Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009376.1 Hibiscus syriacus cultivar Beakdansim tig00113247_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: 93296
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3354 original size:20 final size:20
Alignment explanation
Indices: 3329--3377 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3319 GAAACTAAAA
3329 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
3349 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
3369 TCGTGTTGC
1 TCGCGTTGC
3378 AAATTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.08, C:0.20, G:0.22, T:0.49
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:3942 original size:20 final size:20
Alignment explanation
Indices: 3919--3972 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3909 TGACTTCTGT
3919 GTTGCGAATTACAGATTCAC
1 GTTGCGAATTACAGATTCAC
* *
3939 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCAC
3959 GTTGCGAATT-CAGA
1 GTTGCGAATTACAGA
3973 AAATCGCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCAC
Found at i:4029 original size:20 final size:20
Alignment explanation
Indices: 4004--4044 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3994 ATTCACGTTA
4004 CGAATTTGGAAACTGAGTTG
1 CGAATTTGGAAACTGAGTTG
4024 CGAATTTGGAAACTGAGTTG
1 CGAATTTGGAAACTGAGTTG
4044 C
1 C
4045 AAAATTGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
CGAATTTGGAAACTGAGTTG
Found at i:4052 original size:20 final size:20
Alignment explanation
Indices: 4009--4053 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3999 CGTTACGAAT
* *
4009 TTGGAAACTGAGTTGCGAAT
1 TTGGAAACTGAGTTGCAAAA
4029 TTGGAAACTGAGTTGCAAAA
1 TTGGAAACTGAGTTGCAAAA
4049 TTGGA
1 TTGGA
4054 GTTCGCGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (20 bp):
TTGGAAACTGAGTTGCAAAA
Found at i:4709 original size:58 final size:56
Alignment explanation
Indices: 4621--4740 Score: 134
Period size: 58 Copynumber: 2.1 Consensus size: 56
4611 AAGGACCTTC
* * *
4621 AAATATATAAGGACTAAAATGCTCCTTTTTATAGTAGATGAACT-AAATGAACATCT
1 AAATATATAAGGACTAAAATACTCATTTTTATAGTAGAAGAACTAAAATGAA-ATCT
* * * * *
4677 AAATATAATAAAGGACTAAAATATTTATTTTTATAGTGGAAGGACTAAAATGAAATTT
1 AAATAT-AT-AAGGACTAAAATACTCATTTTTATAGTAGAAGAACTAAAATGAAATCT
4735 AAATAT
1 AAATAT
4741 TGCATAATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 6 0.11
57 2 0.04
58 38 0.72
59 7 0.13
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (56 bp):
AAATATATAAGGACTAAAATACTCATTTTTATAGTAGAAGAACTAAAATGAAATCT
Found at i:20790 original size:23 final size:23
Alignment explanation
Indices: 20764--20810 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20754 TCTTGGATTC
20764 TATATTTTCATCTAAAATCACTT
1 TATATTTTCATCTAAAATCACTT
20787 TATATTTTCATCTAAAATCACTT
1 TATATTTTCATCTAAAATCACTT
20810 T
1 T
20811 GGTCATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTTTCATCTAAAATCACTT
Found at i:21455 original size:32 final size:31
Alignment explanation
Indices: 21380--21456 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
21370 CTAATGTGAC
* * *
21380 TCTTAGGTAGGCTCTGCGGCCTTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
21411 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
21443 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
21457 CATGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:31814 original size:50 final size:50
Alignment explanation
Indices: 31739--31888 Score: 239
Period size: 50 Copynumber: 3.0 Consensus size: 50
31729 AGTGTAGAAC
*
31739 TCTCTAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTATGGAGA
1 TCTCTAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGA
*
31789 TCTCTAGAAGCTTGTGGAAGAGTGT-GAATCCTCTAGAATATTCTGGAGA
1 TCTCTAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGA
* * * *
31838 TGTGTAGAAGCTTGTGGAAGAGTGTGGAATCTTATGGAATATTCTGGAGA
1 TCTCTAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGA
31888 T
1 T
31889 GCGTGAAACC
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 45 0.49
50 47 0.51
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (50 bp):
TCTCTAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGA
Found at i:31889 original size:50 final size:50
Alignment explanation
Indices: 31743--31916 Score: 235
Period size: 50 Copynumber: 3.5 Consensus size: 50
31733 TAGAACTCTC
* * *
31743 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTATGGAGATCTC
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
*
31793 TAGAAGCTTGTGGAAGAGTGT-GAATCCTCTAGAATATTCTGGAGATGTG
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
* * *
31842 TAGAAGCTTGTGGAAGAGTGTGGAATCTTATGGAATATTCTGGAGATGCG
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
* * *
31892 T-GAAACCTTATGGAAGAGTATGGAA
1 TAG-AAGCTTGTGGAAGAGTGTGGAA
31917 GGGAGTGGAA
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
49 46 0.41
50 65 0.59
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.29
Consensus pattern (50 bp):
TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
Found at i:32390 original size:31 final size:31
Alignment explanation
Indices: 32352--32460 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
32342 ATACATAAAG
32352 ATGATATAACATATGTTATATGTTCAAAGTA
1 ATGATATAACATATGTTATATGTTCAAAGTA
*** *
32383 ATGATATAGTTTATGTTATATGTTCAAAGTG
1 ATGATATAACATATGTTATATGTTCAAAGTA
* * * * *
32414 A-GATGTGACACATGTCATATGTACACAAGTA
1 ATGATATAACATATGTTATATGTTCA-AAGTA
* *
32445 ATGATGTGACATATGT
1 ATGATATAACATATGT
32461 CACATTATTA
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 16 0.26
31 33 0.53
32 13 0.21
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (31 bp):
ATGATATAACATATGTTATATGTTCAAAGTA
Found at i:36943 original size:16 final size:16
Alignment explanation
Indices: 36922--36963 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
36912 GACGAGCACG
36922 GATGAGCA-CGGTTAAT
1 GATGAGCATC-GTTAAT
36938 GATGAGCATCGTTAAT
1 GATGAGCATCGTTAAT
36954 GATGAGCATC
1 GATGAGCATC
36964 ATTTATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (16 bp):
GATGAGCATCGTTAAT
Found at i:38449 original size:60 final size:60
Alignment explanation
Indices: 38361--38542 Score: 267
Period size: 60 Copynumber: 3.0 Consensus size: 60
38351 TTACTGATTC
*
38361 AATTTATTTTATAT-TCATTCAATTGGTGAAACGGACACCATTTGATTGGATGAAAAATTT
1 AATTTATTTTCTATCT-ATTCAATTGGTGAAACGGACACCATTTGATTGGATGAAAAATTT
* *
38421 AATTTATTTTCTATCTATTCAATAGGTGAAATGGACACCATTTGATTGGATGAAAAATTT
1 AATTTATTTTCTATCTATTCAATTGGTGAAACGGACACCATTTGATTGGATGAAAAATTT
* * * * *
38481 AATTTATTTTCTATCCATTCAATTGGTGACACGTGGCACCATTCGATTGGATGAAAATTTT
1 AATTTATTTTCTATCTATTCAATTGGTGAAACG-GACACCATTTGATTGGATGAAAAATTT
38542 A
1 A
38543 TTAAATTAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
60 84 0.76
61 26 0.24
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (60 bp):
AATTTATTTTCTATCTATTCAATTGGTGAAACGGACACCATTTGATTGGATGAAAAATTT
Found at i:38937 original size:22 final size:23
Alignment explanation
Indices: 38902--38949 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
38892 CATTTGAAAT
38902 TTTAACTAATTTATAA-TTATATA
1 TTTAACTAATTTATAATTTA-ATA
*
38925 TTTAA-TATTTTATAATTTAATA
1 TTTAACTAATTTATAATTTAATA
38947 TTT
1 TTT
38950 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAATA
Found at i:38944 original size:15 final size:15
Alignment explanation
Indices: 38918--38960 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
38908 TAATTTATAA
38918 TTATATATTTAATATT
1 TTATA-ATTTAATATT
38934 TTATAATTTAATATT
1 TTATAATTTAATATT
*
38949 TTATAAATTAAT
1 TTATAATTTAAT
38961 TTAGTAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:40716 original size:20 final size:20
Alignment explanation
Indices: 40691--40902 Score: 178
Period size: 20 Copynumber: 10.6 Consensus size: 20
40681 GATTTTCCAT
** *
40691 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
40711 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
40731 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
40750 CTATCGCAACGAGTATCCGTA
1 -AATCGCAACGCGAATCCGTA
*
40771 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
40791 AATCGCATCGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
40811 AATCGTAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
*
40831 AATCGCAACGAGAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
40851 AATCGCAATGCGAATACGTAA
1 AATCGCAACGCGAATCCGT-A
*
40872 AATCGCAACG-TATATCCGTA
1 AATCGCAACGCGA-ATCCGTA
40892 AATCGCAACGC
1 AATCGCAACGC
40903 AATTTTTAAA
Statistics
Matches: 153, Mismatches: 32, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.01
20 135 0.88
21 17 0.11
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:40793 original size:60 final size:60
Alignment explanation
Indices: 40710--40902 Score: 205
Period size: 60 Copynumber: 3.2 Consensus size: 60
40700 GCGAATATGA
** * *
40710 AAATCGCAACGCGAA-CATATAAATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGT
1 AAATCGCAACGCGAATC-CGTAAATCGCAACGCGAATACGT-A-AATCGCAACGAGTATCCGT
* * * * * *
40770 AAATCGCAACGCGTATCCGTAAATCGCATCGAGAATACGTAAATCGTAACGCGTATCTGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACGTAAATCGCAACGAGTATCCGT
* *
40830 AAATCGCAACGAGAATCCGTAAATCGCAATGCGAATACGTAAAATCGCAACGTA-TATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACGT-AAATCGCAACG-AGTATCCGT
40891 AAATCGCAACGC
1 AAATCGCAACGC
40903 AATTTTTAAA
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
60 76 0.70
61 32 0.29
62 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACGTAAATCGCAACGAGTATCCGT
Found at i:41514 original size:20 final size:20
Alignment explanation
Indices: 41465--41505 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41455 TTCTAAACTT
*
41465 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
41485 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
41505 A
1 A
41506 CTATCGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:41553 original size:33 final size:33
Alignment explanation
Indices: 41487--41579 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
41477 TGAAAATGAA
* ** *
41487 AATCGCAACACGAAAATGACTATCGCAATGAGAG
1 AATCGCAACGCG-AAATGAAAATCGCAACGAGAG
*
41521 AATCGCAACGCGAAATGAAAATTGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
41554 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
41580 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 40 0.78
34 11 0.22
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:41597 original size:19 final size:19
Alignment explanation
Indices: 41575--41720 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
41565 GAAACCAAAA
*
41575 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
41594 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
41608 TCTCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
41627 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
41641 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
41660 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
41679 TCCGCATTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
41699 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
41719 TC
1 TC
41721 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.19
16 5 0.05
17 5 0.05
19 38 0.38
20 31 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:41620 original size:33 final size:33
Alignment explanation
Indices: 41578--41712 Score: 171
Period size: 33 Copynumber: 3.9 Consensus size: 33
41568 ACCAAAATCG
41578 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
41611 CATTGCGATTTTAATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
41644 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCG
1 CATTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CT
*
41683 CATTGCGATTTTCATTCTCTCGTTGCGATT
1 CATTGCGATTTTCATT-TCGCGTTGCGATT
41713 TTCATTTCAA
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
33 58 0.65
35 2 0.02
38 2 0.02
39 16 0.18
40 11 0.12
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:41697 original size:20 final size:19
Alignment explanation
Indices: 41646--41720 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 19
41636 GATTCTCTCG
41646 TTGCGATTTTCATTT-CGC
1 TTGCGATTTTCATTTCCGC
**
41664 GTTGCGATAGTCATTTCCGC
1 -TTGCGATTTTCATTTCCGC
41684 ATTGCGATTTTCATTCTCTCG-
1 -TTGCGATTTTCATT-TC-CGC
41705 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
41721 AACCAAAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
19 15 0.31
20 29 0.60
21 2 0.04
22 2 0.04
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCCGC
Found at i:43006 original size:24 final size:24
Alignment explanation
Indices: 42972--43025 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
42962 CTGAAAAATC
42972 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
42996 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
43020 ATCAAA
1 ATCAAA
43026 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:43039 original size:24 final size:24
Alignment explanation
Indices: 42972--43039 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
42962 CTGAAAAATC
* * *
42972 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
42996 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
43020 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
43040 TAGTAGTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:43900 original size:20 final size:19
Alignment explanation
Indices: 43879--44115 Score: 136
Period size: 20 Copynumber: 11.8 Consensus size: 19
43869 GCGATAGTCA
43879 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
43898 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
* *
43918 GTATC-CGCATTACGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
43938 GTATTTGCATTGCGATTTAC
1 GAATCT-CGTTGCGATTTAC
* * *
43958 GGATTTGCATTGCGATTTAC
1 GAATCT-CGTTGCGATTTAC
*
43978 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
43998 -AGATACGCGTTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
*
44018 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
44038 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
44059 GTATTGTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
44079 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
*
44100 GGATACTCGTTGCGAT
1 GAAT-CTCGTTGCGAT
44116 AGTCAAAATC
Statistics
Matches: 172, Mismatches: 31, Indels: 28
0.74 0.13 0.12
Matches are distributed among these distances:
18 2 0.01
19 6 0.03
20 125 0.73
21 36 0.21
22 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:43934 original size:40 final size:39
Alignment explanation
Indices: 43887--44096 Score: 217
Period size: 40 Copynumber: 5.2 Consensus size: 39
43877 CAGAATCTCG
*
43887 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATCCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACG-ATACGCA
* * **
43927 TTACGATTTACGTATTTGCATTGCGATTTACGGATTTGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTAC-GATACGCA
* * *
43967 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTAC-GATACGCA
* * *
44007 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTAC-GATACGCA
* *
44047 TTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCG-CATTGCGATTTAC-GATACGCA
44088 TTGCGATTT
1 TTGCGATTT
44097 TACGGATACT
Statistics
Matches: 152, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 112 0.74
41 39 0.26
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (39 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGATACGCA
Found at i:43968 original size:60 final size:60
Alignment explanation
Indices: 43885--44115 Score: 250
Period size: 60 Copynumber: 3.8 Consensus size: 60
43875 GTCAGAATCT
* * * *
43885 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATCCGCATTACGATTTACGTATTTG
1 CGTTGCGATTTACGGATTCGCATTGCGATTTACGTATACGCGTTGCGATTTACGTATTTG
* * * * **
43945 CATTGCGATTTACGGATTTGCATTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTACGGATTCGCATTGCGATTTACGTATACGCGTTGCGATTTAC-GTATTTG
* * * *
44005 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTA-TTG
1 CGTTGCGATTTACGGATTCGCATTGCGATTTACGTATACGCGTTGCGA-TTTACGTATTTG
* * * *
44065 TCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 -CGTTGCGATTTACGGATTCGCATTGCGA-TTTACGTATACGCGTTGCGAT
44116 AGTCAAAATC
Statistics
Matches: 143, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
60 91 0.64
61 33 0.23
62 19 0.13
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACGGATTCGCATTGCGATTTACGTATACGCGTTGCGATTTACGTATTTG
Found at i:44147 original size:20 final size:20
Alignment explanation
Indices: 44124--44176 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
44114 ATAGTCAAAA
*
44124 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
44144 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
44164 TCGCGTTGCGATT
1 TCGCGTTGCGATT
44177 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:44168 original size:40 final size:40
Alignment explanation
Indices: 43947--44176 Score: 180
Period size: 40 Copynumber: 5.7 Consensus size: 40
43937 CGTATTTGCA
* ** * ** *
43947 TTGCGATTTACGGATTTGCATTGCGATTTACGTATTCTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTATATGTTCTCG
** *
43987 TTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTATATGTTCTCG
* * *
44027 TTGCGATTTACGGATACGCGTTGCGATTT-TACGTATTGTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTATA--TGTTCTCG
* * *
44068 TTGCGATTTACGGATACGCGTTGCGATTT-TACGGATACTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTATA-TG-TTCTCG
* * *
44109 TTGCGATAGT-CA-AAATCGCGTTGCGATTTATATGTTCGCG
1 TTGCGAT-TTACAGATA-CGCGTTGCGATTTATATGTTCTCG
* * *
44149 TTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTACAGATACGCGTTGCGATT
44177 ATGGAAAATC
Statistics
Matches: 160, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 91 0.57
41 65 0.41
42 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACAGATACGCGTTGCGATTTATATGTTCTCG
Found at i:45304 original size:26 final size:26
Alignment explanation
Indices: 45268--45325 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
45258 ATAAGTGGAT
*
45268 ATAACATTGTTGAAAAAAATATTCAA
1 ATAATATTGTTGAAAAAAATATTCAA
45294 ATAATATTGTTGAAAAAAATATTCAA
1 ATAATATTGTTGAAAAAAATATTCAA
45320 ATAATA
1 ATAATA
45326 CACTCAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (26 bp):
ATAATATTGTTGAAAAAAATATTCAA
Found at i:55623 original size:24 final size:24
Alignment explanation
Indices: 55573--55623 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
55563 CATATATCAG
* *
55573 TTTATAGCCATTGTTGTAACTGCT
1 TTTATAGCCATTGCTGTAACTACT
* *
55597 TTTATAGCCGTTGCTGTAACTATT
1 TTTATAGCCATTGCTGTAACTACT
55621 TTT
1 TTT
55624 GTTAAATCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (24 bp):
TTTATAGCCATTGCTGTAACTACT
Found at i:57432 original size:24 final size:24
Alignment explanation
Indices: 57400--57452 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
57390 ATTATACACG
*
57400 TTCTGCACCTCAATTTCCTCAATT
1 TTCTGCACCTCAAATTCCTCAATT
57424 TTCTGCACCTCAAATTCCTCAATT
1 TTCTGCACCTCAAATTCCTCAATT
57448 TTCTG
1 TTCTG
57453 TAGTCTCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.32, G:0.06, T:0.42
Consensus pattern (24 bp):
TTCTGCACCTCAAATTCCTCAATT
Found at i:59386 original size:24 final size:24
Alignment explanation
Indices: 59359--59441 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
59349 TGCTTCATCT
*
59359 TCATCTTCACCATCTCCACC-TC-
1 TCATCTTCACCACCTCCACCTTCA
59381 T-ATCATT-ACCACCTCCACCTTCA
1 TCATC-TTCACCACCTCCACCTTCA
* *
59404 CCATCATCACCACCTCCACCTTCA
1 TCATCTTCACCACCTCCACCTTCA
* *
59428 CCATCATCACCACC
1 TCATCTTCACCACC
59442 ATCTTCACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.26
22 5 0.09
23 1 0.02
24 33 0.62
ACGTcount: A:0.24, C:0.51, G:0.00, T:0.25
Consensus pattern (24 bp):
TCATCTTCACCACCTCCACCTTCA
Found at i:61241 original size:24 final size:24
Alignment explanation
Indices: 61191--61241 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
61181 CATATATCAG
* * *
61191 TTTATAGCCGTTGTTGTAACTGCT
1 TTTATAGACGTTGCTGTAACTACT
*
61215 TTTATAGACGTTGCTGTAACTATT
1 TTTATAGACGTTGCTGTAACTACT
61239 TTT
1 TTT
61242 GTTAAATCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
TTTATAGACGTTGCTGTAACTACT
Found at i:63698 original size:32 final size:32
Alignment explanation
Indices: 63662--63725 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
63652 AAGGCAAGGT
63662 CTAAACTCTATGCCCTTCAAGGGAGAGTTTAA
1 CTAAACTCTATGCCCTTCAAGGGAGAGTTTAA
63694 CTAAACTCTATGCCCTTCAAGGGAGAGTTTAA
1 CTAAACTCTATGCCCTTCAAGGGAGAGTTTAA
63726 GACCCACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (32 bp):
CTAAACTCTATGCCCTTCAAGGGAGAGTTTAA
Found at i:68547 original size:6 final size:6
Alignment explanation
Indices: 68536--68638 Score: 197
Period size: 6 Copynumber: 17.2 Consensus size: 6
68526 GACACGTATT
68536 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
68584 ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
68632 ACCACG A
1 ACCACG A
68639 GCCGAGCCGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:68646 original size:5 final size:5
Alignment explanation
Indices: 68636--68689 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
68626 ACCACGACCA
* * * * *
68636 CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGTGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
68686 CGAG
1 CGAG
68690 ACGGACGGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.11, C:0.39, G:0.41, T:0.09
Consensus pattern (5 bp):
CGAGC
Found at i:68651 original size:10 final size:10
Alignment explanation
Indices: 68636--68689 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
68626 ACCACGACCA
*
68636 CGAGCCGAGC
1 CGAGCCGTGC
68646 CGAGCCGTGC
1 CGAGCCGTGC
*
68656 CGTGCCGTGC
1 CGAGCCGTGC
*
68666 CGTGCCGTGC
1 CGAGCCGTGC
*
68676 CGAGCCGAGC
1 CGAGCCGTGC
68686 CGAG
1 CGAG
68690 ACGGACGGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.11, C:0.39, G:0.41, T:0.09
Consensus pattern (10 bp):
CGAGCCGTGC
Found at i:68662 original size:15 final size:15
Alignment explanation
Indices: 68639--68687 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
68629 ACGACCACGA
*
68639 GCCGAGCCGAGCCGT
1 GCCGTGCCGAGCCGT
*
68654 GCCGTGCCGTGCCGT
1 GCCGTGCCGAGCCGT
*
68669 GCCGTGCCGAGCCGA
1 GCCGTGCCGAGCCGT
68684 GCCG
1 GCCG
68688 AGACGGACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.08, C:0.41, G:0.41, T:0.10
Consensus pattern (15 bp):
GCCGTGCCGAGCCGT
Found at i:74555 original size:6 final size:6
Alignment explanation
Indices: 74544--74646 Score: 179
Period size: 6 Copynumber: 17.2 Consensus size: 6
74534 GACACGTATT
*
74544 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AACACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
74592 ACCACG ACCACG ACCTCG ACCACG ACCTCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
74640 ACCACG A
1 ACCACG A
74647 GCCGAGCCGA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.33, C:0.49, G:0.17, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:74654 original size:5 final size:5
Alignment explanation
Indices: 74644--74692 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
74634 ACCACGACCA
* * *
74644 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
74693 ACGGACGGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.14, C:0.39, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:91065 original size:2 final size:2
Alignment explanation
Indices: 91058--91084 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
91048 ATGGTACAAC
91058 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
91085 TGATATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.