Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010073.1 Kokia drynarioides strain JFW-HI SEQ_124851, 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: 47907
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:391 original size:215 final size:215
Alignment explanation
Indices: 13--950 Score: 978
Period size: 215 Copynumber: 4.4 Consensus size: 215
3 TTGTTTACAT
* * * * **
13 AATGGCAACTATTTAGA-CTAAATGATGCGATTT-CTAGAGCATGGAATGT-TCTTAAAATTGCT
1 AATGACAACTATTTAGACCT-AATGATGTGATTTCCCA-AGCATGGACTGTAT-AAAAAATTGCT
* * * * *
75 CAAAGGAATGAATCATCTTGAATAGTTTAAGGAATCAGAGTTATAAAAGAACTCGTAAAAGTTTT
63 CGAAGGAATGGATCGTCTTGAATAGTTTAAGGAATCAAAGTTATAAAAGAACTCGTAAAAGTTTG
* *
140 TCAAGTTCGGAAGTTCGACCGAGAACCAAAAGAGAAACAATTCTCAGCTAAATAAGTTTTTAATT
128 TCAAGTTCGGAAGTTCGACCGAGAAACAAAAGAGAAACAATTCTCACCTAAATAAGTTTTTAATT
205 CAAAGACCAAAAGTAGTTTAAAA
193 CAAAGACCAAAAGTAGTTTAAAA
* * * * * ***
228 AATTACAACTATTTAGGCCTAATGATGTGATCTCCCGAGCATGGACTGTGTGGGAAATTGCTCGA
1 AATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTATAAAAAATTGCTCG-
* * * *
293 AAGG-ATGGATCGTCCTGAATGGTTTAATGAA-CAAAAGTTATAAAAGAACTCGTTAAAGTTTGT
65 AAGGAATGGATCGTCTTGAATAGTTTAAGGAATC-AAAGTTATAAAAGAACTCGTAAAAGTTTGT
* * * * * *
356 CAACTTCGGAAGTTCGGCCTAGAAACAAGAGAGAAACTATTCTCACCTAAAAAAGTTTTTAATTC
129 CAAGTTCGGAAGTTCGACCGAGAAACAAAAGAGAAACAATTCTCACCTAAATAAGTTTTTAATTC
* ** *
421 AAAGACCAAAAGTTGTTTGCAT
194 AAAGACCAAAAGTAGTTTAAAA
** * ** * * * * * ** *
443 AATGGTAATTATTTAGACAAAATGATGCGATTT-CTAGAGCATGCAAT-TTTCTTAAAATTGCTT
1 AATGACAACTATTTAGACCTAATGATGTGATTTCCCA-AGCATGGACTGTAT-AAAAAATTGCTC
* * * *
506 GAAGGAATGGATCGTCTTGAATAATTTAGGGAATCAAAGTTAT-AAAGTAACTCATAAAAGTTTT
64 GAAGGAATGGATCGTCTTGAATAGTTTAAGGAATCAAAGTTATAAAAG-AACTCGTAAAAGTTTG
* *
570 TCAAGTTCGGAAGTTCGACCGAGAACCAAAAGAGAAACAATTCTCACCTAAATAAATTTTTAATT
128 TCAAGTTCGGAAGTTCGACCGAGAAACAAAAGAGAAACAATTCTCACCTAAATAAGTTTTTAATT
* *
635 CGAAGACCAAAAGTTGTTTAAAA
193 CAAAGACCAAAAGTAGTTTAAAA
* *
658 AATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTACAAAAAATTACTCGA
1 AATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTATAAAAAATTGCTCGA
* * *
723 AGGAATGGATCGTCTTGAATACTTTAATGAA-CAAAAGTTATAAAA-ATACTCGTAAAACTTTGT
66 AGGAATGGATCGTCTTGAATAGTTTAAGGAATC-AAAGTTATAAAAGA-ACTCGTAAAAGTTTGT
* * * * **
786 CAAGTTC----G---G-CTGAG-AACGAATAGAAAAATAATTCTCGTCTAAATAAGTTTTTAATT
129 CAAGTTCGGAAGTTCGACCGAGAAAC-AAAAGAGAAACAATTCTCACCTAAATAAGTTTTTAATT
* * * *
842 GAAAAACCAAAAGTAGTATACAA
193 CAAAGACCAAAAGTAGTTTAAAA
* *
865 AATGACAACTATTTAGACCTAATGTTGTGATTTCCCAAGCATGGACTGTATAAAAAATTACTCGA
1 AATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTATAAAAAATTGCTCGA
*
930 AGGAATTGATCGTCTTGAATA
66 AGGAATGGATCGTCTTGAATA
951 CAATCTATTT
Statistics
Matches: 599, Mismatches: 108, Indels: 40
0.80 0.14 0.05
Matches are distributed among these distances:
206 2 0.00
207 136 0.23
208 1 0.00
211 1 0.00
214 14 0.02
215 430 0.72
216 15 0.03
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (215 bp):
AATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTGTATAAAAAATTGCTCGA
AGGAATGGATCGTCTTGAATAGTTTAAGGAATCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCA
AGTTCGGAAGTTCGACCGAGAAACAAAAGAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAA
AGACCAAAAGTAGTTTAAAA
Found at i:3186 original size:6 final size:6
Alignment explanation
Indices: 3177--3201 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3167 GTTCAACAAC
3177 AACACA AACACA AACACA AACACA A
1 AACACA AACACA AACACA AACACA A
3202 CATTAACAAT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AACACA
Found at i:5018 original size:101 final size:101
Alignment explanation
Indices: 4882--5104 Score: 268
Period size: 101 Copynumber: 2.2 Consensus size: 101
4872 GTTCCGTTGT
* * * *
4882 AACTTCA-AGGAGATAAAGAATTGCTTCCATCACTTTAATCTGACCCACTGTAACTTTAGGGGTA
1 AACTTCAGA-GAGATAAAGATTTGCTTCCATCACTTTAATCCGACCCACTGCAACTTCAGGGGTA
* * * *
4946 TAAGATTTGGTGTGGTAGCTTTATCTTGCTCCACTGC
65 TAAGATTTGATGTGGTAGCTTCATCCTACTCCACTGC
* * * * *
4983 AACTTCAGAGAGGTAAAGATTTTCTTTCATGACTTTCATCCGACCCACTGCAACTTCAGGGGTAT
1 AACTTCAGAGAGATAAAGATTTGCTTCCATCACTTTAATCCGACCCACTGCAACTTCAGGGGTAT
* * * *
5048 AGGATTTGATTTTGTAGCTTCATCCTACTCTACTGC
66 AAGATTTGATGTGGTAGCTTCATCCTACTCCACTGC
*
5084 AACTTCAGAGAGATAAGGATT
1 AACTTCAGAGAGATAAAGATT
5105 CACTTTCGTA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 101 0.99
102 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (101 bp):
AACTTCAGAGAGATAAAGATTTGCTTCCATCACTTTAATCCGACCCACTGCAACTTCAGGGGTAT
AAGATTTGATGTGGTAGCTTCATCCTACTCCACTGC
Found at i:5111 original size:101 final size:100
Alignment explanation
Indices: 4882--5153 Score: 264
Period size: 101 Copynumber: 2.7 Consensus size: 100
4872 GTTCCGTTGT
* * * * * *
4882 AACTTCA-AGGAGATAAAGAATT-GCTTCCATCACTTTAATCTGACCCACTGTAACTTTAGGGGT
1 AACTTCAGA-GAGATAAAG-ATTCACTTTCAT-ACTTTCATCCGACCCACTGCAACTTCAGGGGT
* * * * *
4945 ATAAGATTTGGTGTGGTAGCTTTATCTTGCTCCACTGC
63 ATAGGATTTGATGTGGTAGCTTCATCCTACTCCACTGC
* **
4983 AACTTCAGAGAGGTAAAGATTTTCTTTCATGACTTTCATCCGACCCACTGCAACTTCAGGGGTAT
1 AACTTCAGAGAGATAAAGATTCACTTTCAT-ACTTTCATCCGACCCACTGCAACTTCAGGGGTAT
* * *
5048 AGGATTTGATTTTGTAGCTTCATCCTACTCTACTGC
65 AGGATTTGATGTGGTAGCTTCATCCTACTCCACTGC
* * * * *
5084 AACTTCAGAGAGATAAGGATTCACTTTCGTAGC-TTCAATCCAATCCACTGC-ACTTCAGGGATA
1 AACTTCAGAGAGATAAAGATTCACTTTCATA-CTTTC-ATCCGACCCACTGCAACTTCAGGGGTA
5147 TAGGATT
64 TAGGATT
5154 GAGTTTCGTA
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
100 25 0.17
101 117 0.82
102 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (100 bp):
AACTTCAGAGAGATAAAGATTCACTTTCATACTTTCATCCGACCCACTGCAACTTCAGGGGTATA
GGATTTGATGTGGTAGCTTCATCCTACTCCACTGC
Found at i:5118 original size:51 final size:50
Alignment explanation
Indices: 5017--5169 Score: 163
Period size: 49 Copynumber: 3.1 Consensus size: 50
5007 TTTCATGACT
* * *
5017 TTCATCCGAC-CCACTGCAACTTCAGGGGTATAGGATTTGA-TTTTGTAGC
1 TTCATCCTACTCCACTGCAACTTCAGGGATATAGGA-TTGACTTTCGTAGC
* *
5066 TTCATCCTACTCTACTGCAACTTCAGAGAGATA-AGGATTCACTTTCGTAGC
1 TTCATCCTACTCCACTGCAACTTCAG-G-GATATAGGATTGACTTTCGTAGC
* * *
5117 TTCAATCC-AATCCACTGC-ACTTCAGGGATATAGGATTGAGTTTCGTAAC
1 TTC-ATCCTACTCCACTGCAACTTCAGGGATATAGGATTGACTTTCGTAGC
5166 TTCA
1 TTCA
5170 CTCCATTCCA
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
48 5 0.06
49 28 0.32
50 24 0.27
51 24 0.27
52 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (50 bp):
TTCATCCTACTCCACTGCAACTTCAGGGATATAGGATTGACTTTCGTAGC
Found at i:5268 original size:102 final size:99
Alignment explanation
Indices: 5140--5355 Score: 240
Period size: 102 Copynumber: 2.2 Consensus size: 99
5130 ACTGCACTTC
* * *
5140 AGGGATATAGGA-TTGAGTTTCGTAACTTCACTCCATTCCACCATAACTTTAGGGAGATTGAGAT
1 AGGGGTATAGGATTTGAGGTTCGTAACTTCACTCCATTCCACCACAACTTTAGGGAGATTGAGAT
* * * *
5204 CTGATACTG-TTAGTTTTAATCCGCCCCTTTATAACTCT
66 -TCAT--TGCTCA-TTTTAATCCG-CCCTATACAACTCT
** *** *
5242 AGGGGTATAGGATTTGAGGTT-GTAACTTCACTTTATTCCATTGCAACTTTAGGGAGATTGAGGT
1 AGGGGTATAGGATTTGAGGTTCGTAACTTCACTCCATTCCACCACAACTTTAGGGAGATTGAGAT
*
5306 TCATTGCTCATTTTAATCCGCCCTATACAACTTT
66 TCATTGCTCATTTTAATCCGCCCTATACAACTCT
5340 AGGGGTATAGGATTTG
1 AGGGGTATAGGATTTG
5356 TCATTTTGTC
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
98 27 0.28
99 12 0.12
100 2 0.02
101 3 0.03
102 47 0.48
103 7 0.07
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (99 bp):
AGGGGTATAGGATTTGAGGTTCGTAACTTCACTCCATTCCACCACAACTTTAGGGAGATTGAGAT
TCATTGCTCATTTTAATCCGCCCTATACAACTCT
Found at i:9907 original size:17 final size:18
Alignment explanation
Indices: 9887--9923 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9877 TCAGTAGTTG
9887 TCAAG-ACAGT-CAGCAAT
1 TCAAGAACAGTGCAG-AAT
9904 TCAAGAACAGTGCAGAAT
1 TCAAGAACAGTGCAGAAT
9922 TC
1 TC
9924 TACTGATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 10 0.56
19 3 0.17
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (18 bp):
TCAAGAACAGTGCAGAAT
Found at i:10081 original size:24 final size:20
Alignment explanation
Indices: 10052--10111 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
10042 GTACAAGTGT
10052 ATGAACTACCGATACTTCTATA
1 ATGAACTACCGATAC--CTATA
*
10074 AGTAGAACTACCAATACCTATA
1 A-T-GAACTACCGATACCTATA
10096 ATGCAACTACCGATAC
1 ATG-AACTACCGATAC
10112 AACTCAAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.36
22 7 0.21
23 1 0.03
24 12 0.36
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (20 bp):
ATGAACTACCGATACCTATA
Found at i:10970 original size:52 final size:52
Alignment explanation
Indices: 10889--11202 Score: 375
Period size: 52 Copynumber: 6.1 Consensus size: 52
10879 TTCCCATTTA
* * * * *
10889 ATACTCATGATGACACAAAGTCATCGGACCTTA-AATCCGAAAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCG-TAAAGGATTCAT
** * * *
10941 ACGCTCATGATGACACATAGTCATCGGACCTCATAATACGTAAAGTATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
10993 ATACTCACGATGACACATAGTTATTGGCCCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
** * * * *
11045 ATACTCACGATGACACATAGTCATTTGATCTCATAATTCATAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
11097 ATACTCACGATGACAC--AGTCATTGGACCTCATAATCAGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* **
11147 ATACTCACAAT-ACACATAGTCATCAAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
11198 ATACT
1 ATACT
11203 GTGTCATCGG
Statistics
Matches: 225, Mismatches: 34, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
49 4 0.02
50 38 0.17
51 35 0.16
52 143 0.64
53 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:15898 original size:16 final size:17
Alignment explanation
Indices: 15868--15899 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15858 AATAACATTT
15868 TTAGTAAGCTTCAAAGC
1 TTAGTAAGCTTCAAAGC
15885 TTAGTAAG-TTCAAAG
1 TTAGTAAGCTTCAAAG
15900 AATTTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (17 bp):
TTAGTAAGCTTCAAAGC
Found at i:16343 original size:119 final size:118
Alignment explanation
Indices: 16132--16368 Score: 456
Period size: 119 Copynumber: 2.0 Consensus size: 118
16122 GCTGCTCATA
*
16132 TGAGCTATCGAGAATATGCATTTAAGCATAAATCACAGCCATCGTAGGGCCTACAATCCAAAATT
1 TGAGCTATCGAGAATATGCATTTAAGCATAAATCACAGCCATCATAGGGCCTACAATCCAAAATT
16197 TTGGATTCATTTCTCATTTCCAATTTAATACTCACGATGAAACCAAGTCATCC
66 TTGGATTCATTTCTCATTTCCAATTTAATACTCACGATGAAACCAAGTCATCC
16250 NTGAGCTATCGAGAATATGCATTTAAGCATAAATCACAGCCATCATAGGGCCTACAATCCAAAAT
1 -TGAGCTATCGAGAATATGCATTTAAGCATAAATCACAGCCATCATAGGGCCTACAATCCAAAAT
16315 TTTGGATTCATTTCTCATTTCCAATTTAATACTCACGATGAAACCAAGTCATCC
65 TTTGGATTCATTTCTCATTTCCAATTTAATACTCACGATGAAACCAAGTCATCC
16369 GACCTTAAAT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (118 bp):
TGAGCTATCGAGAATATGCATTTAAGCATAAATCACAGCCATCATAGGGCCTACAATCCAAAATT
TTGGATTCATTTCTCATTTCCAATTTAATACTCACGATGAAACCAAGTCATCC
Found at i:16425 original size:52 final size:52
Alignment explanation
Indices: 16343--16737 Score: 587
Period size: 52 Copynumber: 7.6 Consensus size: 52
16333 TTCCAATTTA
* * * * *
16343 ATACTCACGATGAAACCA-AGTCATCCGACCTTA-AATCCGAAAAAGGATCCAT
1 ATACTCACGATGACA-CATAGTCATCGGACCTCATAATCCG-TAAAGGATTCAT
* * * *
16395 ATGCTCACGATAACACATAGTCATCGGACCTAATAATCCGTAAAGGACTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
16447 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
16499 ATACTCACGATGACACATAGTCATCAGATCTCACAATCCTTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* **
16551 ATACTCACGATGACACATAGTCATCAGACCTCATAATTNGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
16603 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
16655 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
16707 ATACTCACGATGACACATAGTCATCAGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
16738 TTTCCGTTTA
Statistics
Matches: 312, Mismatches: 29, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
51 2 0.01
52 304 0.97
53 6 0.02
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:29777 original size:60 final size:61
Alignment explanation
Indices: 29664--29792 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 61
29654 GCTAAATTTG
* * * *
29664 AATTTTTGGAAAGTTTTAAGGGTCAAAATATAATATTCGGAAAATTTAAGGGTTAAAACAT
1 AATTTTTAGAAAGTTTTAAGGGTCAAAACATAATATTCAGAAAATTTAAGGGTTAAAACAC
* * * * *
29725 AATTTTTAGAAAG-TTTAGGGGTCAAAACATAATTTTTAGAAAGTTTAGGGGTTAAAACAC
1 AATTTTTAGAAAGTTTTAAGGGTCAAAACATAATATTCAGAAAATTTAAGGGTTAAAACAC
*
29785 CATTTTTA
1 AATTTTTA
29793 AATAAAATAG
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
60 46 0.79
61 12 0.21
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (61 bp):
AATTTTTAGAAAGTTTTAAGGGTCAAAACATAATATTCAGAAAATTTAAGGGTTAAAACAC
Found at i:29790 original size:30 final size:30
Alignment explanation
Indices: 29664--29792 Score: 141
Period size: 30 Copynumber: 4.3 Consensus size: 30
29654 GCTAAATTTG
* * * *
29664 AATTTTTGGAAAGTTTTAAGGGTCAAAATAT
1 AATTTTTAGAAAG-TTTAGGGGTTAAAACAT
* ** * *
29695 AATATTCGGAAAATTTAAGGGTTAAAACAT
1 AATTTTTAGAAAGTTTAGGGGTTAAAACAT
*
29725 AATTTTTAGAAAGTTTAGGGGTCAAAACAT
1 AATTTTTAGAAAGTTTAGGGGTTAAAACAT
*
29755 AATTTTTAGAAAGTTTAGGGGTTAAAACAC
1 AATTTTTAGAAAGTTTAGGGGTTAAAACAT
*
29785 CATTTTTA
1 AATTTTTA
29793 AATAAAATAG
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 74 0.88
31 10 0.12
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAGGGGTTAAAACAT
Found at i:31721 original size:122 final size:123
Alignment explanation
Indices: 31504--31789 Score: 403
Period size: 122 Copynumber: 2.3 Consensus size: 123
31494 TTGGTCAACC
***
31504 TCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCTTTTTGAGCTCCGCTTCATTGTT
1 TCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGTT
* * * ** *
31569 TTTGTCCACTTCCTTGTATCTCATTAGGAAGATGACCGCTTTGTTG-TTTGATCCACT
66 TTGGTCCACTTCCTTGTATCTCATCAGGAAGATAACCGCTTCATCGTTTTGATCCACT
* * **
31626 TCTCTGTGTCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGTT
1 TCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGTT
* * * *
31691 TTGGTCCACTTCTTTGTATCTCATCAGGAAGATAACTGCTTCATCGTTTTGATTCATT
66 TTGGTCCACTTCCTTGTATCTCATCAGGAAGATAACCGCTTCATCGTTTTGATCCACT
*
31749 TCTCTGCATCTCATCAGGAAGATGGGGTTTGAAGTTTCACT
1 TCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACT
31790 TTACTCCACT
Statistics
Matches: 143, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
122 96 0.67
123 47 0.33
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (123 bp):
TCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGTT
TTGGTCCACTTCCTTGTATCTCATCAGGAAGATAACCGCTTCATCGTTTTGATCCACT
Found at i:31760 original size:48 final size:48
Alignment explanation
Indices: 31679--31771 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
31669 CATTGAGCTT
* * * *
31679 TGCTTCATTGTTTTGGTCCACTTCTTTGTATCTCATCAGGAAGATAAC
1 TGCTTCATCGTTTTGATCCACTTCTCTGCATCTCATCAGGAAGATAAC
* *
31727 TGCTTCATCGTTTTGATTCATTTCTCTGCATCTCATCAGGAAGAT
1 TGCTTCATCGTTTTGATCCACTTCTCTGCATCTCATCAGGAAGAT
31772 GGGGTTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (48 bp):
TGCTTCATCGTTTTGATCCACTTCTCTGCATCTCATCAGGAAGATAAC
Found at i:38834 original size:21 final size:21
Alignment explanation
Indices: 38775--38840 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
38765 GGAGTTTTTA
**
38775 GTATCGATAGAAGTAAGACTT
1 GTATCGATAGAAGTATCACTT
* *
38796 GTATC-AGTAAAAGAATCACTT
1 GTATCGA-TAGAAGTATCACTT
*
38817 GTATCGATAGAACTATCACTT
1 GTATCGATAGAAGTATCACTT
38838 GTA
1 GTA
38841 CCGGTAGGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (21 bp):
GTATCGATAGAAGTATCACTT
Found at i:39109 original size:72 final size:73
Alignment explanation
Indices: 38991--39190 Score: 251
Period size: 72 Copynumber: 2.7 Consensus size: 73
38981 ATAATTTACG
* * * **
38991 ACGTTGAACTTTGCTTCATTGTCTTGATCCATTTCTCTATATCTCATTTGGAAGAT-GTGTTTGA
1 ACGTTGAGCTTCGCTTCATTGT-TTGGTCCATTTCTCTATATCTCATTAAGAAGATGGTGTTT-A
*
39055 AGGTTTC-TC
64 AAGTTTCATC
39064 ACGTTGAGCTTCGCTTCATTGTTTGGTCCATTTCTCTATATCTCATTAAGAAGATGGTGTTTAAA
1 ACGTTGAGCTTCGCTTCATTGTTTGGTCCATTTCTCTATATCTCATTAAGAAGATGGTGTTTAAA
39129 GTTTCATTC
66 GTTTCA-TC
* * * * *
39138 ACATTGAGCTTCGCTTCATTATTTTGGTCCACTTCTTTATATCTCATCAAGAA
1 ACGTTGAGCTTCGCTTCATT-GTTTGGTCCATTTCTCTATATCTCATTAAGAA
39191 AATGACCGCT
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
72 37 0.33
73 26 0.23
74 21 0.19
75 28 0.25
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.43
Consensus pattern (73 bp):
ACGTTGAGCTTCGCTTCATTGTTTGGTCCATTTCTCTATATCTCATTAAGAAGATGGTGTTTAAA
GTTTCATC
Found at i:39288 original size:124 final size:124
Alignment explanation
Indices: 39095--39380 Score: 371
Period size: 124 Copynumber: 2.3 Consensus size: 124
39085 TTTGGTCCAT
* * ** * *
39095 TTCTCTATATCTCATTAAGAAGAT-GGTGTTTAAAGTTTCATTCACATTGAGCTTCGCTTCATTA
1 TTCTCTATATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACACACATTGAACTTCACTTCATTA
* *
39159 TTTTGGTCCACTTCTTTATATCTCATCAAGAAAATGACCGCTTCATCATTTTGAT-TCAC
66 TTTTGGTCCACTTCTCTATATCTAATCAAGAAAATGACCGCTTCATCATTTTGATCT-AC
* * *
39218 TTCTCTATACCTCATCAGGAAGATGGGGGTTTTAAGTTTCACACACATTGAACTTCAC-TCTATT
1 TTCTCTATATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACACACATTGAACTTCACTTC-ATT
* * * * *
39282 GTTTTGGTCTACTTCTCTATATCTAATCAGGAAGATGACCGCTTCATCGTTTTGATCTAC
65 ATTTTGGTCCACTTCTCTATATCTAATCAAGAAAATGACCGCTTCATCATTTTGATCTAC
* *
39342 TTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTT
1 TTCTCTATATCTCATCAAGAAGATGGGGGTTTAAAGTTT
39381 TACTCTACTC
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
123 23 0.16
124 116 0.83
125 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (124 bp):
TTCTCTATATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACACACATTGAACTTCACTTCATTA
TTTTGGTCCACTTCTCTATATCTAATCAAGAAAATGACCGCTTCATCATTTTGATCTAC
Found at i:39492 original size:48 final size:48
Alignment explanation
Indices: 39282--39511 Score: 155
Period size: 48 Copynumber: 4.8 Consensus size: 48
39272 TCACTCTATT
* * * *
39282 GTTTTGGTCTACTTCTCTATATCTAATCAGGAAGATGACCGCTTCATC
1 GTTTTGATCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATC
* *** * * *
39330 GTTTTGATCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGA-A
1 GTTTTGATCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATC
* * * * * ** *
39377 GTTTT-ACTCTACTCCACTGTAAC-C-TCAAGGATGTTGAGCTCTTTTTCATT
1 GTTTTGA-TCTACTTCTCTGTATCTCATC-AGGAAGATGA--TC-GCTTCATC
* * *
39427 GCTTTGCT-TCACTTCTCTATATCTCATCAGGAAGATGATCGCTTCATC
1 GTTTTGATCT-ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATC
* *
39475 GTTTTGATCCACTTCTCTGTATCTCATCAGGATGATG
1 GTTTTGATCTACTTCTCTGTATCTCATCAGGAAGATG
39512 GAGTTTGAAG
Statistics
Matches: 133, Mismatches: 38, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
45 2 0.02
46 8 0.06
47 18 0.14
48 73 0.55
49 7 0.05
50 14 0.11
51 9 0.07
52 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.39
Consensus pattern (48 bp):
GTTTTGATCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATC
Found at i:41498 original size:3 final size:3
Alignment explanation
Indices: 41490--41552 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
41480 GATCATCCCT
41490 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
41538 TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC
41553 ATAACAATGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.