Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003710.1 Hibiscus syriacus cultivar Beakdansim tig00007936_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: 69710
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:15761 original size:32 final size:32
Alignment explanation
Indices: 15725--15787 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
15715 ATGTTATGTT
* *
15725 ATCACTTTGGGTGACATAACATATGTCACATC
1 ATCACTTTAGGTGACATAACACATGTCACATC
* *
15757 ATCACTTTAGGTGATATGACACATGTCACAT
1 ATCACTTTAGGTGACATAACACATGTCACAT
15788 AATTTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (32 bp):
ATCACTTTAGGTGACATAACACATGTCACATC
Found at i:16835 original size:20 final size:20
Alignment explanation
Indices: 16515--16859 Score: 166
Period size: 20 Copynumber: 17.0 Consensus size: 20
16505 TAATAACCAA
16515 CGAATTCGCAACTC-AATTT
1 CGAATTCGCAACTCGAATTT
* ***
16534 CGAATTCGCAACACGAAAAC
1 CGAATTCGCAACTCGAATTT
* * * *
16554 CAAATTCCCAACAC-AGTTTT
1 CGAATTCGCAACTCGA-ATTT
* ***
16574 CGAATTTGCAACAAAAATTT
1 CGAATTCGCAACTCGAATTT
* *
16594 AC-ATTTCGCAACACGAATTT
1 -CGAATTCGCAACTCGAATTT
* * *
16614 ACCAAATTTGCAACTC-AGTTTT
1 --CGAATTCGCAACTCGA-ATTT
** *
16636 TAAATTCACAACTCGAA-TT
1 CGAATTCGCAACTCGAATTT
* *
16655 CGGATTTCACAACTCGAA-TT
1 C-GAATTCGCAACTCGAATTT
*
16675 CGCCAATTTTGCAACTC-AATTTT
1 CG--AA-TTCGCAACTCGAA-TTT
* *
16698 CGAATTCGTAACTTGAATATT
1 CGAATTCGCAACTCGAAT-TT
* * **
16719 -GATTTCGCAACTTGAAAAT
1 CGAATTCGCAACTCGAATTT
*
16738 CGAATTCGCAACTCGAAATT
1 CGAATTCGCAACTCGAATTT
* * **
16758 CAAATTCTCAACTCGAAACT
1 CGAATTCGCAACTCGAATTT
* **
16778 CAAATTCGCAACTCGAAAAT
1 CGAATTCGCAACTCGAATTT
*
16798 CGAATTTGCAACTCGAATTT
1 CGAATTCGCAACTCGAATTT
16818 CGAATTCGCAACTCGAATTT
1 CGAATTCGCAACTCGAATTT
*
16838 AGCGAATTCGCGACTCGAATTT
1 --CGAATTCGCAACTCGAATTT
16860 GGCAAATTTG
Statistics
Matches: 252, Mismatches: 55, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
19 18 0.07
20 177 0.70
21 14 0.06
22 39 0.15
23 4 0.02
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (20 bp):
CGAATTCGCAACTCGAATTT
Found at i:16878 original size:22 final size:20
Alignment explanation
Indices: 16853--16903 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
16843 ATTCGCGACT
*
16853 CGAATTTGGCAAATTTGTGTTG
1 CGAATTTGG-AAA-CTGTGTTG
*
16875 CGAATTCGGAAACTGTGTTG
1 CGAATTTGGAAACTGTGTTG
*
16895 CGAAATTGG
1 CGAATTTGG
16904 TTTTCGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 14 0.56
21 3 0.12
22 8 0.32
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (20 bp):
CGAATTTGGAAACTGTGTTG
Found at i:18479 original size:28 final size:29
Alignment explanation
Indices: 18437--18496 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
18427 ATTTCAATCA
*
18437 TTTTAAAATTCAAGTTTAAA-AATTGTCT
1 TTTTAAAATTCAAGTTTAAACAATTATCT
* *
18465 TTTTAGAATTTAAGTTTAAACAATTATCT
1 TTTTAAAATTCAAGTTTAAACAATTATCT
18494 TTT
1 TTT
18497 ATTTTTCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (29 bp):
TTTTAAAATTCAAGTTTAAACAATTATCT
Found at i:20574 original size:17 final size:16
Alignment explanation
Indices: 20552--20585 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20542 AGTTAGTCAC
20552 AAGAATTCTTACTCTAT
1 AAGAATTCTTACT-TAT
*
20569 AAGAATTTTTACTTAT
1 AAGAATTCTTACTTAT
20585 A
1 A
20586 GGTATAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
AAGAATTCTTACTTAT
Found at i:21383 original size:31 final size:31
Alignment explanation
Indices: 21347--21405 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
21337 AACTTAAAAG
*
21347 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
21378 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
21406 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:21461 original size:22 final size:22
Alignment explanation
Indices: 21428--21894 Score: 491
Period size: 22 Copynumber: 21.6 Consensus size: 22
21418 AATAATAATT
21428 TTTTAAAAATAAATCAATTCATA
1 TTTT-AAAATAAATCAATTCATA
* *
21451 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
21473 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
21495 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
*
21517 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
21539 TTTT--AATAAAT--ATT-TTA
1 TTTTAAAATAAATCAATTCATA
*** *
21556 AAATAAAAT--TT---TTCATA
1 TTTTAAAATAAATCAATTCATA
*
21573 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
21595 TTTTAAAAAAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
21617 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
21639 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
21661 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* ***
21683 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
21705 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
21727 TTTTTAAAATAAATCAA-TCTATA
1 -TTTTAAAATAAATCAATTC-ATA
**
21750 TTTTAAAATAAAT-TTTTCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
21772 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
21794 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
**
21816 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
21838 GTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
21860 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
21882 TTTTAAAATAAAT
1 TTTTAAAATAAAT
21895 TTTAAAATAT
Statistics
Matches: 383, Mismatches: 44, Indels: 35
0.83 0.10 0.08
Matches are distributed among these distances:
16 2 0.01
17 12 0.03
18 2 0.01
19 4 0.01
20 7 0.02
21 3 0.01
22 327 0.85
23 26 0.07
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:21495 original size:44 final size:44
Alignment explanation
Indices: 21428--21894 Score: 587
Period size: 44 Copynumber: 10.8 Consensus size: 44
21418 AATAATAATT
* *
21428 TTTTAAAAATAAATCAATTCATATTTTAAAATAAATTAATCCATA
1 TTTT-AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
*
21473 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
21517 TTTTAAAATAAATCAATCCATA-TTT----T-AAT-AA---ATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
** *
21551 TTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCCATA
* *
21595 TTTTAAAAAAAATCAATTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
21639 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
* *** *
21683 TTTTAAAATAATTTTTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
* *** *
21727 TTTTTAAAATAAATCAATCTATATTTTAAAATAAATTTTTCTATA
1 -TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
***
21772 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
*** * *
21816 TTTTAAAATAAATTTTTCCATAGTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
*
21860 TTTTAAAATAAATCAATCTATATTTTAAAATAAAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAAT
21895 TTTAAAATAT
Statistics
Matches: 368, Mismatches: 41, Indels: 27
0.84 0.09 0.06
Matches are distributed among these distances:
34 17 0.05
35 7 0.02
37 2 0.01
38 3 0.01
39 2 0.01
40 3 0.01
41 2 0.01
43 7 0.02
44 287 0.78
45 38 0.10
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
Found at i:21511 original size:66 final size:65
Alignment explanation
Indices: 21445--21897 Score: 620
Period size: 66 Copynumber: 7.0 Consensus size: 65
21435 AATAAATCAA
* **
21445 TTCATATTTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCA
1 TTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTT
*
21510 ATCAATATTTTAAAATAAATCAATCCATA-TTT----T-AAT-AA---ATATTTTAAAATAAAAT
1 TTC-ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAAT
21565 TT
64 TT
* * *
21567 TTCATATTTTAAAATAAATCAATCCATATTTTAAAAAAAATCAATTCATATTTTAAAATAAATCA
1 TTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-T
*
21632 A
65 T
* *
21633 TCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTT
1 TTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAA-ATT
21698 T
65 T
*
21699 TTCATATTTTAAAATAAATCAATCCATATTTTTAAAATAAATCAATCTATATTTTAAAATAAATT
1 TTCATATTTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATATTTTAAAATAAATT
21764 T
65 T
***
21765 TTCTATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATT
1 TTC-ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATT
21830 T
65 T
* * *
21831 TTCCATAGTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATATTTTAAAATAAATT
1 TT-CATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATT
21896 T
65 T
21897 T
1 T
21898 AAAATATATT
Statistics
Matches: 344, Mismatches: 27, Indels: 33
0.85 0.07 0.08
Matches are distributed among these distances:
56 37 0.11
57 9 0.03
59 2 0.01
60 3 0.01
61 1 0.00
62 3 0.01
63 2 0.01
65 9 0.03
66 219 0.64
67 59 0.17
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (65 bp):
TTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTT
Found at i:21911 original size:11 final size:12
Alignment explanation
Indices: 21878--21908 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21868 TAAATCAATC
21878 TATATTTTAAAA
1 TATATTTTAAAA
*
21890 TAAATTTTAAAA
1 TATATTTTAAAA
21902 TATATTT
1 TATATTT
21909 AAATGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATTTTAAAA
Found at i:21912 original size:22 final size:23
Alignment explanation
Indices: 21856--21920 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 23
21846 TAAATCAATC
* * **
21856 TATATTTTAAAATAA-ATCAATC
1 TATATTTTAAAATAATTTTAAAA
21878 TATATTTTAAAATAAATTTTAAAA
1 TATATTTTAAAAT-AATTTTAAAA
*
21902 TATA-TTT-AAATGATTTTAA
1 TATATTTTAAAATAATTTTAA
21921 TTTTCCCGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.19
22 17 0.47
23 5 0.14
24 7 0.19
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (23 bp):
TATATTTTAAAATAATTTTAAAA
Found at i:22555 original size:13 final size:13
Alignment explanation
Indices: 22534--22593 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
22524 ATTTTGTTAG
22534 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
22547 TATTGTA-TTATT
1 TATTTTATTTAAT
22559 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
22571 TATTTTATTTAAT
1 TATTTTATTTAAT
22584 TATTTTATTT
1 TATTTTATTT
22594 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:22559 original size:21 final size:20
Alignment explanation
Indices: 22534--22598 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
22524 ATTTTGTTAG
22534 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
22555 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
22571 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
22592 TTTTTTA
1 TATTTTA
22599 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:22569 original size:29 final size:29
Alignment explanation
Indices: 22536--22598 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
22526 TTTGTTAGTA
22536 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
22565 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
22594 TTTTA
1 TTTTA
22599 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:22580 original size:16 final size:16
Alignment explanation
Indices: 22538--22580 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
22528 TGTTAGTATT
* *
22538 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
22554 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
22570 TTATTTTATTT
1 TTATTTAATTT
22581 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:22882 original size:12 final size:12
Alignment explanation
Indices: 22849--22887 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
22839 TAACTGTAAA
22849 AAAATAAAATAATT
1 AAAA-AAAATAA-T
*
22863 AAATAAAATAAT
1 AAAAAAAATAAT
22875 AAAAAAAATAAT
1 AAAAAAAATAAT
22887 A
1 A
22888 CAATAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.57
13 7 0.30
14 3 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAAAATAAT
Found at i:22898 original size:33 final size:32
Alignment explanation
Indices: 22846--22914 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
22836 TTATAACTGT
22846 AAAAAAATAAAATAATTAAATAAAATAATAAA
1 AAAAAAATAAAATAATTAAATAAAATAATAAA
* * *
22878 AAAAATAATACAATAATTAAATAAAATACTAAC
1 AAAAA-AATAAAATAATTAAATAAAATAATAAA
22911 AAAA
1 AAAA
22915 TATGATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (32 bp):
AAAAAAATAAAATAATTAAATAAAATAATAAA
Found at i:22905 original size:13 final size:12
Alignment explanation
Indices: 22850--22893 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
22840 AACTGTAAAA
22850 AAATAAAATAATT
1 AAATAAAATAA-T
22863 AAATAAAATAAT
1 AAATAAAATAAT
*
22875 AAAAAAAATAAT
1 AAATAAAATAAT
22887 ACAATAA
1 A-AATAA
22894 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 13 0.46
13 15 0.54
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:43027 original size:2 final size:2
Alignment explanation
Indices: 43020--43050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43010 AGAAACAAAA
43020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43051 AAAGGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50085 original size:16 final size:16
Alignment explanation
Indices: 50064--50094 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50054 TATAAAATTT
*
50064 TTAAATATTCAAAAAA
1 TTAAATATACAAAAAA
50080 TTAAATATACAAAAA
1 TTAAATATACAAAAA
50095 CTAAAACTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAATATACAAAAAA
Found at i:58454 original size:21 final size:21
Alignment explanation
Indices: 58401--58454 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
58391 TCCATTTCAT
* *
58401 CTTCATCATTTAAACAATCTA
1 CTTCATCATCTCAACAATCTA
58422 CTTCATCATCTCAACAATCTA
1 CTTCATCATCTCAACAATCTA
*
58443 CTTCATTATCTC
1 CTTCATCATCTC
58455 CACGACTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (21 bp):
CTTCATCATCTCAACAATCTA
Found at i:58520 original size:76 final size:78
Alignment explanation
Indices: 58425--58632 Score: 244
Period size: 78 Copynumber: 2.7 Consensus size: 78
58415 CAATCTACTT
* * *
58425 CATCATCT-CAACAATCTACTTCATTATCTCCACGACTTCCATCTCCATCTCTACATG-TCC-AC
1 CATCA-CTACAACAATCTACTTCATCATCTCCAAGACTTCCATCTCCATCTCTACATGCACCTAC
58487 CTCCACTCAATCTA
65 CTCCACTCAATCTA
* * * * * *
58501 CATTACTACAATAATCTACTTCATCATCTCCAAGACTTCCATCTCTATATCAATATGCACCTACC
1 CATCACTACAACAATCTACTTCATCATCTCCAAGACTTCCATCTCCATCTCTACATGCACCTACC
* *
58566 TCCACTTAATCTC
66 TCCACTCAATCTA
* * *
58579 CGTCACTACAACAATCTACTTCATCATCTCTATA-ACTTTCATCTCCATCTCTAC
1 CATCACTACAACAATCTACTTCATCATCTCCA-AGACTTCCATCTCCATCTCTAC
58633 CTACATCCAT
Statistics
Matches: 108, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
75 2 0.02
76 46 0.43
77 2 0.02
78 57 0.53
79 1 0.01
ACGTcount: A:0.28, C:0.36, G:0.02, T:0.33
Consensus pattern (78 bp):
CATCACTACAACAATCTACTTCATCATCTCCAAGACTTCCATCTCCATCTCTACATGCACCTACC
TCCACTCAATCTA
Found at i:61742 original size:21 final size:22
Alignment explanation
Indices: 61718--61766 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
61708 GTCTGTTAGG
61718 AACAGTTGA-AACAATAAAAAC
1 AACAGTTGATAACAATAAAAAC
*
61739 AACAAG--GATTACAATAAAAAC
1 AAC-AGTTGATAACAATAAAAAC
61760 AACAGTT
1 AACAGTT
61767 AAAAGGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 4 0.17
21 17 0.74
22 2 0.09
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.16
Consensus pattern (22 bp):
AACAGTTGATAACAATAAAAAC
Found at i:62538 original size:28 final size:28
Alignment explanation
Indices: 62497--62551 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
62487 TGCTGGGTGA
62497 GCCAGATTTCAGAAGAAGAATTAAGCCT
1 GCCAGATTTCAGAAGAAGAATTAAGCCT
* *
62525 GCCAGATTTTAGAAGAAGCATTAAGCC
1 GCCAGATTTCAGAAGAAGAATTAAGCC
62552 CAATCAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (28 bp):
GCCAGATTTCAGAAGAAGAATTAAGCCT
Found at i:66636 original size:11 final size:11
Alignment explanation
Indices: 66580--66636 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
66570 CAATTTAAAC
66580 TATAATAAAAA
1 TATAATAAAAA
*
66591 TATAA-AAATA
1 TATAATAAAAA
66601 TA-AATAAAAA
1 TATAATAAAAA
* * *
66611 AATAATATAAT
1 TATAATAAAAA
*
66622 TATAATAAACA
1 TATAATAAAAA
66633 TATA
1 TATA
66637 TTTTATATAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 2 0.06
10 11 0.31
11 22 0.63
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:67813 original size:13 final size:13
Alignment explanation
Indices: 67797--67825 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
67787 TTTCAAATTC
67797 TAATATAAATTTT
1 TAATATAAATTTT
67810 TAATATAAATTTT
1 TAATATAAATTTT
67823 TAA
1 TAA
67826 ATTCTCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATATAAATTTT
Done.