Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005770.1 Hibiscus syriacus cultivar Beakdansim tig00013504_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: 74968
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1507 original size:22 final size:21
Alignment explanation
Indices: 1481--1521 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1471 GCTGTGGAAA
1481 TGATGGT-CTTGATGGATGAAGT
1 TGATGGTGC-TGAT-GATGAAGT
1503 TGATGGTGCTGATGATGAA
1 TGATGGTGCTGATGATGAA
1522 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 11 0.61
23 1 0.06
ACGTcount: A:0.24, C:0.05, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTGCTGATGATGAAGT
Found at i:4494 original size:24 final size:24
Alignment explanation
Indices: 4467--4517 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4457 TGTGGATCAC
* *
4467 CAAAAGTCATGTCTATTGATTCTT
1 CAAAAGACATGTCTATTGAATCTT
* *
4491 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACATGTCTATTGAATCTT
4515 CAA
1 CAA
4518 CTTGAAGTGA
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:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACATGTCTATTGAATCTT
Found at i:5729 original size:22 final size:22
Alignment explanation
Indices: 5683--5734 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
5673 TTTTCTCTTT
*
5683 TTTCTTTTTTGGGTGCTTTCAA
1 TTTCTTTTTTGAGTGCTTTCAA
* *
5705 TTTCTTCTTTTGAGTGCTTTGAT
1 TTTCTT-TTTTGAGTGCTTTCAA
5728 TTTCTTT
1 TTTCTTT
5735 GCTGGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.08, C:0.13, G:0.15, T:0.63
Consensus pattern (22 bp):
TTTCTTTTTTGAGTGCTTTCAA
Found at i:7209 original size:20 final size:20
Alignment explanation
Indices: 7181--7227 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
7171 TATAGTGATG
*
7181 TGAGTTATATTTGAAGCTCA
1 TGAGCTATATTTGAAGCTCA
*
7201 TGAGCTATATTTGAAGGTCA
1 TGAGCTATATTTGAAGCTCA
7221 TGAGCTA
1 TGAGCTA
7228 ATTATATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (20 bp):
TGAGCTATATTTGAAGCTCA
Found at i:12967 original size:28 final size:30
Alignment explanation
Indices: 12909--12970 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
12899 CACATCTTCC
*
12909 TTTCTTTACTTTCATTTTCCTTGTCTTAAACCT
1 TTTCTTTACTTTCATTTTACTTG---TAAACCT
12942 TTTCTTTACTTTCA-TTTACTTG-AAACCT
1 TTTCTTTACTTTCATTTTACTTGTAAACCT
12970 T
1 T
12971 GTTTCTACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 7 0.25
32 7 0.25
33 14 0.50
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTCTTTACTTTCATTTTACTTGTAAACCT
Found at i:17385 original size:24 final size:23
Alignment explanation
Indices: 17335--17385 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
17325 TTTCTTTGTT
* * *
17335 TTTTCTTCTTTTGAGTGCTGGAT
1 TTTTCTTATTTTGAGTGCTGCAC
*
17358 TTTTCTTTATTTTGAGTGCTTCAC
1 TTTTC-TTATTTTGAGTGCTGCAC
17382 TTTT
1 TTTT
17386 TTTTCTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.10, C:0.14, G:0.16, T:0.61
Consensus pattern (23 bp):
TTTTCTTATTTTGAGTGCTGCAC
Found at i:22324 original size:13 final size:13
Alignment explanation
Indices: 22302--22331 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
22292 ACTAAACACC
22302 TTTC-ACATACCT
1 TTTCAACATACCT
22314 TTTCAACATACCT
1 TTTCAACATACCT
22327 TTTCA
1 TTTCA
22332 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:28185 original size:22 final size:23
Alignment explanation
Indices: 28157--28208 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
28147 ATTTATAAGT
*
28157 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCATGATAA
*
28179 TGGTGATGATATAGGCATGATAA
1 TGGTGATAATATAGGCATGATAA
28202 TGGTGAT
1 TGGTGAT
28209 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCATGATAA
Found at i:28201 original size:36 final size:37
Alignment explanation
Indices: 28159--28274 Score: 134
Period size: 36 Copynumber: 3.2 Consensus size: 37
28149 TTATAAGTTG
*
28159 GTGATAATATAGGCGTGA-TATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
*
28195 ATGAT-A-AT-GGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATAGGTG-T-GACTATGGTGATGATATAGGC
** *
28231 GTGATAATGGAGATG-GACTATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
28267 GTGATAAT
1 GTGATAAT
28275 GGTGATGGAC
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
33 3 0.04
34 3 0.04
35 3 0.04
36 55 0.81
37 1 0.01
39 3 0.04
ACGTcount: A:0.31, C:0.05, G:0.34, T:0.30
Consensus pattern (37 bp):
GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
Found at i:28275 original size:36 final size:36
Alignment explanation
Indices: 28177--28284 Score: 198
Period size: 36 Copynumber: 3.0 Consensus size: 36
28167 ATAGGCGTGA
*
28177 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
28213 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
28249 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
28285 ATATTGTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.30
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:29692 original size:19 final size:20
Alignment explanation
Indices: 29654--29692 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29644 ACCATTCACT
*
29654 TGCATACTATATGATTTTCA
1 TGCATAATATATGATTTTCA
29674 TGCATAATATATG-TTTTCA
1 TGCATAATATATGATTTTCA
29693 CATCTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
TGCATAATATATGATTTTCA
Found at i:30688 original size:19 final size:21
Alignment explanation
Indices: 30664--30715 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
30654 CGGCCAAGAG
*
30664 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
30683 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
30704 CATGTATTTTCA
1 CATGTATTTTCA
30716 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:31088 original size:13 final size:13
Alignment explanation
Indices: 31070--31114 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
31060 CATTGCCATT
*
31070 TCATCATCATCCA
1 TCATCAACATCCA
*
31083 TCATCAACATCCT
1 TCATCAACATCCA
*
31096 TCATCAAGA-CCA
1 TCATCAACATCCA
31108 TCATCAA
1 TCATCAA
31115 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:31460 original size:26 final size:25
Alignment explanation
Indices: 31430--31482 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
31420 TTTAGAGTGC
31430 AAAAATAAAGAAAAAGACA-AAAAGAA
1 AAAAATAAAG-AAAAGA-AGAAAAGAA
**
31456 AAAAATTCAGAAAAGAAGAAAAGAA
1 AAAAATAAAGAAAAGAAGAAAAGAA
31481 AA
1 AA
31483 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 15 0.62
26 8 0.33
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (25 bp):
AAAAATAAAGAAAAGAAGAAAAGAA
Found at i:31469 original size:18 final size:17
Alignment explanation
Indices: 31449--31500 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
31439 GAAAAAGACA
31449 AAAAGAAAAAAATTCAG
1 AAAAGAAAAAAATTCAG
*
31466 AAAAG-AAGAAA---AG
1 AAAAGAAAAAAATTCAG
31479 AAAAGAAAAAAATTCA-
1 AAAAGAAAAAAATTCAG
31495 AAAAGA
1 AAAAGA
31501 GAAAGCAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.24
14 5 0.17
16 11 0.38
17 6 0.21
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAGAAAAAAATTCAG
Found at i:31471 original size:31 final size:29
Alignment explanation
Indices: 31436--31505 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
31426 GTGCAAAAAT
31436 AAAGAAAAAGACAAAAAGAAAAAAATTCAGA
1 AAAGAAAAAGA-AAAAAGAAAAAAATTCA-A
*
31467 AAAGAAGAAA-AGAAAAGAAAAAAATTCAA
1 AAAGAA-AAAGAAAAAAGAAAAAAATTCAA
*
31496 AAAGAGAAAG
1 AAAGAAAAAG
31506 CAAGCCAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 6 0.17
30 16 0.46
31 7 0.20
32 3 0.09
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.06
Consensus pattern (29 bp):
AAAGAAAAAGAAAAAAGAAAAAAATTCAA
Found at i:31484 original size:30 final size:28
Alignment explanation
Indices: 31449--31504 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
31439 GAAAAAGACA
31449 AAAAGAAAAAAATTCAGAAAAGAAGAAAAG
1 AAAAGAAAAAAATTCA-AAAAG-AGAAAAG
31479 AAAAGAAAAAAATTCAAAAAGAGAAA
1 AAAAGAAAAAAATTCAAAAAGAGAAA
31505 GCAAGCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 5 0.19
29 5 0.19
30 16 0.62
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (28 bp):
AAAAGAAAAAAATTCAAAAAGAGAAAAG
Found at i:35140 original size:90 final size:89
Alignment explanation
Indices: 35022--35196 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 89
35012 TCCAGAATAT
* * * * *
35022 TTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATACATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
*
35087 GGTAACTTGTATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
*
35111 TTAAATTCTAATTAATTAAATATACATTTAATTTATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATATACATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
*
35176 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
35197 GTGCGTTAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 7 0.09
90 70 0.91
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATACATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:36729 original size:13 final size:13
Alignment explanation
Indices: 36711--36755 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
36701 CATTGCTATT
*
36711 TCATCATCATCCA
1 TCATCAACATCCA
*
36724 TCATCAACATCCT
1 TCATCAACATCCA
*
36737 TCATCAAGA-CCA
1 TCATCAACATCCA
36749 TCATCAA
1 TCATCAA
36756 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:47655 original size:24 final size:27
Alignment explanation
Indices: 47624--47696 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 27
47614 AAAATTCGGC
*
47624 AAAG-AAATTGAAGCACTCAAAAG-A-
1 AAAGAAAATTCAAGCACTCAAAAGAAG
47648 AAA-AAAATTCAAGCACTCAAAAAGAAG
1 AAAGAAAATTCAAGCACTC-AAAAGAAG
47675 AAAGAAAAGTTCAAGCACTCAA
1 AAAGAAAA-TTCAAGCACTCAA
47697 CAATAAGTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 16 0.38
25 5 0.12
26 1 0.02
27 3 0.07
28 6 0.14
29 11 0.26
ACGTcount: A:0.59, C:0.15, G:0.14, T:0.12
Consensus pattern (27 bp):
AAAGAAAATTCAAGCACTCAAAAGAAG
Found at i:51472 original size:22 final size:22
Alignment explanation
Indices: 51432--51473 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
51422 AAATATGTGG
*
51432 TTCATAATAATAACTTCATACA
1 TTCATAATAATAACATCATACA
* *
51454 TTCATAATATTATCATCATA
1 TTCATAATAATAACATCATA
51474 ACTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATAACATCATACA
Found at i:52414 original size:19 final size:21
Alignment explanation
Indices: 52385--52435 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
52375 GGCCAAGAGA
*
52385 ATGTATCTTCA-TTAAAA-TC
1 ATGTATTTTCATTTAAAAGTC
*
52404 ATGTTTTTTCATTTAAAAGTC
1 ATGTATTTTCATTTAAAAGTC
52425 ATGTATTTTCA
1 ATGTATTTTCA
52436 AAGGCGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 9 0.33
20 6 0.22
21 12 0.44
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAGTC
Found at i:56163 original size:19 final size:21
Alignment explanation
Indices: 56139--56190 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
56129 CGGCCAAGAG
*
56139 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
56158 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
56179 CATGTATTTTCA
1 CATGTATTTTCA
56191 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:61432 original size:19 final size:21
Alignment explanation
Indices: 61408--61459 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
61398 CGGCCAAGAG
*
61408 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
61427 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
61448 CATGTATTTTCA
1 CATGTATTTTCA
61460 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:61894 original size:18 final size:20
Alignment explanation
Indices: 61871--61909 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
61861 TATCATTTAT
61871 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
61889 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
61909 T
1 T
61910 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:61912 original size:22 final size:20
Alignment explanation
Indices: 61867--61915 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
61857 TCTCTATCAT
61867 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
61886 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
61906 TTATATTATT
1 TTATATTATT
61916 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:64754 original size:18 final size:20
Alignment explanation
Indices: 64731--64769 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
64721 TATCATTTAT
64731 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
64749 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
64769 T
1 T
64770 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:64772 original size:22 final size:20
Alignment explanation
Indices: 64727--64775 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
64717 TCTCTATCAT
64727 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
64746 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
64766 TTATATTATT
1 TTATATTATT
64776 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:64948 original size:51 final size:52
Alignment explanation
Indices: 64880--64989 Score: 136
Period size: 51 Copynumber: 2.1 Consensus size: 52
64870 CTAGATCGGG
*
64880 ACAT-AATAAGGCTATCTACTC-TC-TTCCATCAAAGCGTGTAGATTCACCTT
1 ACATCAATAAGGCTATCTACTCTTCTTTCCATCAAAGCGTGTAG-TCCACCTT
* **
64930 ACATCAATCAGGCTATCTACTCTTCTTTTTTATCAAAGCGTGTAGTCCACCTT
1 ACATCAATAAGGCTATCTACTCTTC-TTTCCATCAAAGCGTGTAGTCCACCTT
*
64983 ATATCAA
1 ACATCAA
64990 GCGATAATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 4 0.08
51 16 0.31
52 2 0.04
53 13 0.25
54 16 0.31
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (52 bp):
ACATCAATAAGGCTATCTACTCTTCTTTCCATCAAAGCGTGTAGTCCACCTT
Found at i:65121 original size:19 final size:18
Alignment explanation
Indices: 65090--65154 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 18
65080 AATTGGAGTG
65090 CAAAAAGAA-AGAAAAAGA
1 CAAAAAGAAGAGAAAAA-A
*
65108 CAAAAAGAAGAGAAAAAT
1 CAAAAAGAAGAGAAAAAA
*
65126 CATAAAAGAAGAAAAGAAAA
1 CA-AAAAGAAGAGAA-AAAA
*
65146 GAAAAAGAA
1 CAAAAAGAA
65155 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 11 0.28
19 25 0.62
20 4 0.10
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (18 bp):
CAAAAAGAAGAGAAAAAA
Done.