Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010965.1 Corchorus capsularis cultivar CVL-1 contig10986, 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: 24779
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:4676 original size:33 final size:33
Alignment explanation
Indices: 4595--4713 Score: 125
Period size: 33 Copynumber: 3.5 Consensus size: 33
4585 CCGCGCAACA
* *
4595 CCGGCCACAAGACCGGCCACGCGACATGGATATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
4630 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
4663 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
4696 CCGGCCACAACCGGCCAC
1 CCGGCCACAACCGGCCAC
4714 ACGATCCTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 62 0.86
35 7 0.10
36 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.27, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:7731 original size:36 final size:36
Alignment explanation
Indices: 7643--7831 Score: 226
Period size: 36 Copynumber: 5.3 Consensus size: 36
7633 AGAACATTAG
*
7643 AAGACTGACTTAATTTCAAGGAAATTAAGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
** * * * *
7678 TTGACTGGCATAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
7714 AAGACTGGCTTAATTTCAAGGAAATTAAGT-AA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
7748 AAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAA
1 AAGACTGGCTTAATTTC----AAGGAAATTAAGTAAAGAA
*
7788 AAGATTGGCTTAATTTCAAGGAAATTAAGT-AA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
7822 AAGACTGGCT
1 AAGACTGGCT
7832 CAGTTTTAGG
Statistics
Matches: 130, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
34 30 0.23
35 31 0.24
36 37 0.28
38 12 0.09
39 2 0.02
40 18 0.14
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
Found at i:7791 original size:74 final size:73
Alignment explanation
Indices: 7643--7855 Score: 288
Period size: 74 Copynumber: 2.9 Consensus size: 73
7633 AGAACATTAG
* ** * *
7643 AAGACTGACTTAATTTCAAGGAAATTAAGTAAAGATTGACTGGCATAGTTTC---AAGGAAACTA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AAAGACTGGCTTAGTTTCAGAAAGGAAATTA
7705 GGTAAAGAA
65 GGTAAAGAA
*
7714 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGACTGGCTTAATTTCAAGAAAGGAAATTA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGACTGGCTTAGTTTC-AGAAAGGAAATTA
7779 GGTAAAGAA
65 GGTAAAGAA
* * * *
7788 AAGATTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGACTGGCTCAGTTTTAGGAAAAGAAATTA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGACTGGCTTAGTTTCA-GAAAGGAAATTA
7853 GGT
65 GGT
7856 TAAAACTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
70 14 0.11
71 32 0.25
73 1 0.01
74 79 0.63
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (73 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAGACTGGCTTAGTTTCAGAAAGGAAATTAG
GTAAAGAA
Found at i:7931 original size:36 final size:36
Alignment explanation
Indices: 7884--8248 Score: 283
Period size: 36 Copynumber: 9.8 Consensus size: 36
7874 AATTCTGGGT
7884 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
7920 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
* * * * *
7956 AAATAAGTAAAGTCAGCAAAGATTTAA-TCCA-AAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
* * *
7990 ATGATTAAGTAAGATCAGACAAAGGGCTTAATTTCA-AAG
1 A--ATTAAGTAAAATTAG-CAAA-GACTTAATTTCACAAG
* * * * * ****
8029 AAATTAGGCAAAAGAATATTGAAAGAAGACTGAAAGAAGACTGAAGG
1 -AATTAAG--TAA-AAT-TAG-CA-AAGACT-TAATTTCAC--AA-G
* *
8076 AA-TACTGAAAGAAGTTAGCAAAGACTTAATTTCACAAG
1 AATTA-AGTAA-AA-TTAGCAAAGACTTAATTTCACAAG
*
8114 AATTAAGT-AAATT-GTCAAAGACTCAATTTCACAAG
1 AATTAAGTAAAATTAG-CAAAGACTTAATTTCACAAG
* *
8149 AATTAAGTAAAATTAGCAAAGACTTGATTTCACCAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
*
8185 AATTAAGTAAAATTAGCAAAGACTTAATTTCACGAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
* * *
8221 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAAATTAGCAAAGACTTAAT
8249 CCAAAGATGA
Statistics
Matches: 265, Mismatches: 42, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
34 5 0.02
35 32 0.12
36 154 0.58
37 6 0.02
38 14 0.05
39 10 0.04
40 3 0.01
41 6 0.02
42 12 0.05
43 6 0.02
44 8 0.03
45 3 0.01
46 5 0.02
47 1 0.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (36 bp):
AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
Found at i:8055 original size:11 final size:11
Alignment explanation
Indices: 8048--8089 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
8038 AAAAGAATAT
8048 TGAAAGAAGAC
1 TGAAAGAAGAC
8059 TGAAAGAAGAC
1 TGAAAGAAGAC
* *
8070 TGAAGGAATAC
1 TGAAAGAAGAC
8081 TGAAAGAAG
1 TGAAAGAAG
8090 TTAGCAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.52, C:0.07, G:0.29, T:0.12
Consensus pattern (11 bp):
TGAAAGAAGAC
Found at i:8066 original size:22 final size:22
Alignment explanation
Indices: 8039--8089 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
8029 AAATTAGGCA
* *
8039 AAAGAATATTGAAAGAAGACTG
1 AAAGAAGACTGAAAGAAGACTG
* *
8061 AAAGAAGACTGAAGGAATACTG
1 AAAGAAGACTGAAAGAAGACTG
8083 AAAGAAG
1 AAAGAAG
8090 TTAGCAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.25, T:0.14
Consensus pattern (22 bp):
AAAGAAGACTGAAAGAAGACTG
Found at i:8262 original size:72 final size:72
Alignment explanation
Indices: 8092--8266 Score: 198
Period size: 72 Copynumber: 2.4 Consensus size: 72
8082 GAAAGAAGTT
*
8092 AGCAAAGACTT-AATTTCACAAGAATTAAGT-AAATTGTCAAAGACTCAATTTCACAAGAATTAA
1 AGCAAAGACTTGAA-TCCACAAGAATTAAGTAAAATTGTCAAAGACTCAATTTCACAAGAATTAA
*
8155 GTAAAATT
65 GTAAAATC
* * * * *
8163 AGCAAAGACTTGATTTCACCAGAATTAAGTAAAATTAG-CAAAGACTTAATTTCACGAGAATTAA
1 AGCAAAGACTTGAATCCACAAGAATTAAGTAAAATT-GTCAAAGACTCAATTTCACAAGAATTAA
*
8227 GTAAAGTC
65 GTAAAATC
*
8235 AGCAAAGA-TTTAATCCA-AAGATGATTAAGTAA
1 AGCAAAGACTTGAATCCACAAGA--ATTAAGTAA
8267 GACCAGACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
70 3 0.03
71 32 0.36
72 53 0.60
73 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (72 bp):
AGCAAAGACTTGAATCCACAAGAATTAAGTAAAATTGTCAAAGACTCAATTTCACAAGAATTAAG
TAAAATC
Found at i:8320 original size:11 final size:11
Alignment explanation
Indices: 8304--8393 Score: 108
Period size: 11 Copynumber: 8.1 Consensus size: 11
8294 AAATTAGGCA
*
8304 AAAGAAGATTG
1 AAAGAAGACTG
*
8315 AAAGAAGATTG
1 AAAGAAGACTG
*
8326 AAGGAAGACTG
1 AAAGAAGACTG
*
8337 AAAAAAAGACTG
1 -AAAGAAGACTG
*
8349 AAAGGAGACTG
1 AAAGAAGACTG
*
8360 AAAGAAGACTA
1 AAAGAAGACTG
*
8371 AAAGGAGACTG
1 AAAGAAGACTG
8382 AAAGAAGACTG
1 AAAGAAGACTG
8393 A
1 A
8394 CTTAATTTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
11 58 0.87
12 9 0.13
ACGTcount: A:0.54, C:0.07, G:0.28, T:0.11
Consensus pattern (11 bp):
AAAGAAGACTG
Found at i:8556 original size:39 final size:35
Alignment explanation
Indices: 8382--8801 Score: 413
Period size: 35 Copynumber: 11.8 Consensus size: 35
8372 AAGGAGACTG
* *
8382 AAAGA-AGACTGACTTAATTTAAAGGAAATTAGGT
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * * *
8416 AAAAGA-AGACTGGTTTAGTTTCAAGGAAACTAAGT
1 -AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * *
8451 AAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGT
1 AAAG-ATAGACTGGCTTAATTTCAAGGAAATTAGGT
8487 AAAAAGA-AGACTGGCTTAATTTCAAGGAAATTAGGT
1 --AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
*
8523 AAAGATAGACTGGCTTAATTTCAAGGAAGGAAATTGGGT
1 AAAGATAGACTGGCTTAATTTC----AAGGAAATTAGGT
* * *
8562 AAAGATAGACTGGTTTAATTTCAAGGAAATTAAGC
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
*
8597 AAAGA-AGACTGGCTTAATTTCGAGGAAATTAGGT
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
*
8631 AAAGATAGACTGGCTTAATTTCAAGAAAGGAAATTGGGT
1 AAAGATAGACTGGCTTAATTTC----AAGGAAATTAGGT
* *
8670 AAAGATAGACTGGCTTAATTTCAAGGAAATTAAGC
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * * *
8705 AAAGAAAAGACTGGC-TAGTTTCAGGGAAACTAGGT
1 AAAG-ATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * * * *
8740 AAAGAAAGACTGCCTTAATTTTAAGAAAATTAAGT
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * *
8775 AAA-AGACACAGGCTTAATTTC-AGGAAA
1 AAAGATAGACTGGCTTAATTTCAAGGAAA
8802 GGAAATTAAG
Statistics
Matches: 326, Mismatches: 43, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
33 5 0.02
34 61 0.19
35 126 0.39
36 63 0.19
37 1 0.00
38 4 0.01
39 66 0.20
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (35 bp):
AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
Found at i:8630 original size:108 final size:107
Alignment explanation
Indices: 8382--8766 Score: 483
Period size: 108 Copynumber: 3.6 Consensus size: 107
8372 AAGGAGACTG
* * * *
8382 AAAGAAGACTGACTTAATTTAAAGGAAATTAGGTAAAAGA-AGACTGGTTTAGTTTC---AAGGA
1 AAAGAAGACTGGCTTAATTTCAAGGAAATTAGGT-AAAGATAGACTGGCTTAATTTCAAGAAGGA
* ** * * * * *
8443 AACTAAGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAA
65 AATTGGGTAAAG-ATAGACTGGCTTAATTTCAAGGAAATTAAG--C
8489 AAAGAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAGGAAGGA
1 AAAGAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAA-GAAGGA
*
8554 AATTGGGTAAAGATAGACTGGTTTAATTTCAAGGAAATTAAGC
65 AATTGGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGC
*
8597 AAAGAAGACTGGCTTAATTTCGAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGGA
1 AAAGAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAG-AAGGA
8662 AATTGGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGC
65 AATTGGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGC
* * * * * *
8705 AAAGAAAAGACTGGC-TAGTTTCAGGGAAACTAGGTAAAGAAAGACTGCCTTAATTTTAAGAA
1 AAAG--AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAGAA
8767 AATTAAGTAA
Statistics
Matches: 248, Mismatches: 22, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
106 5 0.02
107 47 0.19
108 110 0.44
109 38 0.15
110 34 0.14
111 14 0.06
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (107 bp):
AAAGAAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAGGAA
ATTGGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGC
Found at i:10300 original size:26 final size:25
Alignment explanation
Indices: 10268--10333 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
10258 AAAATAAGGG
*
10268 AATTTTTTTTAAATCGACGAAAAAGA
1 AATTTTTTTTAAATCGAC-AAAAACA
** *
10294 AATTTTTTTTAAATC-ACAAACCCT
1 AATTTTTTTTAAATCGACAAAAACA
10318 AATTTTTTTTAAATCG
1 AATTTTTTTTAAATCG
10334 CAATTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.51
25 2 0.06
26 15 0.43
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (25 bp):
AATTTTTTTTAAATCGACAAAAACA
Found at i:13074 original size:19 final size:18
Alignment explanation
Indices: 13031--13077 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
13021 TAAATAATAA
13031 ATTTTTAATATTTTTGTT
1 ATTTTTAATATTTTTGTT
**
13049 AAATTTATATATTTGTT-TT
1 ATTTTTA-ATATTT-TTGTT
13068 ATTTTTAATA
1 ATTTTTAATA
13078 ATTGAGTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
ATTTTTAATATTTTTGTT
Found at i:13445 original size:11 final size:11
Alignment explanation
Indices: 13421--13455 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13411 TTGACAACGC
13421 AACAAAAACAA
1 AACAAAAACAA
* *
13432 AACGAAAACGA
1 AACAAAAACAA
13443 AACAAAAACAA
1 AACAAAAACAA
13454 AA
1 AA
13456 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:13937 original size:19 final size:17
Alignment explanation
Indices: 13913--13947 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
13903 AAATACCGCC
13913 CTAATAAATCTAATTAAAA
1 CTAATAAA-CT-ATTAAAA
13932 CTAATAAACTATTAAA
1 CTAATAAACTATTAAA
13948 CAATCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (17 bp):
CTAATAAACTATTAAAA
Found at i:14041 original size:22 final size:22
Alignment explanation
Indices: 13994--14042 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
13984 TAAATTAACT
*
13994 AATTAAAACTAATAAACTAAGC
1 AATTAAAACTAATAAACTAAGA
* *
14016 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
14038 AATTA
1 AATTA
14043 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:14174 original size:33 final size:33
Alignment explanation
Indices: 14093--14183 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
14083 GGGCGGCATA
* * **
14093 CCATGGCCATGCTGCCCATTTTAAGCGGCTTGC
1 CCATGGCCTTGCCGCCCATTTTGGGCGGCTTGC
14126 CCATGG-CTTGCCGCCCATTTTGGGCGGCTTGC
1 CCATGGCCTTGCCGCCCATTTTGGGCGGCTTGC
14158 CCATGGCCTTGCCGCCCATTTTGGGC
1 CCATGGCCTTGCCGCCCATTTTGGGC
14184 CCAGGCTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 28 0.53
33 25 0.47
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.27
Consensus pattern (33 bp):
CCATGGCCTTGCCGCCCATTTTGGGCGGCTTGC
Found at i:15212 original size:29 final size:31
Alignment explanation
Indices: 15173--15247 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
15163 GCCCCAAAAT
*
15173 GCAATTTAGGATATAACGTTAC-AAAA-CAA
1 GCAATTAAGGATATAACGTTACGAAAATCAA
* * *
15202 GCAATTAAGGATTTAATGTTACGAAAATCGA
1 GCAATTAAGGATATAACGTTACGAAAATCAA
*
15233 GCAAATAAGGATATA
1 GCAATTAAGGATATA
15248 GTCCGTTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 19 0.50
30 4 0.11
31 15 0.39
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (31 bp):
GCAATTAAGGATATAACGTTACGAAAATCAA
Found at i:15242 original size:31 final size:29
Alignment explanation
Indices: 15180--15247 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
15170 AATGCAATTT
*
15180 AGGATATAACGTTACAAAACAAGCAATTA
1 AGGATATAACGTTACAAAACAAGCAAATA
* * *
15209 AGGATTTAATGTTACGAAAATCGAGCAAATA
1 AGGATATAACGTTAC-AAAA-CAAGCAAATA
15240 AGGATATA
1 AGGATATA
15248 GTCCGTTAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.24
Consensus pattern (29 bp):
AGGATATAACGTTACAAAACAAGCAAATA
Found at i:15385 original size:29 final size:31
Alignment explanation
Indices: 15319--15393 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
15309 TCTAACGGAC
*
15319 TATATCCTTATTTGCTCGATTTTCGTAACAT
1 TATATCCTTAATTGCTCGATTTTCGTAACAT
* * *
15350 TAAATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACAT
*
15379 TATATCCTAAATTGC
1 TATATCCTTAATTGC
15394 ATTTTGGGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 19 0.50
30 4 0.11
31 15 0.39
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGATTTTCGTAACAT
Found at i:23071 original size:7 final size:7
Alignment explanation
Indices: 23059--23085 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
23049 ACAAACTAAG
23059 CTAGAGC
1 CTAGAGC
23066 CTAGAGC
1 CTAGAGC
23073 CTAGAGC
1 CTAGAGC
23080 CTAGAG
1 CTAGAG
23086 ATGACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (7 bp):
CTAGAGC
Done.