTTCAAACGGGT-
1 C-AATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAACATCTTCAACACTCATGTC
* * * * * **
36533 TGCTCCCTCTTTC-TCTAGGGAGTATAAAACTCGGAC-ATCTTCTT
65 TGCTCCCTATTCCTTC-AGAGAGTATAAGACTCGAACAATCTTCAA
* * * *
36577 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT-AGAACTCGAACATCTTC
1 C-AATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAACATCTTC
36629 TTCTGCTTCA
Statistics
Matches: 220, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
107 54 0.25
108 31 0.14
109 33 0.15
110 95 0.43
111 5 0.02
112 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (109 bp):
CAATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAACATCTTCAACACTCATGTCT
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
Found at i:36556 original size:53 final size:54
Alignment explanation
Indices: 36444--36631 Score: 256
Period size: 54 Copynumber: 3.5 Consensus size: 54
36434 TTCCTTCAGA
** * *
36444 GAGTATA-AGACTCGAACAATCTTCTTCTTATGGGTTCGCTCCCTCTTTCT-TCAGA
1 GAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* *
36499 GAGTATAGAACTTGAATATCTTCTTCAAACGGGTT-GCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
36552 GAGTATAAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
36606 GAGTATAGAACTCGAACATCTTCTTC
1 GAGTATAGAACTCGAACATCTTCTTC
36632 TGCTTCACTA
Statistics
Matches: 118, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
53 46 0.39
54 58 0.49
55 13 0.11
56 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (54 bp):
GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:50697 original size:3 final size:3
Alignment explanation
Indices: 50691--50723 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
50681 TATGTAACAT
*
50691 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
50724 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:50706 original size:6 final size:6
Alignment explanation
Indices: 50678--50737 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
50668 GTAAAAAAAA
* * * * *
50678 TAATAT GTAACAT TAATAA TAATAT TAATAA TAATAA TAATA- TAATTT
1 TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
50726 TAATA- TAATAT T
1 TAATAT TAATAT T
50738 TATAATCCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAATAT
Found at i:53286 original size:3 final size:3
Alignment explanation
Indices: 53278--53309 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53268 GAAGCTCGTA
53278 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
53310 AGAGACCCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:61522 original size:35 final size:35
Alignment explanation
Indices: 61482--61644 Score: 161
Period size: 35 Copynumber: 4.6 Consensus size: 35
61472 AGGAACATCT
61482 AAGAGACACAATGCTTCATCAAAAGGT-TCATTTCC
1 AAGAGACACAATGCTTCATCAAAAGGTATC-TTTCC
* * * *
61517 AAGAGACACAATGTTTCATC-AAAGGATGTCTGTCT
1 AAGAGACACAATGCTTCATCAAAAGG-TATCTTTCC
* * * *
61552 AAGAGACATAATGCTTC-TTAAAAGGGTATTTTTTCT
1 AAGAGACACAATGCTTCATCAAAA-GGTA-TCTTTCC
* **
61588 AAGAGACATAATGCTTCATCAAAAGGTGCCTTTCC
1 AAGAGACACAATGCTTCATCAAAAGGTATCTTTCC
*
61623 AAGAGACACAATGATTCATCAA
1 AAGAGACACAATGCTTCATCAA
61645 GAAACATGAT
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
34 6 0.06
35 66 0.62
36 29 0.27
37 5 0.05
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (35 bp):
AAGAGACACAATGCTTCATCAAAAGGTATCTTTCC
Found at i:61627 original size:71 final size:70
Alignment explanation
Indices: 61482--61644 Score: 186
Period size: 71 Copynumber: 2.3 Consensus size: 70
61472 AGGAACATCT
* *
61482 AAGAGACACAATGCTTCATCAAAAGGTTCATTTCCAAGAGACACAATGTTTCATCAAAGGATGTC
1 AAGAGACACAATGCTTCATCAAAAGGTTCATTTCCAAGAGACACAATGCTTCATCAAAGGATGCC
*
61547 TGTCT
66 TGTCC
* * ** * *
61552 AAGAGACATAATGCTTC-TTAAAAGGGTATTTTTTCTAAGAGACATAATGCTTCATCAAAAGG-T
1 AAGAGACACAATGCTTCATCAAAA-GGT-TCATTTCCAAGAGACACAATGCTTCATC-AAAGGAT
*
61615 GCCTTTCC
63 GCCTGTCC
*
61623 AAGAGACACAATGATTCATCAA
1 AAGAGACACAATGCTTCATCAA
61645 GAAACATGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
69 5 0.07
70 19 0.25
71 44 0.58
72 8 0.11
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (70 bp):
AAGAGACACAATGCTTCATCAAAAGGTTCATTTCCAAGAGACACAATGCTTCATCAAAGGATGCC
TGTCC
Found at i:61694 original size:33 final size:34
Alignment explanation
Indices: 61648--61713 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
61638 TCATCAAGAA
*
61648 ACATGATGCTTCAT-CAAAAGGTGCCTCCAAAAG
1 ACATGATGATTCATCCAAAAGGTGCCTCCAAAAG
* * *
61681 ACATGTTGATTCATCCAAAATGTTCCTCCAAAA
1 ACATGATGATTCATCCAAAAGGTGCCTCCAAAA
61714 TGTTAGAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (34 bp):
ACATGATGATTCATCCAAAAGGTGCCTCCAAAAG
Found at i:68246 original size:61 final size:61
Alignment explanation
Indices: 68148--68306 Score: 183
Period size: 61 Copynumber: 2.6 Consensus size: 61
68138 CCGTAGTGCT
* * * * * * *
68148 ATGACAAATAAGGTTGTGCTCACCAGCTACTCTAAGTTGACACTCTAGTGCTAATCTAGAA
1 ATGACACATAAGGTCGTGCACACCACCTGCTCTAAGTTGACACTCTAGTACTAATCCAGAA
* * * *
68209 ATGACACATAATGTCGTGCACACCACCTGCTCTAAGTTTACACTCTAGTACTGATCCAGAT
1 ATGACACATAAGGTCGTGCACACCACCTGCTCTAAGTTGACACTCTAGTACTAATCCAGAA
* * * *
68270 ATGACACATAAGGTCATGCCCACCTCCTGCACTAAGT
1 ATGACACATAAGGTCGTGCACACCACCTGCTCTAAGT
68307 GTCCTTACAC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 82 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (61 bp):
ATGACACATAAGGTCGTGCACACCACCTGCTCTAAGTTGACACTCTAGTACTAATCCAGAA
Done.