Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015098.1 Corchorus olitorius cultivar O-4 contig15131, 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: 60102
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Found at i:11933 original size:27 final size:26
Alignment explanation
Indices: 11871--11967 Score: 133
Period size: 27 Copynumber: 3.7 Consensus size: 26
11861 AAAAAATTAC
**
11871 CAGGGGCATTTTGGTCATTTTCATCT
1 CAGGGGCATTTTGGTCATTTTCGCCT
11897 CAGGGGCATTTTGGTCATTTATCGCCT
1 CAGGGGCATTTTGGTCATTT-TCGCCT
*
11924 CAAGGGCATTTTGGTCATTTTTCGCCT
1 CAGGGGCATTTTGGTCA-TTTTCGCCT
11951 CAGGGTGC-TTTTGGTCA
1 CAGGG-GCATTTTGGTCA
11968 AAATTGCCAG
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
26 20 0.31
27 39 0.61
28 5 0.08
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.39
Consensus pattern (26 bp):
CAGGGGCATTTTGGTCATTTTCGCCT
Found at i:13791 original size:2 final size:2
Alignment explanation
Indices: 13784--13814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13774 TAAACACAAC
13784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13815 AGCACACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15458 original size:47 final size:47
Alignment explanation
Indices: 15398--15591 Score: 277
Period size: 47 Copynumber: 4.1 Consensus size: 47
15388 AGTAAGTAGA
** *
15398 AAACTAAACAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGATAATT
1 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATT
15445 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATT
1 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATT
**
15492 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAA-T-TACCTAATT
1 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATT
* *
15537 AAACTAAGTAGTAGAAGAAGGAA-AGATTAGTTCAATTCTAGGTAAATT
1 AAACTAAGTAGTAAAAGAA-GAAGAGATTAGTTTAATTCTAGGT-AATT
*
15585 GAACTAA
1 AAACTAA
15592 AGAAGAGGTT
Statistics
Matches: 133, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
45 36 0.27
46 5 0.04
47 82 0.62
48 10 0.08
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (47 bp):
AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATT
Found at i:15574 original size:92 final size:95
Alignment explanation
Indices: 15398--15592 Score: 290
Period size: 92 Copynumber: 2.1 Consensus size: 95
15388 AGTAAGTAGA
*
15398 AAACTAAACAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGATAATTAAACTAAGTAGTAAAAGA
1 AAACTAAACAGTAAAAGAAGAAGAGATTAGTTTAATTCTACATAATTAAACTAAGTAGTAAAAGA
*
15463 AGAAGAGATTAGTTTAATTCTAGGT-AATT
66 AGAAGAGATTAGTTCAATTCTAGGTAAATT
** * *
15492 AAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAA-T-TACCTAATTAAACTAAGTAGTAGAAGA
1 AAACTAAACAGTAAAAGAAGAAGAGATTAGTTTAATTCTACATAATTAAACTAAGTAGTAAAAGA
15555 AGGAA-AGATTAGTTCAATTCTAGGTAAATT
66 A-GAAGAGATTAGTTCAATTCTAGGTAAATT
*
15585 GAACTAAA
1 AAACTAAA
15593 GAAGAGGTTG
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
92 44 0.48
93 14 0.15
94 33 0.36
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (95 bp):
AAACTAAACAGTAAAAGAAGAAGAGATTAGTTTAATTCTACATAATTAAACTAAGTAGTAAAAGA
AGAAGAGATTAGTTCAATTCTAGGTAAATT
Found at i:17062 original size:17 final size:17
Alignment explanation
Indices: 17037--17071 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17027 TGCATAATGT
17037 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
* *
17054 TAATGTACCAACACGAA
1 TAATATACCAACAAGAA
17071 T
1 T
17072 GCACTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:17913 original size:27 final size:26
Alignment explanation
Indices: 17875--18003 Score: 186
Period size: 27 Copynumber: 4.8 Consensus size: 26
17865 CGGCCCGAGG
17875 CGAAGTAGGAGGATCCACTGCTGGGGT
1 CGAAGT-GGAGGATCCACTGCTGGGGT
*
17902 CGAAGTGTGAGGATCCACTGCTGGGTT
1 CGAAGTG-GAGGATCCACTGCTGGGGT
17929 CGAAGTAGGAGGATCCACTGCTGGGGT
1 CGAAGT-GGAGGATCCACTGCTGGGGT
*
17956 CGAAGTGGGAGGATCCACTACTGGGGT
1 CGAAGT-GGAGGATCCACTGCTGGGGT
*
17983 CGAAATGGAAGGATCCACTGC
1 CGAAGTGG-AGGATCCACTGC
18004 GGCAACAGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
26 3 0.03
27 89 0.96
28 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.19
Consensus pattern (26 bp):
CGAAGTGGAGGATCCACTGCTGGGGT
Found at i:17957 original size:54 final size:54
Alignment explanation
Indices: 17875--18003 Score: 206
Period size: 54 Copynumber: 2.4 Consensus size: 54
17865 CGGCCCGAGG
* * *
17875 CGAAGTAGGAGGATCCACTGCTGGGGTCGAAGTGTGAGGATCCACTGCTGGGTT
1 CGAAGTAGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACTGGGGT
17929 CGAAGTAGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACTGGGGT
1 CGAAGTAGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACTGGGGT
*
17983 CGAAAT-GGAAGGATCCACTGC
1 CGAAGTAGG-AGGATCCACTGC
18004 GGCAACAGTC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
53 2 0.03
54 68 0.97
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.19
Consensus pattern (54 bp):
CGAAGTAGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACTGGGGT
Found at i:18080 original size:24 final size:24
Alignment explanation
Indices: 18048--18105 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
18038 ACATCCTCTG
18048 CATTTGCTGCCTCAATGGGGTCGC
1 CATTTGCTGCCTCAATGGGGTCGC
18072 CATTTGCTGCCTCAATGGGGTCGC
1 CATTTGCTGCCTCAATGGGGTCGC
18096 CATTTGCTGC
1 CATTTGCTGC
18106 TAAATCCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.12, C:0.29, G:0.28, T:0.31
Consensus pattern (24 bp):
CATTTGCTGCCTCAATGGGGTCGC
Found at i:18865 original size:2 final size:2
Alignment explanation
Indices: 18858--18894 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18848 AAAGATGTCC
18858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18895 TTTAGCAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19332 original size:2 final size:2
Alignment explanation
Indices: 19327--19358 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19317 TATATATATA
19327 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19359 GAAGAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:23371 original size:163 final size:161
Alignment explanation
Indices: 23112--23505 Score: 457
Period size: 163 Copynumber: 2.4 Consensus size: 161
23102 TATTATAGGC
* * *
23112 GAGGGAATTTTTCCCTCCAAAACAAAGGAAAAAAAATTATCTCACCCCATATATTACAATTGCGG
1 GAGGGAATTTTTCCCTCCAAAA-AAAGGAAAAAAAATTCTCTC-CCCCATATATTAAAATAGCGG
* * * * * *
23177 CGTTTCCCTTCCTAAATACCACTAATTAGCGGCGTCTGGTGAGAAAACGCCACTAATATATTATA
64 CGTTTCACTTCCTAAACACCACTAATTAGCGGCATCCGATGACAAAACGCCACT-ATATATTATA
* * *
23242 CGCGTAGAGTTGGAAATTTTTTTTGTTTTAGGGG
128 CGCATAGAGTTGGAAACTTTCTTTGTTTTAGGGG
* * * *
23276 GAGGGAATTTTTCCCTCTAAAAAACCGGGAAAAAAA-TCTCTCCCTCCATATATTAAAATAGTGG
1 GAGGGAATTTTTCCCTCCAAAAAA-AGGAAAAAAAATTCTCTCCC-CCATATATTAAAATAGCGG
* * * * * * * * *
23340 CGTTTCATTTTCTAGACGCCACTACTTAGCGGCATCCGATGTCTAAACGCCGCTATATATTATAG
64 CGTTTCACTTCCTAAACACCACTAATTAGCGGCATCCGATGACAAAACGCCACTATATATTATAC
23405 GCATAGAGTTGGAAACTTTCTTTGTTTTAGGGG
129 GCATAGAGTTGGAAACTTTCTTTGTTTTAGGGG
* * * *
23438 TAAGGAATTTTTCCCTCCAAAAAAAAGAGAAAAAAAATTCTCTCCCCCATATATTAATATGGCGG
1 GAGGGAATTTTTCCCTCC-AAAAAAAG-GAAAAAAAATTCTCTCCCCCATATATTAAAATAGCGG
23503 CGT
64 CGT
23506 CTTTCAGTCG
Statistics
Matches: 192, Mismatches: 33, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
162 58 0.30
163 96 0.50
164 38 0.20
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (161 bp):
GAGGGAATTTTTCCCTCCAAAAAAAGGAAAAAAAATTCTCTCCCCCATATATTAAAATAGCGGCG
TTTCACTTCCTAAACACCACTAATTAGCGGCATCCGATGACAAAACGCCACTATATATTATACGC
ATAGAGTTGGAAACTTTCTTTGTTTTAGGGG
Found at i:32981 original size:1 final size:1
Alignment explanation
Indices: 32977--33060 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
32967 CATTTTTTGC
* * * * * * * * *
32977 AAAAAAAAACAAAAAAAAACAAAAAAACAAAAACAAAAACAAAAACAAAACAAAACAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * *
33042 GCAAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
33061 CTTTCAAGTT
Statistics
Matches: 58, Mismatches: 25, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:32990 original size:5 final size:5
Alignment explanation
Indices: 32976--33057 Score: 87
Period size: 5 Copynumber: 16.0 Consensus size: 5
32966 CCATTTTTTG
* *
32976 CAAAA AAAAA CAAAA AAAAA C-AAA -AAAA CAAAAA CAAAAA CAAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA C-AAAA C-AAAA C-AAAA
*
33022 CAAAA CAAAA CAAAAA CAAAG CAAAA CAAAA CAAAA
1 CAAAA CAAAA C-AAAA CAAAA CAAAA CAAAA CAAAA
33058 AAACTTTCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
4 6 0.09
5 39 0.58
6 22 0.33
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:32991 original size:10 final size:10
Alignment explanation
Indices: 32976--33058 Score: 96
Period size: 10 Copynumber: 8.0 Consensus size: 10
32966 CCATTTTTTG
32976 CAAAAAAAAA
1 CAAAAAAAAA
32986 CAAAAAAAAA
1 CAAAAAAAAA
32996 CAAAAAAACAA
1 CAAAAAAA-AA
*
33007 -AAACAAAAA
1 CAAAAAAAAA
33016 CAAAAACAAAA
1 CAAAAA-AAAA
33027 CAAAACAAAAA
1 CAAAA-AAAAA
**
33038 CAAAGCAAAA
1 CAAAAAAAAA
33048 CAAAACAAAAA
1 CAAAA-AAAAA
33059 AACTTTCAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
9 2 0.03
10 36 0.58
11 23 0.37
12 1 0.02
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:33000 original size:6 final size:6
Alignment explanation
Indices: 32977--33058 Score: 88
Period size: 6 Copynumber: 14.7 Consensus size: 6
32967 CATTTTTTGC
*
32977 AAAA-A AAAACA AAAA-A AAACAAA AAAACA AAAACA AAAACA AAAAC-
1 AAAACA AAAACA AAAACA AAA-ACA AAAACA AAAACA AAAACA AAAACA
*
33023 AAAAC- AAAACA AAAAC- AAAGC- AAAAC- AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
33059 AACTTTCAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
5 31 0.45
6 34 0.49
7 4 0.06
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:33726 original size:33 final size:30
Alignment explanation
Indices: 33666--33727 Score: 72
Period size: 33 Copynumber: 2.0 Consensus size: 30
33656 TTTTATGTTT
*
33666 TTTATTAATTTAATTAATTCAATTGTAATA
1 TTTATTAATTTAATTAATTCAAGTGTAATA
33696 TTTATTAATTGTTAAATTAAATT-AAGTGTAAT
1 TTTATTAA-T-TT-AATT-AATTCAAGTGTAAT
33728 CATTATCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 8 0.30
31 1 0.04
32 2 0.07
33 12 0.44
34 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTATTAATTTAATTAATTCAAGTGTAATA
Found at i:35495 original size:15 final size:15
Alignment explanation
Indices: 35475--35529 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
35465 TGATTTTCAT
35475 TTATTATTAGTGTTA
1 TTATTATTAGTGTTA
35490 TTATTATTTTTAGTGTTA
1 TTATTA---TTAGTGTTA
*
35508 -T-TTATTATTGTTA
1 TTATTATTAGTGTTA
*
35521 TAATTATTA
1 TTATTATTA
35530 TCATAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 8 0.24
15 12 0.36
16 3 0.09
17 1 0.03
18 9 0.27
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
TTATTATTAGTGTTA
Found at i:35502 original size:18 final size:19
Alignment explanation
Indices: 35475--35516 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
35465 TGATTTTCAT
35475 TTATTATTAGTGTTA-TTA
1 TTATTATTAGTGTTATTTA
*
35493 TTATTTTTAGTGTTATTTA
1 TTATTATTAGTGTTATTTA
35512 TTATT
1 TTATT
35517 GTTATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
TTATTATTAGTGTTATTTA
Found at i:37333 original size:22 final size:23
Alignment explanation
Indices: 37277--37333 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
37267 ATAACCAATA
*
37277 AATTAAATTATTATTTCTTAAAT
1 AATTAAATTAATATTTCTTAAAT
* *
37300 AA-TGAATAAATA-TT-TTATAAT
1 AATTAAATTAATATTTCTTA-AAT
37321 AATTAAATTAATA
1 AATTAAATTAATA
37334 ATAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 3 0.11
21 7 0.26
22 15 0.56
23 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTAAATTAATATTTCTTAAAT
Found at i:37336 original size:15 final size:15
Alignment explanation
Indices: 37316--37405 Score: 58
Period size: 15 Copynumber: 5.8 Consensus size: 15
37306 TAAATATTTT
37316 ATAATAATTAAATTA
1 ATAATAATTAAATTA
* *
37331 ATAATAATAAAAATA
1 ATAATAATTAAATTA
*
37346 ATACCTAATTAAATT-
1 ATA-ATAATTAAATTA
* *
37361 ATAAATAATAATAACTA
1 AT-AATAATTA-AATTA
* *
37378 ATTATTAATT-AATAA
1 A-TAATAATTAAATTA
37393 ATTAATAATTAAA
1 A-TAATAATTAAA
37406 AACCCATAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
15 35 0.62
16 14 0.25
17 6 0.11
18 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATAATTAAATTA
Found at i:37378 original size:25 final size:27
Alignment explanation
Indices: 37316--37401 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 27
37306 TAAATATTTT
*
37316 ATAATAATTAAATTAATAA-TAATAAA-A
1 ATAATAACT-AATT-ATAATTAATAAATA
*
37343 ATAATACCTAATTA-AATT-ATAAATA
1 ATAATAACTAATTATAATTAATAAATA
37368 ATAATAACTAATTATTAATTAATAAATTA
1 ATAATAACTAATTA-TAATTAATAAA-TA
37397 ATAAT
1 ATAAT
37402 TAAAAACCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 7 0.14
25 16 0.32
26 4 0.08
27 11 0.22
28 5 0.10
29 7 0.14
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAATAACTAATTATAATTAATAAATA
Found at i:37402 original size:7 final size:7
Alignment explanation
Indices: 37317--37404 Score: 50
Period size: 7 Copynumber: 13.4 Consensus size: 7
37307 AAATATTTTA
37317 TAATAAT
1 TAATAAT
37324 T-A-AAT
1 TAATAAT
37329 TAATAA-
1 TAATAAT
37335 TAATAA-
1 TAATAAT
*
37341 AAATAA-
1 TAATAAT
*
37347 TACCTAAT
1 TA-ATAAT
37355 T-A-AAT
1 TAATAAT
*
37360 T-ATAAA
1 TAATAAT
37366 TAATAA-
1 TAATAAT
37372 TAACTAAT
1 TAA-TAAT
*
37380 TATTAAT
1 TAATAAT
37387 TAATAAAT
1 TAAT-AAT
37395 TAATAAT
1 TAATAAT
37402 TAA
1 TAA
37405 AAACCCATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
5 9 0.14
6 20 0.31
7 26 0.40
8 10 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
TAATAAT
Found at i:37450 original size:17 final size:17
Alignment explanation
Indices: 37412--37455 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
37402 TAAAAACCCA
*
37412 TAAAATAATTC-AATAGC
1 TAAAATAA-TCAAATACC
37429 T-AAATAATCAAATACC
1 TAAAATAATCAAATACC
37445 TAAAATAATCA
1 TAAAATAATCA
37456 TACAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 12 0.50
17 10 0.42
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAATAATCAAATACC
Found at i:37498 original size:19 final size:19
Alignment explanation
Indices: 37458--37508 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
37448 AATAATCATA
*
37458 CAATAATT-AA-AATAATT
1 CAATAATTAAATAATAAAT
*
37475 TAATAATTAAATAATAAAT
1 CAATAATTAAATAATAAAT
*
37494 CAATAATTAATTAAT
1 CAATAATTAAATAAT
37509 CATAAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 7 0.25
18 2 0.07
19 19 0.68
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
CAATAATTAAATAATAAAT
Found at i:41815 original size:19 final size:19
Alignment explanation
Indices: 41795--41831 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41785 AATTAATTAT
41795 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
41813 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
41832 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:41842 original size:19 final size:19
Alignment explanation
Indices: 41801--41842 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41791 TTATTTTAAT
* * *
41801 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
41820 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
41839 ATTA
1 ATTA
41843 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:44094 original size:22 final size:23
Alignment explanation
Indices: 44065--44122 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
44055 ATAACCCTTC
44065 CTATGAAAATTTTG-TAACCACA
1 CTATGAAAATTTTGTTAACCACA
* *
44087 TTATG-AAATTTTGTTAATCACA
1 CTATGAAAATTTTGTTAACCACA
44109 CTATGAAAAATTTT
1 CTATG-AAAATTTT
44123 AATATAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 8 0.27
22 15 0.50
24 7 0.23
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (23 bp):
CTATGAAAATTTTGTTAACCACA
Found at i:47550 original size:28 final size:29
Alignment explanation
Indices: 47486--47561 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 29
47476 CATTTACACG
*
47486 TCCAGGGGCATTTTGGTCACCTTCGCATG
1 TCCAGGGGCATTTTGGTCACCTTCGCATA
* *
47515 TCCAGGGGCATTTTGGTCA-TTTTGCATA
1 TCCAGGGGCATTTTGGTCACCTTCGCATA
*
47543 TTCAGGGGCATTTTGGTCA
1 TCCAGGGGCATTTTGGTCA
47562 ATTCTTAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 24 0.56
29 19 0.44
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.36
Consensus pattern (29 bp):
TCCAGGGGCATTTTGGTCACCTTCGCATA
Found at i:47883 original size:26 final size:26
Alignment explanation
Indices: 47833--47883 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
47823 TTTACATTTA
* *
47833 GAAAATACAAAAAAATGTGTAAATGG
1 GAAAATACAAAAAAAAGAGTAAATGG
* *
47859 GAAAATATAAAAAAAAGAGTGAATG
1 GAAAATACAAAAAAAAGAGTAAATG
47884 TTCATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.18
Consensus pattern (26 bp):
GAAAATACAAAAAAAAGAGTAAATGG
Found at i:55696 original size:26 final size:26
Alignment explanation
Indices: 55650--55726 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
55640 TTAAGAGTGG
* ** *
55650 ACTTAAAATGACCAACGTGCCCTTGA
1 ACTTAAAATGACTAAAATGCCCCTGA
55676 ACTTAAAATGACTAAAATGCCCCTGA
1 ACTTAAAATGACTAAAATGCCCCTGA
*
55702 A-TATGCAAATGACTAAAATGCCCCT
1 ACT-T-AAAATGACTAAAATGCCCCT
55727 AGGTGACCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 1 0.02
26 24 0.55
27 19 0.43
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (26 bp):
ACTTAAAATGACTAAAATGCCCCTGA
Found at i:58888 original size:21 final size:22
Alignment explanation
Indices: 58864--58904 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
58854 TTGCCTCATA
*
58864 CATTCATTCAT-CATGCCATGG
1 CATTCATTCATGCATCCCATGG
58885 CATTCATTCATGCATCCCAT
1 CATTCATTCATGCATCCCAT
58905 TAAACTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (22 bp):
CATTCATTCATGCATCCCATGG
Done.