Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009602.1 Kokia drynarioides strain JFW-HI SEQ_124318, 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: 26107
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:2030 original size:3 final size:3
Alignment explanation
Indices: 2022--2058 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2012 TTTGTTGATT
2022 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2059 ATGTGAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:7587 original size:17 final size:17
Alignment explanation
Indices: 7561--7609 Score: 89
Period size: 17 Copynumber: 2.8 Consensus size: 17
7551 ATTGCCGCAT
7561 AAAATGCAAAATTCTTAA
1 AAAAT-CAAAATTCTTAA
7579 AAAATCAAAATTCTTAA
1 AAAATCAAAATTCTTAA
7596 AAAATCAAAATTCT
1 AAAATCAAAATTCT
7610 CAACTTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATCAAAATTCTTAA
Found at i:8103 original size:17 final size:17
Alignment explanation
Indices: 8080--8189 Score: 159
Period size: 17 Copynumber: 6.4 Consensus size: 17
8070 CCAAACTCAT
8080 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
8098 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
8115 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
8132 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
8149 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
*
8167 TTTAAATTTATTATAAA
1 TTTAAATTTATTTTAAA
8184 TTTAAA
1 TTTAAA
8190 ATAAATAAAG
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
17 55 0.65
18 29 0.35
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:8119 original size:35 final size:34
Alignment explanation
Indices: 8080--8189 Score: 159
Period size: 35 Copynumber: 3.2 Consensus size: 34
8070 CCAAACTCAT
*
8080 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTT-AAA
*
8115 TTTAAATTTATTTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
*
8149 TTTAAATTTATTTTCAAATTTAAATTTATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTTAAA
8184 TTTAAA
1 TTTAAA
8190 ATAAATAAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
34 17 0.25
35 52 0.75
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:8123 original size:6 final size:6
Alignment explanation
Indices: 8112--8189 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
8102 ATTTGTTTTA
* * *
8112 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
8158 -ATTTT CAAATTT AAATTT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
8190 ATAAATAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 3 0.05
5 13 0.22
6 35 0.60
7 7 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:8129 original size:11 final size:11
Alignment explanation
Indices: 8115--8170 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
8105 TGTTTTAAAA
8115 TTTAAATTTAT
1 TTTAAATTTAT
*
8126 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
8138 TTT-ATTTTAAG
1 TTTAAATTT-AT
8149 TTTAAATTTAT
1 TTTAAATTTAT
8160 TTTCAAATTTA
1 TTT-AAATTTA
8171 AATTTATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 22 0.59
12 15 0.41
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:8142 original size:52 final size:52
Alignment explanation
Indices: 8080--8189 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 52
8070 CCAAACTCAT
* *
8080 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTAAAATTTAAATTTATTATAAA
* *
8132 TTTAAATTTATTTTAAGTTTAAATTTATTTTCAAATTTAAATTTATTATAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTAAAATTTAAATTTATTATAAA
8184 TTTAAA
1 TTTAAA
8190 ATAAATAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (52 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTAAAATTTAAATTTATTATAAA
Found at i:8283 original size:26 final size:24
Alignment explanation
Indices: 8237--8308 Score: 65
Period size: 26 Copynumber: 2.9 Consensus size: 24
8227 GCTCAATTGG
* *
8237 ACCCAAATTCAAATGATCCAAACTAA
1 ACCCAAATTC-AATTACCCAAA-TAA
*
8263 ACCCAAATTACAATTACCCAAATAG
1 ACCCAAATT-CAATTACCCAAATAA
*
8288 GCCCAAA-TCAATTAACCCAAA
1 ACCCAAATTCAATT-ACCCAAA
8309 AGAAGCCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.12
24 8 0.20
25 8 0.20
26 18 0.45
27 1 0.03
ACGTcount: A:0.49, C:0.29, G:0.04, T:0.18
Consensus pattern (24 bp):
ACCCAAATTCAATTACCCAAATAA
Found at i:9318 original size:29 final size:27
Alignment explanation
Indices: 9276--9379 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 27
9266 AAACTTTTTG
* *
9276 AAAATTTCATTTTTACCCTCAAACTTTCTA
1 AAAATTCCA-TTTTACCC-CAAAC-TTCCA
9306 AAAATTCCATTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTT-ACCCC-AAACTTCCA
* * * *
9335 AAAAATACATTTTCCCCCCAACTTCCA
1 AAAATTCCATTTTACCCCAAACTTCCA
*
9362 AAAATTACCCTTTTACCC
1 AAAATT-CCATTTTACCC
9380 TCGGATGTCC
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
27 13 0.21
28 12 0.20
29 20 0.33
30 16 0.26
ACGTcount: A:0.36, C:0.31, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAATTCCATTTTACCCCAAACTTCCA
Found at i:9331 original size:30 final size:29
Alignment explanation
Indices: 9254--9327 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
9244 CCAAAATTAT
* * *
9254 ATTTTAGACCCCAAACTTTTTGAAAATTTC
1 ATTTT-GACCCCAAACTTTCTAAAAATTCC
*
9284 ATTTTTACCCTCAAACTTTCTAAAAATTCC
1 ATTTTGACCC-CAAACTTTCTAAAAATTCC
9314 ATTTTGACCCCAAA
1 ATTTTGACCCCAAA
9328 ACTTCCAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 8 0.21
30 30 0.79
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTGACCCCAAACTTTCTAAAAATTCC
Found at i:9339 original size:30 final size:28
Alignment explanation
Indices: 9276--9379 Score: 86
Period size: 30 Copynumber: 3.6 Consensus size: 28
9266 AAACTTTTTG
* * *
9276 AAAATTTCATTTTTACCCTCAAACTTTCTA
1 AAAATTACA-TTTTACCC-CAAACTTCCAA
*
9306 AAAATTCCATTTTGACCCCAAAACTTCCAA
1 AAAATTACATTTT-ACCCC-AAACTTCCAA
* *
9336 AAAA-TACATTTTCCCCCCAACTTCC-A
1 AAAATTACATTTTACCCCAAACTTCCAA
*
9362 AAAATTACCCTTTTACCC
1 AAAATTA-CATTTTACCC
9380 TCGGATGTCC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
26 5 0.08
27 9 0.15
28 12 0.19
29 12 0.19
30 24 0.39
ACGTcount: A:0.36, C:0.31, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAATTACATTTTACCCCAAACTTCCAA
Found at i:9866 original size:97 final size:97
Alignment explanation
Indices: 9765--9952 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 97
9755 TTTAAAATTC
* * * * * *
9765 AGGCAATATTATTTTATTTCGAATTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA-TTTTTC
1 AGGCAATATT-TCTCATCTCGAATTCTGAAAATTTGTACCTAAACTTACTAGGCACGACTTTTTC
* *
9829 TTCAAATCGAAATAATTGAATATCCTTAAATCG
65 TTCAAATCGAAATAATCGAACATCCTTAAATCG
* * **
9862 AGGCAATGTTTCTCATCTCGGATTCTGAAAATTTGTACCTAAACTTACTAGGTGCGACTTTTTCT
1 AGGCAATATTTCTCATCTCGAATTCTGAAAATTTGTACCTAAACTTACTAGGCACGACTTTTTCT
* *
9927 TTAAATCGAGATAATCGAACATCCTT
66 TCAAATCGAAATAATCGAACATCCTT
9953 TTCAAAAGTG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 38 0.50
97 38 0.50
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (97 bp):
AGGCAATATTTCTCATCTCGAATTCTGAAAATTTGTACCTAAACTTACTAGGCACGACTTTTTCT
TCAAATCGAAATAATCGAACATCCTTAAATCG
Found at i:12944 original size:29 final size:29
Alignment explanation
Indices: 12904--12962 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12894 TCGTGGAAGA
* * *
12904 GGTGGAGAACTTGTTCATTGAGAGTTCGT
1 GGTGAAGAACTTATTCATTGAGAATTCGT
*
12933 GGTGAAGAACTTATTCGTTGAGAATTCGT
1 GGTGAAGAACTTATTCATTGAGAATTCGT
12962 G
1 G
12963 TCAAGGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTATTCATTGAGAATTCGT
Found at i:13040 original size:35 final size:36
Alignment explanation
Indices: 12993--13070 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
12983 GTTATGTTAC
12993 CAAAATTCTAAGAG-ATTGCTTACAAGTCAAGTTAAA
1 CAAAA-TCTAAGAGAATTGCTTACAAGTCAAGTTAAA
*
13029 CAAAATCTAAGAGAATTGCTTTCAAGTCAAGTTAAA
1 CAAAATCTAAGAGAATTGCTTACAAGTCAAGTTAAA
13065 CAAAAT
1 CAAAAT
13071 ATATTATCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 8 0.20
36 32 0.80
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
CAAAATCTAAGAGAATTGCTTACAAGTCAAGTTAAA
Found at i:16997 original size:21 final size:20
Alignment explanation
Indices: 16954--16998 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16944 ATTTCGAAAG
* *
16954 TAAAATTTTGCAGGGTTCCT
1 TAAAATTCTGCAGGCTTCCT
*
16974 TAAAATTCTGCAGTCTTACCT
1 TAAAATTCTGCAGGCTT-CCT
16995 TAAA
1 TAAA
16999 TTTTACGGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
TAAAATTCTGCAGGCTTCCT
Found at i:18015 original size:59 final size:57
Alignment explanation
Indices: 17792--18056 Score: 216
Period size: 58 Copynumber: 4.5 Consensus size: 57
17782 CCCTAAAGGT
* * * * *
17792 CCCTAAACTATCCAAAAA-TATATTTAACCCCTAAACTTTTCCAAAATTATATTTTGAC
1 CCCTAAACTTTTCAAAAATTACATTTTACCCTTAAAC--TTCCAAAATTATATTTTGAC
* * *
17850 CCCTAAACTTTTCCAAAATTATATTTTAACCCTTAAACTTCTCTAAAATTATATTTTAAGC
1 CCCTAAACTTTTCAAAAATTACATTTT-ACCCTTAAACTTC-C-AAAATTATATTTTGA-C
* * ** *
17911 CCC-AAACTTTTCAAAACTTACATTTTACTCTCGAACTTTCCAAAATTCTATTTTTGA-
1 CCCTAAACTTTTCAAAAATTACATTTTACCCTTAAAC-TTCCAAAATTATA-TTTTGAC
* ** * *
17968 CCCTGAACTTTTCAAAAATTACCATTTTACCCTTAAACTTCCTAAAATTCCATTTTAAT
1 CCCTAAACTTTTCAAAAATTA-CATTTTACCCTTAAACTTCC-AAAATTATATTTTGAC
**
18027 CCCT--ACTTTTTGAAAATTACATTTTTACCC
1 CCCTAAACTTTTCAAAAATTACA-TTTTACCC
18057 CGAACTTTCC
Statistics
Matches: 172, Mismatches: 23, Indels: 25
0.78 0.10 0.11
Matches are distributed among these distances:
56 2 0.01
57 24 0.14
58 50 0.29
59 46 0.27
60 46 0.27
61 4 0.02
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (57 bp):
CCCTAAACTTTTCAAAAATTACATTTTACCCTTAAACTTCCAAAATTATATTTTGAC
Found at i:18071 original size:29 final size:29
Alignment explanation
Indices: 17796--18258 Score: 197
Period size: 30 Copynumber: 15.8 Consensus size: 29
17786 AAAGGTCCCT
* * *
17796 AAACTATCCAAAAA-TATA-TTTAACCCC
1 AAACTTTCCAAAAATTACATTTTTACCCC
* *
17823 TAAACTTTTCC-AAAATTATATTTTGACCCC
1 -AAAC-TTTCCAAAAATTACATTTTTACCCC
* * *
17853 TAAACTTTTCC-AAAATTATATTTTAACCCTT
1 -AAAC-TTTCCAAAAATTACATTTTTACCC-C
* * *
17884 AAAC-TTCTCTAAAATTATATTTTAAGCCCC
1 AAACTTTC-CAAAAATTACATTTTTA-CCCC
* * *
17914 AAACTTTTCAAAACTTACA-TTTTACTCTC
1 AAACTTTCCAAAAATTACATTTTTAC-CCC
* *
17943 GAACTTTCC-AAAATT-CTATTTTTGACCCT
1 AAACTTTCCAAAAATTAC-ATTTTT-ACCCC
* * *
17972 GAACTTTTCAAAAATTACCA-TTTTACCCTT
1 AAACTTTCCAAAAATTA-CATTTTTACCC-C
* * * *
18002 AAAC-TTCCTAAAATTCCATTTTAATCCC
1 AAACTTTCCAAAAATTACATTTTTACCCC
* ***
18030 -TACTTTTTGAAAATTACATTTTTACCCC
1 AAACTTTCCAAAAATTACATTTTTACCCC
*
18058 GAACTTTCCAAAAATTACCA-TTTTACCCTC
1 AAACTTTCCAAAAATTA-CATTTTTACCC-C
* *
18088 AATC-TT-CATAAAATTCCATTTTTTACCCC
1 AAACTTTCCA-AAAATTACA-TTTTTACCCC
** * * * *
18117 AATTTTTCTAAAAATTACCA-ATTTACATCT
1 AAACTTTCCAAAAATTA-CATTTTTAC-CCC
*
18147 AAAC-TTCCAAAAATTCCATTTTTTACCCC
1 AAACTTTCCAAAAATTACA-TTTTTACCCC
* ** *
18176 GATTTTTCCAAAACTTACCA-TTTTACCCCC
1 AAACTTTCCAAAAATTA-CATTTTTA-CCCC
* *
18206 AAAC-TTCTAAAAATTCCATTTTTGACCCC
1 AAACTTTCCAAAAATTACATTTTT-ACCCC
*
18235 AAACTTTCCCAAAATTACCATTTT
1 AAACTTTCCAAAAATTA-CATTTT
18259 GCCATTGAGT
Statistics
Matches: 333, Mismatches: 65, Indels: 71
0.71 0.14 0.15
Matches are distributed among these distances:
27 3 0.01
28 46 0.14
29 129 0.39
30 137 0.41
31 17 0.05
32 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTCCAAAAATTACATTTTTACCCC
Found at i:18102 original size:145 final size:145
Alignment explanation
Indices: 17894--18258 Score: 352
Period size: 145 Copynumber: 2.5 Consensus size: 145
17884 AAACTTCTCT
* * * *
17894 AAAATTATATTTTAAGCCCCAAACTTTTCAAAACTTACATTTTACTCTCGAACTTTCCAAAATTC
1 AAAATTACATTTTAAGCCCCAAACTTTCCAAAAATTACATTTTACCCTCGAACTTTCCAAAATTC
* * * * *
17959 TATTTTTGACCCTGAACTTTTC-AAAAATTACCATTTTAC-CCTTAAACTTCCTAAAATTCCATT
66 CATTTTTGACCC-CAACTTTTCTAAAAATTACCAATTTACATC-TAAACTTCCAAAAATTCCATT
18022 TTAATCCCTACTTTTTG
129 TTAATCCCTACTTTTTG
* * *
18039 AAAATTACATTTTTA-CCCCGAACTTTCCAAAAATTACCATTTTACCCTC-AA-TCTTCATAAAA
1 AAAATTACATTTTAAGCCCCAAACTTTCCAAAAATTA-CATTTTACCCTCGAACT-TTC-CAAAA
* *
18101 TTCCATTTTTTACCCCAATTTTTCTAAAAATTACCAATTTACATCTAAACTTCCAAAAATTCCAT
63 TTCCATTTTTGACCCCAACTTTTCTAAAAATTACCAATTTACATCTAAACTTCCAAAAATTCCA-
* * * *
18166 TTTTTACCCCGA-TTTTTCC
127 TTTTAATCCCTACTTTTT-G
* * * *
18185 AAAACTTACCATTTT-ACCCCCAAAC-TTCTAAAAATTCCATTTTTGACCC-CAAACTTTCCCAA
1 AAAA-TTA-CATTTTAAGCCCCAAACTTTCCAAAAATTACA-TTTT-ACCCTCGAACTTT-CCAA
18247 AATTACCATTTT
61 AATT-CCATTTT
18259 GCCATTGAGT
Statistics
Matches: 182, Mismatches: 22, Indels: 28
0.78 0.09 0.12
Matches are distributed among these distances:
143 1 0.01
144 30 0.16
145 80 0.44
146 16 0.09
147 19 0.10
148 27 0.15
149 9 0.05
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (145 bp):
AAAATTACATTTTAAGCCCCAAACTTTCCAAAAATTACATTTTACCCTCGAACTTTCCAAAATTC
CATTTTTGACCCCAACTTTTCTAAAAATTACCAATTTACATCTAAACTTCCAAAAATTCCATTTT
AATCCCTACTTTTTG
Found at i:18123 original size:86 final size:87
Alignment explanation
Indices: 17952--18123 Score: 233
Period size: 86 Copynumber: 2.0 Consensus size: 87
17942 CGAACTTTCC
* * * *
17952 AAAATTCTATTTTTGACCCTGAACTTTTCAAAAATTACCATTTTACCCTTAAACTTCCTAAAATT
1 AAAATTCTATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAAACTTCATAAAATT
* *
18017 CCATTTTAATCCCTACTTTTTG
66 CCATTTTAATCCCCAATTTTTG
*
18039 AAAATTAC-ATTTTT-ACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAATCTTCATAAAAT
1 AAAATT-CTATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAAACTTCATAAAAT
*
18102 TCCATTTT-TTACCCCAATTTTT
65 TCCATTTTAAT-CCCCAATTTTT
18124 CTAAAAATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 1 0.01
86 61 0.81
87 12 0.16
88 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.41
Consensus pattern (87 bp):
AAAATTCTATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAAACTTCATAAAATT
CCATTTTAATCCCCAATTTTTG
Found at i:18136 original size:59 final size:59
Alignment explanation
Indices: 18039--18258 Score: 252
Period size: 59 Copynumber: 3.7 Consensus size: 59
18029 CTACTTTTTG
* *
18039 AAAATTACA-TTTTTACCCCGAA-CTTTCCAAAAATTACCATTTTACCCTCAATCTTCAT
1 AAAATTCCATTTTTTACCCC-AATCTTTCCAAAAATTACCATTTTACCCTCAAACTTCAT
* * * *
18097 AAAATTCCATTTTTTACCCCAATTTTTCTAAAAATTACCAATTTA-CATCTAAACTTCCA-
1 AAAATTCCATTTTTTACCCCAATCTTTCCAAAAATTACCATTTTACCCTC-AAACTT-CAT
* * * *
18156 AAAATTCCATTTTTTACCCCGATTTTTCCAAAACTTACCATTTTACCCCCAAACTTC-T
1 AAAATTCCATTTTTTACCCCAATCTTTCCAAAAATTACCATTTTACCCTCAAACTTCAT
* * *
18214 AAAAATTCCATTTTTGACCCCAAACTTTCCCAAAATTACCATTTT
1 -AAAATTCCATTTTTTACCCCAATCTTTCCAAAAATTACCATTTT
18259 GCCATTGAGT
Statistics
Matches: 137, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
58 14 0.10
59 119 0.87
60 4 0.03
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTTACCCCAATCTTTCCAAAAATTACCATTTTACCCTCAAACTTCAT
Found at i:18187 original size:118 final size:117
Alignment explanation
Indices: 18039--18254 Score: 308
Period size: 118 Copynumber: 1.8 Consensus size: 117
18029 CTACTTTTTG
* *
18039 AAAATTACATTTTTACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAATCTTC-ATAAAATT
1 AAAATTACATTTTTACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAACTTCTA-AAAATT
* ** *
18103 CCATTTTTTACCCCAATTTTTCTAAAAATTACCAATTTACATCTAAACTTCCA
65 CCATTTTTGACCCCAAACTTTCCAAAAATTACCAATTTACATCTAAACTTCCA
* ** *
18156 AAAATTCCATTTTTTACCCCGATTTTTCCAAAACTTACCATTTTACCCCCAAACTTCTAAAAATT
1 AAAATTACA-TTTTTACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATT
*
18221 CCATTTTTGACCCCAAACTTTCCCAAAATTACCA
65 CCATTTTTGACCCCAAACTTTCCAAAAATTACCA
18255 TTTTGCCATT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
117 8 0.09
118 77 0.90
119 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (117 bp):
AAAATTACATTTTTACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATTC
CATTTTTGACCCCAAACTTTCCAAAAATTACCAATTTACATCTAAACTTCCA
Found at i:18301 original size:28 final size:28
Alignment explanation
Indices: 18243--18304 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
18233 CCAAACTTTC
* * *
18243 CCAAAATTACCATTTTGCCATTGAGTGT
1 CCAAAATTACCATTTTACCATCGAGTAT
* *
18271 CCAAAATTACCATTTTACCCTCGGGTAT
1 CCAAAATTACCATTTTACCATCGAGTAT
18299 CCAAAA
1 CCAAAA
18305 ATCACATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCATCGAGTAT
Found at i:19363 original size:3 final size:3
Alignment explanation
Indices: 19355--19386 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19345 ATATCATTTT
19355 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
19387 TCCATTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:20439 original size:21 final size:21
Alignment explanation
Indices: 20403--20448 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
20393 ATCATTTTGT
*
20403 TTTTCTCATTTCATCCTTCA-
1 TTTTCTCATTTCATCCATCAC
20423 TTTTCTCAAGTTT-ATCCATCAC
1 TTTTCTC-A-TTTCATCCATCAC
20445 TTTT
1 TTTT
20449 TTTTCAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTCTCATTTCATCCATCAC
Found at i:24187 original size:22 final size:22
Alignment explanation
Indices: 24159--24200 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
24149 GGTCACTGAT
*
24159 TTAATTATTAATATTGTTAATA
1 TTAATTATTAATACTGTTAATA
24181 TTAATTATTAATACTGTTAA
1 TTAATTATTAATACTGTTAA
24201 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TTAATTATTAATACTGTTAATA
Found at i:24771 original size:12 final size:12
Alignment explanation
Indices: 24736--24794 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
24726 ATTCACGAAC
*
24736 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
24748 AAGCTCATTTAT
1 AAGCTCGTTTAT
24760 AAGCTCGTTTATT
1 AAGCTCGTTTA-T
*
24773 AA-CTCTTTTAT
1 AAGCTCGTTTAT
24784 -AGCTCGTTTAT
1 AAGCTCGTTTAT
24795 TTATTAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 1 0.03
11 9 0.22
12 27 0.68
13 3 0.08
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:24791 original size:23 final size:25
Alignment explanation
Indices: 24736--24795 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
24726 ATTCACGAAC
*
24736 AAGCTCGTTTA-AAAGCTCATTTAT
1 AAGCTCGTTTATTAAGCTCATTTAT
*
24760 AAGCTCGTTTATTAA-CTCTTTTAT
1 AAGCTCGTTTATTAAGCTCATTTAT
24784 -AGCTCGTTTATT
1 AAGCTCGTTTATT
24796 TATTAATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 12 0.36
24 19 0.58
25 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.45
Consensus pattern (25 bp):
AAGCTCGTTTATTAAGCTCATTTAT
Found at i:24931 original size:23 final size:22
Alignment explanation
Indices: 24876--24985 Score: 112
Period size: 23 Copynumber: 4.8 Consensus size: 22
24866 TATTAACATT
* *
24876 GTTCATGAACGTGTTCAATTATA
1 GTTCATGAACATGTTCGATTA-A
*
24899 TGTTCATGAACATGTTCGTTTAA
1 -GTTCATGAACATGTTCGATTAA
*
24922 CGTTCGTGAACATGTTCGATTAA
1 -GTTCATGAACATGTTCGATTAA
**
24945 TGTTTGTGAACATGTTCGATTAA
1 -GTTCATGAACATGTTCGATTAA
*
24968 GTTAAATGAACATGTTCG
1 GTT-CATGAACATGTTCG
24986 TGAACATTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
22 3 0.04
23 54 0.72
24 18 0.24
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (22 bp):
GTTCATGAACATGTTCGATTAA
Found at i:24955 original size:46 final size:46
Alignment explanation
Indices: 24876--24985 Score: 132
Period size: 46 Copynumber: 2.4 Consensus size: 46
24866 TATTAACATT
* * *
24876 GTTCATGAACGTGTTCAATTATATGTTCATGAACATGTTCGTTTAA
1 GTTCATGAACATGTTCGATTATATGTTCATGAACATGTTCGATTAA
* **
24922 CGTTCGTGAACATGTTCGATTA-ATGTTTGTGAACATGTTCGATTAA
1 -GTTCATGAACATGTTCGATTATATGTTCATGAACATGTTCGATTAA
*
24968 GTTAAATGAACATGTTCG
1 GTT-CATGAACATGTTCG
24986 TGAACATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 3 0.06
46 33 0.61
47 18 0.33
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (46 bp):
GTTCATGAACATGTTCGATTATATGTTCATGAACATGTTCGATTAA
Found at i:24995 original size:23 final size:23
Alignment explanation
Indices: 24951--24996 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
24941 TTAATGTTTG
* *
24951 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
24974 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
24997 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Done.