Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012310.1 Kokia drynarioides strain JFW-HI SEQ_127311, 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: 61410
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1419 original size:43 final size:43
Alignment explanation
Indices: 1337--1421 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
1327 ATTAACATGT
* *
1337 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* **
1380 TAAATTATATTACTTTACTTTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
1422 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:2050 original size:38 final size:38
Alignment explanation
Indices: 1999--2071 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1989 CATAGCTCAT
*
1999 CAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCAGCG
1 CAAGCCAAGGATATCAGCCTCAATTTGACGAGCCAGCG
*
2037 CAAGCCAATGATATCAGCCTCAATTTGACGAGCCA
1 CAAGCCAAGGATATCAGCCTCAATTTGACGAGCCA
2072 CCACATTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.18
Consensus pattern (38 bp):
CAAGCCAAGGATATCAGCCTCAATTTGACGAGCCAGCG
Found at i:5655 original size:4 final size:4
Alignment explanation
Indices: 5638--5726 Score: 106
Period size: 4 Copynumber: 21.2 Consensus size: 4
5628 AACACATTAC
* * *
5638 CTTT CTTT CCTT CTTT CTTT CCTTT CATT CTTA CTTT CTTT CTTT CTTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT C-TTT
*
5688 CTTTT CTTC CTTT CTTT CTTT CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT C
5727 CAATTTATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
4 57 0.77
5 17 0.23
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:5663 original size:21 final size:21
Alignment explanation
Indices: 5637--5727 Score: 95
Period size: 21 Copynumber: 4.5 Consensus size: 21
5627 AAACACATTA
5637 CCTTTCTTTCCTTCTTTCTTT
1 CCTTTCTTTCCTTCTTTCTTT
*
5658 CCTTTCATT-CTTACTTTCTTT
1 CCTTTCTTTCCTT-CTTTCTTT
*
5679 -CTTTCTTTTC-T-TTTC-TT
1 CCTTTCTTTCCTTCTTTCTTT
*
5696 CCTTTCTTTCTTTCTTTTCTTT
1 CCTTTCTTTCCTTC-TTTCTTT
5718 -CTTTCTTTCC
1 CCTTTCTTTCC
5728 AATTTATTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
17 2 0.03
18 12 0.21
19 1 0.02
20 11 0.19
21 30 0.52
22 2 0.03
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (21 bp):
CCTTTCTTTCCTTCTTTCTTT
Found at i:5931 original size:27 final size:26
Alignment explanation
Indices: 5885--5936 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
5875 GCCAAGTGGC
*
5885 AAAACACCCCTTAGTGCCGCCACTTA
1 AAAACACCCATTAGTGCCGCCACTTA
*
5911 AAAACACTCCATTGGTGCCGCCACTT
1 AAAACAC-CCATTAGTGCCGCCACTT
5937 CGTGTTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.21
Consensus pattern (26 bp):
AAAACACCCATTAGTGCCGCCACTTA
Found at i:6364 original size:5 final size:6
Alignment explanation
Indices: 6332--6362 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6322 GATATGGTAG
6332 AAAG-A AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
6363 GAGCCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:7692 original size:20 final size:20
Alignment explanation
Indices: 7667--7704 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7657 CACCTCCTCA
7667 TATTTTCCATAAAATTTATT
1 TATTTTCCATAAAATTTATT
* *
7687 TATTTTCCTTTAAATTTA
1 TATTTTCCATAAAATTTA
7705 CTGTCACATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTCCATAAAATTTATT
Found at i:9244 original size:213 final size:213
Alignment explanation
Indices: 8877--9305 Score: 813
Period size: 213 Copynumber: 2.0 Consensus size: 213
8867 TCAATTTGAA
8877 GCAAATAGAGGATAATTAGTTTCCTACTACCGCAAAGAAGAAAGCCAGTTTGCAATCTCACTTAT
1 GCAAATAGAGGATAATTAGTTTCCTACTACCGCAAAGAAGAAAGCCAGTTTGCAATCTCACTTAT
8942 TCTTATTAGAATTTAAAAGATATATTTAAGTGAGAATTAACATTAATTTGGAACAAATACGAAAC
66 TCTTATTAGAATTTAAAAGATATATTTAAGTGAGAATTAACATTAATTTGGAACAAATACGAAAC
9007 CTGAAATGAGAAGATCAGCTCTGTCTCTTACTGGTTTAATTCATAGGAAGGGTTTGCCGTATAGA
131 CTGAAATGAGAAGATCAGCTCTGTCTCTTACTGGTTTAATTCATAGGAAGGGTTTGCCGTATAGA
9072 ATTCCTGGTATGGTTGGG
196 ATTCCTGGTATGGTTGGG
*
9090 GCAAATAGAGGATAATTAGTTTCCTACTACCGCAAAGAAGAAAGTCAGTTTGCAATCTCACTTAT
1 GCAAATAGAGGATAATTAGTTTCCTACTACCGCAAAGAAGAAAGCCAGTTTGCAATCTCACTTAT
* *
9155 TCTTATTAGAATTTAAAAGATATATTTAAGTGAGAATTAACATTAATTTGGAACAAATATGAAGC
66 TCTTATTAGAATTTAAAAGATATATTTAAGTGAGAATTAACATTAATTTGGAACAAATACGAAAC
* *
9220 TTGAAATGAGAAGATCAGCTCTGTCTCTTACTGGTTTAATTCATAGGAAGGGTTTGCCGTGTAGA
131 CTGAAATGAGAAGATCAGCTCTGTCTCTTACTGGTTTAATTCATAGGAAGGGTTTGCCGTATAGA
9285 ATTCCTGGTATGGTTGGG
196 ATTCCTGGTATGGTTGGG
9303 GCA
1 GCA
9306 GATACTCTGA
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
213 211 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (213 bp):
GCAAATAGAGGATAATTAGTTTCCTACTACCGCAAAGAAGAAAGCCAGTTTGCAATCTCACTTAT
TCTTATTAGAATTTAAAAGATATATTTAAGTGAGAATTAACATTAATTTGGAACAAATACGAAAC
CTGAAATGAGAAGATCAGCTCTGTCTCTTACTGGTTTAATTCATAGGAAGGGTTTGCCGTATAGA
ATTCCTGGTATGGTTGGG
Found at i:19936 original size:2 final size:2
Alignment explanation
Indices: 19929--19963 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19919 TTGGCTGCTT
19929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19964 TATTAACCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27945 original size:24 final size:24
Alignment explanation
Indices: 27918--27967 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
27908 GGCAGAGATT
27918 GATCGCAGAACTGAAATGAATGAA
1 GATCGCAGAACTGAAATGAATGAA
27942 GATCGCAGAACTGAAATGAATGAA
1 GATCGCAGAACTGAAATGAATGAA
27966 GA
1 GA
27968 AAGCAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.26, T:0.16
Consensus pattern (24 bp):
GATCGCAGAACTGAAATGAATGAA
Found at i:28336 original size:31 final size:31
Alignment explanation
Indices: 28299--28361 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
28289 TGAGAGTACG
*
28299 TCATATTTAATACTTATATAAATTACATAAA
1 TCATATTTAATACTTAGATAAATTACATAAA
28330 TCATATTTAATACTTAGATAAATTACATAAA
1 TCATATTTAATACTTAGATAAATTACATAAA
28361 T
1 T
28362 AGTCATTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.41
Consensus pattern (31 bp):
TCATATTTAATACTTAGATAAATTACATAAA
Found at i:29328 original size:16 final size:17
Alignment explanation
Indices: 29293--29330 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29283 TCCATGTAAT
*
29293 TATAATAAAAAATATTA
1 TATAATAAAAAATATGA
*
29310 TATAATAAAAGATA-GA
1 TATAATAAAAAATATGA
29326 TATAA
1 TATAA
29331 AATTATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
TATAATAAAAAATATGA
Found at i:31771 original size:151 final size:151
Alignment explanation
Indices: 31497--31800 Score: 581
Period size: 151 Copynumber: 2.0 Consensus size: 151
31487 GCTTTAGCTA
31497 AAGTAACTCTACCGGTAAAAGAGAGAGTCTGAGCTTTTCACCTTGTAAGTTTTTGTTGCATCTGT
1 AAGTAACTCTACCGGTAAAAGAGAGAGTCTGAGCTTTTCACCTTGTAAGTTTTTGTTGCATCTGT
* *
31562 TGGAGAATGTATTGATACGTTGCATTAGTTACTCTTTTATGAAGAAGAGGAACACCAAGATATCT
66 TGGAGAATGTATCGATACGTTGCATTAGTTACTCTTTTATGAAGAAGAAGAACACCAAGATATCT
31627 CCCCAAGTCTACAACACTAAC
131 CCCCAAGTCTACAACACTAAC
*
31648 AAGTAACTCTACCGGTAAAAGAGAGAGTGTGAGCTTTTCACCTTGTAAGTTTTTGTTGCATCTGT
1 AAGTAACTCTACCGGTAAAAGAGAGAGTCTGAGCTTTTCACCTTGTAAGTTTTTGTTGCATCTGT
31713 TGGAGAATGTATCGATACGTTGCATTAGTTACTCTTTTATGAAGAAGAAGAACACCAAGATATCT
66 TGGAGAATGTATCGATACGTTGCATTAGTTACTCTTTTATGAAGAAGAAGAACACCAAGATATCT
31778 CCCCAAGTCTACAACACTAAC
131 CCCCAAGTCTACAACACTAAC
31799 AA
1 AA
31801 AACCAAGGGC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (151 bp):
AAGTAACTCTACCGGTAAAAGAGAGAGTCTGAGCTTTTCACCTTGTAAGTTTTTGTTGCATCTGT
TGGAGAATGTATCGATACGTTGCATTAGTTACTCTTTTATGAAGAAGAAGAACACCAAGATATCT
CCCCAAGTCTACAACACTAAC
Found at i:34355 original size:65 final size:65
Alignment explanation
Indices: 34242--34374 Score: 196
Period size: 65 Copynumber: 2.0 Consensus size: 65
34232 ATGTCAGCTC
* * *
34242 ACTCATATGTGCTCAGACTTGCTTTAAAATCATAATTCGATTTGGAAGTTTATCTTCTAACAAGG
1 ACTCATATGTGCTCAGACGTGCTTTAAAATCATAATTCAATTTGGAAGTTTATCTTCCAACAAGG
* * *
34307 ACTCATATGTGCTCAGACGTGCTTTAGAATCGTAATTCAAATTT-GAAGTTTATCTTCCAACGAG
1 ACTCATATGTGCTCAGACGTGCTTTAAAATCATAATTC-AATTTGGAAGTTTATCTTCCAACAAG
34371 G
65 G
34372 ACT
1 ACT
34375 TTGTATTTCT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 57 0.93
66 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (65 bp):
ACTCATATGTGCTCAGACGTGCTTTAAAATCATAATTCAATTTGGAAGTTTATCTTCCAACAAGG
Found at i:37826 original size:20 final size:21
Alignment explanation
Indices: 37785--37827 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
37775 AAATTAATAA
* *
37785 TAGGTATGGATGGAATCTGAT
1 TAGGTATAGAGGGAATCTGAT
37806 TAGGTATAGAGGGAA-CTGAT
1 TAGGTATAGAGGGAATCTGAT
37826 TA
1 TA
37828 CACAATTATT
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:0.33, C:0.05, G:0.33, T:0.30
Consensus pattern (21 bp):
TAGGTATAGAGGGAATCTGAT
Found at i:42798 original size:3 final size:3
Alignment explanation
Indices: 42790--42818 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42780 TTTGTTTCTC
42790 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42819 TCCATTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43438 original size:17 final size:18
Alignment explanation
Indices: 43406--43439 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43396 AAATTTTATT
*
43406 TTTTAAAGTTGATTAAAA
1 TTTTAAAGTGGATTAAAA
43424 TTTTAAA-TGGATTAAA
1 TTTTAAAGTGGATTAAA
43440 TTTATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTTAAAGTGGATTAAAA
Found at i:44931 original size:31 final size:31
Alignment explanation
Indices: 44896--44957 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
44886 ACAATCACTC
* * * *
44896 TTACATTAGGACCTGAACTTGATAATTATTT
1 TTACATTAAGACCTAAACTTAACAATTATTT
*
44927 TTACATTAAGACTTAAACTTAACAATTATTT
1 TTACATTAAGACCTAAACTTAACAATTATTT
44958 CCAAGTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (31 bp):
TTACATTAAGACCTAAACTTAACAATTATTT
Found at i:45376 original size:24 final size:24
Alignment explanation
Indices: 45348--45410 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
45338 AGAAATAATC
45348 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* * *
45372 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
45396 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
45411 TCTTAGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:47355 original size:24 final size:24
Alignment explanation
Indices: 47326--47376 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
47316 AGAAATAATC
*
47326 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
47350 TTTCAATTAAACTTTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
47374 TTT
1 TTT
47377 AAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:47385 original size:24 final size:25
Alignment explanation
Indices: 47326--47392 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
47316 AGAAATAATC
* *
47326 TTTCAATTAAACTC-TGTTTATTTG
1 TTTCAATCAAACTCTTATTTATTTG
*
47350 TTTCAATTAAACT-TTATTTATTTG
1 TTTCAATCAAACTCTTATTTATTTG
47374 TTT-AAGTCAAACTCTTATT
1 TTTCAA-TCAAACTCTTATT
47393 AGTCTAGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
23 2 0.05
24 31 0.82
25 5 0.13
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (25 bp):
TTTCAATCAAACTCTTATTTATTTG
Found at i:49343 original size:24 final size:24
Alignment explanation
Indices: 49315--49379 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
49305 TAAGAAATAA
49315 TGTTTCAGTTAAACTCTGTTTAAT
1 TGTTTCAGTTAAACTCTGTTTAAT
* *
49339 TGTTTCAATTAAACTCTGTTTATT
1 TGTTTCAGTTAAACTCTGTTTAAT
* *
49363 TGTTTGAGTCAAACTCT
1 TGTTTCAGTTAAACTCT
49380 TATTAGTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (24 bp):
TGTTTCAGTTAAACTCTGTTTAAT
Found at i:49762 original size:23 final size:23
Alignment explanation
Indices: 49735--49781 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
49725 CTCTAACATA
49735 TATTTATATTTTATATTCTTTAT
1 TATTTATATTTTATATTCTTTAT
49758 TATTTATATTTTATATTCTTTAT
1 TATTTATATTTTATATTCTTTAT
49781 T
1 T
49782 TCATACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATATTTTATATTCTTTAT
Found at i:49763 original size:16 final size:16
Alignment explanation
Indices: 49732--49814 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
49722 GATCTCTAAC
49732 ATATATTTATA-T-TTT
1 ATAT-TTTATATTATTT
49747 ATATTCTT-TATTATTT
1 ATATT-TTATATTATTT
*
49763 ATATTTTATATTCTTT
1 ATATTTTATATTATTT
*
49779 AT-TTCATACTATT-TTAAT
1 ATATT-TTA-TATTATT--T
49797 ATATTTTATATTATTT
1 ATATTTTATATTATTT
49813 AT
1 AT
49815 TTATACTGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
14 3 0.05
15 11 0.20
16 24 0.44
17 8 0.15
18 7 0.13
19 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTTTATATTATTT
Found at i:49804 original size:34 final size:33
Alignment explanation
Indices: 49762--49827 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
49752 CTTTATTATT
*
49762 TATATTTTATATTCTTTATTTCATACTATTTTAA
1 TATATTTTATATTATTTATTT-ATACTATTTTAA
*
49796 TATATTTTATATTATTTATTTATACTGTTTTA
1 TATATTTTATATTATTTATTTATACTATTTTA
49828 TGTCATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.64
Consensus pattern (33 bp):
TATATTTTATATTATTTATTTATACTATTTTAA
Found at i:51718 original size:2 final size:2
Alignment explanation
Indices: 51713--51740 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51703 TGTGTGTGTG
51713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51741 AACAAGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55142 original size:6 final size:6
Alignment explanation
Indices: 55131--55167 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
55121 CTCCCAAGTA
*
55131 GCAGAG GCAGAG GCAGAG GCAGAG GCAGAG ACAGAG G
1 GCAGAG GCAGAG GCAGAG GCAGAG GCAGAG GCAGAG G
55168 ATCAGAACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.49, T:0.00
Consensus pattern (6 bp):
GCAGAG
Found at i:58837 original size:21 final size:18
Alignment explanation
Indices: 58811--58854 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
58801 ATGCAACCAT
58811 TTACACATGTAAATAAATATA
1 TTACACAT-T-AAT-AATATA
*
58832 TTACACATTTATAATATA
1 TTACACATTAATAATATA
58850 TTACA
1 TTACA
58855 TAATCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 2 0.09
20 1 0.05
21 8 0.36
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (18 bp):
TTACACATTAATAATATA
Found at i:60668 original size:23 final size:23
Alignment explanation
Indices: 60642--60689 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
60632 ATATCCGTAG
60642 GCACAC-AAGATGCGAAACAGTAA
1 GCACACGAAG-TGCGAAACAGTAA
60665 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
60688 GC
1 GC
60690 GCGCTTGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.08
Consensus pattern (23 bp):
GCACACGAAGTGCGAAACAGTAA
Done.