Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014917.1 Corchorus capsularis cultivar CVL-1 contig14938, 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: 22342
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:2191 original size:19 final size:18
Alignment explanation
Indices: 2159--2196 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2149 TTGAAATAAT
*
2159 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
2177 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
2196 T
1 T
2197 AATCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:2192 original size:11 final size:11
Alignment explanation
Indices: 2175--2206 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2165 ATTGTCTTCA
2175 AATCTTCAAAT
1 AATCTTCAAAT
*
2186 TATCTTCAAAT
1 AATCTTCAAAT
2197 AATCTTCAAA
1 AATCTTCAAA
2207 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:2203 original size:22 final size:22
Alignment explanation
Indices: 2147--2206 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
2137 AATTTTTACT
* *
2147 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
2169 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
2188 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
2207 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:3757 original size:22 final size:20
Alignment explanation
Indices: 3724--3768 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
3714 CTTCTATTAC
3724 CTTAATTCTCAAATTCACTCA
1 CTTAATTCTCAAATTCACT-A
* *
3745 CTTAGATTTTCAATTTCACTA
1 CTTA-ATTCTCAAATTCACTA
3766 CTT
1 CTT
3769 CATCAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.44
Consensus pattern (20 bp):
CTTAATTCTCAAATTCACTA
Found at i:6218 original size:40 final size:40
Alignment explanation
Indices: 6149--6224 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
6139 AAGGTTTAAA
* *
6149 AAAATAACTTCCGAAAGCAAAGCCGAAAGTGGAAACCATG
1 AAAACAACTTCCGAAAGCAAAGCCAAAAGTGGAAACCATG
*
6189 AAAACAACTTCCGAAAGCAGAGCCAAAAGTGGAAAC
1 AAAACAACTTCCGAAAGCAAAGCCAAAAGTGGAAAC
6225 TATAGAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.11
Consensus pattern (40 bp):
AAAACAACTTCCGAAAGCAAAGCCAAAAGTGGAAACCATG
Found at i:7344 original size:18 final size:18
Alignment explanation
Indices: 7311--7346 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7301 ACTTCTTTGT
*
7311 AATTCAATTCGAATGCAA
1 AATTCAATTCCAATGCAA
*
7329 AATTCAATTCCTATGCAA
1 AATTCAATTCCAATGCAA
7347 GAATAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (18 bp):
AATTCAATTCCAATGCAA
Found at i:8042 original size:72 final size:72
Alignment explanation
Indices: 7917--8135 Score: 339
Period size: 72 Copynumber: 3.0 Consensus size: 72
7907 CTAGCCGGTG
* * * * *
7917 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCTGGTCTCACGGGACCCTTAAGAGGGT
1 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGC
7982 TCTTCAT
66 TCTTCAT
* * *
7989 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAACCGATATCTCTGGACCCTTAAAAGGGC
1 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGC
8054 TCTTCAT
66 TCTTCAT
* *
8061 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTACCAGTCGGTATCTCTGGACCCTTAAGAGGGC
1 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGC
*
8126 TCTTGAT
66 TCTTCAT
8133 CCG
1 CCG
8136 GTCTTACTAC
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 133 1.00
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.25
Consensus pattern (72 bp):
CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGTATCTCTGGACCCTTAAGAGGGC
TCTTCAT
Found at i:8358 original size:50 final size:49
Alignment explanation
Indices: 8315--8464 Score: 228
Period size: 50 Copynumber: 3.0 Consensus size: 49
8305 TTACTGTCGT
* *
8315 ATGATCAATGCTCGTCGGTCTTATGGCCCGTCATGGGGTCTTACGGCCG
1 ATGATCGATGCTCGTCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCG
*
8364 ATCAGTCGATGCTCGTCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCG
1 ATGA-TCGATGCTCGTCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCG
* * *
8414 ATCGGTTGATGCTCGTTGGTCTTACGGCCCGTCATGGGGTCTTACGGCCG
1 AT-GATCGATGCTCGTCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCG
8464 A
1 A
8465 GAATGATCAA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 3 0.03
50 89 0.97
ACGTcount: A:0.13, C:0.27, G:0.32, T:0.28
Consensus pattern (49 bp):
ATGATCGATGCTCGTCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCG
Found at i:8387 original size:30 final size:28
Alignment explanation
Indices: 8351--8442 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 28
8341 CCCGTCATGG
8351 GGTCTTACGGCCGATCAGTCGATGCTCGT
1 GGTCTTACGGCCGATC-GTCGATGCTCGT
8380 CGGTCTTACGGCC---CGTC-ATG---G-
1 -GGTCTTACGGCCGATCGTCGATGCTCGT
*
8401 GGTCTTACGGCCGATCGGTTGATGCTCGTT
1 GGTCTTACGGCCGATC-GTCGATGCTCG-T
8431 GGTCTTACGGCC
1 GGTCTTACGGCC
8443 CGTCATGGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
20 12 0.24
22 1 0.02
23 1 0.02
24 2 0.04
25 6 0.12
26 3 0.06
27 1 0.02
28 1 0.02
30 24 0.47
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (28 bp):
GGTCTTACGGCCGATCGTCGATGCTCGT
Found at i:8406 original size:20 final size:20
Alignment explanation
Indices: 8381--8462 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
8371 GATGCTCGTC
8381 GGTCTTACGGCCCGTCATGG
1 GGTCTTACGGCCCGTCATGG
*
8401 GGTCTTACGGCCGATCGGTTGATGCTCG
1 GGTCTTACGGCC---C-G-TCATG---G
8429 TTGGTCTTACGGCCCGTCATGG
1 --GGTCTTACGGCCCGTCATGG
8451 GGTCTTACGGCC
1 GGTCTTACGGCC
8463 GAGAATGATC
Statistics
Matches: 50, Mismatches: 2, Indels: 20
0.69 0.03 0.28
Matches are distributed among these distances:
20 24 0.48
22 1 0.02
23 1 0.02
24 1 0.02
25 8 0.16
26 1 0.02
27 1 0.02
28 1 0.02
30 12 0.24
ACGTcount: A:0.10, C:0.28, G:0.34, T:0.28
Consensus pattern (20 bp):
GGTCTTACGGCCCGTCATGG
Found at i:8785 original size:90 final size:90
Alignment explanation
Indices: 8629--8860 Score: 281
Period size: 90 Copynumber: 2.6 Consensus size: 90
8619 GTACAAGTAC
** * * * * *
8629 TAAGCATATACCACCACCAAAATATGATAAAACATGTAAGCATGTTTAAACGATGCTCTTGCATG
1 TAAGCATATACTTCCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTCTTGCATG
*
8694 ATCATATTAA-CTCAATTTATACATA
66 ATCATA-AAAGCTCAATTTATACATA
* *
8719 TAGGCATATACTTCCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTTTTGCATG
1 TAAGCATATACTTCCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTCTTGCATG
*
8784 ATCATAAAAGCTCAATTTATGCATA
66 ATCATAAAAGCTCAATTTATACATA
* *
8809 TAAGCACATGCTTTTCC-T-AAAAAATGATAAAAGGCATGTTATCATGCTTAAA
1 TAAGCATATAC--TTCCATCAAAAAATGATAAAA--CATGTTATCATGCTTAAA
8861 GGATCATATT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
89 2 0.02
90 98 0.80
91 1 0.01
92 22 0.18
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (90 bp):
TAAGCATATACTTCCATCAAAAAATGATAAAACATGTTATCATGCTTAAACGATGCTCTTGCATG
ATCATAAAAGCTCAATTTATACATA
Found at i:10871 original size:11 final size:11
Alignment explanation
Indices: 10857--10890 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
10847 ATAAAGAAGG
10857 AAAAAAAAGAA
1 AAAAAAAAGAA
10868 AAAAGAAAAGAA
1 AAAA-AAAAGAA
*
10880 AAGAAAAAGAA
1 AAAAAAAAGAA
10891 GCAAATGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:10890 original size:16 final size:16
Alignment explanation
Indices: 10856--10887 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
10846 AATAAAGAAG
10856 GAAAAAAAAGAAAAAA
1 GAAAAAAAAGAAAAAA
10872 GAAAAGAAAAGAAAAA
1 GAAAA-AAAAGAAAAA
10888 GAAGCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAGAAAAAA
Found at i:11224 original size:13 final size:13
Alignment explanation
Indices: 11206--11230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11196 TCGTATATTT
11206 TCCCCAATTTTTC
1 TCCCCAATTTTTC
11219 TCCCCAATTTTT
1 TCCCCAATTTTT
11231 TTCTTAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (13 bp):
TCCCCAATTTTTC
Found at i:12065 original size:22 final size:22
Alignment explanation
Indices: 12037--12082 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12027 TCAAAAGTGT
12037 AAAAAATAAGGCGGTGTTTAGC
1 AAAAAATAAGGCGGTGTTTAGC
*
12059 AAAAAATAGGGCGGTGTTTAGC
1 AAAAAATAAGGCGGTGTTTAGC
12081 AA
1 AA
12083 CAGCCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.22
Consensus pattern (22 bp):
AAAAAATAAGGCGGTGTTTAGC
Found at i:12150 original size:21 final size:21
Alignment explanation
Indices: 12126--12168 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12116 CAAATGGGAG
* **
12126 TTACTATTTACCGTCCCCTTT
1 TTACTACTTACCACCCCCTTT
12147 TTACTACTTACCACCCCCTTT
1 TTACTACTTACCACCCCCTTT
12168 T
1 T
12169 GACACTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.37, G:0.02, T:0.44
Consensus pattern (21 bp):
TTACTACTTACCACCCCCTTT
Found at i:14916 original size:487 final size:487
Alignment explanation
Indices: 14003--14976 Score: 1626
Period size: 487 Copynumber: 2.0 Consensus size: 487
13993 TGGATACCAG
** * * * * *
14003 ATTGACTATCACAAAGCAGAAGAATTGGGGATGGAGGTTGAACTTGTAAGTCTGTTAGAAGATAT
1 ATTGACTATCACAAAGCAGAAGAATTAAGGATAGAAGTTGAACTTATAAGTCTGTTAAAAGATAC
* *
14068 TGAATCCATTGAAGCTCACATGTGGTTGAAGTTAGAGCTCTATATTCTGCTTCAGAGGAGCTACG
66 TGAATCCATTGAAGCTCACATGTGGTTGAAGCTAGAGCTCTATATTCTGCTTCAGAGGAACTACG
* *
14133 ACTTATTGTATTCTACTTTTTACTTTTCCAGGAGACTAAAGCATCACCAATTAGAACACAAAAAC
131 ACTTATTGTATTCTACTTTTTACTTTTCCAGGAGACCAAAACATCACCAATTAGAACACAAAAAC
* * *
14198 TAGTGATAGACCTTCTGGTATCTACACAAGTGCCCCAATCACTATCTGAGAAAGCCTTAAGCTAC
196 CACTGATAGACCTTCTGGTATCTACACAAGTGCCCCAATCACTATCTGAGAAAGCCTCAAGCTAC
* * *
14263 AAACTGTTGTTAGCAGGAAGGAATAATCCTTGTCCTATGCTTCCTTTCAAATATCTGAAAACTCT
261 AAACTGTTGTTAGCACGAAAGAATAATCCTTGTCATATGCTTCCTTTCAAATATCTGAAAACTCT
*
14328 ATGAATAGCTACCAAATGAAAATCAGTGGGTGCATTAAGGAACTGAGCCAGCTGTTGTACTACAA
326 ATGAATAGCTACCAAATGAAAATCAGTGGGTGCATCAAGGAACTGAGCCAGCTGTTGTACTACAA
* *
14393 AACTTTAATCTAGTCGAGTAGTTGTAAGATATTGAAGCTTTCCCACTAACTTTCTATACTGGGTA
391 AACTTAAATCTAGTCGAGTAGTTGTAAGATATTGAAGCTTTCCCACTAACATTCTATACTGGGTA
14458 GAATCAGCTAACAATGTGCCTCCTTCTTTAGA
456 GAATCAGCTAACAATGTGCCTCCTTCTTTAGA
** *
14490 ATTGACTATCACAAAGCAGGGGAATTAAGGCTAGAAGTTGAACTTATAAGTCTGTTAAAAGATAC
1 ATTGACTATCACAAAGCAGAAGAATTAAGGATAGAAGTTGAACTTATAAGTCTGTTAAAAGATAC
*
14555 TGAATCCATTGAAGCTCACATGTGGTTGAAGCTAGAGCTCTATATTCTTCTTCAGAGGAACTACG
66 TGAATCCATTGAAGCTCACATGTGGTTGAAGCTAGAGCTCTATATTCTGCTTCAGAGGAACTACG
* * *
14620 ACTTATTGTATTCTGCTTTTTACTTTTTCGGGAGACCAAAACATCACCAATTAGAACACAAAAAC
131 ACTTATTGTATTCTACTTTTTACTTTTCCAGGAGACCAAAACATCACCAATTAGAACACAAAAAC
*
14685 CACTGATAGACCTTCTGGTATCTACACAAGTGCCCCAATCACTATCTGAGAAAGCCTCAAGCTGC
196 CACTGATAGACCTTCTGGTATCTACACAAGTGCCCCAATCACTATCTGAGAAAGCCTCAAGCTAC
*
14750 AAACTGTTGTTAGCACGAAAGAAT-ATCCCTTGTCATATGCTTCCTTTCAAATATCTTAAAACTC
261 AAACTGTTGTTAGCACGAAAGAATAAT-CCTTGTCATATGCTTCCTTTCAAATATCTGAAAACTC
* *
14814 TATGAATAGCTGCCAAATGAAGATCAGTGGGTGCATCAAGGAACTGAGCCAGCTGTTGTACTACA
325 TATGAATAGCTACCAAATGAAAATCAGTGGGTGCATCAAGGAACTGAGCCAGCTGTTGTACTACA
* * *
14879 AAACTTAAATCTGGTCGATTAGTTGTACGATATTGAAGCTTTCCCACTAACATTCTATACTGGGT
390 AAACTTAAATCTAGTCGAGTAGTTGTAAGATATTGAAGCTTTCCCACTAACATTCTATACTGGGT
14944 AGAATCAGCTAACAATGTGCCTCCTTCTTTAGA
455 AGAATCAGCTAACAATGTGCCTCCTTCTTTAGA
14977 TAATCTGGTT
Statistics
Matches: 452, Mismatches: 34, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
486 2 0.00
487 450 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (487 bp):
ATTGACTATCACAAAGCAGAAGAATTAAGGATAGAAGTTGAACTTATAAGTCTGTTAAAAGATAC
TGAATCCATTGAAGCTCACATGTGGTTGAAGCTAGAGCTCTATATTCTGCTTCAGAGGAACTACG
ACTTATTGTATTCTACTTTTTACTTTTCCAGGAGACCAAAACATCACCAATTAGAACACAAAAAC
CACTGATAGACCTTCTGGTATCTACACAAGTGCCCCAATCACTATCTGAGAAAGCCTCAAGCTAC
AAACTGTTGTTAGCACGAAAGAATAATCCTTGTCATATGCTTCCTTTCAAATATCTGAAAACTCT
ATGAATAGCTACCAAATGAAAATCAGTGGGTGCATCAAGGAACTGAGCCAGCTGTTGTACTACAA
AACTTAAATCTAGTCGAGTAGTTGTAAGATATTGAAGCTTTCCCACTAACATTCTATACTGGGTA
GAATCAGCTAACAATGTGCCTCCTTCTTTAGA
Found at i:20152 original size:14 final size:14
Alignment explanation
Indices: 20123--20179 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 14
20113 AAAAAGACTC
20123 AAAACC-TTT-TTG
1 AAAACCATTTCTTG
20135 AAAACTCATTTC-TG
1 AAAAC-CATTTCTTG
20149 AAAACCATTTCTTG
1 AAAACCATTTCTTG
*
20163 AAAA-CATTTTTTG
1 AAAACCATTTCTTG
20176 AAAA
1 AAAA
20180 ATGTCTCTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 5 0.12
13 19 0.47
14 16 0.40
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAACCATTTCTTG
Found at i:20159 original size:13 final size:13
Alignment explanation
Indices: 20123--20171 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
20113 AAAAAGACTC
*
20123 AAAACC-TTTTTG
1 AAAACCATTTCTG
20135 AAAACTCATTTCTG
1 AAAAC-CATTTCTG
20149 AAAACCATTTCTTG
1 AAAACCATTTC-TG
20163 AAAA-CATTT
1 AAAACCATTT
20172 TTTGAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 5 0.15
13 12 0.36
14 16 0.48
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (13 bp):
AAAACCATTTCTG
Found at i:20176 original size:13 final size:13
Alignment explanation
Indices: 20129--20179 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
20119 ACTCAAAACC
20129 TTTTTGAAAAC-T
1 TTTTTGAAAACAT
*
20141 CATTTCTGAAAACCAT
1 --TTTTTGAAAA-CAT
*
20157 TTCTTGAAAACAT
1 TTTTTGAAAACAT
20170 TTTTTGAAAA
1 TTTTTGAAAA
20180 ATGTCTCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 12 0.39
14 17 0.55
15 1 0.03
16 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTTTGAAAACAT
Found at i:21337 original size:26 final size:26
Alignment explanation
Indices: 21308--21384 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 26
21298 TTAGGGTCAC
*
21308 CCAGGGGCATTTTGGTTATTTTAAAT
1 CCAGGGGCATTTTGGTCATTTTAAAT
* **
21334 CCAGGGGCATTTTTGTCATTTTTGTAT
1 CCAGGGGCATTTTGGTCA-TTTTAAAT
* *
21361 TCAGGGACATTTTGGTCATTTTAA
1 CCAGGGGCATTTTGGTCATTTTAA
21385 GACCACTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.44
Consensus pattern (26 bp):
CCAGGGGCATTTTGGTCATTTTAAAT
Done.