Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008037.1 Hibiscus syriacus cultivar Beakdansim tig00110524_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: 111676
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1579 original size:30 final size:30
Alignment explanation
Indices: 1538--1615 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
1528 TTTGGTCCAA
*
1538 AGCTCCCCCAGCTAAGTTCAGCTACATGCT
1 AGCTCCTCCAGCTAAGTTCAGCTACATGCT
1568 AGCTCCTCCAGCTAAGTTCAGCTACATGCT
1 AGCTCCTCCAGCTAAGTTCAGCTACATGCT
1598 AGCTCCTCCAGCTAAGTT
1 AGCTCCTCCAGCTAAGTT
1616 GAAGTTCTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.26
Consensus pattern (30 bp):
AGCTCCTCCAGCTAAGTTCAGCTACATGCT
Found at i:7862 original size:19 final size:21
Alignment explanation
Indices: 7819--7870 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
7809 GAAACCCCTT
*
7819 TGAAAATTCATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
7840 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
7859 TGAAGATACATG
1 TGAAAATACATG
7871 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:9620 original size:19 final size:20
Alignment explanation
Indices: 9596--9646 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
9586 CGGCCAAGAG
*
9596 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
*
9615 CATGTATTTTCATTTAAAGT
1 CATGTATTTTCATTTAAAAT
9635 CATGTATTTTCA
1 CATGTATTTTCA
9647 AAGGGTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:13659 original size:18 final size:20
Alignment explanation
Indices: 13636--13682 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
13626 CGGCCAAGAG
13636 CATGTATCTTCA-TT-AAA-T
1 CATGTAT-TTCATTTAAAAGT
13654 CATGTATTTCATTTAAAAGT
1 CATGTATTTCATTTAAAAGT
13674 CATGTATTT
1 CATGTATTT
13683 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 3 0.12
20 10 0.38
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAGT
Found at i:16395 original size:2 final size:2
Alignment explanation
Indices: 16388--16434 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
16378 AGTTATTTTC
*
16388 AT AT AT AT CT 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 AT AT AT
*
16430 CT AT A
1 AT AT A
16435 GTTATTATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17718 original size:22 final size:21
Alignment explanation
Indices: 17681--17722 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
17671 CCATCTCCAT
17681 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
17702 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
17723 TTCTGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:19076 original size:25 final size:27
Alignment explanation
Indices: 19026--19078 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
19016 CTAAAGGACC
19026 CAACAAGAGAGAATTGAGAGGAAAAAGG
1 CAACAAGAGAGAATTGAGA-GAAAAAGG
19054 CAAC-AGAGAG-ATTGAGA-ACAAAAGG
1 CAACAAGAGAGAATTGAGAGA-AAAAGG
19079 GGATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.04
25 6 0.25
26 7 0.29
27 6 0.25
28 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.30, T:0.08
Consensus pattern (27 bp):
CAACAAGAGAGAATTGAGAGAAAAAGG
Found at i:24305 original size:11 final size:13
Alignment explanation
Indices: 24273--24302 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24263 TGGCCAAAGA
24273 TGAAAAGGTATGT
1 TGAAAAGGTATGT
24286 TGAAAAGGTATG-
1 TGAAAAGGTATGT
24298 TGAAA
1 TGAAA
24303 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:29420 original size:36 final size:36
Alignment explanation
Indices: 29368--29480 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
29358 GATACTATTT
* *
29368 TCATGACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
29404 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
29440 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
29475 ACATCA
1 TCATCA
29481 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:29423 original size:13 final size:11
Alignment explanation
Indices: 29401--29466 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
29391 TATCACGCCT
29401 ATATCATCACC
1 ATATCATCACC
29412 ATAGTCCATCACC
1 ATA-T-CATCACC
*
29425 ATTATCA-CGCC
1 A-TATCATCACC
29436 TATATCATCACC
1 -ATATCATCACC
29448 ATATTCCATCACC
1 ATA-T-CATCACC
29461 ATATCA
1 ATATCA
29467 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:29495 original size:33 final size:33
Alignment explanation
Indices: 29380--29519 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
29370 ATGACCATAA
* * *
29380 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
29414 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
29452 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
29485 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
29518 TC
1 TC
29520 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:29890 original size:17 final size:17
Alignment explanation
Indices: 29870--29913 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
29860 CAAAAGCAAC
*
29870 AAAAAGAAA-AAAAAAG
1 AAAAAAAAAGAAAAAAG
*
29886 AAAAAAAAAGAAAGAAG
1 AAAAAAAAAGAAAAAAG
*
29903 AAAAGAAAAGA
1 AAAAAAAAAGA
29914 CTCCTACAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:29913 original size:10 final size:10
Alignment explanation
Indices: 29870--29911 Score: 66
Period size: 10 Copynumber: 4.0 Consensus size: 10
29860 CAAAAGCAAC
29870 AAAAAGAAAA
1 AAAAAGAAAA
29880 AAAAAGAAAA
1 AAAAAGAAAA
29890 AAAAAGAAAGA
1 AAAAAGAAA-A
29901 AGAAAAGAAAA
1 A-AAAAGAAAA
29912 GACTCCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 19 0.63
11 3 0.10
12 8 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:31380 original size:20 final size:20
Alignment explanation
Indices: 31355--31396 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31345 TGGAAAAGGG
31355 GTACATTCGAGAAAGCCTAA
1 GTACATTCGAGAAAGCCTAA
31375 GTACATTCGAGAAAGCCTAA
1 GTACATTCGAGAAAGCCTAA
31395 GT
1 GT
31397 CCATGTGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
GTACATTCGAGAAAGCCTAA
Found at i:35174 original size:36 final size:36
Alignment explanation
Indices: 35122--35234 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
35112 GATACTATTT
*
35122 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
35158 TCATCACCGTAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
35194 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
35229 ACATCA
1 TCATCA
35235 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 17 0.24
36 53 0.76
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:35249 original size:33 final size:33
Alignment explanation
Indices: 35134--35273 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
35124 ATCACCATAA
* * *
35134 TCCATCTCCATTATCACGCCTATATCATCA-CCGT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
35168 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
35206 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
35239 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
35272 TC
1 TC
35274 ATTCATCAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.47
38 1 0.01
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:40758 original size:12 final size:13
Alignment explanation
Indices: 40732--40760 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40722 CATGTAATGC
40732 ATAAATAAGTAAA
1 ATAAATAAGTAAA
40745 ATAAATAA-TAAA
1 ATAAATAAGTAAA
40757 ATAA
1 ATAA
40761 GGCAAGACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
ATAAATAAGTAAA
Found at i:52609 original size:6 final size:6
Alignment explanation
Indices: 52598--52627 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
52588 TTCAACTTTC
52598 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
52628 CCTCTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:52633 original size:18 final size:18
Alignment explanation
Indices: 52598--52634 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52588 TTCAACTTTC
**
52598 TTTCTTTTTCTTTTTCTT
1 TTTCTTTTTCTTCCTCTT
52616 TTTCTTTTTCTTCCTCTT
1 TTTCTTTTTCTTCCTCTT
52634 T
1 T
52635 GAGTGCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTTTTTCTTCCTCTT
Found at i:52662 original size:23 final size:23
Alignment explanation
Indices: 52632--52675 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
52622 TTTCTTCCTC
52632 TTTGAGTGCTTTCAATTTCTTAT
1 TTTGAGTGCTTTCAATTTCTTAT
* *
52655 TTTGAGTGCTTTGATTTTCTT
1 TTTGAGTGCTTTCAATTTCTT
52676 TGCTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (23 bp):
TTTGAGTGCTTTCAATTTCTTAT
Found at i:59387 original size:11 final size:11
Alignment explanation
Indices: 59368--59403 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
59358 AATTTATCTC
59368 TTTTTATCTTG
1 TTTTTATCTTG
* *
59379 TTTTAATCTTA
1 TTTTTATCTTG
59390 TTTTTATCTTG
1 TTTTTATCTTG
59401 TTT
1 TTT
59404 CCAGCACCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.72
Consensus pattern (11 bp):
TTTTTATCTTG
Found at i:59752 original size:23 final size:21
Alignment explanation
Indices: 59719--59781 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
59709 TGCTATTTTT
*
59719 TAAAAACAAAAAACAAAAAAA
1 TAAAAAAAAAAAACAAAAAAA
59740 GGTAAAAAAAAAAAA-AAAAAAA
1 --TAAAAAAAAAAAACAAAAAAA
* *
59762 -ACACAAAAAAAACAAAAAAA
1 TAAAAAAAAAAAACAAAAAAA
59782 CCAAAATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.28
20 7 0.19
22 7 0.19
23 12 0.33
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (21 bp):
TAAAAAAAAAAAACAAAAAAA
Found at i:59773 original size:18 final size:18
Alignment explanation
Indices: 59747--59787 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
59737 AAAGGTAAAA
*
59747 AAAAAAAAAAAAAAAACAC
1 AAAAAAAACAAAAAAAC-C
59766 AAAAAAAACAAAAAAACC
1 AAAAAAAACAAAAAAACC
59784 AAAA
1 AAAA
59788 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAAAAAAACC
Found at i:59799 original size:1 final size:1
Alignment explanation
Indices: 59720--59781 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
59710 GCTATTTTTT
* * *** * * *
59720 AAAAACAAAAAACAAAAAAAGGTAAAAAAAAAAAAAAAAAAAACACAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59782 CCAAAATTTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:64328 original size:20 final size:22
Alignment explanation
Indices: 64299--64338 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
64289 GGGAGAGCTT
64299 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
64319 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
64339 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:65203 original size:33 final size:33
Alignment explanation
Indices: 65124--65227 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
65114 ATACAATCTG
* *
65124 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
65160 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
65193 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
65226 TC
1 TC
65228 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:66067 original size:11 final size:11
Alignment explanation
Indices: 66053--66093 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
66043 TTCCAATTCA
66053 TTTATCTTTTT
1 TTTATCTTTTT
66064 TTTATCTTTTT
1 TTTATCTTTTT
* *
66075 TTAATCTTATT
1 TTTATCTTTTT
66086 TTTATCTT
1 TTTATCTT
66094 GTTCCAGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATCTTTTT
Found at i:67361 original size:11 final size:11
Alignment explanation
Indices: 67345--67371 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
67335 AATAAAAACA
67345 AAGTGCAAGTG
1 AAGTGCAAGTG
67356 AAGTGCAAGTG
1 AAGTGCAAGTG
67367 AAGTG
1 AAGTG
67372 AAAAGTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.37, T:0.19
Consensus pattern (11 bp):
AAGTGCAAGTG
Found at i:67431 original size:22 final size:25
Alignment explanation
Indices: 67403--67455 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
67393 AAATCCAACA
67403 AAGAAA-TCAAAGCACTC-AAAA-G
1 AAGAAATTCAAAGCACTCAAAAAGG
*
67425 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAATTCAAAGCACTCAAAAAGG
67450 AAGAAA
1 AAGAAA
67456 AAGAAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 6 0.22
23 10 0.37
24 4 0.15
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.09
Consensus pattern (25 bp):
AAGAAATTCAAAGCACTCAAAAAGG
Found at i:67461 original size:25 final size:23
Alignment explanation
Indices: 67411--67461 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
67401 CAAAGAAATC
**
67411 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAAAAG
67434 AAAGCACTCAAAAAGGAAGAAAAAG
1 AAAGCACTC-AAAA-GAAGAAAAAG
67459 AAA
1 AAA
67462 ACAAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 4 0.17
25 11 0.46
ACGTcount: A:0.63, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:70439 original size:19 final size:20
Alignment explanation
Indices: 70392--70442 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
70382 GAAACCCCTT
**
70392 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
70412 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
70431 TGAAGATACATG
1 TGAAAATACATG
70443 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:78777 original size:19 final size:20
Alignment explanation
Indices: 78730--78780 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
78720 GAAACCCCTT
**
78730 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
78750 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
78769 TGAAGATACATG
1 TGAAAATACATG
78781 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:81367 original size:35 final size:37
Alignment explanation
Indices: 81321--81398 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 37
81311 TGAGAATTTT
*
81321 GTGATGATATAGGCGTGAT-ATGG-TGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGAAGATGGACTATG
*
81356 GTGATGATATAGGCGTGATAATGGAAGATGGATTATG
1 GTGATGATATAGGCGTGATAATGGAAGATGGACTATG
81393 GTGATG
1 GTGATG
81399 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 19 0.49
36 4 0.10
37 16 0.41
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (37 bp):
GTGATGATATAGGCGTGATAATGGAAGATGGACTATG
Found at i:83393 original size:36 final size:36
Alignment explanation
Indices: 83341--83453 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
83331 GATACTATTT
*
83341 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
83377 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
83413 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
83448 ACATCA
1 TCATCA
83454 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:83396 original size:13 final size:11
Alignment explanation
Indices: 83341--83439 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
83331 GATACTATTT
83341 TCATCACCATAA
1 TCATCACCAT-A
*
83353 TCCATCTCCATTA
1 T-CATCACCA-TA
*
83366 TCA-CGCCTATA
1 TCATCACC-ATA
83377 TCATCACCATA
1 TCATCACCATA
83388 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
83402 TCA-CGCCTATA
1 TCATCACC-ATA
83413 TCATCACCATA
1 TCATCACCATA
83424 TTCCATCACCATA
1 -T-CATCACCATA
83437 TCA
1 TCA
83440 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:83468 original size:33 final size:33
Alignment explanation
Indices: 83353--83492 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
83343 ATCACCATAA
* * *
83353 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
83387 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
83425 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
83458 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
83491 TC
1 TC
83493 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:87785 original size:22 final size:20
Alignment explanation
Indices: 87760--87799 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
87750 ATGTTTGTTT
87760 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
87782 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
87800 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:88032 original size:15 final size:15
Alignment explanation
Indices: 88009--88044 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
87999 ACTAATATTC
* *
88009 TTATCATAATATATA
1 TTATAATAACATATA
88024 TTATAATAACATATA
1 TTATAATAACATATA
88039 TTATAA
1 TTATAA
88045 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:92062 original size:22 final size:20
Alignment explanation
Indices: 92037--92076 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
92027 ATGTTTGTTT
92037 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
92059 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
92077 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:92309 original size:15 final size:15
Alignment explanation
Indices: 92286--92321 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
92276 ACTAATATTC
* *
92286 TTATCATAATATATA
1 TTATAATAACATATA
92301 TTATAATAACATATA
1 TTATAATAACATATA
92316 TTATAA
1 TTATAA
92322 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:95003 original size:36 final size:36
Alignment explanation
Indices: 94951--95063 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
94941 GATACTATTT
*
94951 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
94987 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
95023 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
95058 ACATCA
1 TCATCA
95064 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:95006 original size:13 final size:11
Alignment explanation
Indices: 94951--95049 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
94941 GATACTATTT
94951 TCATCACCATAA
1 TCATCACCAT-A
*
94963 TCCATCTCCATTA
1 T-CATCACCA-TA
*
94976 TCA-CGCCTATA
1 TCATCACC-ATA
94987 TCATCACCATA
1 TCATCACCATA
94998 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
95012 TCA-CGCCTATA
1 TCATCACC-ATA
95023 TCATCACCATA
1 TCATCACCATA
95034 TTCCATCACCATA
1 -T-CATCACCATA
95047 TCA
1 TCA
95050 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:95078 original size:33 final size:33
Alignment explanation
Indices: 94963--95102 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
94953 ATCACCATAA
* * *
94963 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
94997 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
95035 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
95068 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
95101 TC
1 TC
95103 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:100585 original size:13 final size:13
Alignment explanation
Indices: 100563--100592 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
100553 ACTAAACACC
100563 TTTC-ACATACCT
1 TTTCAACATACCT
100575 TTTCAACATACCT
1 TTTCAACATACCT
100588 TTTCA
1 TTTCA
100593 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:106422 original size:35 final size:37
Alignment explanation
Indices: 106376--106455 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
106366 TTTGAGAATT
*
106376 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
106411 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
106448 TGGGGATG
1 TGGTGATG
106456 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:109508 original size:27 final size:27
Alignment explanation
Indices: 109459--109515 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
109449 GAAAATTAGA
*
109459 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCAAAAAG-AAG
* *
109487 AAAGAAATT-CAGCATTCAAAAAGAAG
1 AAAGAAATTGAAGCACTCAAAAAGAAG
109513 AAA
1 AAA
109516 AACAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 11 0.42
28 9 0.35
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (27 bp):
AAAGAAATTGAAGCACTCAAAAAGAAG
Done.