Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012950.1 Kokia drynarioides strain JFW-HI SEQ_127968, 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: 27301
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2469 original size:26 final size:27
Alignment explanation
Indices: 2431--2482 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
2421 ATTGAACAAA
2431 AAAAAAGAATAAAAACAAAAA-ATTTT
1 AAAAAAGAATAAAAACAAAAACATTTT
* *
2457 AAAAAAGAGTAAAAATAAAAACATTT
1 AAAAAAGAATAAAAACAAAAACATTT
2483 AATTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAAAAGAATAAAAACAAAAACATTTT
Found at i:4294 original size:99 final size:100
Alignment explanation
Indices: 4093--4300 Score: 240
Period size: 100 Copynumber: 2.1 Consensus size: 100
4083 CAGGAAAATG
* ** * * * *
4093 GGATTTGGTGTTGAAGCTTCTTTCTATTCCACTGTAACCTCAGGAACATTGAGATCTACTTCATT
1 GGATTTGGTGTTGAAACTTCACTCCATTACACTGTAACCTCAGGAACACTGAGATCTACTTCATC
* *
4158 ATTTTAATCTGACCCACTACAACTTCAGGGGTATA
66 ATTTTAATCTGACCCACTACAACTTCAAGGATATA
* * * *
4193 GGATTTGGTGTTTAAACTTCACTCCATTACACTGTAACCTTAGGGACACTGAGATCT-GTT-ACT
1 GGATTTGGTGTTGAAACTTCACTCCATTACACTGTAACCTCAGGAACACTGAGATCTACTTCA-T
* * *
4256 CATTTTGATCTGATCCACTGCAACTTCAAGGATATA
65 CATTTTAATCTGACCCACTACAACTTCAAGGATATA
*
4292 GGATCTGGT
1 GGATTTGGT
4301 TCTTCATTCC
Statistics
Matches: 90, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
98 1 0.01
99 41 0.46
100 48 0.53
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (100 bp):
GGATTTGGTGTTGAAACTTCACTCCATTACACTGTAACCTCAGGAACACTGAGATCTACTTCATC
ATTTTAATCTGACCCACTACAACTTCAAGGATATA
Found at i:4355 original size:93 final size:96
Alignment explanation
Indices: 4109--4356 Score: 236
Period size: 93 Copynumber: 2.6 Consensus size: 96
4099 GGTGTTGAAG
* * * * * *
4109 CTTCTTTCTATTCCACTGTAACCTCAGGAACATTGAGATCTACTTCATTATTTTAATCTGACCCA
1 CTTCATTCCATTCCACTGTAACCTCAGG-ACATTGAGATCTGCTAC-CTATTTTGATCTGACCCA
* * *
4174 CTACAACTTCAGGGGTATAGGATTTGGTGTTTAAA
64 CTACAACTTCAAGGATATAGGATCTGGTGTTT--A
* * * * * *
4209 CTTCACTCCATTACACTGTAACCTTAGGGACACTGAGATCTGTTA-CTCATTTTGATCTGATCCA
1 CTTCATTCCATTCCACTGTAACCTCA-GGACATTGAGATCTGCTACCT-ATTTTGATCTGACCCA
*
4273 CTGCAACTTCAAGGATATAGGATCT-G-G-TT-
64 CTACAACTTCAAGGATATAGGATCTGGTGTTTA
* *
4302 CTTCATTCCATTCCATTGTAACCTCAGAGACATTGAGATCTGCTACCTGTTTTGA
1 CTTCATTCCATTCCACTGTAACCTCAG-GACATTGAGATCTGCTACCTATTTTGA
4357 CCCACTTCAT
Statistics
Matches: 121, Mismatches: 23, Indels: 15
0.76 0.14 0.09
Matches are distributed among these distances:
92 1 0.01
93 43 0.36
94 2 0.02
96 2 0.02
97 1 0.01
98 2 0.02
99 35 0.29
100 33 0.27
101 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (96 bp):
CTTCATTCCATTCCACTGTAACCTCAGGACATTGAGATCTGCTACCTATTTTGATCTGACCCACT
ACAACTTCAAGGATATAGGATCTGGTGTTTA
Found at i:4725 original size:49 final size:49
Alignment explanation
Indices: 4659--5258 Score: 395
Period size: 49 Copynumber: 12.3 Consensus size: 49
4649 TCATCTTCAG
** ** **
4659 GGTATAAGATTTGTCGTTGTAGCTTCAATCTTTCCTTTCACATCTCTAA
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * *
4708 GGTATAAGATTCATCGTTACGGCTTCAACCTTTCCCTTTACATCTCTAA
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * * *
4757 GGTAAAAGGTTCGTCGTTGCGGCTTCATTCTTTCCCATCACGTTTCTAA
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * *
4806 TGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCC-TCTACATCTCTAC
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATC-ACATCTCTAA
* ** *
4855 GGTATAAGATTCGTTATTACGGCTTCAATCTTTCCCATCACATCTCTAA
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * * *
4904 GGTAAAAGGTTCATCGTTGCGGGTTCAA-CATTTCCC-TCCATATCTTTAG
1 GGTATAAGATTCATCGTTGCGGCTTCAATC-TTTCCCAT-CACATCTCTAA
* * * * * * * *
4953 GGTATAAGGTTCGTTGTTTCGGCTTCAACCTTTCCC-TCCATATCTTTAG
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCAT-CACATCTCTAA
* * ** * *
5002 GGCACAAGATTTGTCGTTGCGACTTCAATCTTTCCCATCATATCTCTAA
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
** * * * * * * * *
5051 GGTGCAAGGTTC-GCAGTTACGGTTTTAACCTTTCCC-TCTACATCCCCAA
1 GGTATAAGATTCATC-GTTGCGGCTTCAATCTTTCCCATC-ACATCTCTAA
* * * * * * * *
5100 TGTATAATATTTACCTTTGCGGCTTTAATCTTTCCCTTCACATCTCTAG
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * * *
5149 GGCATGAGATTCATCGTTACGGCTTAAATCTTTCCCTTCACATCTCTAG
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
* * * * * * ** *
5198 GGCATGAGATTCGTCATTGCGACTTCAATCTCTCCTTTCACATCTCTAG
1 GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
5247 GGTAT-AGATTCA
1 GGTATAAGATTCA
5259 ATGTTTTTTC
Statistics
Matches: 435, Mismatches: 106, Indels: 21
0.77 0.19 0.04
Matches are distributed among these distances:
48 13 0.03
49 415 0.95
50 7 0.02
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (49 bp):
GGTATAAGATTCATCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAA
Found at i:4898 original size:147 final size:146
Alignment explanation
Indices: 4680--5196 Score: 488
Period size: 147 Copynumber: 3.5 Consensus size: 146
4670 TGTCGTTGTA
* * * * *
4680 GCTTCAATCTTT-CCTTTCACATCTCTAAGGTATAAGATTCATCGTTACGGCTTCAACCTTTCCC
1 GCTTCAACCTTTCCCTCTCACATCTCTAGGGCATAAGATTCATCGTTACGGCTTCAATCTTTCCC
* * * *
4744 TTTACATCTCTAAGGTAAAAGGTTCGTCGTTGCGGCTTCATTCTTTCCCATCACGTTTCTAATGT
66 ATCACATCTCTAAGGTAAAAGGTTCGTCGTTGCGGCTTCA-ACTTTCCC-TCACATTTCTAATGT
4809 ATAAGGTTCACCGTTGCG
129 ATAAGGTTCACCGTTGCG
* * * **
4827 GCTTCAACCTTTCCCTCT-ACATCTCTACGGTATAAGATTCGTTATTACGGCTTCAATCTTTCCC
1 GCTTCAACCTTTCCCTCTCACATCTCTAGGGCATAAGATTCATCGTTACGGCTTCAATCTTTCCC
* * * **
4891 ATCACATCTCTAAGGTAAAAGGTTCATCGTTGCGGGTTCAACATTTCCCTC-CATATCTTTAGGG
66 ATCACATCTCTAAGGTAAAAGGTTCGTCGTTGCGGCTTCAAC-TTTCCCTCACAT-T-TCTAATG
*** *
4955 TATAAGGTTCGTTGTTTCG
128 TATAAGGTTCACCGTTGCG
* * * ** * *
4974 GCTTCAACCTTTCCCTC-CATATCTTTAGGGCACAAGATTTGTCGTTGCGACTTCAATCTTTCCC
1 GCTTCAACCTTTCCCTCTCACATCTCTAGGGCATAAGATTCATCGTTACGGCTTCAATCTTTCCC
* ** * * * ** *
5038 ATCATATCTCTAAGGTGCAAGGTTCG-CAGTTACGGTTTTAACCTTTCCCTCTACATCCCCAATG
66 ATCACATCTCTAAGGTAAAAGGTTCGTC-GTTGCGGCTTCAA-CTTTCCCTC-ACATTTCTAATG
** * *
5102 TATAATATTTACCTTTGCG
128 TATAAGGTTCACCGTTGCG
* * * *
5121 GCTTTAATCTTTCCCT-TCACATCTCTAGGGCATGAGATTCATCGTTACGGCTTAAATCTTTCCC
1 GCTTCAACCTTTCCCTCTCACATCTCTAGGGCATAAGATTCATCGTTACGGCTTCAATCTTTCCC
*
5185 TTCACATCTCTA
66 ATCACATCTCTA
5197 GGGCATGAGA
Statistics
Matches: 296, Mismatches: 64, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
145 2 0.01
146 5 0.02
147 281 0.95
148 5 0.02
149 3 0.01
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (146 bp):
GCTTCAACCTTTCCCTCTCACATCTCTAGGGCATAAGATTCATCGTTACGGCTTCAATCTTTCCC
ATCACATCTCTAAGGTAAAAGGTTCGTCGTTGCGGCTTCAACTTTCCCTCACATTTCTAATGTAT
AAGGTTCACCGTTGCG
Found at i:6209 original size:7 final size:7
Alignment explanation
Indices: 6184--6249 Score: 66
Period size: 7 Copynumber: 9.7 Consensus size: 7
6174 TGACCTCTCC
6184 TTTTTCT
1 TTTTTCT
*
6191 TCTTTC-
1 TTTTTCT
*
6197 TATTTCT
1 TTTTTCT
6204 TTTTTCT
1 TTTTTCT
6211 TTTTTCT
1 TTTTTCT
6218 TTTTT-T
1 TTTTTCT
*
6224 TTCTT-T
1 TTTTTCT
*
6230 TTTCTCT
1 TTTTTCT
6237 TTTTATCT
1 TTTT-TCT
6245 TTTTT
1 TTTTT
6250 GGTGAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
6 14 0.29
7 28 0.57
8 7 0.14
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:6226 original size:24 final size:25
Alignment explanation
Indices: 6183--6249 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
6173 TTGACCTCTC
6183 CTTTTTCTTCTTTCTATTTCTTTTTTCT
1 CTTTTTCTT-TTT-T-TTTCTTTTTTCT
6211 -TTTTTCTTTTTTTTTCTTTTTTCT
1 CTTTTTCTTTTTTTTTCTTTTTTCT
* *
6235 CTTTTTATCTTTTTT
1 CTTTTTCTTTTTTTT
6250 GGTGAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 12 0.33
25 13 0.36
26 3 0.08
27 8 0.22
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (25 bp):
CTTTTTCTTTTTTTTTCTTTTTTCT
Found at i:6228 original size:17 final size:17
Alignment explanation
Indices: 6184--6249 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 17
6174 TGACCTCTCC
*
6184 TTTTTCTTCTTTCTATTTCT
1 TTTTTCTT-TTT-TCTTT-T
6204 TTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
*
6221 TTTTTCTTTTTTCTCTT
1 TTTTTCTTTTTTCTTTT
*
6238 TTTATCTTTTTT
1 TTTTTCTTTTTT
6250 GGTGAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
17 28 0.65
18 4 0.09
19 3 0.07
20 8 0.19
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTT
Found at i:6240 original size:10 final size:9
Alignment explanation
Indices: 6203--6249 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
6193 TTTCTATTTC
6203 TTTTTTCTT
1 TTTTTTCTT
*
6212 TTTTCT-TT
1 TTTTTTCTT
6220 TTTTTTCTT
1 TTTTTTCTT
*
6229 TTTTCTC-T
1 TTTTTTCTT
*
6237 TTTTATCTT
1 TTTTTTCTT
6246 TTTT
1 TTTT
6250 GGTGAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 14 0.44
9 18 0.56
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:13562 original size:7 final size:7
Alignment explanation
Indices: 13546--13579 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
13536 TCTTTTCAAT
*
13546 CATCATC
1 CATCACC
13553 CATCACC
1 CATCACC
13560 CATCACC
1 CATCACC
13567 CATCA-C
1 CATCACC
13573 CATCACC
1 CATCACC
13580 TTTTCGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (7 bp):
CATCACC
Found at i:14310 original size:26 final size:25
Alignment explanation
Indices: 14275--14329 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
14265 TCTCAATTAT
*
14275 TTTTATTATTTATATTTGTT-TGTTTA
1 TTTTAGTATTTA-ATTT-TTATGTTTA
*
14301 TTTTAGTATTTAATTTTTATTTTTA
1 TTTTAGTATTTAATTTTTATGTTTA
14326 TTTT
1 TTTT
14330 TCTGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 13 0.50
26 11 0.42
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTTAGTATTTAATTTTTATGTTTA
Found at i:14330 original size:103 final size:102
Alignment explanation
Indices: 14174--14359 Score: 229
Period size: 103 Copynumber: 1.8 Consensus size: 102
14164 TTCTTTTTTA
*
14174 TTATTACTTATATTTAGTTGTTTATATTGACATTTAATTTATTGATTTTTTTTTGTTTATTTATT
1 TTATTACTTATATTTAGTTGTTTATATTGACATTTAATTTATTGA-TTTTTTTT-TCTATTTATT
14239 TAT-TTGTCATTTATTTTCATGTCTGATCTCAATTATTT
64 TATCTTGTCATTTATTTTCATGTCTGATCTCAATTATTT
* * * *
14277 TTATTATTTATATTT-GTTTGTTTAT-TTTAGTATTTAATTT-TT-ATTTTTATTTTTCTGTTTA
1 TTATTACTTATATTTAG-TTGTTTATATTGA-CATTTAATTTATTGA-TTTT-TTTTTCTATTTA
*
14338 TTTATCTTGTTATTTATTTTCA
62 TTTATCTTGTCATTTATTTTCA
14360 GATCATTTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
101 17 0.23
102 25 0.34
103 31 0.42
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (102 bp):
TTATTACTTATATTTAGTTGTTTATATTGACATTTAATTTATTGATTTTTTTTTCTATTTATTTA
TCTTGTCATTTATTTTCATGTCTGATCTCAATTATTT
Found at i:14352 original size:41 final size:39
Alignment explanation
Indices: 14271--14357 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
14261 CTGATCTCAA
* *
14271 TTATTTTTATTATTTATATTTGTTTGTTTATTTTAGTAT
1 TTATTTTTATTATTTATATTTGTTTATTTATCTTAGTAT
*
14310 TTAATTTTTATT-TTTATTTTTCTGTTTATTTATCTT-GTTAT
1 TT-ATTTTTATTATTTA-TATT-TGTTTATTTATCTTAG-TAT
14351 TTATTTT
1 TTATTTT
14358 CAGATCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
39 6 0.15
40 18 0.44
41 17 0.41
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (39 bp):
TTATTTTTATTATTTATATTTGTTTATTTATCTTAGTAT
Found at i:14564 original size:16 final size:16
Alignment explanation
Indices: 14540--14575 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14530 AATGCATTTA
14540 ATATATTTATTTATTG
1 ATATATTTATTTATTG
* *
14556 ATATTTTTATTTATTT
1 ATATATTTATTTATTG
14572 ATAT
1 ATAT
14576 GTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATATATTTATTTATTG
Found at i:15601 original size:15 final size:15
Alignment explanation
Indices: 15577--15606 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15567 ATTTGTGATC
*
15577 CTTTGTATTTTATTG
1 CTTTGCATTTTATTG
15592 CTTTGCATTTTATTG
1 CTTTGCATTTTATTG
15607 AATATATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
CTTTGCATTTTATTG
Found at i:19700 original size:49 final size:49
Alignment explanation
Indices: 19647--19780 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 49
19637 AGGTTCAAGT
* * *
19647 TGCAACGACGAACCTTACACCCTAAAACTGAATAGGGAAAGATTAAAGC
1 TGCAACGACGAATCTTACACCCTAAAACTGAAGAGGAAAAGATTAAAGC
* * * *
19696 TGCAACGACGGATCTAACACTCTAAAACTGAAGAGGAAAAGATTGAAGC
1 TGCAACGACGAATCTTACACCCTAAAACTGAAGAGGAAAAGATTAAAGC
* * *
19745 TGTAAC-AGCGAATCTTACACCTTAAAACTAAAGAGG
1 TGCAACGA-CGAATCTTACACCCTAAAACTGAAGAGG
19781 GGTAGGTTGA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 70 0.99
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (49 bp):
TGCAACGACGAATCTTACACCCTAAAACTGAAGAGGAAAAGATTAAAGC
Found at i:20511 original size:158 final size:158
Alignment explanation
Indices: 20174--20502 Score: 455
Period size: 158 Copynumber: 2.1 Consensus size: 158
20164 ACAATTACAA
* *
20174 CTCGTATGAGCATTACAGGTTATATGGGTGCTGGTCTTAAATGTCTTACCGATGGCTGAGGTCCT
1 CTCGTGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAAATGTCCTACCGATGGCTGAGGTCCT
* *
20239 GCATTTGTTACGGATTCTCCACAGCTCGTCTTAGAAGCATCGCGTAGCCTAACATCTCGACCCAA
66 GCATTTATTACGGATTCTCCACAGCTCGTCTTAGAAGCATCGCGTAGCCCAACATCTCGACCCAA
*
20304 GGCTCGTGTGAGCAGACCCATTTCATAG
131 GGCTCGTGTGAGCAGACCCATTTCACAG
* * * *
20332 CTCGTGTGAGCATTACAGGTTATATTGGTGCTGGTCTTAGATGTCCTATCGATGGCTGAGGTTC-
1 CTCGTGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAAATGTCCTACCGATGGCTGAGGTCCT
** * * * * * * *
20396 GACATTTATTGTGGATTCTTCATAGCTCGTGTTAGCAGCATCGTGTAGCCCCACATCTCGATCCA
66 G-CATTTATTACGGATTCTCCACAGCTCGTCTTAGAAGCATCGCGTAGCCCAACATCTCGACCCA
*
20461 CA-GCTTGTGTGAGCAGACCCATTTCACAG
130 -AGGCTCGTGTGAGCAGACCCATTTCACAG
20490 CTCGTGTGAGCAT
1 CTCGTGTGAGCAT
20503 ATATGGTTAC
Statistics
Matches: 150, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
157 1 0.01
158 148 0.99
159 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (158 bp):
CTCGTGTGAGCATTACAGGTTATATGGGTGCTGGTCTTAAATGTCCTACCGATGGCTGAGGTCCT
GCATTTATTACGGATTCTCCACAGCTCGTCTTAGAAGCATCGCGTAGCCCAACATCTCGACCCAA
GGCTCGTGTGAGCAGACCCATTTCACAG
Found at i:23108 original size:14 final size:14
Alignment explanation
Indices: 23089--23115 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23079 CTAAGCAAAG
23089 TTATCTTATGTAAT
1 TTATCTTATGTAAT
23103 TTATCTTATGTAA
1 TTATCTTATGTAA
23116 AGACATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (14 bp):
TTATCTTATGTAAT
Found at i:24456 original size:13 final size:13
Alignment explanation
Indices: 24430--24479 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
24420 GCATTTAATT
*
24430 TTTATTTTTATTTA
1 TTTA-TTTTGTTTA
24444 TTTATTTTGTTTA
1 TTTATTTTGTTTA
*
24457 TTTATCTTGCTGTTA
1 TTTATTTTG-T-TTA
24472 TTTATTTT
1 TTTATTTT
24480 CAGACCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 16 0.52
14 5 0.16
15 10 0.32
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:24679 original size:16 final size:16
Alignment explanation
Indices: 24638--24679 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
24628 TTTATGAATG
24638 CATTTCATATATTTATT
1 CATTT-ATATATTTATT
*
24655 CATTGATATATTTATT
1 CATTTATATATTTATT
*
24671 TATTTATAT
1 CATTTATAT
24680 GTCATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (16 bp):
CATTTATATATTTATT
Found at i:25718 original size:15 final size:17
Alignment explanation
Indices: 25680--25769 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 17
25670 TTAAAATTTA
25680 ATTTATTACTTTAAATTG
1 ATTTATT-CTTTAAATTG
25698 ATTTATTCTTTAAA-T-
1 ATTTATTCTTTAAATTG
* *
25713 ATTTATTCTTTTAATTAA
1 ATTTATTCTTTAAATT-G
* *
25731 ATTTTATT-TTGTAATTTA
1 A-TTTATTCTT-TAAATTG
25749 ACTTTATTCCTTTAAATTG
1 A-TTTATT-CTTTAAATTG
25768 AT
1 AT
25770 ATTTTAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
15 13 0.22
16 2 0.03
17 7 0.12
18 19 0.32
19 16 0.27
20 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTATTCTTTAAATTG
Found at i:25739 original size:71 final size:70
Alignment explanation
Indices: 25629--25769 Score: 178
Period size: 71 Copynumber: 2.0 Consensus size: 70
25619 AAATAATTTA
* *
25629 TTATTCTTTAAATATGTCTTAGTTAATTTAAATTATATTTTTTAAAATTTAA-TTTATTACTTTA
1 TTATTCTTTAAATATGTATTAGTTAATTTAAATTATATTTTGT--AATTTAACTTTATTACTTTA
25693 AATTGAT
64 AATTGAT
* ** * *
25700 TTATTCTTTAAATATTTATTCTTTTAA-TTAAATTTTATTTTGTAATTTAACTTTATTCCTTTAA
1 TTATTCTTTAAATATGTATT-AGTTAATTTAAATTATATTTTGTAATTTAACTTTATTACTTTAA
25764 ATTGAT
65 ATTGAT
25770 ATTTTAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
69 7 0.11
70 18 0.30
71 32 0.52
72 4 0.07
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (70 bp):
TTATTCTTTAAATATGTATTAGTTAATTTAAATTATATTTTGTAATTTAACTTTATTACTTTAAA
TTGAT
Found at i:26469 original size:29 final size:30
Alignment explanation
Indices: 26426--26484 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
26416 TTTTTAACCA
* *
26426 GGATCATTTATGT-AAATAACAAATTTTTT
1 GGATCATTTAGGTAAAATAACAAATCTTTT
* *
26455 GGATCATTTGGGTAAAATAACCAATCTTTT
1 GGATCATTTAGGTAAAATAACAAATCTTTT
26485 ATTACAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (30 bp):
GGATCATTTAGGTAAAATAACAAATCTTTT
Done.