Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012154.1 Kokia drynarioides strain JFW-HI SEQ_127155, 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: 132088
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Warning! 137 characters in sequence are not A, C, G, or T
Found at i:2861 original size:21 final size:21
Alignment explanation
Indices: 2835--2877 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2825 TAGGGTCCAT
*
2835 TTGCCCCGGAGGAGTAGAGTA
1 TTGCCCCGGAGGAATAGAGTA
*
2856 TTGCCCGGGAGGAATAGAGTA
1 TTGCCCCGGAGGAATAGAGTA
2877 T
1 T
2878 CGCGATGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (21 bp):
TTGCCCCGGAGGAATAGAGTA
Found at i:3002 original size:45 final size:45
Alignment explanation
Indices: 2883--3008 Score: 180
Period size: 45 Copynumber: 2.8 Consensus size: 45
2873 AGTATCGCGA
* * ** * *
2883 TGGCTCGTCAAACTTAGCCTGATATCCTTCCCTTGAGTATTGCGG
1 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTACCG
*
2928 TGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTACCG
1 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTACCG
*
2973 TGGCTCGTCAAACTGAGGCTAATATCCTTGGCTTGA
1 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
3009 TTAGCTATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (45 bp):
TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTACCG
Found at i:4975 original size:14 final size:17
Alignment explanation
Indices: 4941--4987 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
4931 GATGTGGATT
4941 TTTTTTATAATTAATTA
1 TTTTTTATAATTAATTA
4958 TTTTTTAT-ATT-A-TA
1 TTTTTTATAATTAATTA
*
4972 -TTTTGATAATTAATTA
1 TTTTTTATAATTAATTA
4988 GCTAGATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.23
14 5 0.19
15 2 0.08
16 5 0.19
17 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTTATAATTAATTA
Found at i:5273 original size:20 final size:21
Alignment explanation
Indices: 5248--5290 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5238 TACTTACTAC
5248 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
5268 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
5289 TA
1 TA
5291 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:5649 original size:9 final size:9
Alignment explanation
Indices: 5635--5691 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
5625 TATTTTTTTT
5635 TTCTTCTCC
1 TTCTTCTCC
*
5644 TTCTTCCCC
1 TTCTTCTCC
*
5653 TTCTTCCCC
1 TTCTTCTCC
*
5662 ATCTTCTCC
1 TTCTTCTCC
5671 TTC-T-TCC
1 TTCTTCTCC
5678 TTC-T-TCC
1 TTCTTCTCC
5685 TTCTTCT
1 TTCTTCT
5692 TTCTTTCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 13 0.31
8 2 0.05
9 27 0.64
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:5680 original size:7 final size:7
Alignment explanation
Indices: 5664--5696 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5654 TCTTCCCCAT
5664 CTTC-TC
1 CTTCTTC
5670 CTTCTTC
1 CTTCTTC
5677 CTTCTTC
1 CTTCTTC
5684 CTTCTTC
1 CTTCTTC
*
5691 TTTCTT
1 CTTCTT
5697 TCTTTCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (7 bp):
CTTCTTC
Found at i:5695 original size:4 final size:4
Alignment explanation
Indices: 5688--5726 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
5678 TTCTTCCTTC
*
5688 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
5727 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:5699 original size:25 final size:26
Alignment explanation
Indices: 5671--5730 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
5661 CATCTTCTCC
5671 TTCTTCCTTCT-TCCTTCTTCTTTCT
1 TTCTTCCTTCTCTCCTTCTTCTTTCT
* * *
5696 TTCTTTCTT-TCTCTTTTTTCTTTCT
1 TTCTTCCTTCTCTCCTTCTTCTTTCT
*
5721 TTTTTCCTTC
1 TTCTTCCTTC
5731 AATTTTCGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (26 bp):
TTCTTCCTTCTCTCCTTCTTCTTTCT
Found at i:5710 original size:21 final size:20
Alignment explanation
Indices: 5686--5730 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
5676 CCTTCTTCCT
5686 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
5707 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
5727 -CTTC
1 TCTTC
5731 AATTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:10770 original size:5 final size:5
Alignment explanation
Indices: 10760--10787 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10750 TGGTTCGGAA
10760 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
10788 GATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:14080 original size:28 final size:29
Alignment explanation
Indices: 14033--14112 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 29
14023 ATGACCCCTT
* *
14033 AAAATAAT-AAAATTTCAATTTAATCTC-A
1 AAAATAATAAAAAATT-AATTTAACCTCTA
*
14061 AAAATAATAAAAAATTAATTTAACCTCTT
1 AAAATAATAAAAAATTAATTTAACCTCTA
* *
14090 AAAATTATAAAAATATAAATTTA
1 AAAATAATAAAAA-ATTAATTTA
14113 TCACTAATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 18 0.41
29 18 0.41
30 8 0.18
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATAATAAAAAATTAATTTAACCTCTA
Found at i:22195 original size:2 final size:2
Alignment explanation
Indices: 22188--22228 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
22178 CCCTAAACCC
*
22188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22229 TATTATCACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22447 original size:32 final size:33
Alignment explanation
Indices: 22385--22450 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
22375 TGAACTGATG
* *
22385 TATAAATTTTTAAATAATTTTTTTAATTATTGT
1 TATAAAATTTTAAATAATTTATTTAATTATTGT
*
22418 TATAAAATTTTAACT-ATTTATTTAATTATTGT
1 TATAAAATTTTAAATAATTTATTTAATTATTGT
22450 T
1 T
22451 GGACTAGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (33 bp):
TATAAAATTTTAAATAATTTATTTAATTATTGT
Found at i:24056 original size:21 final size:21
Alignment explanation
Indices: 24030--24070 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24020 CACCTACAAT
24030 GGTATCGCT-ATATCCACCTTG
1 GGTATCG-TGATATCCACCTTG
24051 GGTATCGTGATATCCACCTT
1 GGTATCGTGATATCCACCTT
24071 CCAAGAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (21 bp):
GGTATCGTGATATCCACCTTG
Found at i:28947 original size:22 final size:22
Alignment explanation
Indices: 28922--28966 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28912 TTTTAAATGC
28922 ATTTTACCTTTTAAAAATAATA
1 ATTTTACCTTTTAAAAATAATA
*** *
28944 ATTTTTTTTTTTAAAAATTATA
1 ATTTTACCTTTTAAAAATAATA
28966 A
1 A
28967 AAATATAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTACCTTTTAAAAATAATA
Found at i:48462 original size:20 final size:20
Alignment explanation
Indices: 48425--48480 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
48415 GCTTAAAAAG
* ** *
48425 TAGTTCTTGAATAATATTTT
1 TAGTTCTTAAATTTTATTGT
48445 TAGTTCTTAAATTTTATTGT
1 TAGTTCTTAAATTTTATTGT
* *
48465 GAGTTCTAAAATTTTA
1 TAGTTCTTAAATTTTA
48481 ATTCTTTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (20 bp):
TAGTTCTTAAATTTTATTGT
Found at i:51962 original size:3 final size:3
Alignment explanation
Indices: 51954--52006 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
51944 TCTGACTTTA
* * * * *
51954 TAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT TGT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52002 TAT TA
1 TAT TA
52007 AAGTATAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:53848 original size:23 final size:23
Alignment explanation
Indices: 53797--53854 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
53787 TTGATATTTA
**
53797 AAAATTGTAAAACTATAAGATGAT
1 AAAA-TGTAAAACTATAAGACAAT
*
53821 GAAATGTAAAACTATAAGACAAT
1 AAAATGTAAAACTATAAGACAAT
53844 AAAATGGTAAA
1 AAAAT-GTAAA
53855 TTTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (23 bp):
AAAATGTAAAACTATAAGACAAT
Found at i:59283 original size:23 final size:23
Alignment explanation
Indices: 59256--59300 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
59246 TCAAATTTTT
* *
59256 TTTTTTAAATAATAAAATATATAA
1 TTTTATAAA-AATAAAAAATATAA
*
59280 TTTTATTAAAATAAAAAATAT
1 TTTTATAAAAATAAAAAATAT
59301 TTACGATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTATAAAAATAAAAAATATAA
Found at i:62880 original size:5 final size:5
Alignment explanation
Indices: 62867--62897 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
62857 CTTATCTGGT
*
62867 TTTTT TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
62898 GAGCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:67907 original size:4 final size:4
Alignment explanation
Indices: 67898--67943 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
67888 TTTTGCTTTC
*
67898 AATA AATA AATA AATA TATA AATTA AATTA AATTA AATA AATA AAT
1 AATA AATA AATA AATA AATA AA-TA AA-TA AA-TA AATA AATA AAT
67944 GAATTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 25 0.64
5 14 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (4 bp):
AATA
Found at i:67935 original size:27 final size:26
Alignment explanation
Indices: 67900--67950 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
67890 TTGCTTTCAA
*
67900 TAAATAAATAAATATATAAATTAAAT
1 TAAATAAATAAATAAATAAATTAAAT
*
67926 TAAATTAAATAAATAAATGAATTAA
1 TAAA-TAAATAAATAAATAAATTAA
67951 TATTTAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAATAAATAAATAAATAAATTAAAT
Found at i:69421 original size:13 final size:13
Alignment explanation
Indices: 69403--69428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69393 AAAGAACCAA
69403 CTTTGATTCTTTG
1 CTTTGATTCTTTG
69416 CTTTGATTCTTTG
1 CTTTGATTCTTTG
69429 TTGTAGCTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (13 bp):
CTTTGATTCTTTG
Found at i:82220 original size:4 final size:4
Alignment explanation
Indices: 82203--82235 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
82193 CAAGAATGCC
*
82203 AGAT AGAT AAAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
82236 TAGATATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:83528 original size:20 final size:20
Alignment explanation
Indices: 83500--83539 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
83490 CTCTAATCAG
*
83500 AATCTCTAAAAATCAGCTAT
1 AATCCCTAAAAATCAGCTAT
* *
83520 AATCCCTAAAGATTAGCTAT
1 AATCCCTAAAAATCAGCTAT
83540 TCAATGCTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCCCTAAAAATCAGCTAT
Found at i:85159 original size:71 final size:71
Alignment explanation
Indices: 85037--85177 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 71
85027 ATCTTAGATC
* * * *
85037 AGTGATAGCTTCACTCCAATCGTGTAGAACAGACATAGAGAACAAAAACAAAGCAAAAGCTCTAT
1 AGTGATAGCTTCACTCCAACCCTGTAGAACAAACATAGAGAACAAAAACAAAGCAAAAACTCTAT
*
85102 GGGATT
66 AGGATT
* * * **
85108 AGTGATAGCTTCTCTCCAACCCTGTGGAACAAACATTGAGAACAAGGACAAAGCAAAAACTCTAT
1 AGTGATAGCTTCACTCCAACCCTGTAGAACAAACATAGAGAACAAAAACAAAGCAAAAACTCTAT
85173 AGGAT
66 AGGAT
85178 GGGGATAAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (71 bp):
AGTGATAGCTTCACTCCAACCCTGTAGAACAAACATAGAGAACAAAAACAAAGCAAAAACTCTAT
AGGATT
Found at i:87806 original size:164 final size:163
Alignment explanation
Indices: 87535--87862 Score: 586
Period size: 164 Copynumber: 2.0 Consensus size: 163
87525 ATCCCTACAA
* *
87535 TCCACAAGCCTTGATAAACAACAAGCAAGACCTTGACCAAGCAAGTTAATTACGTCCATCAAGCT
1 TCCACAAGCCTCGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCT
*
87600 TCACAAGGCTAATTTGTAACGAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTTGACATA
66 TCACAAGGCTAATTTGTAACGAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATA
87665 ATACTAAAAAAAAAACTAGTACCCAAAAAACTGC
131 ATACT-AAAAAAAAACTAGTACCCAAAAAACTGC
87699 TCCACAAGCCTCGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCT
1 TCCACAAGCCTCGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCT
* *
87764 TCA-TAGGACTAATTTGTAATGAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACAT
66 TCACAAGG-CTAATTTGTAACGAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACAT
87828 AATACTAAAAAAAAACTAGTACCCAAAAAACTGC
130 AATACTAAAAAAAAACTAGTACCCAAAAAACTGC
87862 T
1 T
87863 TGGAAAAATT
Statistics
Matches: 158, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
163 32 0.20
164 126 0.80
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (163 bp):
TCCACAAGCCTCGATAAACAACAAGCAAGACCTTGACCAAGCAAGGTAATTACGTCCATCAAGCT
TCACAAGGCTAATTTGTAACGAGGGATTATCGGATACAATCATGAGCTTCTCATCCTTCGACATA
ATACTAAAAAAAAACTAGTACCCAAAAAACTGC
Found at i:97312 original size:51 final size:51
Alignment explanation
Indices: 97236--97337 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
97226 AAATAAAGAA
97236 AGAAAATCAGTTGATAAAGGGCAGTACCAGAGATTAGTTGGTAAGTTAATC
1 AGAAAATCAGTTGATAAAGGGCAGTACCAGAGATTAGTTGGTAAGTTAATC
97287 AGAAAATCAGTTGATAAAGGGCAGTACCAGAGATTAGTTGGTAAGTTAATC
1 AGAAAATCAGTTGATAAAGGGCAGTACCAGAGATTAGTTGGTAAGTTAATC
97338 TACTTATCAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (51 bp):
AGAAAATCAGTTGATAAAGGGCAGTACCAGAGATTAGTTGGTAAGTTAATC
Found at i:97325 original size:27 final size:27
Alignment explanation
Indices: 97244--97326 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
97234 AAAGAAAATC
97244 AGTTGATAAAGGGCAGTACCAGAGATT
1 AGTTGATAAAGGGCAGTACCAGAGATT
* ** * * *
97271 AGTTGGT-AA-GTTA--ATCAGAAAATC
1 AGTTGATAAAGGGCAGTACCAG-AGATT
97295 AGTTGATAAAGGGCAGTACCAGAGATT
1 AGTTGATAAAGGGCAGTACCAGAGATT
97322 AGTTG
1 AGTTG
97327 GTAAGTTAAT
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
23 4 0.10
24 9 0.23
25 4 0.10
26 4 0.10
27 14 0.36
28 4 0.10
ACGTcount: A:0.37, C:0.10, G:0.28, T:0.25
Consensus pattern (27 bp):
AGTTGATAAAGGGCAGTACCAGAGATT
Found at i:107650 original size:17 final size:17
Alignment explanation
Indices: 107625--107670 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
107615 TGGCACTATA
*
107625 TGGGTACTGTTCACACT
1 TGGGAACTGTTCACACT
107642 TGGGAACTGTTCACACT
1 TGGGAACTGTTCACACT
107659 TGGGAACTGTTC
1 TGGGAACTGTTC
107671 GGGTTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (17 bp):
TGGGAACTGTTCACACT
Found at i:131538 original size:17 final size:17
Alignment explanation
Indices: 131516--131548 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
131506 TTGAAGGAAA
131516 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
*
131533 AAAGAAAGAAAGAAGA
1 AAAGAAAGAAAAAAGA
131549 AGGAAGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Found at i:131561 original size:28 final size:27
Alignment explanation
Indices: 131512--131566 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
131502 AAAATTGAAG
131512 GAAAAAAGAAAGAAAAAAGAGAAAGAAA
1 GAAAAAAGAAAGAAAAAAGAG-AAGAAA
* * * *
131540 GAAAGAAGAAGGAAGAAGGAGAAGAAA
1 GAAAAAAGAAAGAAAAAAGAGAAGAAA
131567 CGGAAGAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (27 bp):
GAAAAAAGAAAGAAAAAAGAGAAGAAA
Done.