Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007571.1 Hibiscus syriacus cultivar Beakdansim tig00021568_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: 56413
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3419 original size:13 final size:13
Alignment explanation
Indices: 3401--3429 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3391 CTGTCATTAA
3401 TAATTTAATAAAG
1 TAATTTAATAAAG
3414 TAATTTAATAAAG
1 TAATTTAATAAAG
3427 TAA
1 TAA
3430 AAACCGTTGA
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:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
TAATTTAATAAAG
Found at i:4662 original size:23 final size:23
Alignment explanation
Indices: 4589--4662 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
4579 CCGTATATGT
*
4589 TATAAAACATGTATTCAAACTCG
1 TATAAAACATGTATTCGAACTCG
* * *
4612 TATATAACGATTTGGT-TTCGTA-T-T
1 TATAAAAC-A--T-GTATTCGAACTCG
4636 TATAAAACATGTATTCGAACTCG
1 TATAAAACATGTATTCGAACTCG
4659 TATA
1 TATA
4663 TATTCATCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
20 2 0.05
21 6 0.16
22 1 0.03
23 12 0.32
24 8 0.22
25 1 0.03
26 5 0.14
27 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TATAAAACATGTATTCGAACTCG
Found at i:11478 original size:5 final size:5
Alignment explanation
Indices: 11468--11549 Score: 146
Period size: 5 Copynumber: 16.4 Consensus size: 5
11458 TGCCTCAACC
* *
11468 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTTT ATTTT ATTCT ATTCT
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT
11518 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT AT
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT AT
11550 CACCATCAGC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 75 1.00
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTCT
Found at i:22599 original size:34 final size:30
Alignment explanation
Indices: 22561--22629 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
22551 TTGATATAAC
22561 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
22595 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
22624 AATTTA
1 AATTTA
22630 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:22640 original size:29 final size:30
Alignment explanation
Indices: 22570--22629 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
22560 CAATTTAAGG
22570 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
22601 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
22630 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:22735 original size:21 final size:21
Alignment explanation
Indices: 22709--22764 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
22699 AGGGTGTCAA
*
22709 AGTGCATCTATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
22730 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
22751 AGTGCATCCATGCA
1 AGTGCATCCATGCA
22765 ACTGCACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:22871 original size:20 final size:20
Alignment explanation
Indices: 22829--22924 Score: 147
Period size: 20 Copynumber: 4.7 Consensus size: 20
22819 ATGCATTTAG
22829 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCAT-CTTGCCA
*
22850 TGCATCGATGCATCTGGCCA
1 TGCATCGATGCATCTTGCCA
*
22870 TGCATCCATGCATCCTTGCCA
1 TGCATCGATGCAT-CTTGCCA
22891 TGCATCGATGCATCTTGCCA
1 TGCATCGATGCATCTTGCCA
*
22911 TGCATCCATGCATC
1 TGCATCGATGCATC
22925 AAGGCTGCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
20 38 0.55
21 31 0.45
ACGTcount: A:0.20, C:0.33, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATCTTGCCA
Found at i:22881 original size:41 final size:41
Alignment explanation
Indices: 22829--22924 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
22819 ATGCATTTAG
*
22829 TGCATCGATGCATCCTTGCCATGCATCGATGCATCTGGCCA
1 TGCATCCATGCATCCTTGCCATGCATCGATGCATCTGGCCA
*
22870 TGCATCCATGCATCCTTGCCATGCATCGATGCATCTTGCCA
1 TGCATCCATGCATCCTTGCCATGCATCGATGCATCTGGCCA
22911 TGCATCCATGCATC
1 TGCATCCATGCATC
22925 AAGGCTGCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.33, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCATCCATGCATCCTTGCCATGCATCGATGCATCTGGCCA
Found at i:23724 original size:24 final size:23
Alignment explanation
Indices: 23667--23731 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
23657 TTCCCCTTGA
23667 AGTGCATCGATGCATT-C-T-AC
1 AGTGCATCGATGCATTCCTTAAC
*
23687 AGTGTATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATTCCTTAAC
*
23710 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCATTCCTTA
23732 TGCATCGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 15 0.39
21 1 0.03
22 1 0.03
23 3 0.08
24 18 0.47
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (23 bp):
AGTGCATCGATGCATTCCTTAAC
Found at i:27420 original size:23 final size:23
Alignment explanation
Indices: 27352--27412 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
27342 ACATTTTATA
*
27352 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
* *
27375 CGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
27398 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
27413 TTTATACGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:27609 original size:28 final size:28
Alignment explanation
Indices: 27556--27610 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
27546 AATGAATTGT
* * *
27556 ATTATATGATTTATATGATGATATGTGG
1 ATTATATGATTTAAATGATCAAATGTGG
27584 ATTATATGA-TTAAATGAGTCAAATGTG
1 ATTATATGATTTAAATGA-TCAAATGTG
27611 TTAAATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (28 bp):
ATTATATGATTTAAATGATCAAATGTGG
Found at i:30175 original size:23 final size:22
Alignment explanation
Indices: 30140--30211 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 22
30130 CCACTAGGGG
*
30140 CTATGAATTTGTCCCGAAGGATCA
1 CTATGAA-ATGTCCCGAAGGA-CA
*
30164 CTATGAAATGTCCCGAATGAC-
1 CTATGAAATGTCCCGAAGGACA
*
30185 C-ACTG-TATGTCCCGAAGGAC-
1 CTA-TGAAATGTCCCGAAGGACA
30205 CTATGAA
1 CTATGAA
30212 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 17 0.43
21 4 0.10
22 1 0.03
23 11 0.28
24 7 0.17
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (22 bp):
CTATGAAATGTCCCGAAGGACA
Found at i:31236 original size:15 final size:15
Alignment explanation
Indices: 31216--31272 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
31206 AACTGGGTAT
31216 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
31231 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
31248 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
31263 CGGGTACCCG
1 CGGGTACCCG
31273 TAACATCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:31252 original size:17 final size:16
Alignment explanation
Indices: 31216--31284 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
31206 AACTGGGTAT
**
31216 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
31231 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
31248 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
31263 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
31280 CGGGT
1 CGGGT
31285 CGGGACACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:31257 original size:32 final size:32
Alignment explanation
Indices: 31216--31284 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
31206 AACTGGGTAT
31216 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
31248 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
31280 CGGGT
1 CGGGT
31285 CGGGACACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:31342 original size:15 final size:16
Alignment explanation
Indices: 31310--31364 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
31300 AAAATCGTCG
*
31310 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
31327 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
*
31342 ACCCGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
31358 ACCCGGA
1 ACCCGGA
31365 TTTGCACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.41
16 12 0.35
17 8 0.24
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:31871 original size:75 final size:76
Alignment explanation
Indices: 31674--31871 Score: 256
Period size: 75 Copynumber: 2.6 Consensus size: 76
31664 AATTACAAAT
* * **
31674 TGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTTTGGCTCCG
1 TGCTCGGAGGGAACCGATTCCCCCCC-TAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCG
*
31739 AGATTTCCATAA
65 AGAATTCCATAA
* * * *
31751 TGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATTTTTGTTCCGA
1 TGCTCGGAGGGAACCGATTCCCCCCCTAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGA
31815 GAATTCCAGT-A
66 GAATTCCA-TAA
* * *
31826 TGCTCGGAGGGAACCGATTCCCCCCCCAGGGGGTACCGATTCCCCC
1 TGCTCGGAGGGAACCGATTCCCCCCCTAGGAGGAACCGATTCCCCC
31872 ATGTTCAACG
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
75 60 0.57
76 28 0.26
77 18 0.17
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.21
Consensus pattern (76 bp):
TGCTCGGAGGGAACCGATTCCCCCCCTAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGA
GAATTCCATAA
Found at i:35028 original size:26 final size:26
Alignment explanation
Indices: 34992--35044 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
34982 ATCTATTTAT
34992 GTAACAATAGAACTAGAAGCTCAACA
1 GTAACAATAGAACTAGAAGCTCAACA
35018 GTAACAATAGAACTAGAAGCTCAACA
1 GTAACAATAGAACTAGAAGCTCAACA
35044 G
1 G
35045 GATTTAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (26 bp):
GTAACAATAGAACTAGAAGCTCAACA
Found at i:36068 original size:14 final size:14
Alignment explanation
Indices: 36049--36077 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
36039 CAAATATATA
36049 ATAATTTATAGTTT
1 ATAATTTATAGTTT
36063 ATAATTTATAGTTT
1 ATAATTTATAGTTT
36077 A
1 A
36078 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:36089 original size:6 final size:6
Alignment explanation
Indices: 36078--36102 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36068 TTATAGTTTA
36078 AATATT AATATT AATATT AATATT A
1 AATATT AATATT AATATT AATATT A
36103 TGATTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:38836 original size:13 final size:13
Alignment explanation
Indices: 38818--38842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38808 AACATATTAA
38818 TATAATTTAAATC
1 TATAATTTAAATC
38831 TATAATTTAAAT
1 TATAATTTAAAT
38843 ATTAATATTA
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:38847 original size:30 final size:31
Alignment explanation
Indices: 38778--38850 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
38768 TTATTTAAAT
*
38778 AATATTAGA-ATAATTTAAATTATTTATGTTA
1 AATATTA-ATATAATTTAAATTATTAATGTTA
38809 ACATATTAATATAATTTAAATCTA-TAAT-TTA
1 A-ATATTAATATAATTTAAAT-TATTAATGTTA
38840 AATATTAATAT
1 AATATTAATAT
38851 TATTATATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.26
31 6 0.16
32 20 0.53
33 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
AATATTAATATAATTTAAATTATTAATGTTA
Found at i:39150 original size:19 final size:20
Alignment explanation
Indices: 39122--39165 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
39112 AATTTAAGAA
*
39122 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
39141 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
39161 TAAAT
1 TAAAT
39166 CAATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:39174 original size:26 final size:26
Alignment explanation
Indices: 39145--39208 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
39135 AATATTTAAA
39145 TAATATTATAATA-ATTTAA-ATCAATT
1 TAATATTATAATATA-TTAATAT-AATT
*
39171 TAAT-TTAAGAATATATTAATATAATT
1 TAATATT-ATAATATATTAATATAATT
*
39197 TAAAATTATAAT
1 TAATATTATAAT
39209 TTAAATGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 2 0.06
26 24 0.77
27 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TAATATTATAATATATTAATATAATT
Found at i:39208 original size:60 final size:57
Alignment explanation
Indices: 39081--39194 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 57
39071 AATCCTTATT
*
39081 ATATTTAA-AA-ATTATATAAATTAATTAATTTAATTTAAGAATAAATTATATAAAA
1 ATATTTAATAATATTATATAAATTAATCAATTTAATTTAAGAATAAATTATATAAAA
* *
39136 ATATTTAAATAATATTATAATAATTTAAATCAATTTAATTTAAGAATATATTAATATAA
1 ATATTT-AATAATATTAT-ATAAATT-AATCAATTTAATTTAAGAATAAATT-ATATAA
39195 TTTAAAATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
55 6 0.12
56 2 0.04
57 2 0.04
58 5 0.10
59 6 0.12
60 23 0.46
61 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (57 bp):
ATATTTAATAATATTATATAAATTAATCAATTTAATTTAAGAATAAATTATATAAAA
Found at i:39416 original size:372 final size:368
Alignment explanation
Indices: 38763--39466 Score: 931
Period size: 372 Copynumber: 1.9 Consensus size: 368
38753 TAATTTAATT
* *
38763 TAAAATTATTTAAATAATATTAGAATAATTTAAATTATTTATGTTAACATATTAATATAATTTAA
1 TAAAAATATTTAAATAATATTAGAATAATTTAAATAATTTATGTTAACATATTAATATAATTTAA
** * *
38828 ATCTATAATTTAAATATTAATATTATTATATAGGGCAGGATCTAATTATATTGTGTAAAACTCTT
66 ATCTATAATTTAAATATTAATATTATTATATAGGGCAAAATCCAATTATAGTGTGTAAAACTCTT
* * ** * *
38893 TTAGTTTATACCATTTTAAGACCAATAGATGGGAGAAATTAAAGAGTGAAATTAATAGTGGAAAA
131 TAAGTTTACACCATTTTAAGACCAATAGATGAAAAAAATTAAAGACTGAAATTAATAGTGGAAAA
* * *
38958 TGAAAAGATATTCACTAAAAAAACTAATTAATCTCAATCTTTGATTTATCTTAATCCAATGGCTC
196 TGAAAAGATATTCACTAAAAAAACGAATTAATCTCAATCTTTGATTTATCTCAATCCAATGGCAC
* ***
39023 TAAAAATGTGTAAAACTAAAAGAGTTTTACATTGTATAAATAGATCCTAATCCTTATTATATTTA
261 TAAAAATGTGCAAAACTAAAAGAGTTTTACACAATATAAATAGATCCTAATCCTTATTATATTTA
39088 AAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
326 AAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
* *
39131 TAAAAATATTTAAATAATATTATAATAATTTAAATCAATTTAAT-TTAAGAATATATTAATATAA
1 TAAAAATATTTAAATAATATTAGAATAATTTAAAT-AATTT-ATGTT---AACATATTAATATAA
* *
39195 TTTAAAAT-TATAATTTAAATGTTAATATTATTATATGGGGGCAAAATCCAATTATAGTGTGTAA
61 TTT-AAATCTATAATTTAAATATTAATATTATTATAT-AGGGCAAAATCCAATTATAGTGTGTAA
* * * *
39259 AACTCTTTAATTTTACATCATTTTAGGACC-ATTGAATGAAAAAAATTAAAGACT-AAGATTAAC
124 AACTCTTTAAGTTTACACCATTTTAAGACCAATAG-ATGAAAAAAATTAAAGACTGAA-ATTAA-
* * *
39322 TA-TGGAAAATGAACAGATATTCACT-AAAAAACGAATTAATCTTAA-CATTTGATTTCTCTCAA
186 TAGTGGAAAATGAAAAGATATTCACTAAAAAAACGAATTAATCTCAATC-TTTGATTTATCTCAA
* *
39384 TCCAATGAG-ACTAAAAA-GATGCAAACCTAAAAGAGTTTTACACAATATAAATGGATCCTAATC
250 TCCAATG-GCACTAAAAATG-TGCAAAACTAAAAGAGTTTTACACAATATAAATAGATCCTAATC
*
39447 CTTATTATATTTATAAATTA
313 CTTATTATATTTAAAAATTA
39467 ATTAATTTAA
Statistics
Matches: 290, Mismatches: 33, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
368 33 0.11
369 6 0.02
370 2 0.01
371 2 0.01
372 151 0.52
373 94 0.32
374 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (368 bp):
TAAAAATATTTAAATAATATTAGAATAATTTAAATAATTTATGTTAACATATTAATATAATTTAA
ATCTATAATTTAAATATTAATATTATTATATAGGGCAAAATCCAATTATAGTGTGTAAAACTCTT
TAAGTTTACACCATTTTAAGACCAATAGATGAAAAAAATTAAAGACTGAAATTAATAGTGGAAAA
TGAAAAGATATTCACTAAAAAAACGAATTAATCTCAATCTTTGATTTATCTCAATCCAATGGCAC
TAAAAATGTGCAAAACTAAAAGAGTTTTACACAATATAAATAGATCCTAATCCTTATTATATTTA
AAAATTATATAAATTAATTAATTTAATTTAAGAATAAATTATA
Found at i:39490 original size:21 final size:20
Alignment explanation
Indices: 39466--39519 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
39456 TTTATAAATT
39466 AATTAATTTAAATTAAGAATA
1 AATTAATTTAAATTAAG-ATA
* *
39487 AATTAATTTAATTTATGATA
1 AATTAATTTAAATTAAGATA
**
39507 TTTTAATTTAAAT
1 AATTAATTTAAAT
39520 AAATAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTAATTTAAATTAAGATA
Found at i:40030 original size:13 final size:13
Alignment explanation
Indices: 40012--40038 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40002 TCTAGAAAAC
40012 TGCCCAATCTGTA
1 TGCCCAATCTGTA
40025 TGCCCAATCTGTA
1 TGCCCAATCTGTA
40038 T
1 T
40039 CGCTTACAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (13 bp):
TGCCCAATCTGTA
Found at i:45456 original size:26 final size:26
Alignment explanation
Indices: 45427--45481 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
45417 CACAATTCAC
* *
45427 ATCATAATCCGAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAATAATA
* *
45453 ATCATTATCCAAATCAAACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
45479 ATC
1 ATC
45482 CGAGTTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:45546 original size:26 final size:26
Alignment explanation
Indices: 45516--45566 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
45506 TTAAGAATAA
45516 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
45542 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
45567 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:46161 original size:23 final size:22
Alignment explanation
Indices: 46132--46213 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 22
46122 TAGAGTGTAT
46132 TTTAATTAATTATAATAATTAAA
1 TTTAATTAATTATAA-AATTAAA
*
46155 TTTAATTTAATT-TAAGAATT-TA
1 TTTAA-TTAATTATAA-AATTAAA
* *
46177 -TTAATATAATTTTAAATTTATAA
1 TTTAAT-TAATTATAAAATTA-AA
*
46200 TTTAAATAATTATA
1 TTTAATTAATTATA
46214 TATGGGGCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 4 0.09
23 20 0.43
24 10 0.21
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TTTAATTAATTATAAAATTAAA
Found at i:46186 original size:21 final size:20
Alignment explanation
Indices: 46156--46197 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
46146 ATAATTAAAT
*
46156 TTAATTTAATTTAAGAATTTA
1 TTAATATAATTTAA-AATTTA
*
46177 TTAATATAATTTTAAATTTA
1 TTAATATAATTTAAAATTTA
46197 T
1 T
46198 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATATAATTTAAAATTTA
Found at i:46606 original size:15 final size:17
Alignment explanation
Indices: 46564--46603 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
46554 ATGATATTTT
*
46564 ATAATTTATAATTTATAA
1 ATAATTTA-ATTTTATAA
46582 ATAATTTAATTTTA-AA
1 ATAATTTAATTTTATAA
46598 ATAATT
1 ATAATT
46604 AATAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 5 0.24
18 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATTTAATTTTATAA
Done.