Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010378.1 Kokia drynarioides strain JFW-HI SEQ_125251, 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: 88898
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:550 original size:4 final size:4
Alignment explanation
Indices: 529--577 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
519 TTACCTCTCA
* * * *
529 TTCT TCCT TCCT TCCT TTCT TTCT TTCT TTATT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT
578 CGTTTATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 37 0.93
5 3 0.08
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (4 bp):
TTCT
Found at i:3857 original size:22 final size:22
Alignment explanation
Indices: 3817--3875 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
3807 TTTATATTTT
*
3817 TTTAATGAATTT-AAAAAAT-A
1 TTTAATTAATTTAAAAAAATAA
3837 TATTAA-TAATTTGAAAAAAATAA
1 T-TTAATTAATTT-AAAAAAATAA
3860 TTTAATTAATTTAAAA
1 TTTAATTAATTTAAAA
3876 TCAGTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 6 0.18
21 4 0.12
22 15 0.45
23 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
TTTAATTAATTTAAAAAAATAA
Found at i:6865 original size:32 final size:32
Alignment explanation
Indices: 6804--6865 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
6794 GTTTTCGGGA
*
6804 TTTTTTTTTATTAAGGTTTTCAAATTTTTTTT
1 TTTTTTTTTATAAAGGTTTTCAAATTTTTTTT
*
6836 TTTTTTTTTA-AAATGGTTATTTAAATTTTT
1 TTTTTTTTTATAAA-GGTT-TTCAAATTTTT
6866 ATAATCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 2 0.08
32 14 0.54
33 10 0.38
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (32 bp):
TTTTTTTTTATAAAGGTTTTCAAATTTTTTTT
Found at i:7022 original size:23 final size:23
Alignment explanation
Indices: 6996--7040 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
6986 CTTAAGAGAA
*
6996 AAAAATTATAAATCATATAATTG
1 AAAAATTATAAATAATATAATTG
7019 AAAAATTATAAATAATATAATT
1 AAAAATTATAAATAATATAATT
7041 AATCGTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAATTATAAATAATATAATTG
Found at i:10058 original size:14 final size:15
Alignment explanation
Indices: 10028--10060 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10018 TTTACAATCA
*
10028 TTTAATTTTTAATTT
1 TTTAATTTGTAATTT
10043 TTTAATTTGT-ATTT
1 TTTAATTTGTAATTT
10057 TTTA
1 TTTA
10061 TCAAATCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTAATTTGTAATTT
Found at i:11290 original size:18 final size:19
Alignment explanation
Indices: 11255--11295 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
11245 ATTAAATAAT
* *
11255 TCGAGTTATTTGAGTTAA-
1 TCGAGTTATTCGAATTAAC
11273 TCGAGTTATTCGAATTAAC
1 TCGAGTTATTCGAATTAAC
11292 TCGA
1 TCGA
11296 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGAGTTATTCGAATTAAC
Found at i:29175 original size:16 final size:20
Alignment explanation
Indices: 29120--29182 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
29110 TTATAAAATT
* *
29120 TATAAAATATAATTTTAATTA
1 TATAAAA-ATTATTTTATTTA
29141 T-TAAAAATTATTTTATTTA
1 TATAAAAATTATTTTATTTA
29160 -ATAAAAA-TA-TTT-TTTA
1 TATAAAAATTATTTTATTTA
29176 TATAAAA
1 TATAAAA
29183 TTCAAACCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.11
17 9 0.24
18 2 0.05
19 17 0.45
20 5 0.13
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAAAAATTATTTTATTTA
Found at i:35965 original size:24 final size:24
Alignment explanation
Indices: 35919--35965 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35909 TGAATTGCAA
* *
35919 GTATCGGTAGTTATGTGTTTTGTT
1 GTATCGGTAGTTATGTATCTTGTT
35943 GTATCGGTAGTT-TGTATACTTGT
1 GTATCGGTAGTTATGTAT-CTTGT
35966 ATCAGTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.15, C:0.06, G:0.28, T:0.51
Consensus pattern (24 bp):
GTATCGGTAGTTATGTATCTTGTT
Found at i:37346 original size:61 final size:58
Alignment explanation
Indices: 37238--37370 Score: 178
Period size: 61 Copynumber: 2.2 Consensus size: 58
37228 AATCACTTTA
*
37238 ATATTAAATTAATATAATAGTTTTCAAGATAAATATTAAATTAAATTTAATATTAAAT
1 ATATTAAATTAATAGAATAGTTTTCAAGATAAATATTAAATTAAATTTAATATTAAAT
* * *
37296 CTATTAAATTAATAGAATATTTATTTACAA-ATTAAGTATTAAATTAAATTTAATATTAAAT
1 ATATTAAATTAATAGAATA-GT-TTT-CAAGA-TAAATATTAAATTAAATTTAATATTAAAT
*
37357 ATATTAAAATAATA
1 ATATTAAATTAATA
37371 TTATTTTTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
58 17 0.26
59 1 0.02
60 4 0.06
61 43 0.66
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (58 bp):
ATATTAAATTAATAGAATAGTTTTCAAGATAAATATTAAATTAAATTTAATATTAAAT
Found at i:39380 original size:31 final size:30
Alignment explanation
Indices: 39327--39384 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
39317 TAAAGGTTTT
*
39327 TTTTATTTAATTAAATATTTGAATTTAAAC
1 TTTTATTTAATTAAATACTTGAATTTAAAC
39357 TTTTAGTTTAAATT-AATACTTGAATTTA
1 TTTTA-TTT-AATTAAATACTTGAATTTA
39385 GTTTTATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.20
31 16 0.64
32 4 0.16
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTATTTAATTAAATACTTGAATTTAAAC
Found at i:39501 original size:18 final size:18
Alignment explanation
Indices: 39478--39534 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
39468 GAACCAAAAT
39478 ATTAAATTTAAATATTTA
1 ATTAAATTTAAATATTTA
* *
39496 ATTAAA--TAAA-AATAA
1 ATTAAATTTAAATATTTA
* *
39511 ATTAAGTTCAAATATTTA
1 ATTAAATTTAAATATTTA
39529 ATTAAA
1 ATTAAA
39535 CAAAAAGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
15 8 0.28
16 4 0.14
17 3 0.10
18 14 0.48
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTAAATTTAAATATTTA
Found at i:39524 original size:33 final size:33
Alignment explanation
Indices: 39478--39540 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
39468 GAACCAAAAT
* *
39478 ATTAAATTTAAATATTTAATTAAATAAAAATAA
1 ATTAAATTCAAATATTTAATTAAACAAAAATAA
*
39511 ATTAAGTTCAAATATTTAATTAAACAAAAA
1 ATTAAATTCAAATATTTAATTAAACAAAAA
39541 GAAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (33 bp):
ATTAAATTCAAATATTTAATTAAACAAAAATAA
Found at i:40532 original size:28 final size:26
Alignment explanation
Indices: 40470--40532 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
40460 TAACTTTTCA
* * *
40470 AATATATAAGGATTAAAATGTTTTTTT
1 AATATA-AAGGAATAAAATGATTTTAT
40497 AATAATAAAGAGAATAAAATGGATTTTAT
1 AAT-ATAAAG-GAATAAAAT-GATTTTAT
40526 AATATAA
1 AATATAA
40533 CACAAGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.20
28 15 0.50
29 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (26 bp):
AATATAAAGGAATAAAATGATTTTAT
Found at i:40695 original size:3 final size:3
Alignment explanation
Indices: 40687--40722 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
40677 TCTGATAATT
40687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40723 AAAGTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40979 original size:4 final size:4
Alignment explanation
Indices: 40972--41008 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
40962 CCAGCCAGCA
*
40972 AAAG AAAG AAAG AAAG AAAG -AAG AAA- AAGG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
41009 ATTGGCAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 5 0.17
4 24 0.83
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:50188 original size:12 final size:12
Alignment explanation
Indices: 50171--50254 Score: 57
Period size: 12 Copynumber: 6.7 Consensus size: 12
50161 TTGAAATTAA
*
50171 TTATGTTTATGT
1 TTATGTTTATAT
50183 TTATGTTTATAT
1 TTATGTTTATAT
50195 TTAAT-TAATTATAT
1 TT-ATGT--TTATAT
*
50209 TTATGTTTGTAT
1 TTATGTTTATAT
50221 TTAAT-TAATTATAT
1 TT-ATGT--TTATAT
*
50235 TTATGCTTT-TGT
1 TTATG-TTTATAT
50247 TTATGTTT
1 TTATGTTT
50255 GGGGTATGGG
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 3 0.05
12 29 0.49
13 10 0.17
14 16 0.27
15 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.10, T:0.64
Consensus pattern (12 bp):
TTATGTTTATAT
Found at i:50206 original size:32 final size:30
Alignment explanation
Indices: 50165--50254 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 30
50155 ATGAATTTGA
50165 AATTAATTATGTTTATGTTTATGTTTATATTT
1 AATTAATTATGTTTATGTTTATGTTTA-A-TT
* * *
50197 AATTAATTATATTTATGTTTGTATTTAATT
1 AATTAATTATGTTTATGTTTATGTTTAATT
50227 AATTATATTTATGCTTT-TGTTTATGTTT
1 AATTA-A-TTATG-TTTATGTTTATGTTT
50255 GGGGTATGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 7 0.14
31 2 0.04
32 37 0.76
33 3 0.06
ACGTcount: A:0.28, C:0.01, G:0.09, T:0.62
Consensus pattern (30 bp):
AATTAATTATGTTTATGTTTATGTTTAATT
Found at i:50208 original size:14 final size:14
Alignment explanation
Indices: 50189--50237 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
50179 ATGTTTATGT
50189 TTATATTTAATTAA
1 TTATATTTAATTAA
50203 TTATATTT-ATGT--
1 TTATATTTAAT-TAA
*
50215 TTGTATTTAATTAA
1 TTATATTTAATTAA
50229 TTATATTTA
1 TTATATTTA
50238 TGCTTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (14 bp):
TTATATTTAATTAA
Found at i:50249 original size:26 final size:26
Alignment explanation
Indices: 50177--50239 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
50167 TTAATTATGT
*
50177 TTATGTTTATGTTTATATTTAATTAA
1 TTATATTTATGTTTATATTTAATTAA
*
50203 TTATATTTATGTTTGTATTTAATTAA
1 TTATATTTATGTTTATATTTAATTAA
50229 TTATATTTATG
1 TTATATTTATG
50240 CTTTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTATATTTATGTTTATATTTAATTAA
Found at i:50400 original size:21 final size:21
Alignment explanation
Indices: 50361--50415 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
50351 CCTATACTCA
*
50361 AAACCCATAAAATCTTAAACCCT
1 AAACCC-T-AAATCATAAACCCT
*
50384 AAACCCTAAATCATAAACTCT
1 AAACCCTAAATCATAAACCCT
*
50405 AAACACTAAAT
1 AAACCCTAAAT
50416 TCTAAACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 22 0.76
22 1 0.03
23 6 0.21
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAATCATAAACCCT
Found at i:50414 original size:14 final size:14
Alignment explanation
Indices: 50376--50429 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
50366 CATAAAATCT
* *
50376 TAAACCCTAAACCC
1 TAAACACTAAACTC
50390 TAAATCA-TAAACTC
1 TAAA-CACTAAACTC
*
50404 TAAACACTAAATTC
1 TAAACACTAAACTC
*
50418 TAAACATTAAAC
1 TAAACACTAAAC
50430 CCCAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 2 0.06
14 30 0.91
15 1 0.03
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACACTAAACTC
Found at i:50638 original size:26 final size:26
Alignment explanation
Indices: 50589--50649 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
50579 ATACAAAGAT
50589 TAATTAATTAAATAAAAACATAAAAA
1 TAATTAATTAAATAAAAACATAAAAA
* * ** *
50615 TTATTAATTAAATACAAATTTAAATA
1 TAATTAATTAAATAAAAACATAAAAA
50641 TAATTAATT
1 TAATTAATT
50650 CCAAATTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATTAATTAAATAAAAACATAAAAA
Found at i:52799 original size:39 final size:39
Alignment explanation
Indices: 52755--52876 Score: 192
Period size: 39 Copynumber: 3.1 Consensus size: 39
52745 GACCATCCGG
*
52755 GACCTCTTCATTCAGGCCTTCCTCGTCGATATCATTCGA
1 GACCTCTTCATTCAGGCCTTCCTCATCGATATCATTCGA
*
52794 GACCTCTTCATTCAAGCCTTCCTCATCGATATCATTC-A
1 GACCTCTTCATTCAGGCCTTCCTCATCGATATCATTCGA
* *
52832 GGACCTCTTCATTCAGGCCTTCCTCATCGATATCATCCGG
1 -GACCTCTTCATTCAGGCCTTCCTCATCGATATCATTCGA
52872 GACCT
1 GACCT
52877 AGTCCACGTC
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
38 1 0.01
39 75 0.99
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (39 bp):
GACCTCTTCATTCAGGCCTTCCTCATCGATATCATTCGA
Found at i:57927 original size:19 final size:20
Alignment explanation
Indices: 57895--57937 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
57885 TCATGTTGAC
* * *
57895 AAATAATTTTAAAATTATAA
1 AAATAATTTAAAAAATAAAA
57915 AAAT-ATTTAAAAAATAAAA
1 AAATAATTTAAAAAATAAAA
57934 AAAT
1 AAAT
57938 TCATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATTTAAAAAATAAAA
Found at i:58979 original size:20 final size:21
Alignment explanation
Indices: 58953--59000 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
58943 TTTATATTAT
58953 TTAAAAATAAAT-TAAAAAA-
1 TTAAAAATAAATATAAAAAAG
*
58972 TCTAAAAA-ACATATAAAAAAG
1 T-TAAAAATAAATATAAAAAAG
58993 TTAAAAAT
1 TTAAAAAT
59001 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (21 bp):
TTAAAAATAAATATAAAAAAG
Found at i:62695 original size:20 final size:20
Alignment explanation
Indices: 62667--62716 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
62657 CAAGATAAAA
*
62667 CCAACACTACATCCTCACCT
1 CCAAGACTACATCCTCACCT
*
62687 CCAAGACTACATCCTCGCCT
1 CCAAGACTACATCCTCACCT
62707 CCAAGACTAC
1 CCAAGACTAC
62717 TTGATGATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.46, G:0.06, T:0.18
Consensus pattern (20 bp):
CCAAGACTACATCCTCACCT
Found at i:66082 original size:3 final size:3
Alignment explanation
Indices: 66065--66114 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
66055 TTTAGGATTT
* * *
66065 AAG AAG -AG AAA AAG AAG AAG AAG AGG AAG AAG AAAG AAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
66110 AAG AA
1 AAG AA
66115 AAAAAAATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:67795 original size:41 final size:41
Alignment explanation
Indices: 67735--67817 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
67725 TACAAGCAAA
*
67735 TTACAAATATATGTATCACCAAAAACATTAATTTGTCTTAG
1 TTACAAATATATGTATCACCAAAAACACTAATTTGTCTTAG
*
67776 TTACAAATATATGTCTCACCAAAAACACTAATTTGTCTTAG
1 TTACAAATATATGTATCACCAAAAACACTAATTTGTCTTAG
67817 T
1 T
67818 GGCAATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (41 bp):
TTACAAATATATGTATCACCAAAAACACTAATTTGTCTTAG
Found at i:73712 original size:16 final size:18
Alignment explanation
Indices: 73682--73716 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
73672 TACACAGATG
73682 AAAAATCAACACCCCAAA
1 AAAAATCAACACCCCAAA
73700 AAAAATC-AC-CCCCAAA
1 AAAAATCAACACCCCAAA
73716 A
1 A
73717 CACCAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.60, C:0.34, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAATCAACACCCCAAA
Found at i:75223 original size:8 final size:8
Alignment explanation
Indices: 75210--75243 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
75200 TTCAACATAC
75210 AAAATATT
1 AAAATATT
75218 AAAATATT
1 AAAATATT
*
75226 AAATATATA
1 AAA-ATATT
75235 AAAATATT
1 AAAATATT
75243 A
1 A
75244 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:75241 original size:10 final size:11
Alignment explanation
Indices: 75226--75258 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
75216 TTAAAATATT
75226 AAATA-TATAA
1 AAATATTATAA
75236 AAATATTATAA
1 AAATATTATAA
75247 AAA-ATTATAA
1 AAATATTATAA
75257 AA
1 AA
75259 TTACTTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATTATAA
Found at i:77346 original size:84 final size:82
Alignment explanation
Indices: 77196--77348 Score: 193
Period size: 84 Copynumber: 1.8 Consensus size: 82
77186 TTGGAGATTG
* * * *
77196 AAATTAAATTATATATTTTTATGATAATAAAAATATAATTTTATTATTTAATAATTTATATCTTT
1 AAATTAAATTATATATTTTTAGGATAATAAAAATACAATTTGATTATTTAATAATTTAAATCTTT
77261 ATAACTTTTAAAAAATT
66 ATAACTTTTAAAAAATT
* *
77278 AAATTAAATTATTATTATTTTTGAGGA-AATTAAAATACAATTTGATTA-TTATTAATTTAAAAT
1 AAATTAAATTA-TA-TATTTTT-AGGATAATAAAAATACAATTTGATTATTTAATAATTT-AAAT
*
77341 TTTTATAA
62 CTTTATAA
77349 ATTAAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 11 0.18
83 11 0.18
84 35 0.58
85 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (82 bp):
AAATTAAATTATATATTTTTAGGATAATAAAAATACAATTTGATTATTTAATAATTTAAATCTTT
ATAACTTTTAAAAAATT
Found at i:80541 original size:181 final size:182
Alignment explanation
Indices: 80236--80600 Score: 696
Period size: 181 Copynumber: 2.0 Consensus size: 182
80226 CTAATGCATC
*
80236 GTTACCCTCTGCCAATTTGAAGCAGTTAAAAGCCCAAATATATCCACCAACCCCTGAATTGAAAA
1 GTTACCCTCTGCCAATTTGAAGCAGTTAAAAGCACAAATATATCCACCAACCCCTGAATTGAAAA
80301 GCTTTAGTCGAATTTGCAACTGCTTCCAATGAACCACAACCGTCTAACCATAGTTTTATGCTTGC
66 GCTTTAGTCGAATTTGCAACTGCTTCCAATGAACCACAACCGTCTAACCATAGTTTTATGCTTGC
80366 TGGTAGCTCGGGCAATGATTTAAGCCTTTTGCAGTCAGTCAGTACTAGACTA
131 TGGTAGCTCGGGCAATGATTTAAGCCTTTTGCAGTCAGTCAGTACTAGACTA
*
80418 GTTACCCTCTGCCAATTTGAAGCAGTTAAAAGCACAAATATATCCATCAACCCCTGAATTG-AAA
1 GTTACCCTCTGCCAATTTGAAGCAGTTAAAAGCACAAATATATCCACCAACCCCTGAATTGAAAA
80482 GCTTTAGTCGAATTTGCAACTGCTTCCAATGAACCACAACCGTCTAACCATAGTTTTATGCTTGC
66 GCTTTAGTCGAATTTGCAACTGCTTCCAATGAACCACAACCGTCTAACCATAGTTTTATGCTTGC
*
80547 TGGTAGGTCGGGCAATGATTTAAGCCTTTTGCAGTCAGTCAGTACTAGACTA
131 TGGTAGCTCGGGCAATGATTTAAGCCTTTTGCAGTCAGTCAGTACTAGACTA
80599 GT
1 GT
80601 AAGCTTGGAA
Statistics
Matches: 180, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
181 121 0.67
182 59 0.33
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (182 bp):
GTTACCCTCTGCCAATTTGAAGCAGTTAAAAGCACAAATATATCCACCAACCCCTGAATTGAAAA
GCTTTAGTCGAATTTGCAACTGCTTCCAATGAACCACAACCGTCTAACCATAGTTTTATGCTTGC
TGGTAGCTCGGGCAATGATTTAAGCCTTTTGCAGTCAGTCAGTACTAGACTA
Found at i:84388 original size:80 final size:80
Alignment explanation
Indices: 84255--84414 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
84245 CTCATTTTAT
84255 CGAGTCTGAGCAACAAAGAACTGGAGCTCAATTCCTCTTTCTAATTTCTCATCCATATTTGAAAG
1 CGAGTCTGAGCAACAAAGAACTGGAGCTCAATTCCTCTTTCTAATTTCTCATCCATATTTGAAAG
84320 AAAAAGTATGGATAA
66 AAAAAGTATGGATAA
84335 CGAGTCTGAGCAACAAAGAACTGGAGCTCAATTCCTCTTTCTAATTTCTCATCCATATTTGAAAG
1 CGAGTCTGAGCAACAAAGAACTGGAGCTCAATTCCTCTTTCTAATTTCTCATCCATATTTGAAAG
84400 AAAAAGTATGGATAA
66 AAAAAGTATGGATAA
84415 TGTTTTTTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (80 bp):
CGAGTCTGAGCAACAAAGAACTGGAGCTCAATTCCTCTTTCTAATTTCTCATCCATATTTGAAAG
AAAAAGTATGGATAA
Done.