Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011250.1 Corchorus capsularis cultivar CVL-1 contig11271, 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: 117427
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:157 original size:18 final size:19
Alignment explanation
Indices: 134--170 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
124 CTCACCAATT
134 TTTTTTTAA-AAAAATATA
1 TTTTTTTAATAAAAATATA
152 -TTTTTTAATAAAAATATA
1 TTTTTTTAATAAAAATATA
170 T
1 T
171 GACGTGGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTTTAATAAAAATATA
Found at i:6126 original size:2 final size:2
Alignment explanation
Indices: 6119--6157 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6109 CATCATAATA
6119 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
6158 CTATTTAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:14592 original size:26 final size:26
Alignment explanation
Indices: 14562--14629 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
14552 TTTCTTCATT
14562 TTAATCATAAACTAATTAAATACGAA
1 TTAATCATAAACTAATTAAATACGAA
*
14588 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACGAA
*
14614 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
14630 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.32
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACGAA
Found at i:14604 original size:15 final size:14
Alignment explanation
Indices: 14562--14629 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
14552 TTTCTTCATT
14562 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
*
14577 TTAA-AT--ACGAA
1 TTAACATAAACTAA
14588 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
14603 TTAA-AT--ACTAA
1 TTAACATAAACTAA
14614 TTAAACATAAACTAA
1 TT-AACATAAACTAA
14629 T
1 T
14630 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 15 0.35
12 2 0.05
13 8 0.19
15 18 0.42
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.32
Consensus pattern (14 bp):
TTAACATAAACTAA
Found at i:14700 original size:9 final size:10
Alignment explanation
Indices: 14683--14730 Score: 71
Period size: 10 Copynumber: 4.7 Consensus size: 10
14673 CTAATTAATA
14683 TTAAAAAAAT
1 TTAAAAAAAT
14693 TTAAAAAAAT
1 TTAAAAAAAT
14703 TTAAAAAAA-
1 TTAAAAAAAT
14712 TTAAAGAAAACT
1 TTAAA-AAAA-T
14724 TTAAAAA
1 TTAAAAA
14731 TCCTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.14
10 23 0.66
11 2 0.06
12 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:15885 original size:15 final size:15
Alignment explanation
Indices: 15858--15922 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
15848 GCTTAAGTCA
*
15858 GGTCGGTTGAATTTG
1 GGTCGGTTGAATTCG
15873 GGTCAGGTT-AATTCG
1 GGTC-GGTTGAATTCG
* *
15888 GGTTTGGGTTGAATTTG
1 GG--TCGGTTGAATTCG
15905 GGTCTGGTT-AATTCG
1 GGTC-GGTTGAATTCG
15920 GGT
1 GGT
15923 TCGGGTTCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 20 0.50
16 12 0.30
17 8 0.20
ACGTcount: A:0.14, C:0.08, G:0.38, T:0.40
Consensus pattern (15 bp):
GGTCGGTTGAATTCG
Found at i:15903 original size:32 final size:32
Alignment explanation
Indices: 15862--15929 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
15852 AAGTCAGGTC
*
15862 GGTTGAATTTGGGTCAGGTTAATTCGGGTTTG
1 GGTTGAATTTGGGTCAGGTTAATTCGGGTTCG
*
15894 GGTTGAATTTGGGTCTGGTTAATTCGGGTTCG
1 GGTTGAATTTGGGTCAGGTTAATTCGGGTTCG
15926 GGTT
1 GGTT
15930 CAGTTTGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.13, C:0.07, G:0.38, T:0.41
Consensus pattern (32 bp):
GGTTGAATTTGGGTCAGGTTAATTCGGGTTCG
Found at i:15937 original size:32 final size:32
Alignment explanation
Indices: 15862--15937 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
15852 AAGTCAGGTC
* *
15862 GGTTGAATTTGGGTCAGGTTAATTCGGGTTTG
1 GGTTCAATTTGGGTCAGGTTAATTCGGGTTCG
* *
15894 GGTTGAATTTGGGTCTGGTTAATTCGGGTTCG
1 GGTTCAATTTGGGTCAGGTTAATTCGGGTTCG
*
15926 GGTTCAGTTTGG
1 GGTTCAATTTGG
15938 ATTTTGGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.13, C:0.08, G:0.38, T:0.41
Consensus pattern (32 bp):
GGTTCAATTTGGGTCAGGTTAATTCGGGTTCG
Found at i:16290 original size:15 final size:17
Alignment explanation
Indices: 16270--16301 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16260 CAATTGCGTG
16270 AGATAAA-A-AGGAAAA
1 AGATAAATAGAGGAAAA
16285 AGATAAATAGAGGAAAA
1 AGATAAATAGAGGAAAA
16302 TGATTTCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (17 bp):
AGATAAATAGAGGAAAA
Found at i:23303 original size:12 final size:12
Alignment explanation
Indices: 23286--23310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23276 TTAAAGTAAC
23286 CCCTATTAAATG
1 CCCTATTAAATG
23298 CCCTATTAAATG
1 CCCTATTAAATG
23310 C
1 C
23311 ATTCCAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CCCTATTAAATG
Found at i:46002 original size:16 final size:16
Alignment explanation
Indices: 45983--46091 Score: 87
Period size: 16 Copynumber: 6.4 Consensus size: 16
45973 TGTAGTTTTT
*
45983 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTC
*
45999 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
*
46015 TCGGGTCGTTCGCGTTCCGGGTC
1 TC-GG--G-T--CATT-CGGGTC
46038 TCGGGTCATTCGGGT-
1 TCGGGTCATTCGGGTC
46053 TCCGGGTCATTCGGGTC
1 T-CGGGTCATTCGGGTC
*
46070 TCGGGTC-TACCGGGTC
1 TCGGGTCAT-TCGGGTC
46086 TCGGGT
1 TCGGGT
46092 TGGGCGGGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.03
16 53 0.69
17 6 0.08
19 2 0.03
20 2 0.03
22 4 0.05
23 8 0.10
ACGTcount: A:0.05, C:0.25, G:0.39, T:0.32
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:46035 original size:23 final size:22
Alignment explanation
Indices: 45992--46091 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 22
45982 TTCGGGTCAT
*
45992 TCGGGT-TTCGGGTTATTCGGGTC
1 TCGGGTCTTCGGG-T-TCCGGGTC
*
46015 TCGGGTCGTTCGCGTTCCGGGTC
1 TCGGGTC-TTCGGGTTCCGGGTC
46038 TCGGGTCATTCGGGTTCCGGGTC
1 TCGGGTC-TTCGGGTTCCGGGTC
46061 ATTCGGGTC-TCGGGTCTACCGGGTC
1 --TCGGGTCTTCGGGT-T-CCGGGTC
46086 TCGGGT
1 TCGGGT
46092 TGGGCGGGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
23 46 0.69
24 2 0.03
25 19 0.28
ACGTcount: A:0.04, C:0.25, G:0.39, T:0.32
Consensus pattern (22 bp):
TCGGGTCTTCGGGTTCCGGGTC
Found at i:46568 original size:21 final size:21
Alignment explanation
Indices: 46538--46585 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
46528 TAGCCAATTT
*
46538 ATAATAGGTAAAATCATAATA
1 ATAATAGGTAAAATCATAACA
* *
46559 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
46580 ATAATA
1 ATAATA
46586 TAAACGAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:48009 original size:2 final size:2
Alignment explanation
Indices: 48002--48031 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47992 ACTCTAATTC
48002 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48032 GGTTCTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:52263 original size:21 final size:22
Alignment explanation
Indices: 52225--52266 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
52215 AACCGACGGG
52225 TCGGTTCCGTCAGGTTCTCGGA
1 TCGGTTCCGTCAGGTTCTCGGA
*
52247 TCGGTTCCG-CGGGTTCTCGG
1 TCGGTTCCGTCAGGTTCTCGG
52267 GTCGAGTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.05, C:0.29, G:0.36, T:0.31
Consensus pattern (22 bp):
TCGGTTCCGTCAGGTTCTCGGA
Found at i:52345 original size:15 final size:15
Alignment explanation
Indices: 52314--52434 Score: 91
Period size: 13 Copynumber: 8.5 Consensus size: 15
52304 TATAAAAGTA
*
52314 AATATATATTTATTAT
1 AATATATA-TAATTAT
52330 AATATATATAATTAT
1 AATATATATAATTAT
*
52345 AATTTATATAA-TA-
1 AATATATATAATTAT
52358 AATATATATAA--AGT
1 AATATATATAATTA-T
52372 AA-ATATATAATTACT
1 AATATATATAATTA-T
* *
52387 -TTATATAT-ATTGT
1 AATATATATAATTAT
*
52400 -ATATATA-AAGTA-
1 AATATATATAATTAT
*
52412 AATACATATAATTAT
1 AATATATATAATTAT
52427 AATATATA
1 AATATATA
52435 ATTTATATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.01
13 33 0.39
14 11 0.13
15 31 0.37
16 8 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:52354 original size:24 final size:26
Alignment explanation
Indices: 52316--52363 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
52306 TAAAAGTAAA
*
52316 TATATATTTATTATAATATATATAAT
1 TATATATTTATTATAATAAATATAAT
52342 TATA-ATTTA-TATAATAAATATA
1 TATATATTTATTATAATAAATATA
52364 TATAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 5 0.24
26 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATATTTATTATAATAAATATAAT
Found at i:52367 original size:22 final size:23
Alignment explanation
Indices: 52315--52368 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
52305 ATAAAAGTAA
*
52315 ATATAT-ATTTATTATAATATAT
1 ATATATAATTTATTATAATAAAT
52337 ATAATTATAATTTA-TATAATAAAT
1 AT-A-TATAATTTATTATAATAAAT
52361 ATATATAA
1 ATATATAA
52369 AGTAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.25
23 2 0.07
24 14 0.50
25 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATAATTTATTATAATAAAT
Found at i:52390 original size:39 final size:39
Alignment explanation
Indices: 52333--52442 Score: 111
Period size: 39 Copynumber: 2.8 Consensus size: 39
52323 TTATTATAAT
52333 ATATATAATTATAATTTATATA-ATAAATATATATAAAGTAA
1 ATATATAA-T-TAATTTATATATAT-AATATATATAAAGTAA
* **
52374 ATATATAATTACTTTATATATATTGTATATATAAAGTAA
1 ATATATAATTAATTTATATATATAATATATATAAAGTAA
* *
52413 ATACAT-A-TAA-TTATAATATATAATTTATAT
1 ATATATAATTAATTTAT-ATATATAATATATAT
52443 TTATTATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
36 4 0.07
37 14 0.24
38 1 0.02
39 29 0.49
40 3 0.05
41 8 0.14
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (39 bp):
ATATATAATTAATTTATATATATAATATATATAAAGTAA
Found at i:52394 original size:41 final size:38
Alignment explanation
Indices: 52333--52442 Score: 102
Period size: 41 Copynumber: 2.8 Consensus size: 38
52323 TTATTATAAT
52333 ATATATAATTATAATTTATATAATAAATATATATAAAGTAA
1 ATATATAATTAT-ATTTATAT-AT-AATATATATAAAGTAA
**
52374 ATATATAATTACT-TTATATATATTGTATATATAAAGTAA
1 ATATATAATTA-TATT-TATATATAATATATATAAAGTAA
*
52413 ATACATATAATTATA---ATATATAATTTATAT
1 AT--ATATAATTATATTTATATATAATATATAT
52443 TTATTATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
37 12 0.20
39 16 0.27
40 5 0.08
41 25 0.42
42 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (38 bp):
ATATATAATTATATTTATATATAATATATATAAAGTAA
Found at i:53193 original size:16 final size:16
Alignment explanation
Indices: 53172--53274 Score: 127
Period size: 16 Copynumber: 6.4 Consensus size: 16
53162 GGTTAATGTC
*
53172 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
53188 TCGGGTCATACGAGTT
1 TCGGGTCATTCGGGTT
*
53204 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTT
53220 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
53236 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* * *
53252 ACGAGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
53268 TCGGGTC
1 TCGGGTC
53275 GGATGGGTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
15 2 0.03
16 71 0.95
17 2 0.03
ACGTcount: A:0.11, C:0.19, G:0.36, T:0.34
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:53251 original size:32 final size:32
Alignment explanation
Indices: 53183--53292 Score: 125
Period size: 32 Copynumber: 3.5 Consensus size: 32
53173 CGGGTTATTC
* *
53183 GGGTTTCGGGTCATACGAGTTTCGGGTCATAC-
1 GGGTTTCGGGTCATTCGGGTTTCGGGTCAT-CT
53215 GGGTTTCGGGTCATTCGGGTTTCGGGTCATCT
1 GGGTTTCGGGTCATTCGGGTTTCGGGTCATCT
* * * ***
53247 GGGTTACGAGTCATTCGGGTCTCGGGTCGGAT
1 GGGTTTCGGGTCATTCGGGTTTCGGGTCATCT
53279 GGG-TTCGGGTCATT
1 GGGTTTCGGGTCATT
53293 TACTTTTTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 10 0.15
32 57 0.85
ACGTcount: A:0.11, C:0.18, G:0.38, T:0.33
Consensus pattern (32 bp):
GGGTTTCGGGTCATTCGGGTTTCGGGTCATCT
Found at i:53283 original size:48 final size:48
Alignment explanation
Indices: 53169--53274 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
53159 TCGGGTTAAT
* * *
53169 GTCTCGGGTTATTCGGGTTTCGGGTCATACGAGTTTCGGGTCATACGG
1 GTCTCGGGTCATTCGGGTTTCGGGTCATACGAGTTACGAGTCATACGG
* * *
53217 GTTTCGGGTCATTCGGGTTTCGGGTCAT-CTGGGTTACGAGTCATTCGG
1 GTCTCGGGTCATTCGGGTTTCGGGTCATAC-GAGTTACGAGTCATACGG
53265 GTCTCGGGTC
1 GTCTCGGGTC
53275 GGATGGGTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.10, C:0.20, G:0.36, T:0.34
Consensus pattern (48 bp):
GTCTCGGGTCATTCGGGTTTCGGGTCATACGAGTTACGAGTCATACGG
Found at i:54421 original size:2 final size:2
Alignment explanation
Indices: 54414--54443 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54404 AATTAGAAGA
54414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54444 TAGGGCATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61672 original size:4 final size:4
Alignment explanation
Indices: 61665--61694 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
61655 TAATTAAAAA
61665 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
61695 GTATATATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:66233 original size:29 final size:28
Alignment explanation
Indices: 66196--66267 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 28
66186 TTTTTGGTTC
*
66196 TTTATATTTATTTTCTTAATTTTTAGTA
1 TTTATATTTATTTTCTTAAGTTTTAGTA
66224 TTTATAATTTATTTTCTTAAGTTTTAGTA
1 TTTAT-ATTTATTTTCTTAAGTTTTAGTA
66253 TTTATTTATTTATTT
1 TTTA--TATTTATTT
66268 ATAATATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 5 0.12
29 26 0.65
30 8 0.20
31 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (28 bp):
TTTATATTTATTTTCTTAAGTTTTAGTA
Found at i:72026 original size:32 final size:32
Alignment explanation
Indices: 71990--72051 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
71980 GACAAATAAT
*
71990 ATGGGACGGAGGTTTCCTCAAAAAAAAAAAAA
1 ATGGGACGAAGGTTTCCTCAAAAAAAAAAAAA
72022 ATGGGACGAAGGTTTCCTCAAAAAAAAAAA
1 ATGGGACGAAGGTTTCCTCAAAAAAAAAAA
72052 GGGACGGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.50, C:0.13, G:0.21, T:0.16
Consensus pattern (32 bp):
ATGGGACGAAGGTTTCCTCAAAAAAAAAAAAA
Found at i:72055 original size:28 final size:30
Alignment explanation
Indices: 71990--72062 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 30
71980 GACAAATAAT
71990 ATGGGACGGAGGTTTCCTCAAAAAAAAAAAAA
1 ATGGGACGGAGGTTTCCTC--AAAAAAAAAAA
*
72022 ATGGGACGAAGGTTTCCTC-AAAAAAAAAA
1 ATGGGACGGAGGTTTCCTCAAAAAAAAAAA
72051 A-GGGACGGAGGT
1 ATGGGACGGAGGT
72063 ATATGTTACT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 10 0.26
29 11 0.28
32 18 0.46
ACGTcount: A:0.45, C:0.12, G:0.27, T:0.15
Consensus pattern (30 bp):
ATGGGACGGAGGTTTCCTCAAAAAAAAAAA
Found at i:88383 original size:32 final size:32
Alignment explanation
Indices: 88342--88402 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
88332 ATGTACCAAA
88342 AAGATTACCAATTTTCTATCTAATTTTTTATG
1 AAGATTACCAATTTTCTATCTAATTTTTTATG
*
88374 AAGATTACCAATTTTCTATCTATTTTTTT
1 AAGATTACCAATTTTCTATCTAATTTTTT
88403 TTTGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (32 bp):
AAGATTACCAATTTTCTATCTAATTTTTTATG
Found at i:88753 original size:32 final size:31
Alignment explanation
Indices: 88717--88780 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
88707 TTCATTAATG
88717 GTGAAGATCACCAATTTTCTATCTAATTTTTT
1 GTGAAGATCACCAATTTTCTATCT-ATTTTTT
** *
88749 GTGAAGATTGCCAATTTTCTATCTTTTTTTT
1 GTGAAGATCACCAATTTTCTATCTATTTTTT
88780 G
1 G
88781 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.50
Consensus pattern (31 bp):
GTGAAGATCACCAATTTTCTATCTATTTTTT
Found at i:89278 original size:27 final size:27
Alignment explanation
Indices: 89247--89303 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
89237 TTTTAATTTT
89247 ATTATTTTATTGTATGTATATATAAAC
1 ATTATTTTATTGTATGTATATATAAAC
89274 ATTATTTTATTGTATGTATATATAAAC
1 ATTATTTTATTGTATGTATATATAAAC
89301 ATT
1 ATT
89304 TTCAATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (27 bp):
ATTATTTTATTGTATGTATATATAAAC
Found at i:107472 original size:15 final size:15
Alignment explanation
Indices: 107452--107481 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
107442 CACACTATCA
107452 TATTAATTTCCTTGT
1 TATTAATTTCCTTGT
107467 TATTAATTTCCTTGT
1 TATTAATTTCCTTGT
107482 ATATCGTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
TATTAATTTCCTTGT
Found at i:110025 original size:2 final size:2
Alignment explanation
Indices: 110018--110042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
110008 AGTCTGATTT
110018 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
110043 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:110425 original size:50 final size:50
Alignment explanation
Indices: 110349--110460 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 50
110339 CTATAGACCT
*
110349 ATGAAGAAGATTCAAGATTCTTGATC-AAATGTATACAACTCATCCGGTC
1 ATGAAGAAGATTCAAGATTCTCGATCAAAATGTATACAACTCATCCGGTC
* *
110398 ATGAAGTAAGGTTCAAGATTCTCGATCAAAATGTATATAACTCATCCGGTC
1 ATGAAG-AAGATTCAAGATTCTCGATCAAAATGTATACAACTCATCCGGTC
110449 ATGAAGCAAGAT
1 ATGAAG-AAGAT
110461 CTAGATTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 6 0.11
50 18 0.32
51 32 0.57
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (50 bp):
ATGAAGAAGATTCAAGATTCTCGATCAAAATGTATACAACTCATCCGGTC
Found at i:115322 original size:19 final size:19
Alignment explanation
Indices: 115298--115338 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
115288 TGCAATCTGG
* *
115298 TTTATCAAGGTCTAGATGA
1 TTTATCAAGATCTAGACGA
115317 TTTATCAAGATCTAGACGA
1 TTTATCAAGATCTAGACGA
115336 TTT
1 TTT
115339 CATTCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (19 bp):
TTTATCAAGATCTAGACGA
Done.